| Type | Keyword |
| Use | As "PDF", but 'cut off' (ignore) all phonon contributions greater than |
| a given "wmax" ("pdf "block input option) or less than a given "wmin" | |
| ("pdf" block input option). | |
| See also | PDFkeep pdf nowidth nofreq rmax rbins wmin wmax units |
| Type | Keyword |
| Use | As "PDFcut", but 'keep' all phonon contributions greater than a given |
| "wmax" (pdf block input option) or less than a given "wmin" (pdf block | |
| input option) by setting w=wmax or w = wmin respectively. | |
| See also | PDFcut pdf nowidth nofreq rmax rbins wmin wmax units |
| Type | Keyword |
| Use | Compute the thermal conductivity using Alamode. For this to work |
| Alamode must be installed on your computer and the environment | |
| variable ALAMODE_DIR set to point to the root directory of Alamode. | |
| In this mode GULP will call the program alm to obtain the finite | |
| difference patterns required for the system, compute the forces | |
| for these displacements, and fit the force constants using alm. | |
| The cost of this process depends on the force constant cutoffs | |
| and the precision is determined by the displacement magnitude. | |
| See also | thermalconductivity ala_disp ala_cutoff ala_shrink ala_processors |
| Type | Keyword |
| Use | When using eembond GULP tries to find the minimal set of bonds |
| need for EEM that avoid rings that cause the inversion of the EEM | |
| matrix to become singular. Specifying this keyword forces the code | |
| to work with all bonds. However, this means iterative solution has | |
| to be used and prevents the use of analytic second derivatives. | |
| See also | eembond |
| Type | Keyword |
| Default | Do not allow partial occupancies on a site to exceed 1. |
| Use | Tells GULP to allow the sum of partial occupancies on a |
| given site to be allowed to exceed one without treating | |
| the particles as separate entities that have accidentally | |
| been superimposed. | |
| NB: This option should be used with caution as it physically | |
| not usually sensible to have a site occupancy greater than | |
| one. The main use is to allow different atom types to be | |
| constrained to move together to allow the construction of | |
| more complex potential forms. |
| Type | Keyword |
| Use | Print out all valid three-body angles found for the three-body |
| potentials. |
| Type | Keyword |
| Use | Given contents of unit cell find possible atomic coordinates |
| by implementing an algorithm which simulates annealing. | |
| Generally a local minimisation is performed on the best configuration. | |
| See also | predict cost global temperature |
| Type | Keyword |
| Use | Causes the atomic stresses to be output at the final geometry. |
| These are the atomic contributions to the strain derivatives. | |
| For 3D systems the stresses in GPa are output, while for all | |
| cases the strain derivative per atom is output in eV. | |
| NB: This feature requires that symmetry is turned off during | |
| the calculation. | |
| See also | stress_out catomic_stress |
| Type | Keyword |
| Use | Causes the average bond lengths between pairs of species to be printed |
| out after a bond length analysis. | |
| See also | bond distance |
| Type | Keyword |
| Use | Print out bond length analysis at beginning and end of run. |
| NOTE : The way in which this keyword works has changed for | |
| version 1.4. Whereas in older versions all distances less | |
| than the sum of the covalent radii multiplied by a tolerance | |
| were considered to be bonded, now only the atoms which are | |
| bonded in the calculation are listed. This therefore allows | |
| for the influence of the "nobond" and "connect" options. | |
| See also | distance average nobond connect bondtype |
| Type | Keyword |
| Use | Set flags for radii only optimisation . It is still necessary to |
| specify either "conp" or "conv" so that the cell flags are correctly | |
| set. | |
| See also | conp conv noflags shell nobreathe cellonly isotropic ocell |
| Type | Keyword and option |
| Format | broaden_dos <scale/gaussian> b |
| Default | b = 0.2 |
| Units | cm-1 (default) or fractional (scale) |
| Use | An approximation to the delta function is used in order to line |
| Lorentzian broaden the phonon density of states peaks. If given | |
| as a keyword then the default broadening is applied or if used | |
| as an option the user may specify their own broadening factor. | |
| e.g. broaden 0.3 | |
| The expression used for the broadening is: | |
| w(f) = b/[pi*(1 + (b*(f - f0))**2)] | |
| where w is the fractional weight at frequency f of a peak at | |
| frequency f0. b is the broadening factor and is the inverse | |
| of the half-width at half-maximum parameter. | |
| Note, the smaller the factor, the greater the broadening. | |
| The range of the plot is automatically extended when broadening is | |
| turned on to allow the highest frequency peak to decay to 1/100th of | |
| its original magnitude. | |
| In the case of thermal conductivity calculations, there is the | |
| option to have a fixed broadening (default) or to scale the | |
| average frequency difference (if scale is specified). | |
| If "gaussian" is specified then Gaussian broadening will be used: | |
| w(f) = b/sqrt(pi) * exp(-(b*(f-f0))**2) | |
| See also | phonon project output lorentzian_tolerance thermalconductivity |
| box |
| Type | Keyword |
| Use | Stops GULP from performing optimisations during the bulk run |
| - this is of use when performing defect calculations when | |
| you only want the runtype to apply to the defect section. | |
| See also | defect centre size region_1 noanisotropic_2b |
| Type | Keyword |
| Use | The dispersion energy, as represented by 1/r**6 terms |
| as part of the Buckingham, Lennard-jones and General | |
| potentials, is actually quite slow to converge in | |
| real space. By specifying this keyword the C6 terms | |
| are evaluated using an Ewald-like approach, thus | |
| achieving much greater accuracy in the energy for | |
| only a small amount of extra computational expense. | |
| When this option is used the rmax value for the | |
| potential only influences the short range repulsion | |
| component. As the truncation distance for these terms | |
| is also controlled by the program, the best thing is | |
| to just specify a large cutoff and let the program | |
| decide. |
| Type | Keyword |
| Use | Set flags for cell optimisation while keeping internal coordinates |
| fixed. If cellonly, conv or conp are not specified for a calculation | |
| that requires derivatives - individual flags are needed. | |
| See also | conv conp noflags breathe nobreathe shell isotropic ocell |
| strain cellstrain |
| Type | Keyword |
| Default | no comparison |
| Use | Causes a table comparing the initial and final structures to be printed |
| out both for bulk and defects. |
| Type | Keyword |
| Use | Use conjugate gradients to optimise geometry, instead of second |
| derivative based methods. | |
| See also | dfp numdiag unit positive lbfgs steepest |
| and | |
| Type | Option |
| Format | conjugate n |
| Default | never |
| Use | Part of genetic section. After n iterations the odd top 5 |
| configurations are minimised locally using a method of conjugate | |
| gradients. |
| Type | Keyword |
| Use | Set flags for constant pressure optimisation. |
| If conv, cellonly or conp are not specified for a calculation | |
| that requires derivatives - individual flags are needed. | |
| See also | conv cellonly breathe nobreathe noflags shell isotropic ocell |
| Type | Keyword |
| Use | Causes the conserved quantity for the MD ensemble to be output where |
| applicable. |
| Type | Keyword |
| Use | Set flags for constant volume optimisation. |
| If cellonly, conv or conp are not specified for a calculation | |
| that requires derivatives - individual flags are needed. | |
| See also | conp cellonly breathe nobreathe noflags shell isotropic |
| Type | Keyword |
| Use | Outputs atomic information on all atoms (cores, not shells, if using shell model) |
| used in phonon calculations. Details given for each core in the primitive cell. | |
| Lists species mass, neutron scattering length (bbar), incoherent and coherent | |
| neutron scattering area, and atomic position in both Cartesian and Fractional | |
| coordinates. This option is purely for information, and does not change the | |
| behaviour of GULP. Where partial occupancies used, output is for the mean- | |
| field atom on each site. | |
| See also | Keywords: makeEigenArrays |
| Type | Keyword |
| Use | Invokes a modified form of the COSMO algorithm that |
| imposes the constraint of an Integral Charge (normally | |
| zero) on the system. This is important for periodic | |
| systems where charge neutral is a requirement for a | |
| converged lattice sum. | |
| If a surface is non-charge neutral then the net surface | |
| charge is balanced by the net charge on the solvent | |
| accessible surface. This requires the "qok" keyword | |
| to be specified. | |
| See also | pointsperatom segmentsperatom solventepsilon |
| solventradius solventrmax vdw nosasinitevery | |
| cosmoframe cosmoshape rangeforsmooth qsas | |
| sasparticles qiterative cwolf pureQ cosmo | |
| matrix_format |
| Type | Keyword |
| Use | Causes a solvation energy calculation to be performed |
| using the COSMO model. For details of the method see: | |
| A. Klamt and G. Schueuermann, JCS Perkin Trans 2, 799 (1993) | |
| Here the system is immersed in an effective continuum | |
| solvent with a user-specified dielectric constant and | |
| solvent molecule radius. A solvent-accessible surface | |
| is then constructed around the molecule/surface where | |
| charges are induced that interact with the underlying | |
| material. | |
| See also | pointsperatom segmentsperatom solventepsilon |
| solventradius solventrmax vdw nosasinitevery | |
| cosmoframe cosmoshape rangeforsmooth qsas | |
| sasparticles qiterative cwolf pureQ cosmic | |
| matrix_format |
| Type | Keyword |
| Use | Calculate the cost function rather than energy during global |
| optimisation. If no other potential form given then use cost | |
| function for local minisation as well. | |
| For a single point run calculate cost function as well as | |
| energy. | |
| See also | predict genetic anneal |
| and | |
| Type | Genetic Option |
| Format | cost <kb value_kb> <kc value_kc> <kq value_kq> <ks value_ks> |
| Default | kb=1.0 kc=1.0 kq=1.0 ks=0.0 |
| Use | Specify a weighting factor for the various components of the cost |
| function, where kb represent the bond valence contribution, kc | |
| the coordination contribution, kq the Coulombic repulsion between | |
| like charged ions and ks a sort of bond valence term between like | |
| charged ions. |
| Type | Keyword |
| Use | Calculate the first derivatives of the atomic charges |
| with respect to the coordinates of the atoms (and strain) | |
| as calculated according to either the EEM or QEq | |
| electronegativity equalisation schemes. | |
| See also | eem qeq noqeem |
| Type | Keyword |
| Use | Could do anything! For programmers' use only. |
| Type | Keyword |
| Default | Use fractions in output where appropriate. |
| Use | Specifying this keyword suppresses the use of fractions in |
| output from GULP. |
| Type | Keyword |
| Use | When used as a keyword this causes a defect calculation to be |
| performed at the end of any bulk calculations. This option | |
| cannot currently be used in conjuction with the background | |
| neutralising charge for non-charge neutral unit cells, or | |
| with the dipole correction energy. | |
| See also | region_1 centre size regi_before vacancy |
| impurity interstitial frequency noanisotropic save | |
| restore gdcrit bulk_noopt |
| Type | Keyword |
| Use | For crystals where there is a dipole moment within the |
| unit cell it adds the correction term to the energy: | |
| E = 2*pi*D**2 / 3.V | |
| where D is the dipole per unit cell and V is the volume. | |
| When delta_dipole is specified the dipole D is defined | |
| relative to the dipole for the initial configuration | |
| being zero. This is useful where an electric field is | |
| applied to an equilibrium system, generating a net dipole. | |
| Note that defect calculations cannot be performed when | |
| this term is present. | |
| NB: delta_dipole and dipole are mutually exclusive - if | |
| both are specified then delta_dipole will be applied | |
| See also | field dipole initial_dipole |
| Type | Keyword |
| Use | Debugging keyword that causes GULP to output the internal-internal |
| second derivative matrix when second derivatives are generated. | |
| See also | derv3 |
| Type | Keyword |
| Use | Debugging keyword that causes GULP to output the internal-strain |
| second derivative matrix when second derivatives are generated. | |
| See also | derv2 |
| Type | Keyword |
| Use | Use the Davidon-Fletcher-Powell updating formula instead of BFGS. |
| See also | unit numdiag positive conjugate lbfgs steepest |
| Type | Keyword |
| Use | For crystals where there is a dipole moment within the |
| unit cell it adds the correction term to the energy: | |
| E = 2*pi*D**2 / 3.V | |
| where D is the dipole per unit cell and V is the volume. | |
| By default the Ewald sum assumes that there is no dipole | |
| moment across the crystal, while this term is applicable | |
| to cases where there is a permenant dipole. Note | |
| that the dipole is ambiguous in many cases because it | |
| depends on the termination of the crystal at the surface | |
| and hence this correction should be used with care! | |
| Note that defect calculations cannot be performed when | |
| this term is present. | |
| NB: delta_dipole and dipole are mutually exclusive - if | |
| both are specified then delta_dipole will be applied | |
| See also | field delta_dipole |
| Type | Keyword |
| Use | Print out distance analysis at beginning and end of run. |
| Default search radius is 2.0 Angstroms - this can be changed | |
| by using "cutd". For bond length search see "bond". |
| Type | Keyword |
| Use | Causes GULP to output the dynamical matrix from a phonon calculation. |
| See also | phonon |
| Type | Keyword |
| Use | For molecules it causes an Eckart transformation to be performed |
| on dynamical matrix. This removes the rotational and translational | |
| contamination of the vibration modes. Currently only applies to | |
| 0-D systems. | |
| See also | phonon raman inten msd |
| Type | Keyword |
| Use | Calculate charges by Mortiers EEM. |
| oldeem invokes the original set of parameters. | |
| Only available for H, C, N, O, F, Si, Al and P. | |
| If specified with optimise then the charges will be recalculated at | |
| every point of the optimisation. | |
| NB Electronegativity equalisation schemes should NOT | |
| be used in combination with Coulomb subtraction of | |
| any form otherwise the calculation of the charges and | |
| the energy will not be self-consistent. This leads to | |
| all derivatives being incorrect as dE/dQ is no longer | |
| zero. If Coulomb subtracted potentials are to be used | |
| then charges must be calculated for the initial geometry | |
| and then frozen. | |
| Note: Phonon calculations are limited with the EEM keyword | |
| to the gamma point without the LO/TO splitting. | |
| Note: Only region 1 atoms are included in EEM and fixed | |
| charges will be taken for region 2. | |
| See also | qeq dcharge sm electronegativity gasteiger qbond pacha noqeem |
| eembond |
| Type | Keyword |
| Use | Calculate charges by split bond charge electronegativity |
| This is closely related to EEM and can use many of the same | |
| variants such as QEq, SM, and pacha. The major difference is | |
| that charge is only transfered between atoms that are bonded | |
| and so the charge on an atom is the sum of its bond charges. | |
| This means that the total charge within a molecule is conserved | |
| and long-distance unphysical charge transfer is prevented. | |
| However, there are some restrictions: | |
| 1) This approach can only be applied to charge neutral systems | |
| at present since a net charge cannot be automatically | |
| redistributed. | |
| 2) The energy surface is discontinuous if a bond breaks or forms. | |
| 3) The iterative QEq special case for hydrogen is not available | |
| in this form at present, though increasingly this is not used. | |
| See also | qeq dcharge sm electronegativity gasteiger qbond pacha noqeem |
| eem allbonds |
| Type | Keyword |
| Use | Print out electric field gradients at the atomic sites. Currently |
| this is not compatible with the use of the cell multipole method | |
| - in such cases the exact electric field gradients will be calculated. | |
| The principal components of the EFG tensor and the asymmetry parameter | |
| are now also output as part of an efg calculation. | |
| See also | pot potential |
| Type | Keyword |
| Use | Calculate the implicit harmonic relaxation energy, but do not optimise. |
| This uses the Hessian and forces to compute the energy of optimisation | |
| if the system was perfectly harmonic, but without iteratively refining | |
| the coordinates. It allows a single point calculation to provide an | |
| estimate of the energy that would result from optimisation. | |
| See also | conp conv cellonly isotropic finite unfix shell single |
| optimise md montecarlo gradient ocell |
| Type | Keyword |
| Use | Generate eigenvectors as well as eigenvalues during a phonon |
| calculation. This option is automatically implied when projected | |
| phonon densities of states are required. | |
| Both real and imaginary components of the eigenvectors are | |
| output, but remember that when two or more frequencies are | |
| degenerate there are an infinite number of possible vectors | |
| that can be created by taking linear combinations. | |
| All eigenvectors output are orthonormal. | |
| See also | phonon lower symmetry project_dos eckart intensity msd |
| Type | Keyword |
| Default | Don't print region energies |
| Use | Causes GULP to output the energy broken down into regions. |
| NB Not all potential types currently support this feature and | |
| for many body potentials it may not be meaningful where they | |
| span multiple regions. Use with care! |
| Type | Keyword |
| Use | Switch the algorithm for bond order potential calculations (including |
| EDIP, Brenner and ReaxFF) to a faster finite difference approach. | |
| See also |
| Type | Keyword |
| Use | Perform fitting run using full BFGS method. This involves |
| the calculation of the full numerical Hessian instead of | |
| just the diagonal elements. | |
| See also | fit |
| Type | Keyword |
| Use | Perform fitting run using unit matrix with BFGS method. |
| See also | simul relax genetic fbfgs delta simplex |
| Type | Keyword |
| Use | When a molecule keyword is included, the bonding list |
| defining the connectivity is checked at every geometry | |
| and the cell index references recalculated. If an atom | |
| which was previously bonded exceeds the bond length | |
| cutoff then the calculation is normally abandoned. By | |
| using the fix_molecule (can be abbreviated to "fix") | |
| option the connectivity is fixed by the initial | |
| geometry and not updated subsequently. This can | |
| prevent the calculation from being abandoned. However | |
| it has the side effect that a restarted job may have | |
| a different energy due to changes in connectivity - so | |
| beware! | |
| See also | molecule molmec molq rtol inter intra both |
| Type | Keyword |
| Use | Causes an optimisation run to use the gradient norm as the quantity for minimisation |
| rather than the energy. Useful for situation where the absolute energy is not well | |
| defined, such as systems under uniaxial stress. | |
| See also | anisotropic_pressure |
| Type | Keyword |
| Default | Use coordinates as input |
| Use | Causes the coordinates of a 0-D system (molecule) to be rotated to the |
| standard frame of reference based on the non-mass weighted moment of | |
| inertia tensor of the cores. | |
| NB: Use of this keyword is not compatible with the use of flags and | |
| constraints at present. It is recommend that a single point calculation | |
| is used to change the frame first and then any flag/constraints specified | |
| using the restart file. | |
| See also | cartesian |
| Type | Keyword |
| Use | Use Gibbs free-energy as the quantity to be calculated/optimised |
| instead of the internal energy. This uses the phonon density of | |
| states to calculate the vibrational partition function and thereby | |
| the free energy. Note: It is best not to use gamma point phonons | |
| in such calculations since the Born charge correction is not applied | |
| in a free energy minimisation. Hence the default k point (if none | |
| specified) is (1/4,1/4,1/4). However, the use of the "shrink" option | |
| is recommended to converge the free energy. | |
| See also | phonon nozeropt static_first zsisa scmaxsearch lowest_mode shrink |
| Type | Keyword |
| Use | Causes GULP to compute the frequencies for a defect calculation |
| in the Mott-Littleton scheme. | |
| NB: This is approximate since it assumes that regions 1 and 2 | |
| are uncoupled with respect to their vibrations. | |
| See also | phonon |
| Type | Keyword |
| Use | Causes the nosymmetry keyword to produce the full, instead of the |
| primitive, unit cell. | |
| See also | nosymmetry |
| Type | Keyword |
| Use | Indicates that Gasteiger charges should be calculated according |
| to the method in Tetrahedron, 36, 3219-3288 (1980). The Gasteiger | |
| charges are geometry independent and only depend on the connectivity | |
| of the molecule. Hence it is important to ensure that the bonding | |
| is correct at the start of the calculation and the "fix" keyword | |
| is also recommended to avoid potential discontinuities. Parameters | |
| are available for H, C, N, O, S and the halogens. For C, N and O | |
| the electronegativities used depend on the hybridisation. In the | |
| absence of formal atom typing, GULP makes the approximation that | |
| the hybridisation state is the obvious one for the coordination | |
| number, i.e. for C, 4 bonds => sp3, 3 bonds => sp2, 2 bonds => sp, | |
| for N, 3 bonds => sp3, 2 bonds => sp2, 1 bond => sp, and for O, | |
| 2 bonds => sp3, 1 bond => sp2. | |
| See also | eem qeq molq fix bond gasttol gastiter qbond pacha gastparam |
| gastdamping noqeem eembond |
| Type | Keyword |
| Use | Given contents of unit cell use a genetic algorithm to find |
| possible atomic coordinates. (global optimiser) | |
| A local minimisation can then be performed on the best configurations | |
| See also | predict anneal contents global cost |
| Type | Keyword |
| Use | When using the fc_supercell approach to compute phonons based on |
| finite differencing of first derivatives there can be problems | |
| for some models where images of the same atom interact with each | |
| other. The main case where this occurs is for bond order potentials, | |
| including brenner, EDIP, ReaxFF. Note that for brenner analytic | |
| second derivatives are available and so there is no need to use | |
| finite differences, whereas for EDIP and ReaxFF this is not the case. | |
| The solution to this problem is to compute the force constants for a | |
| supercell (specified using this option) and then the ghostcell keyword | |
| tells the code to compute the phonons as though they were for the | |
| original smaller cell from which the supercell was constructed. | |
| NB: At present this keyword can only be used in serial. | |
| See also | phonon fc_supercell ghost_supercell |
| Type | Keyword |
| Use | After finding possible crystal coordinates (because keyword |
| predict specified) dump out restart files before performing local | |
| minimisation of the best structures. | |
| See also | predict genetic anneal |
| Type | Keyword |
| Use | Calculate gradients but do not optimise, provided the single |
| keyword is not specified. | |
| See also | conp conv cellonly isotropic finite unfix shell single |
| optimise md montecarlo eharmonic fix_atom ocell |
| Type | Keyword |
| Use | Calculate the group velocities of the phonons at each k point |
| See also | thermalconductivity broaden_dos temperature lorentzian_tolerance |
| Type | Keyword |
| Use | Calculate the Grueneisen parameters for the phonons |
| See also | phonon groupvelocity thermal_conductivity shrink kpoint |
| Type | Keyword |
| Use | Causes details of the Hessian matrix to be output. For calculations |
| employing the RFO method then the eigenvalues, eigenvectors and the | |
| gradients transformed into the local modes are output for every cycle. | |
| For Newton-Raphson calculations, the inverse Hessian is output after | |
| each exact recalculation, but not after updating. | |
| See also | optimise matrix_format |
| Type | Keyword |
| Use | Causes a rhombohedral structure to be output in |
| hexagonal form in the dumpfile. |
| Type | Keyword |
| Default | Show shell coordinates and other details in the output. |
| Use | Causes the output of details of the shells to be suppressed in the output. |
| See also | noaddshells |
| Type | Keyword |
| Default | Reuss convention for bulk/shear modulus |
| Use | Specifies that the Hill convention is used for the bulk |
| modulus. The Hill convention takes the average of the | |
| Reuss and Voigt values. | |
| See also | bulk_modulus shear_modulus elastic fit observables |
| voigt young poisson |
| Type | Keyword |
| Default | Imaginary frequencies excluded from DOS / dispersion |
| Use | Specifies that imaginary frequencies should be included |
| in the output of density of states or dispersion plots. | |
| See also | phonon nodensity |
| Type | Keyword |
| Info | Infra-red phonon intensities are output when the eigenvectors |
| have been calculated using "eigen". This keyword also triggers | |
| the printing of intensity. Intensities are in nominal | |
| units of charge**2. Raman intensities are also now output. | |
| However, it should be noted that they are approximate and only | |
| valid for systems with a single type of bond in (such as a | |
| silicate). | |
| NB: From version 4.0.5 onwards the IR intensities are computed | |
| using the Born effective charge tensor, where available, | |
| rather than the sum of core and shell charges. For simple rigid | |
| ion models there is no difference, but for more complex models | |
| there may be some change. | |
| NNB: Intensities should usually be calculated at the gamma point | |
| and to ensure the proper symmetry it is recommended to specify | |
| nononanal as a keyword to turn off the non-analytic correction. | |
| See also | oldintensity eigen nononanal eckart msd |
| Type | Keyword |
| Use | Only allow isotropic cell expansion and contraction during |
| optimisation. For molecular dynamics this keyword requires the | |
| use of the default integrator (stochastic). | |
| See also | conp conv orthorhombic ocell |
| Type | Keyword |
| Default | eV |
| Use | Output the energy components in kcal rather than eV. |
| Useful for comparing energies against other programs | |
| See also | kjmol |
| Type | Keyword |
| Use | When the unit cell is centred, the K points specified are taken |
| as being for the primitive cell by default. When this keyword | |
| is specified, the K points given by the kpoints and dispersion | |
| options are taken to be for the full centred cell instead. Note | |
| the calculation is still performed using the primitive cell, but | |
| at the points in reciprocal space that relate to the full cell. | |
| See also | kpoints dispersion |
| Type | Keyword |
| Default | eV |
| Use | Output the energy components in kJ/mol rather than eV. |
| Useful for comparing energies against other programs | |
| See also | kcal |
| Type | Keyword |
| Use | Use limited memory BFGS for optimisation. This is useful where |
| a system is too large to allow the storage of the full Hessian | |
| matrix and so a limited part of it is stored instead. The size | |
| of the memory used depends on the value of lbfgs_order which | |
| is set as an option. | |
| See also | numdiag dfp positive conjugate unit lbfgs_order |
| Type | Keyword |
| Use | Indicates that library symbols should be dumped to a restart |
| file. NB This option will create an a restart file that is | |
| incompatible with GULP at the moment. | |
| See also | library libff |
| Type | Keyword |
| Use | Indicates that fitting flags should be read from any library |
| files if this is a fitting run. | |
| See also | library libdump |
| Type | Keyword |
| Default | no printing |
| Use | Print out details of line minimisations. |
| Type | Keyword |
| Use | Use imaginary phonon modes to lower the symmetry of a structure. |
| This is particularly useful when an optimised structure has | |
| imaginary frequencies and help is needed as to how to distort the | |
| geometry to obtain the true minimum. This keyword requires a | |
| phonon run to be performed and the calculation of eigenvectors | |
| is required, though from version 5.1 onwards these will not be | |
| output unless eigenvectors is explicitly specified as a keyword. | |
| NB: If applying to molecules then it is recommended that the | |
| eckart keyword is also used to ensure that rotations are not | |
| included in the frequencies calculated. | |
| See also | phonon eigenvectors slower optlower switch frqtol |
| Type | Keyword |
| Use | If the cell is cubic, then a Madelung correction can be |
| applied to the electrostatics of a charged system to | |
| put the energy to zero. This assumes a single point ion | |
| excess charge (e.g. one charged ion in a box). The | |
| energy correction is given by: | |
| E = 1/2 alpha*Q**2/(epsilon_0*L) | |
| where alpha is the Madelung constant (2.8373 for a simple | |
| cubic case), Q is the excess charge and L the side of the | |
| cubic box. | |
| See also | qok |
| Type | Keyword |
| Use | Stores phonon information (frequencies and eigenvectors) in internal arrays for |
| further calculations. This information is generated by phonon and eigen | |
| keywords (automatically called if makeEigenArrays is set). This keyword | |
| should not need to be explicitly set unless testing. It is not currently | |
| compatible with parallel runs. | |
| See also | pdf nowidth nofreq |
| Type | Keyword |
| Use | Changes the way that many body terms are apportioned between regions 1 |
| and 2 to match the convention that Marvin adopts (i.e. all 3-/4- body | |
| interactions involving a region 1 atom are assigned to the region 1 | |
| energy) |
| Type | Keyword |
| Use | Specifies that a molecular dynamics run is to be performed |
| See also | timestep temperature equilibration production sample |
| tscale write cutp integrator nolist_md minimum_image | |
| nomolecularinternalke momentum_correct mdmaxtemp tether |
| Type | Keyword |
| Use | Requests that GULP prints out a decomposition of the mean kinetic |
| energy of vibration projected onto each lattice site. Note that | |
| this keyword requires that a phonon calculation be specified and | |
| that the temperature is non-zero. Furthermore, this will only | |
| currently work for a single temperature rather than a temperature | |
| range. | |
| See also | phonon eigenvector msd |
| Type | Keyword |
| Use | Requests that the real space components of the energy for |
| a solid are calculated using the minimum image convention | |
| during a molecular dynamics or conjugate gradient simulation. | |
| For large unit cells this can accelerate the real space | |
| calculation of the program by reducing the work done in | |
| searching for interactions, especially for right angled unit cells. | |
| NB: The minimum image approach is incompatible with the spatial | |
| algorithm and so if both are specified the spatial algorithm will | |
| be used. | |
| See also | md spatial |
| Type | Keyword |
| Default | no molecules |
| Use | Program locates molecules based on either an input connectivity or |
| by automatically locating bonds based on covalent radii and removes the | |
| Coulombic interactions within the molecule. See "molq" if you wish | |
| to retain the Coulomb terms. This option allows intra- and inter- | |
| molecular potentials to be specified. | |
| See also | molq molmec fix_molecule rtol nobond inter intra both |
| 14_scale noautobond bondtype |
| Type | Keyword |
| Default | no molecules |
| Use | Program locates molecules based on either an input connectivity or |
| by automatically locating bonds based on covalent radii and subtracts | |
| Coulomb terms between bonded atoms and between atoms bonded to | |
| a common third atom. This option is needed when using molecular | |
| mechanics potentials, such as in the CVFF forcefield. Works for | |
| isolated molecules and 1,2 and 3-D periodic molecules provided | |
| repeat directions lie parallel to crystallographic axes, where | |
| appropriate. | |
| See also | molq molecule rtol fix_molecule nobond inter intra both |
| 14_scale noautobond bondtype |
| Type | Keyword |
| Default | no molecules |
| Use | Program locates molecules based on either an input connectivity or |
| by automatically locating bonds based on covalent radii, but retains the | |
| Coulombic interactions within the molecule. See "molecule" if you wish | |
| to remove the Coulomb terms. This option allows intra- and inter- | |
| molecular potentials to be specified. Works for isolated molecules | |
| and 1, 2 and 3-D periodic molecules provided repeat directions | |
| lie parallel to crystallographic axes, where appropriate. | |
| See also | molecule molmec rtol fix_molecule nobond inter intra both |
| 14_scale noautobond bondtype |
| Type | Keyword |
| Use | Specifies that a Monte Carlo calculation is to be performed. |
| See also | mccreate mcdestroy mcmove mcrotate mctrial mcoutfreq |
| mcsample gcmcspecies gcmcmolecule mcstrain mcswap nomcediff |
| Type | Keyword |
| Info | Compute the mean-squared displacements for atoms based on the |
| phonon calculation. The three Cartesian components are output | |
| based on the sum over all k points (where applicable). | |
| See also | phonon intensity eigenvector meanke |
| Type | Keyword |
| Use | Invokes a Nudged Elastic Band run to map out the minimum energy |
| pathway between two structures. A limited memory BFGS run is used to | |
| converge the replicas to the path. See the papers of G. Henkelman | |
| and H. Jonsson (e.g. J. Chem. Phys., 113, 9978 (2000)). By default | |
| the Doubly Nudged Elastic Band form is used. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Keyword |
| Use | if specified this selects the new defect algorithm |
| in which all ions in region 2 that interact with | |
| region 1 are stored. The advantage of this approach | |
| is that there is no need to add and then subtract | |
| contributions from the non-defective region 1 to the | |
| short range energy. This leads to increased numerical | |
| stability, but tends to be slower than the old | |
| algorithm except where numerical problems slow down | |
| the rate of convergence. The other downside is that | |
| the storage needed for region 2a will be larger. | |
| When using the Embedded Atom Model this algorithm | |
| must be used and will therefore automatically be | |
| selected. | |
| See also | defect |
| Type | Keyword |
| Default | Add shells where they are missing in the input. |
| Use | If specified then no shells will be added. |
| See also | hideshells |
| Type | Keyword |
| Use | The region 2b energy is calculated for an anisotropic solid by |
| default using ra*rb/r**6. This keyword forces the program to | |
| use the isotropic formula 1/r**4. The only real use for this | |
| keyword is when trying to compare with CASCADE results which | |
| use the more approximate isotropic form. | |
| See also | mode2a defect centre region_1 vacancy impurity |
| interstitial bulk_noopt |
| Type | Keyword |
| Default | Automatically locate bonds in molecules based on covalent radii |
| Use | Specifies that GULP should not try to automatically locate bonds |
| based on the sum of covalent radii. Bonds are then completely | |
| controlled by the "connectivity" option. | |
| See also | molecule molq rtol fix_molecule nobond inter intra both |
| 14_scale molmec bondtype |
| Type | Keyword |
| Use | Excludes radii from the optimisation variables. |
| See also | conp conv noflags shell breathe cellonly isotropic ocell |
| Type | Keyword |
| Use | Turns off the use of symmetry for second derivatives in |
| bulk and defect calculations. Primarily of use for debugging | |
| purposes. If using variable charges this option is used | |
| implicitly. | |
| See also | defect nod3 |
| Type | Keyword |
| Use | Turns off the calculation of third derivatives for ShengBTE |
| output. Allows just the second derivatives to be obtained. | |
| See also | output num3 |
| Type | Keyword |
| Use | Do not write phonon density of states curve to output channel. |
| Type | Keyword |
| Use | Turns off the doubly nudged elastic band method and uses the singly |
| nudged formalism. | |
| See also | nebspring nebtolerance neb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Keyword |
| Use | When performing a calculation of the site potentials for region 1 |
| in a defect calculation, the values are normally only output for | |
| the asymmetric unit. If this keyword is specified then symmetry | |
| is still used in the defect calculation, but the site potentials | |
| are output for all sites in region 1. | |
| See also | pot |
| Type | Keyword |
| Use | Switches off the use of symmetry in defect calculations. |
| See also | defect |
| Type | Keyword |
| Use | Turns off the Ewald summation/Coulomb interaction even when charges |
| are present in the input. This is mainly used when a screened | |
| Coulomb potential is being used, such as "qerfc", which requires | |
| the charges to be present but replaces the normal energy term. | |
| See also | qerfc qwolf |
| Type | Keyword |
| Use | Do not calculate energy. |
| Type | Keyword |
| Use | Do not freeze out atoms with no degrees of freedom from first and |
| and second derivative calculations during optimisation. For systems | |
| where the number of frozen atoms is small then turning off this | |
| option may increase the performance of the program as it allows | |
| variable tuning of eta for each level of derivatives to be used. | |
| See also | unfreeze |
| Type | Keyword |
| Default | do first point |
| Use | Requests that the translate option exclude the initial |
| starting structure from the calculation and only does | |
| the translated calculations. | |
| See also | translate |
| Type | Keyword |
| Use | Stops input processor looking for flags in the absence of conp, conv, |
| shell or cellonly and sets all flags to zero. Mainly of use for | |
| fitting energy hypersurfaces when the gradients are not to be fitted. | |
| See also | conv cellonly breathe nobreathe shell isotropic ocell |
| Type | Keyword |
| Use | Causes the frequencies not to be output after a phonon calculation. |
| This is useful when calculating phonon dispersion curves which can | |
| involve large numbers of k points and frequencies. | |
| See also | kpoints dispersion shrink phonon |
| Type | Keyword |
| Use | Prevents output of list of k points for each configuration. |
| Type | Keyword |
| Use | Turns off the use of Brillouin zone symmetry to reduce the number of |
| k points associated with a given shrinking factor. Generally there is | |
| never any reason to do this, except for checking purposes. | |
| See also | phonon shrink |
| Type | Keyword |
| Use | By default list based methods are used for three and four |
| body terms in molecular dynamics to avoid problems with | |
| discontinuities in the energy as atoms move over cutoffs. | |
| It also increases the speed of the three and four body | |
| terms dramatically. Specifying "nolist" will cause the | |
| program to use the standard non-list based method. | |
| See also | three-body four md |
| Type | Keyword |
| Use | Controls the algorithm used for calculating the energy difference |
| during a trial move. By default, GULP will try to use the energy | |
| change associated only with the atoms that are affected by the | |
| trial step, where possible. Specifying this keyword forces the full | |
| calculation of the total energy at each step, which is more expensive. | |
| This option is mainly for debug checking. | |
| See also | montecarlo |
| Type | Keyword |
| Use | Prevents the use of mod on the input coordinates for most purposes. |
| The mod function is used to place fractional coordinates into the | |
| central unit cell. Note that this option applies to all steps of a | |
| calculation. |
| Type | Keyword |
| Use | Causes the initial velocites of atoms within a molecule to |
| be initialised to the same average value thereby resulting | |
| in no internal kinetic energy. | |
| See also | md |
| Type | Keyword |
| Use | If present, then the non-analytic correction to the phonons at |
| the gamma point is excluded. This was always true for versions | |
| of GULP prior to 1.4 and so this keyword allows backwards | |
| compatability while leading to an incorrect LO/TO splitting. | |
| From version 4.2.0 the default has been changed and this correction | |
| is no longer included for a configuration unless the | |
| gamma_direction_of_approach is explicitly input or a dispersion | |
| curve is requested. | |
| Note: The Born effective charges are not presently available | |
| with electronegativity equalisation and therefore this keyword | |
| will automatically be set. | |
| See also | phonon gamma_direction_of_approach gamma_angular_steps intensity |
| Type | Keyword |
| Use | Used in conjuction with PDF keywords, suppresses output of partial pair |
| distributions. | |
| See also | PDFcut PDFkeep nowidth |
| Type | Keyword |
| Use | Causes the electrostatic contribution to be excluded from the EEM |
| calculation. Invoke this will make the charge calculation geometry | |
| independent. | |
| See also | eem qeq dcharge sm electronegativity gasteiger qbond pacha |
| eembond |
| Type | Keyword |
| Use | Turns off some timesaving changes to the searching algorithm for |
| pairs of distances. Should have no effect, but this is still | |
| under evaluation! |
| Type | Keyword |
| Use | Do not calculate real space contributions to the energy and |
| derivatives. | |
| See also | norecip |
| Type | Keyword |
| Use | Do not calculate reciprocal space contributions to the energy and |
| derivatives. | |
| See also | noreal |
| Type | Keyword |
| Use | GULP automatically introduces a cutoff for exponential |
| repulsive terms when they become less than the accuracy | |
| factor (default=10**-8) to save computer time where the | |
| Buckingham potential has a large cutoff due to the more | |
| slowly convergent C term. This option tells the program | |
| to rigorously enforce the cutoff given in the input file. | |
| See also | cutp accuracy |
| Type | Keyword |
| Use | If specified then this turns off the calculation of charges within ReaxFF |
| See also | reaxff_chi reaxff_mu reaxff_gamma qiterative |
| Type | Keyword |
| Use | Causes the SAS calculation not to be reinitialised at |
| every step of the calculation. It is generally recommended | |
| to reinitialise to ensure that calculation results are | |
| independent of the starting point. It also avoids potential | |
| energy surface discontinuities due to the history of segment | |
| creation. | |
| See also | cosmo |
| Type | Keyword |
| Use | Stops the use of symmetry in calculating the first derivatives, but |
| not the energy during line searches. This causes the program to | |
| revert to behaving like GULP0.4 and earlier versions. The user should | |
| never need to use this option as it will slow down the code and is | |
| only useful for algorithm checking purposes. |
| Type | Keyword |
| Use | Switches off symmetry after generating unit cell. |
| For non-primitive systems the final unit cell is primitive. | |
| See also | spacegroup origin valid_spacegroups symmetry_operator |
| Type | Keyword |
| Use | Used in conjunction with PDF keywords, prevents output of individual |
| pairwise contributions to the PDF peak widths in a .wid file | |
| See also | PDFcut PDFkeep nowidth nofreq |
| Type | Keyword |
| Use | Stops coordinates from being wrapped back into the unit cell |
| This is a pseudonym for the nomodcoord keyword. | |
| See also | nomodcoord |
| Type | Keyword |
| Use | Exclude zero point energy term from phonon/free energy calculation |
| - this has the advantage that the conventional energy minimised | |
| structure corresponds to the zero kelvin structure. | |
| See also | phonon free_energy lowest_mode |
| Type | Keyword |
| Use | Forces the use of numerical third derivatives for force constant evaluation |
| even when analytic third derivatives are available. This is only needed | |
| for debugging purposes. At present this keyword only applies to the calculation | |
| of force constants for output to ShengBTE. | |
| See also | numerical output shopt threshold nod3 |
| Type | Keyword |
| Use | Use numerical estimates of the diagonal elements as a starting point |
| for the Hessian. Can be useful when exact Hessian is ill-conditioned. | |
| See also | unit dfp positive conjugate lbfgs steepest |
| Type | Keyword |
| Use | Forces the use of numerical second derivatives for property evaluation |
| even when analytic second derivatives are available. This is only needed | |
| for debugging purposes. | |
| NB: If using numerical in combination with fc_supercell it is important | |
| to make sure that the interaction range for a given force term is less | |
| than the size of the unit cell being used. If this is not the case then | |
| there will be some error in the phasing of the second derivatives. In | |
| other words, the gamma point results will be correct, but the dispersion | |
| away from gamma may contain errors. This problem is most likely to happen | |
| for small cells when using bondorder or manybody potentials since | |
| interactions become coupled over longer ranges. | |
| NB: Numerical derivatives can be in error in cases where the finite | |
| differences go across cutoff boundaries! | |
| See also | property sfinite pfinite fc_supercell num3 |
| Type | Keyword |
| Use | Use cell parameters instead of strains for optimisation of the cell |
| By default GULP uses strain derivatives for unit cell optimisation. | |
| However, if you wish to fix cell parameters with flags then this will | |
| be easier with this keyword since the flags will refer directly to | |
| the cell parameters rather than strains. | |
| See also | conv cellonly breathe nobreathe noflags shell isotropic scan_cell |
| strain |
| Type | Keyword |
| Use | Specifies that the old IR intensities, as per pre-GULP-4.0.5, |
| be computed instead of the new values based on the Born effective | |
| charge tensor. | |
| See also | intensity eigen msd |
| Type | Keyword |
| Use | The default units of elastic constants have now changed to GPa |
| in order to be consistent and modern. This keyword is included | |
| to maintain backwards compatibility. |
| Type | Keyword |
| Use | In order to make parallelisation of the second derivatives easier |
| the order of variables in optimisation has been changed such that | |
| internal coordinates appear before cell variables. Specifying this | |
| keyword returns the order to that used in earlier versions of GULP | |
| for backward compatibility. Note that the order shouldn't change | |
| the answers and so this keyword is primarily for debugging and code | |
| verification. | |
| See also | optimise |
| Type | Keyword |
| Use | Causes the program to print out the rotation matrix and shifts for |
| all bulk symmetry operators. Primarily a debugging keyword. |
| Type | Keyword |
| Use | Invokes geometry optimisation using the NR/BFGS minimiser. |
| The exact Hessian is used where necessary and subsequently updated | |
| unless a failure occurs in which case a cycle of steepest descents | |
| is used to continue the optimisation. | |
| See also | conp conv cellonly shell transition_state rfo unfix single md montecarlo |
| eharmonic fix_atom oldvarorder hessian ocell |
| Type | Keyword |
| Use | Causes an optimisation to be performed after the lower_symmetry |
| task has been performed as part of the same run. Note that it is | |
| normally worthwhile using the switch option to get the minimiser | |
| to change to rfo after lower_symmetry has been performed. | |
| See also | phonon eigenvectors slower lower_symmetry switch |
| Type | Keyword |
| Use | Only allow cell lengths to change, but not angles, during |
| optimisation or MD. | |
| See also | conp conv isotropic cellonly ocell |
| Type | Keyword |
| Use | By default any contraints generated by the program automatically |
| are not dumped to the restart file unless the user has also added | |
| some constraints. This is to prevent errors when users use the | |
| restart file, but with nosym specified. Specifying outcon on the | |
| keyword line will cause the program to dump all constraints | |
| regardless. | |
| See also | constrain |
| Type | Keyword |
| Use | Turns on calculation of variable charges using the formulation |
| of Marc Henry known as Pacha. See ChemPhysChem, 3, 561-569 | |
| (2002) for more details. At present the parameters for this | |
| method in GULP are limited to elements below number 102 in the periodic | |
| table. | |
| See also | sm eem qeq gasteiger noqeem external_potential |
| eembond |
| Type | Keyword |
| Use | Calculate the Pair Distribution Function up to a given maximum radius (rmax) |
| by summing peak widths calculated for each atomic pair. Makes use of the | |
| theory of Chung and Thorpe for calculating PDFs from phonon information | |
| Phonon information will be generated according to a full Monkhorst-Pack grid, | |
| with a specified density (using the shrink option). It is essential that all | |
| k-points are evaluated within a single gamma-centred Brillouin Zone; this | |
| is automatically enforced through the use of the "shift" keyword. | |
| See also | PDFcut PDFkeep nowidth nofreq optimise rmax rbins shrink bbar siginc |
| Type | Keyword |
| Use | Causes the phonon frequencies to be calculated for each structure |
| with k points specified at the end of each run. If no k points are | |
| explicitly given the phonons are calculated at the gamma point. | |
| Note: For materials with charges it is important to consider the | |
| effect of the LO/TO splitting. | |
| See also | kpoints dispersion shrink eigenvectors lower_symmetry box |
| project_dos output nozeropt gamma_direction_of_approach omega | |
| dynamical_matrix meanke frequencies eckart box fc_supercell | |
| msd ghostcell alamode ala_disp ala_cutoff groupvelocity | |
| grueneisen threshold |
| Type | Keyword |
| Use | Ensure that the Hessian always behaves as positive definite during |
| Newton-Raphson by ensuring the search vector has the same sign as | |
| as the gradient vector. | |
| See also | unit numdiag dfp conjugate lbfgs steepest |
| Type | Keyword |
| Use | Print out electrostatic site potentials and their first derivatives. |
| If cell multipole method is specified then this technique will be | |
| also used in the calculation of the potential for clusters. Note | |
| that the potential calculated is not corrected for Coulomb subtract | |
| options in the two-body potentials or molecule options. However, in | |
| a core-shell model the potential due to the other component of an | |
| atom is excluded. | |
| It is now possible to also use "pot" for defect | |
| calculations in which case GULP returns the electrostatic | |
| potential at the sites of the asymmetric unit of region 1. | |
| This potential does not include the displacements in | |
| region 2a. | |
| Note : when using pot in combination with QEq the potential calculated | |
| is that resulting from q/r, not the integral expression used within a | |
| QEq determination of the charges. | |
| See also | efg potential nodpsym potsites potgrid |
| Type | Keyword |
| Use | General Algorithm for Structure Prediction Pre-gulp routine. |
| Given contents of unit cell atomic coordinates are found using a | |
| global optimiser (simulated annealing or genetic algorithm). | |
| See also | genetic anneal contents global cost |
| and | |
| Type | Option |
| Use | Start of global optimiser options section, closed by "end" |
| See also | minimum maximum discrete configurations conjugate |
| tournament crossover mutation seed grid |
| Type | Keyword |
| Use | If present, this causes the force on each region to be output. |
| See also | sfractional |
| Type | Keyword |
| Use | If charges are given in a library or via the species command these |
| can potentially overwrite charges input on the end of a coordinate | |
| line. By specifying this keyword GULP preserves the state of the | |
| charges from the coordinate input and prevents overwriting. Note | |
| that if fitting of charges is specified or a method that generates | |
| charges, such as eem or qeq, these options will still lead to the | |
| charges being modified. | |
| See also | species library |
| Type | Keyword |
| Default | properties not calculated |
| Use | Causes properties to be calculated and output. |
| For 3-D systems this includes the elastic constants, dielectric | |
| constants, piezoelectric constants, sound wave velocities, bulk | |
| and shear moduli, and Youngs modulus. | |
| For 0-D systems this leads to the calculation of the moment of | |
| inertia tensor and, if the temperature is greater than zero, | |
| the calculation of the rotational and translational partition | |
| functions, plus the free energy. Because the rotational partition | |
| function depends on the symmetry number, this can be input by the | |
| user, otherwise it will default to 1. | |
| See also | numerical temperature pressure symmetry_number raman |
| Type | Keyword |
| Use | Output the density and energy associated with atoms during an EAM calculation. |
| For a MEAM calculation, the density printed is the total when summed over the | |
| component orders. | |
| See also | eam_functional eam_density prt_two prt_four prt_three prt_six |
| Type | Keyword |
| Use | Output the fourbody energy contributions. The atoms are output in |
| the order of the torsion, 1-2-3-4, or with the middle atom as number 1 | |
| for the out of plane terms. | |
| See also | prt_eam prt_two prt_three prt_six |
| Type | Keyword |
| Use | Output the sixbody energy contributions. |
| See also | prt_eam prt_four prt_three prt_two |
| Type | Keyword |
| Use | Output the threebody energy contributions. Atom 1 is the pivot atom |
| when output. | |
| See also | prt_eam prt_two prt_four prt_six |
| Type | Keyword |
| Use | Output the real space twobody energy contributions. |
| See also | prt_eam prt_four prt_three prt_six |
| Type | Keyword |
| Use | By default, a Wolf sum is used to evaluate the Coulomb |
| potential in periodic systems when applied to the SAS | |
| - SAS interaction matrix (A) in COSMO/COSMIC. For | |
| consistency, this is retained in 0-D where it is not | |
| necessary. This keyword causes a pure 1/r Coulomb | |
| potential to be used instead. | |
| See also | cosmo cosmic cwolf |
| Type | Keyword |
| Use | Indicates that charges should be calculated using bond increments. |
| Here the charge on the site is the sum of the increments associated | |
| with each bond. These increments are specified using the qincrement | |
| option. | |
| See also | qeq eem gasteiger qincrement noqeem eembond |
| Type | Keyword |
| Use | Calculate charges by Rappe and Goddard's QEq scheme. |
| This differs from Mortier's scheme in that the Coulomb | |
| interaction is replaced by the integral over two s | |
| type Slater orbitals for small distances. It is also | |
| available for the whole periodic table up to Lr (103). | |
| If specified with optimise then the charges will be | |
| recalculated at every point of the optimisation. | |
| NB Electronegativity equalisation schemes should NOT | |
| be used in combination with Coulomb subtraction of | |
| any form otherwise the calculation of the charges and | |
| the energy will not be self-consistent. This leads to | |
| all derivatives being incorrect as dE/dQ is no longer | |
| zero. If Coulomb subtracted potentials are to be used | |
| then charges must be calculated for the initial geometry | |
| and then frozen. | |
| Note: it is important to investigate the effect of | |
| qeqradius on the degree of convergence and CPU time. | |
| Note: Phonon calculations are limited with the QEq keyword | |
| to the gamma point without the LO/TO splitting. | |
| Note: Only region 1 atoms are included in QEq and fixed | |
| charges will be taken for region 2. | |
| See also | eem qeqtol qeqiter qeqradius dcharge sm qelectronegativity |
| gasteiger pacha noqeem external_potential |
| Type | Keyword |
| Use | Try to extrapolate the charges forward during MD with the reaxFF algorithm. Only works |
| when qiterative is also specified. | |
| See also | reaxff_chi reaxff_mu reaxff_gamma reaxff_qshell qiterative |
| Type | Keyword |
| Use | Invokes the use of an iterative method to solve for charges in a |
| variable charge scheme, rather than matrix inversion. This applies | |
| both COSMO/COSMIC calculations, where the charge is induced on the | |
| solvent accessible surface, and to variable charge schemes including | |
| ReaxFF, EEM, and QEq. This algorithm is usually superior for large | |
| systems, especially in the case of ReaxFF where it offers linear-scaling | |
| due to sparsity. For parallel calculations this option must be used | |
| for variable charge algorithms since parallel matrix inversion is not | |
| yet implemented. | |
| NB: To obtain precise second derivatives by finite differences then | |
| it is best NOT to use this keyword since it will generate more numerical | |
| noise. | |
| See also | cosmo cosmic reaxff_mu reaxff_chi reaxff_gamma qsolver qiterations |
| Type | Keyword |
| Use | if specified this allows a periodic calculation to be |
| run when a solid is not charge neutral. This implies | |
| that a neutralising uniform charge background will be | |
| added. | |
| Note that defect calculation cannot be performed when | |
| this term is present. | |
| See also | madelung |
| Type | Keyword |
| Use | Causes the charges on the segments of the solvent |
| accessible surface to be output, as well as the total | |
| charge and dipole(s). | |
| See also | cosmo cosmic qonsas |
| Type | Keyword |
| Default | Raman susceptibilities not calculated |
| Use | Causes Raman susceptibilities to be calculated and output. |
| The quantities output are the derivatives of: | |
| (1/(4*pi))(epsilon_infinity - delta_ab) | |
| Here epsilon_infinity is the high frequency dielectric | |
| constant tensor and delta_ab is the delta function that is | |
| one for xx, yy, zz and otherwise 0. This quantity is the | |
| same as q.(D**-1).q, where q is the vector shell charges, | |
| and D is the matrix of shell-shell second derivatives. | |
| Note that this will only have an effect if a shell model is | |
| used since it involves the high frequency polarisability. | |
| It also requires that a property calculation is performed | |
| since it uses the high frequency dielectric constant tensor. | |
| NB: The calculation of this quantity requires analytical | |
| third derivatives and so is only available for certain | |
| potential models (pairwise, three- and four-body terms). | |
| See also | property rdirection eckart |
| Type | keyword |
| Use | print out region 2a in the output |
| See also | region_1 regi_before defect |
| Type | Keyword |
| Default | output region 1 only after a minimisation |
| Use | Output region 1 list before the start of a defect calculation. |
| See also | defect centre size region_1 bulk_noopt |
| Type | Keyword |
| Default | no relaxation during fitting |
| Use | Invokes fitting to structural displacements on relaxation rather than |
| to the derivatives. This also means any observables are fitted at the | |
| optimised rather than experimental structure. There is no need to give | |
| "simul" as an option if relax fitting. This method should only be used | |
| once a reasonable set of potentials have been obtained by conventional | |
| fitting, otherwise the optimisations may fail. It is also an order of | |
| magnitude more expensive in cputime! | |
| See also | fit simultaneous |
| Type | Keyword |
| Use | Changes the eigenvector phases so the component with the largest magnitude is |
| all real for all eigenvectors, and renormalizes to unity. This makes visualisation | |
| of eigenvectors simpler. Called as a dependent keyword by other keywords, for | |
| example PDF. | |
| See also |
| Type | Keyword |
| Use | Causes the region 2 matrices, derived from the bulk |
| second derivatives, to be restored from disk (fort.44) | |
| for use in restarts. This is important for large | |
| bulk materials where the second derivatives are | |
| expensive to recalculate. The fort.44 file must have | |
| been generated in a previous run. | |
| See also | save defect |
| Type | Keyword |
| Use | Invoke the Rational Function Optimisation (RFO) method for searching |
| for stationary points. By default the optimiser searches for the | |
| minimum and may prove advantageous over the standard optimiser if the | |
| Hessian is ill-conditioned. Also the Newton-Raphson method will yield | |
| transition states if started too close to one, whereas the RFO method | |
| will find the minimum. | |
| Transition_state is a special case of rfo, in which the optimiser is | |
| to converge to a first order transition state. | |
| For transition state calculations, the updating scheme is DFP by | |
| default instead of BFGS as the former is not biased towards positive | |
| definiteness of the Hessian. | |
| See also | optimise transition_state |
| Type | Keyword |
| Use | Causes the region 2 matrices, derived from the bulk |
| second derivatives, to be saved to disk as fort.44 | |
| for use in restarts. This is important for large | |
| bulk materials where the second derivatives are | |
| expensive to recalculate. | |
| See also | restore defect |
| Type | Keyword |
| Use | Set flags for shell only optimisation (equivalent to optical |
| calculation). It is still necessary to specify "conp" or "conv" | |
| so that the cell flags are correctly set. | |
| See also | conp conv noflags breathe nobreathe cellonly isotropic ocell |
| Type | Keyword |
| Use | If numerical third derivatives are being used to determine the force constants |
| for output to ShengBTE then this uses an algorithm in which only the cores are | |
| finite differenced and the shells are optimised at every point. This is typically | |
| less numerically precise than the default method where the shells are handled by | |
| matrix multiplication. | |
| See also | numerical output num3 |
| Type | Keyword |
| Use | Use the simplex algorithm for fitting instead of unit matrix with BFGS method. |
| See also | fit simul relax genetic fbfgs delta |
| Type | Keyword |
| Default | no relaxation |
| Use | Allows simultaneous relaxation of shells during fitting, |
| including both position and radius. | |
| See also | relax fit breathe noflags |
| Type | Keyword |
| Use | Calculate energy only - default calculation. |
| See also | optimise gradient md montecarlo |
| Type | Keyword |
| Default | site energies not printed |
| Use | Tells GULP to write out the site energies if possible. |
| Currently this is implemented in routines that compute | |
| the forces and so you should use "gradients", "opti" | |
| or "md" in the run type to ensure there is some output. | |
| See also | gradients optimise md |
| Type | Keyword |
| Use | Turns on calculation of variable charges using the formulation |
| of Streitz and Mintmire. Here the charge is partitioned into a | |
| fixed nuclear point charge and a variable charge distribution | |
| with the shape of a 1s orbital. To use this option parameters | |
| must be specified with the smelectronegativity option too. | |
| If the keyword is given as "smzz" then the Znuc_i-Znuc_j energy | |
| term given by Streitz and Mintmire, but neglected as part of the | |
| two-body energy is included explicitly. | |
| See also | smelectronegativity eem qeq pacha gasteiger noqeem external_potential |
| eembond |
| Type | Keyword |
| Use | Specifies that the details of shell optimisations during MD be output |
| See also | shellmass iterations md |
| Type | Keyword |
| Use | Requests that a spatial decomposition algorithm is used wherever |
| possible to try to achieve linear scaling with system size. | |
| NB: The minimum image approach is incompatible with the spatial | |
| algorithm and so if both are specified the spatial algorithm will | |
| be used. | |
| See also | rcspatial minimum_image |
| Type | Keyword |
| Use | Use the smoothed particle mesh Ewald sum where possible instead of the |
| standard Ewald sum. Note that this option only currently has first | |
| derivatives and does not support the calculation of site energies or | |
| use of multiple regions. The main use for molecular dynamics or optimisation | |
| of large systems. Note that the values of rspeed and qgrid should be tuned | |
| to give the best performance for the desired precision. | |
| NB: This keyword is currently incompatible with variable charge models, | |
| calculation of site energies and atomic stresses. | |
| See also | accuracy rspeed qgrid bspline |
| Type | Keyword |
| Use | Run a static optimisation first before the free energy energy minimisation. |
| This should always be done unless restarting a job from a previously | |
| optimised structure. However, because this would negate the effects of a | |
| restart the default action is not to do this. | |
| See also | phonon nozeropt free_energy zsisa lowest_mode |
| Type | Keyword |
| Use | Use steepest descents weighted by the average diagonal Hessian |
| element instead of the diagonal elements multiplying the gradients. | |
| See also | unit numdiag positive conjugate lbfgs dfp |
| Type | Keyword |
| Use | Use algorithms, where possible, that involve storing a table of |
| interatomic vectors that lie within the cutoff distance. Currently | |
| this applies only to molecular dynamics. The idea is that by reducing | |
| the frequency with which the vectors are searched for, the calculation | |
| will be considerably speeded up in return for a small loss of precision. | |
| The frequency of updating, controlled by the "resetvectors" option, | |
| should be tested for the particular system of study. | |
| See also | resetvectors extracutoff |
| Type | Keyword |
| Use | Instead of using the actual unit cell as input/output, a reference |
| cell is used along with a specified set of strains to record the | |
| change in the cell. | |
| See also | scan_cell ocell vectors cell cellstrain |
| Type | Keyword |
| Use | Causes the stresses to be output at the final geometry. This is |
| the same as the strain derivatives divided by the volume and | |
| converted to GPa, plus correction for any external pressure. | |
| See also | atomic_stress |
| Type | Keyword |
| Use | Calculate the thermal conductivity of a solid at a given |
| temperature. This method uses a gamma point phonon calculation | |
| for a supercell to estimate the thermal conductivity using the | |
| method of Allen and Feldman, Phys. Rev. B, 48, 12581 (1993). | |
| The output includes the mode diffusivities, Di (in cm^2/s), | |
| and the overall thermal conductivity (in W/(m.K)). Note that | |
| in this approximation the precise value obtained depends on | |
| the degree of broadening of the density of states, controlled | |
| by the broaden_dos option, the drop tolerance for the Lorentzian | |
| broadening function, the temperature used, and finally the size | |
| of the supercell (until converged with increasing size). Also | |
| note that the non-analytic correction to the phonons at gamma | |
| is turned off for a thermal conductivity calculation. | |
| In order to correctly allow for the acoustic mode contribution | |
| to thermal conductivity then a lower bound frequency should be | |
| specified for the Allen-Feldman contribution and an analytic | |
| integration used, as described under the omega_af option. | |
| NB: Here the heat capacity for the modes is computed using the | |
| full quantised expression from lattice dynamics, rather than | |
| approximating the value from equipartition, as used in some | |
| other work. | |
| If the thermal conductivity is required more accurately and for | |
| ordered solids then GULP can write out the files required for | |
| use with the program ShengBTE that implements the Boltzmann | |
| Transport Equations. To obtain the thermal conductivity via this | |
| route the steps are: | |
| 1) Run a GULP calculation to optimise the structure and compute | |
| the gamma point phonons with the option "output shengbte" | |
| specified. Note that the third order force constants will be | |
| computed analytically if possible, or numerically if they are | |
| not available. To force the use of numerical third derivatives | |
| the keyword "num3" can be specified. It is important to note | |
| that the range of third order force constants output depends | |
| on the size of the supercell specified using the "super" option. | |
| 2) Modify the file CONTROL to ensure that the correct temperature | |
| k point sampling (ngrid) and broadening are specified for your | |
| system. | |
| 3) Use the files CONTROL, FORCE_CONSTANTS_2ND and FORCE_CONSTANTS_3RD | |
| as the inputs for ShengBTE. | |
| 4) Assuming the run is successful then the final overall thermal | |
| conductivity will be given in the file BTE.kappa_scalar as the | |
| last line (converged value from final iteration). | |
| Alternatively GULP can use Alamode (if installed) to compute the | |
| thermal conductivity and phonon lifetimes. To do this it is important | |
| to set the environment variable ALAMODE_DIR to point to the root | |
| directory of Alamode. | |
| See also | broaden_dos temperature lorentzian_tolerance omega_af |
| groupvelocity output num3 supercell ghost_supercell | |
| alamode ala_disp ala_cutoff |
| Type | Keyword |
| Use | Invoke RFO optimisation to find nearest stationary point with one |
| negative Hessian eigenvalue. More general optimisations to transition | |
| states of any order can be performed using the RFO method. | |
| Important note - a transition state optimisation will only lead to | |
| one negative phonon frequency if the calculation is run without any | |
| crystal symmetry. | |
| See also | optimise rfo |
| Type | Keyword |
| Use | By default the UFF generation rules use a harmonic potential for the |
| bonded interaction. By specifying this keyword, the Morse potential | |
| is used instead of harmonic. | |
| See also | uff1 |
| Type | Keyword |
| Use | By default, if GULP sets the flags for a system automatically then one |
| atom will be fixed to remove translational invariance, which would be | |
| fatal to a Hessian based optimiser. For first derivative methods, there | |
| is no such need and they may work better by not fixing any atoms. The | |
| unfix keyword tells GULP not to fix any of the atoms. | |
| See also | optimise noflags conp conv fix_atom |
| Type | Keyword |
| Use | Use unit diagonal matrix as starting point for Hessian. |
| Can be useful when exact Hessian is ill-conditioned. | |
| See also | numdiag dfp positive conjugate lbfgs |
| Type | Keyword |
| Use | Specifies that an alternative reciprocal space algorithm is used in |
| which the inner loop is over k vectors and the outer (parallelised) | |
| loop is over atoms. This may scale better on some platforms, but is | |
| usually slower overall. | |
| See also | rspeed accuracy index_k ewaldrealradius |
| Type | Keyword |
| Default | Reuss convention for bulk/shear modulus |
| Use | Specifies that the Voigt convention is used for the bulk |
| modulus. The Voigt convention takes the average of the | |
| elastic constants in the 1-3 x 1-3 block. | |
| See also | bulk_modulus shear_modulus elastic fit observables |
| hill young poisson |
| Type | Keyword |
| Use | Sets the average potential across all lattice sites to be |
| zero. This allows comparison of the site potentials to be | |
| made more readily between the bulk and molecular/surface | |
| situations. | |
| See also | potential |
| Type | Keyword |
| Use | perform free energy minimisation in the Zero Static Internal Stress |
| Approximation (ZSISA) - this implies that only the strain derivatives | |
| with respect to the free energy are used while the internal derivatives | |
| neglect the free energy contribution. This approach is equivalent to | |
| the old numerical method of free energy minimisation. Note this keyword | |
| does not apply to molecules! | |
| See also | free lowest_mode shrink |
| Type | Option |
| Format | 3coulomb <intra/inter> <bond> <nbeq/nbne nbond> |
| atom1 atom2 atom3 scale <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 | |
| Units | scale in fractional, distances in Angstroms |
| Use | Coulomb subtraction between atoms that are connected by a three-body term: |
| E(three) = - scale.q2.q3/r23 | |
| where q2 and q3 are the charges of the atoms 2 and 3. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger bcross lin3 |
| urey-bradley murrell-mottram bacross hydrogen-bond equatorial | |
| uff3 bagcross |
| Type | Option |
| Format | absdipolemoment |
| value <weight> | |
| Units | Debye |
| Default | no dipole moment to be fitted |
| Use | Subsection of observables, used for specifying an experimental |
| absolute dipole moment for fitting. Here the square root of the | |
| dipole moment components along each axis are used so that the | |
| quantity is rotationally invariant. | |
| See also | observables |
| Type | Option |
| Format | absolute_coordinates |
| atom_no x y z | |
| Units | Angstroms |
| Use | Specifies the absolute Cartesian coordinates of the atoms. Used for |
| restarting MD calculations and determining properties, such as | |
| diffusion coefficients, where the migration across cell boundaries | |
| must be correctly tracked. | |
| See also | md initial_coordinates |
| Type | Option |
| Format | accelerations <no._of_accelerations> |
| atom_no (acceleration_x acceleration_y acceleration_z) x no. of accelerations | |
| Units | Angstroms / ps in powers appropriate to order |
| Default | None |
| Use | Specifies the current Cartesian accelerations in an MD simulation and |
| can be used for restarting such a run. Can also be used to set the | |
| initial values. Depending on the algorithm, different orders of acceleration | |
| are required. For example, Gear fifth order requires 4, and velocity | |
| Verlet requires 1. | |
| See also | md velocities |
| Type | Option |
| Format | accuracy <exponent> <<Euler-Maclaurin_order> <maximum-cell> <acc-1D>> |
| Units | none |
| Default | 12.0 < 4 50 8.0> |
| Use | Controls the accuracy of the electrostatic summations. Note : the last two |
| values only apply to 1-D systems. The first value is the target number of | |
| converged significant figures in the electrostatic energy or the fractional | |
| uncertainty in the electrostatic energy, where the value is used as an | |
| exponent (i.e. 10**-(exponent)). This determines the real and reciprocal | |
| space cut-offs of the Ewald sum (3-D) and Parry sum (2-D) for a given value | |
| of rspeed. | |
| For 1-D systems a direct real space approach is used, as per CRYSTAL. Here | |
| the energy is converged to the precision specified by acc-1D by searching | |
| for the number of neutral cells that must be included in each direction in | |
| the sum. The maximum-cell indicates the upper bound to be used while the | |
| second optional parameter is the order of the series used in the numerical integrals. | |
| Generally the default values should be sufficient. | |
| See also | rspeed veck index_k spme |
| Type | Option |
| Format | ala_cutoff cutoff_harm cutoff_cubic <none> <au> |
| Units | Angstrom, unless au is specified in which case it will be atomic units |
| Default | 8.0 Angstroms for both harmonic and cubic force constants. |
| Use | Specifies the force constant cutoff (distance beyond which force |
| constants are assumed to be zero) for the thermal conductivity | |
| calculation with Alamode. Note that the cost increases rapidly | |
| with the size of the cutoff since larger supercells are needed and | |
| more terms must be computed. Separate values can be specified for | |
| harmonic (cutoff_harm) and cubic (cutoff_cubic) terms, or a single | |
| value for both. If "none" is specified then no cutoff is applied | |
| (i.e. the cutoff is determined by the size of the cell input). | |
| See also | alamode ala_disp thermal_conductivity ala_shrink ala_processors |
| Type | Option |
| Format | ala_disp disp_harm disp_cubic <au> |
| Units | Angstrom, unless au is specified in which case it will be atomic units |
| Default | 0.005 / 0.01 for harmonic and cubic force constants, respectively. |
| Use | Specifies the displacements for finite difference calculation of the |
| harmonic (disp_harm) and cubic (disp_cubic) force constants when | |
| using Alamode. | |
| See also | alamode ala_cutoff thermal_conductivity ala_shrink ala_processors |
| Type | Option |
| Format | ala_processors ncore |
| Units | None |
| Default | Same number of cores as GULP is running on. |
| Use | Specifies the number of processors that will be used by Alamode. |
| Since the thermal conductivity calculation can be more expensive | |
| than the force constant evaluation, this allows more processors | |
| to be used for the Alamode part of the calculation. | |
| See also | alamode thermalconductivity ala_disp ala_cutoff ala_shrink |
| Type | Option |
| Format | ala_shrink ix <iy> <iz> |
| Units | ix, iy and iz are dimensionless integers |
| Default | 1 1 1 |
| Use | Specifies the shrinking factors in reciprocal space. The higher the |
| shrinking factor the more extensively k space is sampled. One value | |
| may be given, in which case the shrinking factor is used isotropically | |
| or three anisotropic values can be given. These shrinking factors will | |
| be used for calls to Alamode. | |
| See also | alamode thermalconductivity ala_disp ala_cutoff ala_processors |
| Type | Option |
| Format | anisotropic_pressure P_xx P_yy P_zz P_yz P_xz P_xy (for 3-D) |
| anisotropic_pressure P_xx P_yy P_xy (for 2-D) | |
| anisotropic_pressure P_xx (for 1-D) | |
| Units | GPa |
| Default | No anisotropic pressure |
| Use | This option allows the user to apply a general constant stress, such |
| as a uniaxial stress. Because the energy is not defined for anisotropic | |
| pressure, except via a set of integrals between states, then the use | |
| of force minimisation, rather than energy minimisation is required for | |
| optimisation. | |
| If both pressure and anisotropic pressure are specified then | |
| the two are added together. For anisotropic pressure, this must be | |
| specified after the structure otherwise the information may not be | |
| correctly processed since this depends on the dimensionality. | |
| Note that stresses are dependent on the cell orientation and so take | |
| care when specifying. | |
| See also | pressure force_minimisation |
| Type | Option |
| Format | ashift <ev/au/kcal/kjmol-1> |
| atomic_symbol value <1xflag> | |
| Units | eV (default), au, kcal or kJmol-1 |
| Default | 0.0 |
| Use | Specifies a species specific energy shift (i.e. a one-body potential). |
| Usually this term is not needed since it is just a constant. However, | |
| it may prove useful during fitting of ab initio energy surfaces. | |
| e.g. | |
| ashift | |
| O2 0.34 | |
| The above would apply an energy shift to each O2 atom in a structure | |
| of 0.34 eV. | |
| See also | shift sshift |
| Type | Option |
| Format | atomab |
| <Atomic_symbol/atomic_number> A B <2 x flags for fitting> | |
| Units | eV*Angs**m and eV*Angs**n |
| Use | Specifies A and B values for each species type to be used in |
| combination rules to obtain Lennard-Jones potential parameters | |
| where specified. | |
| See also | epsilon lennard |
| Type | Option |
| Format | aver sum_velocity_squared sum_energy sum_virial sum_temperature sum_cons |
| sum_cst no_of_averaging_points | |
| Units | Angstroms and ps as appropriate. |
| Use | Specifies various sum of values required for correct restarting of the |
| averages during MD. | |
| See also | md caver cfaver current_time absolute_coordinates |
| Type | Option |
| Format | axilrod-teller <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) <rmin(2-3)> | |
| rmax(2-3) <flag> | |
| Units | k in eV*Angstroms**9, rmin & rmax in Angstroms |
| Default | none |
| Use | Axilrod-Teller three-body potential: |
| E(three) = k (1+3*cos(theta1)*cos(theta2)*cos(theta3)) | |
| ------------------------------------------- | |
| (r12*r13*r23)**3 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2, 2-3 and 1-3 are bonded. | |
| See also | three-body angle exponential stillinger-weber bcross urey-bradley |
| murrell-mottram bacross hydrogen-bond equatorial uff3 lin3 3coulomb | |
| bagcross |
| Type | Option |
| Format | bacoscross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K1 K2 r1 r2 theta0 <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <5*flags> | |
| Units | K1 and K2 in eV/Angs, r1 and r2 in Angstroms, theta0 in degrees |
| Use | Bond-angle cosine cross term three body potential |
| E(three) = [K1*(r12 - r1) + K2*(r13 - r2)].(cos(theta)-cos(theta0)) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bcross hydrogen-bond equatorial lin3 uff3 bacross | |
| 3coulomb bagcross |
| Type | Option |
| Format | bacross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol/degree> |
| atom1 atom2 atom3 K1 K2 r1 r2 theta0 <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <5*flags> | |
| Units | K1 and K2 in eV/(Angs*rad), r1 and r2 in Angstroms, theta0 in degrees |
| Use | Bond-angle cross term three body potential |
| E(three) = [K1*(r12 - r1) + K2*(r13 - r2)].(theta-theta0) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bcross hydrogen-bond equatorial lin3 uff3 | |
| bacoscross 3coulomb bagcross |
| Type | Option |
| Format | bagcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K r1 r2 theta0 m n p <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <4*flags> | |
| Units | K in eV/((Angs**(m+n))*(rad**p)), r1 and r2 in Angstroms, theta0 in degrees |
| Use | Bond-angle general cross term three body potential: |
| E(three) = K*[(r12 - r1)**m]*[(r13 - r2)**n].(theta-theta0)**p | |
| This potential is designed to represent general anharmonic coupling | |
| terms for a force field up to three-body terms. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bcross hydrogen-bond equatorial lin3 uff3 | |
| bacoscross 3coulomb bacross balcross |
| Type | Option |
| Format | balcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K r1 r2 isign n m p <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <3*flags> | |
| Units | K in eV/(Angs**(m+p))), r1 and r2 in Angstroms |
| Use | Bond-angle linear cross term three body potential: |
| E(three) = K*[(r12 - r1)**m]*[(r13 - r2)**p].(1 + isign*cos(n*theta)) | |
| This potential is designed to represent anharmonic coupling | |
| terms for a force field up to three-body terms for linear angles. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bcross hydrogen-bond equatorial lin3 uff3 | |
| bacoscross 3coulomb bacross bagcross |
| Type | Option |
| Format | baskes <a4> <n> |
| atom1 atom2 Ec A alpha r0 Z1 wF d <rmin> rmax <5xflags> | |
| Z2S_1 s_1 Z2S_2 s_2 | |
| if the potential is specified as "baskes a4" then the format is: | |
| atom1 atom2 Ec A alpha r0 Z1 wF d gamma lambda <rmin> rmax <7xflags> | |
| Z2S_1 s_1 Z2S_2 s_2 | |
| Z2S and s are only input if n > 0 | |
| Units | Ec in eV; gamma and r0 in Angstroms; A, Z1, Z2S, s, alpha, d, wF and lambda are unitless |
| Default | None, n=0 |
| Use | This option specifies the two-body potential between atoms need for the MEAM |
| method. The form is constructed based on the difference between the Rose | |
| equation of state and the form of the embedding function for a reference | |
| structure (such as fcc, bcc, hcp, etc). | |
| The form of the potential is: | |
| E = - (2/Z1)*Ec*{(1+a+d*a**3)*exp(-a) + A*(rho_ref(r)/rho0)*ln((rho_ref(r)/rho0))} | |
| unless "a4" is specified in which case there is an extra term: | |
| E = - (2/Z1)*Ec*{(1+a+d*a**3+gamma*a**4*exp(-lambda*a**2)/r)*exp(-a) + | |
| A*(rho_ref(r)/rho0)*ln((rho_ref(r)/rho0))} | |
| where: | |
| Z1 = the number of nearest neighbours in the reference structure (NB no fitting flag) | |
| Ec = cohesive energy of the reference structure | |
| r0 = equilibrium distance in the reference structure | |
| rho0 = density for equilibrium reference structure (comes from meam_functional) | |
| rho_ref(r) = density for reference structure when distance is r. | |
| a = (alpha/r0)*(r-r0) | |
| d = unitless factor that modifies shape of equation - usually 0.0 | |
| wF = unitless factor that weights the i vs j contributions - for pure phases this is | |
| 1.0, but for alloys will be 0 < wF < 1. For phase of composition AB3 with atoms | |
| input in the order A then B, then wF will be 0.25 (the weight for component A). | |
| If B is input first then it would be 0.75. | |
| gamma = distance factor that modifies shape of equation | |
| lambda = exponent that modifies the shape of the equation | |
| The value of rho_ref(r) is given by the following expression: | |
| rho_ref(r) = sqrt[ sum(l=0->3) s_l*t_l*rho_l(r)**2 ] | |
| where rho_l = exp(-(b_l/r0)*(r-r0)) | |
| here t_l is the coefficient of the l'th order density square in MEAM and s_l is a | |
| geometric factor for the reference structure in question that depends on the l'th | |
| order. Note that s_0 is equal to Zd**2 in the notation of Baskes and co-workers. | |
| NB: In earlier versions of GULP the b and t coefficients were specified explicitly | |
| for this potential. However, they are now obtained directly from the MEAM density | |
| in order to avoid duplication. Similarly the rho0 used to be specified, but this is | |
| now obtained from the MEAM functional. | |
| If n = 0 (default) then the 1NN form of MEAM is used. | |
| If n > 0, then the 2NN form of MEAM is selected instead. Here the pair potential | |
| is generated according to: | |
| phi(R) = psi(R) + sum(i=1,n) (-Z2S/Z1)**i.psi(s**i.R) | |
| where: | |
| Z2S = the number of second neighbours in the reference structure x screening function, S | |
| s = is the scale factor for the second neighbour distance relative to the first one | |
| phi = effective pair potential | |
| psi = (2/Z1)*(Ec(R)-F(rho(R)) | |
| See also | meam_functional meam_density |
| Type | Option |
| Format | bbar at.no. <bbar> |
| Units | Angstrom |
| Use | Used within element option input block, overwrites the default neutron |
| scattering length for a specified element. (at. no. or symbol may be used) | |
| See also | coreinfo element siginc |
| Type | Option |
| Format | bcoscross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K b m n r1 r2 <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <4*flags> | |
| Units | K in eV/Angs**2, r1 and r2 in Angstroms, b, m and n are unitless. |
| Use | Bond-bond cross term three body potential with cosine angle dependance: |
| E(three) = K * (1 + b*cos(n.theta)**m) * (r12 - r1) * (r13 - r2) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bacross bcross hydrogen-bond equatorial lin3 uff3 | |
| 3coulomb bagcross |
| Type | Option |
| Format | bcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K r1 r2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> | |
| rmax23 <3*flags> | |
| Units | K in eV/Angs**2, r1 and r2 in Angstroms |
| Use | Bond-bond cross term three body potential: |
| E(three) = K * (r12 - r1) * (r13 - r2) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger urey-bradley |
| murrell-mottram bacross hydrogen-bond equatorial lin3 uff3 3coulomb | |
| bagcross |
| Type | Option |
| Format | becke_johnson_c6 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 C6 r0 <rmin> rmax <2*flags> | |
| Units | C6 in eV*Angs**6, r0 in Angs |
| Default | None |
| Use | Specifies potential parameters for the Becke-Johnson form of damped C6 term. |
| The energy is of the form: | |
| E = - C6/(r**6 + r0**6) | |
| See also | damped_dispersion grimme_c6 |
| Type | Option |
| Format | best n <every_m> <only> |
| Default | Best 2 candidates at the end of global search may be optimised. |
| Use | Part of ga options section. If used then the best 'n' candidates |
| found (after every m iterations) may be optimised at the end. | |
| If 'only' specified then a maximum of n candidates may be optimised | |
| ie the best n from iterations m, 2m, 3m, ... | |
| See also | genetic predict |
| Type | Option |
| Format | blocksize <atoms/sas> nblocksize |
| Default | atoms = 1, sas = 12 |
| Units | none |
| Use | This parameter is an integer that decides how the second |
| derivatives are divided over the processes when running | |
| in parallel. The number is used to control the efficiency | |
| of the parallel work in Scalapack / Blacs, but also in | |
| GULP itself. The real number used for atoms is actually | |
| 3*nblocksize in order to divide the coordinates of the atoms | |
| so that the x, y, z components of an atom are all on the same | |
| node. If nblocksize is too large then load balance will | |
| be an issue, while if it is too small then Scalapack will | |
| lose efficiency. | |
| Specifying atoms or sas allows control over the individual | |
| blocksizes for matrices relating to atoms, or the solvent | |
| accessible surface, respectively. | |
| NB: The blocksize must be a factor of the number of atoms, | |
| and the number of shells, if appropriate, in each configuration. | |
| Therefore 1 is a safe value that will always work, but other | |
| values may be possible depending on the system. | |
| See also | matrix_format maths |
| Type | Option |
| Format | boattractive <zrl> |
| atom1 <atom2> alpha m n lambda <3*flags> | |
| or | |
| boattractive theta <zrl> | |
| atom1 <atom2> alpha m n lambda c d h <6*flags> | |
| or | |
| boattractive kumagai <zrl> | |
| atom1 <atom2> alpha m n lambda c1 c2 c3 c4 c5 h <9*flags> | |
| or | |
| boattractive mmp <zrl> | |
| atom1 <atom2> alpha m n lambda c0 c1 c2 c3 c4 <8*flags> | |
| NB The value of m cannot be fitted and therefore there is no flag | |
| Units | lambda in 1/Angstroms |
| All other quantities are unitless. | |
| Default | If atom2 is not given then it will be set to be atom1 |
| Use | Sets the parameters for the bond-order in the attractive term as |
| given by | |
| BOa = (1 + (alpha*zeta)**n)**(-1/2n) | |
| For case without "theta" sub-option; | |
| zeta = Sum(rik) [f(rik).exp(lambda**m.(rij-rik)**m)] | |
| else; | |
| zeta = Sum(rik) [f(rik).g(theta).exp(lambda**m.(rij-rik)**m)] | |
| f(rik) = cosine taper function | |
| g(theta) = 1 + (c/d)**2 - c**2/[d**2 + (h - cos(theta))**2] | |
| Note that the cut-offs are derived from the values for the corresponding | |
| botwobody potential. | |
| If the "zrl" sub-option is specified then the alternative form | |
| of Billeter et al (Phys. Rev. B, 73, 155329 (2006)) is used in which | |
| the exponential part of zeta becomes: | |
| exp((lambda_ij*rij - lambda_ik*rik)**m) | |
| Because lambda is now specific to each pair of atoms, it is recommended | |
| that the zrl form is specified for all bond-order potentials or none, | |
| rather than mixing forms. | |
| If the "kumagai" sub-option is specified then the theta term becomes: | |
| g(theta) = c1 + g_o(theta)*g_a(theta) | |
| g_o(theta) = c2*(h - cos(theta))**2/(c3 + (h - cos(theta))**2) | |
| g_a(theta) = 1 + c4*exp(-c5*(h-cos(theta))**2) | |
| If the "mmp" sub-option is specified then the theta term becomes: | |
| g(theta) = (sum(n=0->4) c_n*cos(n*theta))**2 | |
| This is the form of the angular potential required for the MMP potential | |
| as given in Monteverde et al, J. Phys. Condens. Matter, 25, 425801 (2013) | |
| NB: Because of the introduction of pair-wise specific terms, input files | |
| from earlier versions will needed to be changed for mixed element systems. | |
| See also | botwobody borepulsive bocharge boselfenergy bocoordination |
| Type | Option |
| Format | bocharge <staper> |
| atom1 atom2 deltaQ Rmin Rmax | |
| Units | au |
| Default | None for potential / use cosine taper |
| Use | Specifies the parameters for the taper function used in determining |
| bond order charges as a function of environment. The charge on an | |
| ion is determined as: | |
| Atom 1: Q = sum [ - deltaQ*H(r) ] | |
| Atom 2: Q = sum [ + deltaQ*H(r) ] | |
| Here the sum is over all atoms of the approriate type within the | |
| cutoff radius, Rmax. H(r) is taper function that acts between Rmin | |
| and Rmax. In the original paper of Jiang and Brown a cosine taper | |
| is used and this is the default. However, the sub-option allows the | |
| sine taper of Watanabe et al (Jpn. J. Appl. Phys. 38, L367 (1999)) | |
| to be used which has better behaviour for the second derivatives at | |
| the cutoff. | |
| See also | botwobody borepulsive boattractive boselfenergy sw2jb sw3jb |
| bocoordination |
| Type | Option |
| Format | bocnswitch zb zt |
| Units | None |
| Default | zb = 0.20039, zt = 0.49751 |
| Use | Specifies the 2 universal values that are used in the coordination |
| switching function in the Tersoff ZRL model. See paper below for | |
| more information, and this is the source of the default values: | |
| Billeter et al, Phys. Rev. B, 73, 155329 (2006). | |
| NB: zt+zb must be less than 1 and zt-zb must be greater than 0 | |
| NNB: The original switching function in the above paper leads to | |
| a highly discontinuous energy and so a modified form is implemented | |
| here in 2 ways (the int(z) term is left out and sin is replaced by cos) | |
| See also | botwobody borepulsive boattractive bocharge sw2jb sw3jb |
| boselfenergy bocoordination bocntolerance |
| Type | Option |
| Format | bocntolerance tol |
| Units | None |
| Default | tol = 0.000001 |
| Use | Specifies the tolerance on the coordination number from an |
| integer to trigger calculating derivatives. | |
| See also | botwobody borepulsive boattractive bocharge sw2jb sw3jb |
| boselfenergy bocoordination bocnswitch |
| Type | Option |
| Format | bocoordination |
| atom1 c1 c2 z0 E0 <4*flags> | |
| Units | c1, c2 and E0 in eV |
| Default | c1, c2 = 0, E0 = 0, z0 = 0 |
| Use | Specifies the Tersoff augmentation term based on coordination number, as |
| well as the self energy. These were proposed in the Tersoff ZRL form of | |
| Billeter et al, Phys. Rev. B, 73, 155329 (2006). | |
| E = c1*delta_z + c2*(delta_z**2) + E0 | |
| See also | botwobody borepulsive boattractive bocharge sw2jb sw3jb |
| boselfenergy bocnswitch bocntolerance |
| Type | Option |
| Format | bondtype species1 species2 type_of_bond <regular/cyclic/exocyclic> |
| Default | type_of_bond = single |
| Use | Sets the default type of bond between two species. |
| Valid bond types are: single, double, triple, quadruple, resonant, | |
| amide, custom, half, quarter, and third. For example, a default | |
| double bond between two carbons of type C2 can be specified as: | |
| bondtype C2 C2 double | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | molecule molq molmec bond connect noautobond nobond |
| Type | Option |
| Format | borepulsive <zrl> |
| atom1 <atom2> alpha m n lambda <3*flags> | |
| or | |
| borepulsive theta <zrl> | |
| atom1 <atom2> alpha m n lambda c d h <6*flags> | |
| or | |
| borepulsive kumagai <zrl> | |
| atom1 <atom2> alpha m n lambda c1 c2 c3 c4 c5 h <9*flags> | |
| or | |
| borepulsive mmp <zrl> | |
| atom1 <atom2> alpha m n lambda c0 c1 c2 c3 c4 <8*flags> | |
| NB The value of m cannot be fitted and therefore there is no flag | |
| Units | lambda in 1/Angstroms |
| All other quantities are unitless. | |
| Default | If atom2 is not given then it will be set to be atom1 |
| Use | Sets the parameters for the bond-order in the repulsive term as |
| given by | |
| BOr = (1 + (alpha*zeta)**n)**(-1/2n) | |
| For case without "theta" sub-option; | |
| zeta = Sum(rik) [f(rik).exp(lambda**m.(rij-rik)**m)] | |
| else; | |
| zeta = Sum(rik) [f(rik).g(theta).exp(lambda**m.(rij-rik)**m)] | |
| f(rik) = cosine taper function | |
| g(theta) = 1 + (c/d)**2 - c**2/[d**2 + (h - cos(theta))**2] | |
| Note that the cut-offs are derived from the values for the corresponding | |
| botwobody potential. | |
| If the "zrl" sub-option is specified then the alternative form | |
| of Billeter et al (Phys. Rev. B, 73, 155329 (2006)) is used in which | |
| the exponential part of zeta becomes: | |
| exp((lambda_ij*rij - lambda_ik*rik)**m) | |
| Because lambda is now specific to each pair of atoms, it is recommended | |
| that the zrl form is specified for all bond-order potentials or none, | |
| rather than mixing forms. | |
| If the "kumagai" sub-option is specified then the theta term becomes: | |
| g(theta) = c1 + g_o(theta)*g_a(theta) | |
| g_o(theta) = c2*(h - cos(theta))**2/(c3 + (h - cos(theta))**2) | |
| g_a(theta) = 1 + c4*exp(-c5*(h-cos(theta))**2) | |
| If the "mmp" sub-option is specified then the theta term becomes: | |
| g(theta) = (sum(n=0->4) c_n*cos(n*theta))**2 | |
| This is the form of the angular potential required for the MMP potential | |
| as given in Monteverde et al, J. Phys. Condens. Matter, 25, 425801 (2013) | |
| NB: Because of the introduction of pair-wise specific terms, input files | |
| from earlier versions will needed to be changed for mixed element systems. | |
| See also | botwobody boattractive bocharge boselfenergy bocoordination |
| Type | Option |
| Format | bornq n |
| i <xx/yy/zz/xy/xz/yz> Zeff <weight> | |
| Units | atomic units |
| Default | no Born effective charges to be fitted |
| Use | Subsection of observables, used for specifying values of |
| Born effective charges for fitting. Note that i is the | |
| atom number in the unit cell, not the asymmetric unit, | |
| and the two letter code indicates the tensorial component | |
| to be considered. Note: The Born effective charge tensor is | |
| antisymmetric (i.e. Zxy = - Zyx ) | |
| Example: | |
| bornq 1 | |
| 1 xx 1.95 | |
| Here n (after bornq) represents the number of lines of input | |
| to follow. | |
| Note: Born effective charges cannot currently be calculated | |
| with electronegativity equalisation. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| monopoleq qreaxff young poisson |
| Type | Option |
| Format | boselfenergy |
| atom1 Kq <rho> q0 | |
| Units | Kq in eV, rho in a.u., q0 in a.u. |
| Default | Rho = 1.0 |
| Use | Specifies the self energy for bond order charges, as introduced by |
| Jiang and Brown: | |
| E = Kq*exp(-rho/(q - q0)) if q > q0 for q0 > 0 | |
| or | |
| E = Kq*exp(rho/(q - q0)) if q > q0 for q0 < 0 | |
| else E = 0 | |
| See also | botwobody borepulsive boattractive bocharge sw2jb sw3jb |
| bocoordination |
| Type | Option |
| Default | both |
| Use | All subsequent potentials to be treated as both intra- |
| and intermolecular when molecule option is active. | |
| See also | molecule molq molmec inter intra |
| Type | Option |
| Format | botwobody <kcal/kjmol> <cosine/mdf/murty> |
| atom1 atom2 A B za zb rtaper rmax <4*flags> | |
| or | |
| botwobody combine <cosine/mdf/murty> | |
| atom1 atom2 chiR chiA <2*flags> | |
| Units | A and B in eV, za and zb in 1/Angstroms, rtaper and rmax in Angs |
| Default | none, taper = mdf |
| Use | Specifies the parameters for the twobody form of a bond-order |
| potential of the Tersoff form: | |
| E = f(r)[A.exp(-za.r).(BOr) - B.exp(-zb.r).(BOa)] | |
| where f(r) is a taper function that smooths the decay from rtaper | |
| to rmax, BOr and BOa are the bond orders for the repulsive and | |
| attractive terms, respectively. These terms are set by separate | |
| options. If the combine sub-option is specified then the parameters | |
| are generated using Tersoff's combination rules from the values for | |
| the corresponding element's self-self interaction. The chi values | |
| then scale the repulsive and attractive terms. | |
| The sub-options cosine, mdf and murty are used to select the form of | |
| taper that is used. Early versions of GULP used the cosine taper, but | |
| this leads to numerical instabilities in the second derivatives for some | |
| cases. For backwards compatibility it may be necessary to use cosine | |
| to reproduce results. The murty taper form was used by Kumagai et al | |
| in their form of the Tersoff potential along with the corresponding | |
| modified angular term. | |
| See also | borepulsive boattractive bocharge boselfenergy bocoordination |
| Type | Option |
| Format | box <dispersion/density> <size/number> value |
| Units | size in cm-1 |
| Default | number for dispersion = 25 |
| number for density = 64 | |
| Use | Allows the user to change the box size or number of boxes used for |
| outputting the phonon density of states or/and phonon dispersion | |
| curves. | |
| For example, to change the resolution of the phonon density of | |
| states to 10 cm^-1: | |
| box density size 10 | |
| See also | phonon dispersion shrink broaden_dos |
| Type | Option |
| Format | brenner |
| Use | Specifies that the REBO forcefield of Brenner et al (2002 variant) be |
| included in the energy calculation. Note that this is only available | |
| for the elements C, H, and O. The parameters for O are from the work | |
| of Ni, Lee and Sinnott (J. Phys.: Condens. Matter, 16, 7261 (2004), but | |
| with some changes from the authors that lead to improvements. Parameters | |
| are also available for F, but should not be used if oxygen is present. | |
| The option REBO is a synonym for this option. | |
| If the model number is given as 1 (i.e. "brenner 1") then the original | |
| Brenner model will be used. This option has parameters for C, H and Si | |
| using the extended parameter set given in Dyson and Smith, Surf. Sci., | |
| 355, 140 (1996) | |
| See also | spatial |
| Type | option |
| Format | bsm <exponential> <single_exponential> <kcal/kjmol> |
| if harmonic form: | |
| atom_symbol/atomic_number <core/shel> K r0 <2 x flags> | |
| if exponential form: | |
| atom_symbol/atomic_number <core/shel> K rho r0 <3 x flags> | |
| if single_exponential form: | |
| atom_symbol/atomic_number <core/shel> K rho r0 <3 x flags> | |
| Units | K in eVAngs**-2, r0 in Angstroms |
| K in eV, rho in Angstroms**-1 | |
| Defaults | Type = harmonic |
| Use | Specifies the breathing shell force constant, K, and |
| equilibrium radius, r0, for the spherical breathing | |
| shell model. | |
| E(bs) = 1/2 * K * (r - r0)**2 | |
| or the constants of the exponential restoring term: | |
| E(bs) = K * [exp(rho*(r-r0)) + exp(-rho*(r-r0))] | |
| or the constants of the single_exponential restoring term: | |
| E(bs) = K * exp(rho*(r-r0)) | |
| See also | breathe nobreathe simultaneous |
| Type | Option |
| Format | bspline norder |
| Units | none |
| Default | norder = 8 |
| Use | Specifies the B-spline interpolation order in SPME. |
| See also | rspeed veck accuracy ewaldrealradius spme qgrid |
| Type | Option |
| Format | buck4 <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 A rho C <rmin> cut1 rminimum cut2 rmax <4*flags> | |
| Units | A in eV, rho in Angs, C in eV*Angs**6, distances in Angstroms |
| Default | none |
| Use | Four range Buckingham potential - optimisation flags for fitting (0/1) |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| The form of the potential is: | |
| from rmin to cut1 : E=Aexp(-r/rho) | |
| from cut1 to rminimum: E=a0+a1*r+a2*r**2+a3*r**3+a4*r**4+a5*r**5 | |
| from rminimum to cut2: E=b0+b1*r+b2*r**2+b3*r**3 | |
| from cut2 to rmax : E=-C/r**6 | |
| The potentials are subjected to the constraint that the functions and | |
| their first and second derivatives must be continuous at the boundary | |
| points, and also that the function must have a stationary point at | |
| rminimum (hopefully a minimum!). | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| Type | Option |
| Format | buckingham <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> |
| atom1 atom2 A rho C <rmin> rmax <3*flags> | |
| Units | A in eV, rho in Angs, C in eV*Angs**6 |
| If kcal is given : A in kcal, rho in Angs, C in kcal*Angs**6 | |
| If kjmol is given: A in kJmol-1, rho in Angs, C in kJmol*Angs**6 | |
| Default | none |
| Use | Buckingham potential - optimisation flags for fitting (0/1). |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A.exp(-r/rho) - C/r**6 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | c6 mm3buck slater |
| Type | Option |
| Format | buffered_lj <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 epsilon r0 delta gamma <rmin> rmax <4*flags> | |
| Units | epsilon in eV, r0, rmin and rmax in Angs |
| Default | none |
| Use | This option specifies the use of a buffer 14-7 Lennard-Jones potential. |
| The form is that used by AMOEBA for interactions: | |
| E = epsilon*[((1+delta)/(rho+delta))**7]*[(1+gamma)/(rho**7+gamma)-2] | |
| where rho = r/r0 | |
| See also | epsilon atomab c6 lennard |
| Type | Option |
| Format | bulk_modulus <weight> |
| Units | GPa |
| Default | bulk modulus not to be fitted |
| Use | Subsection of observables, used for specifying the experimental |
| bulk modulus for fitting. By default, the Reuss definition of | |
| the bulk modulus is used. However, the Voigt and Hill definitions | |
| can be used by specifying the appropriate keyword. | |
| See also | observables elastic sdlc hfdlc shear_modulus weight bornq |
| hill voigt young poisson |
| Type | Option |
| Format | cartesian <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> <angs/au> |
| at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> <%/T> | |
| or | |
| at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> <%/T> | |
| or | |
| at.sym. <species_type> x y z <charge> <occupancy> <radius> <3 x flags> <%/T> | |
| Units | Angstrom (default) or au for coordinates and electrons for charge, |
| radius in Angstroms | |
| Use | Cartesian coordinates and charges for all species in the unit cell. |
| Either the atomic number or the symbol may be supplied, followed | |
| by the species type. If the species type is omitted then it is | |
| assumed to be a core. Individual charges may be supplied for each | |
| ion or the charges for each type of species given using the | |
| species option. If the charges are given, then optionally site | |
| occupancies may also be specified. Optimisation flags are only | |
| needed if cellonly, conv, bulk, conp or shell are not specified. | |
| If the "region" sub-option is specified, then this tells the program | |
| the region number for the following atoms. In a surface calculation | |
| region 2 is held fixed. If the "rigid" sub-option is also specified | |
| after "region" then the region is created as a rigid body so that | |
| all atoms are constrained with respect to each other. By specifying | |
| a string after this containing x, y and/or z, the region may be | |
| allowed to move in particular directions. For example, in an interface | |
| calculation, a region could be specified that is allowed to only relax | |
| in the z direction by using: | |
| cart region 3 rigid z | |
| NB: The "region" sub-option must come before any of the other related | |
| sub-options. | |
| If a "T" is specified then the atom is marked for the translate option | |
| If a "%" is specified then the atom is part of a growth slice if it | |
| is in region 1 of a surface calculation. | |
| See also | fractional ditto spacegroup frame |
| Type | Option |
| Format | catomic_stress |
| 1 xx yy zz yz xz xy | |
| 2 xx yy zz yz xz xy | |
| etc | |
| Units | eV |
| Default | None |
| Use | Gives the current average of the atomic stresses needed from MD |
| Used for MD restart or information. | |
| See also | atomic_stress |
| Type | Option |
| Format | caver sum_a sum_b sum_c |
| sum_alpha sum_beta sum_gamma sum_vol | |
| Units | Angstroms for distances / degrees for angles |
| Use | The cumulative sum of all cell parameters and the volume is |
| specified so that the averages can be correctly determined | |
| on restarting. | |
| See also | md aver cfaver current_time absolute_coordinates |
| Type | Option |
| Format | cell <angs/au> |
| a b c alpha beta gamma <6 x optimisation flags> | |
| Units | Angstrom (default) or au for a, b, c and degrees for angles |
| Use | Crystallographic unit cell. Either "vectors" or "cell" |
| must be given. For optimisations or fitting, | |
| flags must be set unless cellonly, conp or conv are specified. | |
| See also | vectors scan_cell |
| Type | Option |
| Format | cellstrain strain_1 <strain_2> ... <strain_6> |
| Units | None |
| Default | 0.0 |
| Use | Specifies the initial strains to be applied to the unit cell. |
| The number of expected input values depends on the dimensionality of | |
| the system: | |
| 3-D => 6 strains (1=xx,2=yy,3=zz,4=yz,5=xz,6=xy) | |
| 2-D => 3 strains (1=xx,2=yy,3=xy) | |
| 1-D => 1 strain (1=xx) | |
| NB: These values are only used if strain is specified as a keyword. | |
| See also | strain cell vectors ocell scan_cell |
| Type | Option |
| Format | centre <atomic_symbol> <atom_number> <mol no.> <cart/frac> <x y z> |
| Use | Defines the location of the defect centre for a defect calculation. |
| The location can be specified in one of 4 ways; | |
| (1) Atomic symbol - places the defect centre at the atom site as | |
| specified at the start of the defect calculation. | |
| e.g. centre Mg1 shel | |
| (2) Atom number - places the defect centre at the site of the atom | |
| given by the number in the asymmetric unit. | |
| e.g. centre 3 | |
| (3) Cartesian coordinates - explicit specification of centre | |
| e.g. centre cartesian 0.2 1.3 0.53 | |
| (4) Fractional coordinates - explicit specification of centre | |
| based on the fractional coordinates. If "cart" or "frac" | |
| is not specified, this is the default. | |
| e.g. centre 0.25 0.25 0.25 | |
| (5) Molecule number - places the defect centre at the centre of | |
| the molecule whose number has been given. | |
| e.g. centre mol 2 | |
| See also | defect size region_1 regi_before |
| impurity vacancy impurity interstitial frequency bulk_noopt |
| Type | Option |
| Format | cfaver sum_lambdaR sum_lambdaV |
| Units | eV/Angstrom |
| Use | Specifies the sum of the values for the constraint force during an MD |
| run. Used to restart average values correctly. LambdaR is the distance | |
| constraint force in the velocity Verlet algorithm, while LambdaV is the | |
| velocity constraint force. | |
| See also | aver caver md |
| Type | Option |
| Format | cfm_fermi <kcal/kjmol> |
| atom1 atom2 k zeta r0 R w rmax <5*flags> | |
| Units | k in eV, r0, w and R in Ang, zeta in Ang**-1 |
| Default | none |
| Use | Specifies a Fermi-Dirac like inter potential for the central force model |
| as described by Bresme (J. Chem. Phys. 115, 7564 (2001)). | |
| E = [k/(1+exp(zeta*(r - r0)))]*t(r) | |
| where | |
| t(r) = 0.5*(1 + tanh((r-R)/w)) | |
| See also | cfm_harmonic cfm_power cfm_gaussian |
| Type | Option |
| Format | cfm_gaussian <kcal/kjmol> |
| atom1 atom2 k zeta r0 R w rmax <5*flags> | |
| Units | k in eV, r0, w and R in Ang, zeta in Ang**-2 |
| Default | none |
| Use | Specifies a Gaussian inter potential for the central force model |
| E = [k*exp(-zeta*(r - r0)**2)]*t(r) | |
| where | |
| t(r) = 0.5*(1 + tanh((r-R)/w)) | |
| NB: If w < 0 then t(r) = 1 | |
| See also | cfm_harmonic cfm_power cfm_fermi |
| Type | Option |
| Format | cfm_harmonic <kcal/kjmol> |
| atom1 atom2 k r0 R w rmax <4*flags> | |
| Units | k in eV/Ang**2, r0, w and R in Ang |
| Default | none |
| Use | Specifies a harmonic intra potential for the central force model |
| as described by Bresme (J. Chem. Phys. 115, 7564 (2001)). | |
| E = [0.5*k*(r - r0)**2]*[1 - t(r)] | |
| where | |
| t(r) = 0.5*(1 + tanh((r-R)/w)) | |
| NB: If w < 0 then t(r) = 1 | |
| See also | cfm_power cfm_gaussian cfm_fermi |
| Type | Option |
| Format | cfm_power <kcal/kjmol> |
| atom1 atom2 A power R w rmax <4*flags> | |
| Units | k in eV*Ang**power, w and R in Ang, power is unitless |
| Default | none |
| Use | Specifies a power-law inter potential for the central force model |
| as described by Bresme (J. Chem. Phys. 115, 7564 (2001)). | |
| E = [A/r**power]*t(r) | |
| where | |
| t(r) = 0.5*(1 + tanh((r-R)/w)) | |
| NB: If w < 0 then t(r) = 1 | |
| See also | cfm_harmonic cfm_gaussian cfm_fermi |
| Type | Option |
| Format | charge <number of charges to be varied> |
| list of labels whose charges are to be varied | |
| Units | none |
| Default | charges fixed |
| Use | Allows charges to be varied during fitting. Charge neutrality of |
| the lattice is automatically maintained, or no change in the | |
| total charge in the case of charged molecular systems. | |
| This directive must be part of the variables section. | |
| NB: DO NOT specify charges on the coordinate line for the atoms | |
| that you wish to be influenced by this option since they will be | |
| held fixed as they are NOT overwritten by the species option. | |
| See also | fit observables monopoleq |
| Type | Option |
| Format | chemshell_mode <init/calc> |
| Default | No chemshell output |
| Use | Sets the ChemShell output mode to be init or calc. |
| NB: Only is used if GULP has been compiled to work with | |
| recent versions of ChemShell. | |
| See also |
| Type | Option |
| Format | cmm <monopole/dipole/quadrupole/octopole> <cell_size> |
| Use | The cell multipole method (cmm) is a technique for speeding |
| up calculations on large systems by approximating all | |
| long range interactions by multipole expansions for | |
| all species within a given box. Because of the general | |
| nature of GULP a one level strategy is currently used | |
| with larger boxes than normal. The idea is that the | |
| short range cutoff is used to decide the box length | |
| so that all potentials only act between neighbouring | |
| boxes (given that not all potentials are readily | |
| expanded as a series in inverse distance). All other | |
| boxes act through the multipole expansion. At the | |
| moment this method is only available for clusters, as | |
| different techniques are more appropriate for periodic | |
| systems. | |
| After the option cmm the highest term included in the | |
| expansion can be given. Currently the octopole moment | |
| is the highest allowed and the quadrupole moment is | |
| the default. In cases where there are no short range | |
| potentials the cell size may be specified by the user. | |
| Note that because of the nature of the cell multipole | |
| method, second derivatives are not available with this | |
| technique. Correspondingly the minimiser will therefore | |
| default to BFGS starting from a unit Hessian. | |
| NOTE: cmm cannot be used in conjunction with EEM | |
| or QEq at the moment. |
| Type | Option |
| Format | configurations n <max_configs> <stepsize> |
| Default | 10 <10> <0 or 2> |
| Use | Part of ga options section. Specifies the number of configurations |
| to be used in the genetic algorithm procedure. Number of | |
| configurations must be even. If maximum number of configurations | |
| is greater than n then population will expand by stepsize (default | |
| 2) every iteration until <n=max> after which <stepsize> new random | |
| configurations will replace current <stepsize> worst configurations. | |
| <stepsize> also specifies how many of the best configurations | |
| survive into the next iteration without changing! | |
| See also | genetic predict |
| Type | Option |
| Format | connect atom1 atom2 <type_of_bond> <imageX> <imageY> <imageZ> |
| Default | If imageX, imageY, imageZ are not specified then take the nearest |
| image. | |
| Use | Forces a bond to be formed between atom1 and atom2 where atom1 and |
| atom2 are the numbers of atoms in the full unit cell. Requires one | |
| of the molecule keywords to be included to have any affect. The | |
| parameters imageX, imageY and imageZ specify which translational | |
| image of atom 2 should be used. Valid values are usually -1, 0, 1, | |
| where 0 means the image in the central cell, -1 means the image in | |
| the negative direction and +1 in the positive one. | |
| e.g. | |
| connect 1 2 1 0 -1 | |
| Optionally, the type of bond can be specified and this information | |
| can be used in applying the correct force field terms where applicable. | |
| Valid bond types are: single, double, triple, quadruple, resonant, | |
| amide, custom, half, quarter, third, cyclic, and exocyclic. For example, | |
| an exocyclic double bond can be specified as: | |
| connect 1 2 double exocyclic 1 0 -1 | |
| If not specified, the bonds are assumed to be single bonds. Note that | |
| the bond order used in UFF for each type_of_bond can be set using the | |
| option uff_bondorder. | |
| NB: For the connect information to be used one of the molecule | |
| keywords must be specified. | |
| See also | molecule molq molmec nobond bond noautobond uff_bondorder bondtype |
| Type | Option |
| Format | For geometric or (non-)linear fit: |
| constrain <fit> <no._of_constraints> | |
| nvari nfix coefficient <offset> <power> | |
| For geometric mean fit: | |
| constrain <fit> <no._of_constraints> | |
| nvari1 nvari2 mean nfix <coefficient> | |
| Default | no constraints, <coefficient>=1.0 |
| Use | Allows geometrical variables within configuration to be |
| constrained to be equal to preserve symmetry. By also specifying | |
| "fit" this allows the constraint of fitted parameters instead. | |
| option within variables section. | |
| nvari = no. of variable(s) to allow to vary | |
| nfix = no. of variable to be constrained | |
| coefficient = multiplier that relates values | |
| which is normally 1 or -1. | |
| offset = additive shift between the coordinates | |
| power = power to which value is raised (1 for a linear case) | |
| Geometric constraints: | |
| Variable numbers are coded as strains = 1-6, internal variable | |
| n of atom i = 3*(i-1)+n+6, n=1,3 => x,y,z and radius of atom | |
| i = 6+3*nasym+i, where nasym = no. of atoms in asymmetric unit. | |
| Now nvari and nfix can be entered as: | |
| atom1 x/y/z atom2 x/y/z coefficient offset | |
| e.g. 3 x 6 z 1.0 0.0 | |
| Radii can be entered as: | |
| atom1 r atom2 r coefficient offset | |
| e.g. 3 r 6 r 1.0 0.2 | |
| Additive use of geometric constraints is allowed so that an | |
| atom may be fixed at the centroid of two other atoms. When | |
| this is the case for 3-D systems, there is an ambiguity | |
| due to the presence of periodic replications. GULP will | |
| use the two nearest images for the constraints. | |
| Fitting constraints: | |
| Variable numbers refer to the number of the parameter as included | |
| in the variables table, which in general is the same as the order | |
| of specification in the input. If nvar1=nvar2 for geometric mean | |
| constraints then the square root of just one parameter is taken. | |
| Note that the variable numbers for the constraint command in | |
| fitting may be changed in the restart file relative to those in | |
| the input. This is to take account of the reordering of potentials. | |
| To input multiple constraints the number can be | |
| added after the constraint command. | |
| Note: The ability to raise the variable to power is currently only | |
| available for fitting constraint, though it shouldn't be needed | |
| for geometric variables anyway. | |
| See also | outcon |
| Type | Option |
| Format | contents |
| at no. <x> <y> <z> charge <coordination> | |
| at.sym. <species_type> <x> <y> <z> charge <coordination> | |
| Units | Fractional, electrons and dimensionless |
| Use | Internal contents of the first atom, charges and coordination |
| numbers for all species in the unit cell. Either the atomic | |
| number or the symbol may be supplied, followed by the species | |
| type. For now the species type can only be a core. Individual | |
| charges and coodination number may be supplied for each ion or | |
| for each type of species given using the species option. The | |
| average observed coodination numbers are used as default. | |
| Can only be used when keyword predict included or when a single | |
| calculation required and all coordinates are known/supplied. |
| Type | Option |
| Format | coordno <n> |
| i rcut cn <weight> | |
| Units | Angstroms for rcut |
| Default | no coordination numbers to be fitted |
| Use | Subsection of observables, used for specifying values of |
| coordination numbers for fitting. Here i is the atom number | |
| whose coordination number is to be fitted, rcut is the cutoff | |
| distance for including neighbours in the coordination shell, | |
| and cn is the target value of the coordination number. | |
| Example: | |
| coordno 1 | |
| 3 2.4 6 1000.0 | |
| NB This option is intended for use with relax fitting. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq qreaxff fbond fangle relax reaction |
| Type | Option |
| Format | cosh-spring <kcal/kjmol> |
| atom1 k2 d <2 x flags> | |
| Eqn | E = k2*d**2*(cosh(r/d) - 1) |
| Units | k2 in eV/Angs*2, d in Angs |
| Default | None |
| Use | Core-shell spring potential with cosh functional form. |
| Cosh-spring potential does not need cutoffs as the maximum is set by cuts | |
| and the minimum is zero. | |
| Only atom1 needs to be specified as this potential is specifically | |
| for core shell pairs. Atom1 can be given either by atomic number | |
| or symbol which in the latter case can be followed by a species | |
| type. If no species type is given then type is assumed to be core. | |
| See also | spring |
| Type | Option |
| Format | cosmoframe |
| M(1,1) M(2,1) M(3,1) | |
| M(1,2) M(2,2) M(3,2) | |
| M(1,3) M(2,3) M(3,3) | |
| Units | none |
| Default | Current local frame |
| Use | Specifies the local frame for the system as used in a |
| previous run so that a job can be restarted consistently. | |
| See also | cosmo |
| Type | Option |
| Format | cosmoshape <octahedron/dodecahedron> |
| Units | none |
| Default | octahedron |
| Use | Specifies the basic polyhedron used to construct the SAS |
| used in COSMO. The original approach used a dodecahedron | |
| but an octahedron is more symmetric. | |
| See also | cosmoframe pointsperatom segmentsperatom |
| Type | Option |
| Format | coulomb_subtract <intra/inter> <bond/x12/x13/x14/o14/g14> <scale14> |
| atom1 atom2 <scale> <rmin> rmax <flag> | |
| Units | rmin and rmax in Angs, scale in fractional |
| Default | scale = 1.0 |
| Use | Coulomb subtraction potential only |
| Coulomb potential does not need Coulomb offset | |
| when acting as a core-shell spring, see cuts | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = - scale*qi.qj/rij | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction - this can also be achieved through the command molmec. | |
| o14 => only act between atoms which are 1-4, i.e. separated by | |
| 3 bonds | |
| When specified as bonded potential cutoffs are omitted from input. | |
| See also | molmec 3coulomb |
| Type | Option |
| Format | covalent at.no. <radius> |
| Units | Angstroms |
| Default | standard literature value |
| Use | Allows covalent radii to be changed. |
| Used in bond and molecule calculations. | |
| Command is part of element section. | |
| See also | element |
| Type | Option |
| Format | covexp <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> |
| atom1 atom2 D a r0 <rmin> rmax <3*flags> | |
| Units | D in eV, a in Angs**-1, r0, rmin and rmax in Angs |
| Default | none |
| Use | Covalent-exponential potential form (see Phys. Rev. B, 60, 7234 (1999)) |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = -D*exp(-a*(r-r0)**2/(2r)) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| Type | Option |
| Format | crossover initial <final> <stepsize> |
| Default | 0.4 <0.4> <0.0> |
| Use | Part of ga options section. Specifies the crossover probability. |
| The higher the value, the more likely it is that crossover will | |
| occur. If <initial> value is less than <final> value then after | |
| 20 iterations tournament is incremented by <stepsize>. If the optimisation | |
| is stuck in a local minimum then if stepsize non-zero tournament is reset | |
| to <initial>. | |
| See also | genetic anneal tpxo |
| Type | Option |
| Format | current_time time <ps> |
| Units | ps |
| Use | Specifies the current total time during an MD simulation, so that |
| restarting can be performed from the correct time step. | |
| See also | md aver caver absolute_coordinates |
| Type | Option |
| Format | cutd cutoff_distance <angs/au> |
| Units | Angstrom (default) or au |
| Default | 2.0 Angstroms |
| Use | Controls search for bond lengths. |
| See also | bond |
| Type | Option |
| Format | cutp cutoff_scale_factor |
| Units | Fractional |
| Default | 0.5 |
| Use | Manybody calculations with EAM and MEAM can be accelerated when |
| second derivatives are being used in optimisation by reducing the | |
| cutoff for cross-terms that only contribute to Hessian matrix but | |
| not the energy or first derivatives. This scale factor can be used | |
| to choose the balance between being exact (1.0) and fast (0.0). | |
| Usually a good local approximation to the Hessian is sufficient | |
| and so fractions much less than 1 can still converge quickly while | |
| speed ups of an order of magnitude can be obtained. | |
| See also | cutp cuts manybody |
| Type | Option |
| Format | cutp cutoff_distance <polynomial/cosine/voter/exponential/mdf/p7> <taper_range> <angs/au> |
| Units | Angstrom (default) or au |
| Default | Use individual potential values / polynomial |
| Use | Maximum interatomic potential cutoff if less than individual value |
| This can be optionally followed by a taper range. If this is set | |
| to a non-zero value then all short range potentials are tapered | |
| smoothly to zero over this range such that the energy, first and | |
| second derivatives remain continuous. This facility is particularly | |
| useful for MD where discontinuities can lead to drift in the energy/ | |
| temperature. Note that tapering does not apply to Coulomb subtracts, | |
| Stillinger-Weber potentials (as these go to zero at the cut-off any | |
| way) and spline potentials (which can be constructed to go to zero | |
| as well). The types of taper that can be used are: | |
| polynominal => 5th order polynomial | |
| p7 => 7th order polynomial over whole range (as per ReaxFF) | |
| cosine => cosine function | |
| exponential => exponential function - see below | |
| voter => form suggested by Voter - see below | |
| mdf => form suggested by Mei-Davenport-Fernando - see below | |
| The form of the Voter taper is: | |
| E_smooth(r) = E(r) - E(rcut) + (rcut/m)*(1 - (r/rcut)**m)*(dE(rcut)/dR) | |
| The form of the exponential taper is: | |
| E_smooth(r) = E(r)*f_cut(r) | |
| where f_cut(r) = exp(-1/(rcut-r)) for r < rcut and = 0 for r >= rcut | |
| Note that in the case of the Voter, exponential and p7 tapers there is | |
| no taper range since it applies over the whole range. | |
| The form of the MDF (Mei-Davenport-Fernando) taper is: | |
| E_smooth(r) = E(r)*f_cut(r) | |
| where f_cut(r) = 1.0 for r < r_m and = 0 for r >= rcut. | |
| In between it takes the value f_cut(r) = ((1 - x)**3)*(1+3x+6x**2), where | |
| x = (r-r_m)/(rcut-r_m). Here r_m is the start of the taper range. | |
| See also | cutmany cuts |
| Type | Option |
| Format | cuts cutoff_distance <angs/au> |
| Units | Angstrom (default) or au |
| Default | 0.8 Angstroms |
| Use | Core-shell cutoff distance - should be set to be the same as the |
| maximum core-shell harmonic distance. If spring potential is used | |
| then cutoff is set equal to cuts to avoid errors. | |
| See also | cutp cutmany |
| Type | Option within "observables" |
| Format | Cv |
| value <weight> <j/kmol> | |
| Units | eV/(Kmol) (default) or J/(Kmol) |
| Default | Heat capacity not to be fitted |
| Use | Specifies the experimental heat capacity (Cv) for |
| fitting. Remember that it is important to set the | |
| temperature for the structure otherwise the heat | |
| capacity will be zero. Also you should ensure that | |
| sufficient K points are sampled to give an accurate | |
| value. Remember that the value should be per mole of | |
| primitive unit cells, not just per mole when Z does | |
| not equal 1. | |
| See also | observables entropy elastic sdlc hfdlc bulk shear |
| young poisson bornq weight |
| Type | Option |
| Format | cvec no_of_vector x y z |
| Units | Angstroms |
| Use | For constant pressure MD, specifies the Cartesian cell vectors at the |
| current time step of a MD simulation so that the cell dynamics can be | |
| restarted. | |
| See also | md caver aver current_time |
| Type | Option |
| Format | cwolf <eta> <rmax> |
| Units | eta in inverse Angstroms and rmax in Angstroms |
| Default | none |
| Use | The particle - particle Coulomb interaction matrix for |
| the COSMO/COSMIC method is determined using the Wolf | |
| sum in real space. This option controls the eta value | |
| and cutoff for this summation. Small eta and large | |
| cutoff leads to convergence towards the Ewald / Parry | |
| result for periodic systems. | |
| See also | cosmo cosmic pureQ |
| Type | Option |
| Format | damped <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 C6 C8 C10 <b6> <b8> <b10> <rmin> rmax <6*flags> | |
| Units | C6 in eV*Angs**6, C8 in eV*Angs**8, C10 in eV*Angs**10 |
| b6, b8 and b10 in Angs**-1 | |
| Default | C8=0, C10=0, b6=0, b8=0, b10=0 |
| Use | Specifies potential parameters for damped dispersion potential |
| form of Tang and Toennies (J. Chem. Phys. 80, 3726 (1984)). | |
| If the coefficients b6 and b8 are zero then the potential is | |
| undamped. The functional form is: | |
| E = -(C6/r**6)*f6(r) -(C8/r**8)*f8(r) -(C10/r**10)*f10(r) | |
| where f2n(r) is given by: | |
| f2n(r) = 1 - { sum(k=0->2n) [(b*r)**k]/k!} * exp(-b*r) | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| Note that this potential cannot yet be used with the c6 keyword. | |
| See also | grimme_c6 becke_johnson_c6 |
| Type | Option |
| Format | default_weight <type> weight |
| where type is one of angle, bond, cell_length, cell_angle, coord, | |
| dipole, elastic, energy, dielectric, frac, freq, grad, modulus, stress | |
| Units | None |
| Use | Changes the default weights for the structure or properties. |
| The following are the types of weights that can be changed and | |
| their default values: | |
| angle angle observable 1.0 | |
| bond bond length observable 1.0 | |
| cell_length cell parameter weight in relax fit 1000.0 | |
| cell_angle cell parameter weight in relax fit 1000.0 | |
| coord Cartesian coordinate weight (0-2-D) 1000.0 | |
| dipole dipole moment 10.0 | |
| elastic elastic constant tensor component 0.01 | |
| energy energy (absolute or reaction) 1.0 | |
| frac fractional coordinate in relax fit (3-D) 10000.0 | |
| freq vibrational frequency or phonon mode 1.0 | |
| grad gradient in a conventional fit 1.0 | |
| modulus bulk or Young's modulus 1.0 | |
| stress stress value in conventional fit 1.0 | |
| See also | weight |
| Type | Option |
| Format | deflist nvacancy ninterstitial |
| nvacancy x atom numbers, ninterstitial x atom numbers | |
| Use | Used by the program to enable restarts when mode2a |
| is greater than or equal to 3. Normally this should | |
| only need to be written by GULP, rather than the | |
| user. | |
| See also | defect reldef centre region restore save size |
| Type | Option |
| Format | delay_field value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - default is time in picoseconds. |
| Default | 0.0 |
| Use | Specifies a delay time before any time-dependent field is |
| applied to the simulation. Can be used to prevent the | |
| field being applied during equilibration. | |
| See also | md production sample write temperature timestep |
| tscale nolist equilibration external_force | |
| td_external_force end_force td_field field end_field |
| Type | Option |
| Format | delay_force value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - default is time in picoseconds. |
| Default | 0.0 |
| Use | Specifies a delay time before any external force is |
| applied to the simulation. Can be used to prevent the | |
| force being applied during equilibration. | |
| See also | md production sample write temperature timestep |
| tscale nolist equilibration external_force | |
| td_external_force end_force |
| Type | Option |
| Format | delf energy_change |
| Units | eV |
| Default | none |
| Use | Maximum change per step of minimisation of the function before |
| Hessian is recalculated. |
| Type | Option |
| Format | delta <fit> <real value> |
| Units | fractional |
| Default | 0.00001 for ordinary fitting / 0.0001 for relax fitting |
| Use | Differencing interval used in numerical procedures. |
| One delta value is possible according to the sub-option word | |
| supplied. This value corresponds to the differencing interval | |
| for gradients during fitting (fit). Previously values were | |
| also possible in connection with free energy minimisation. | |
| However, these are no long needed with analytical derivatives. |
| Type | Option |
| Format | dhkl <width of growth slice> <au> |
| Units | Angstrom |
| Use | This specifies the spacing of the hkl planes which is equivalent to the |
| width of the growth slice for the calculation of the attachment energy. | |
| This should only be specified for an unrelaxed surface. For a general | |
| surface the growth slice can be marked by adding a "%" sign to the end | |
| of the coordinate line. | |
| See also | sfractional cartesian |
| Type | Option |
| Format | discrete <no._to_set>=N |
| <variables_to_be_set>xN | |
| <discretation_number>xN | |
| Default | 6 |
| Use | Part of genetic options section. When two is raised to the power |
| of this number it gives the discretisation interval for a fitted | |
| variable. The higher the value, the greater the resolution of the | |
| fitting. | |
| See also | genetic |
| Type | Option |
| Format | dispersion <no. of lines, default=1> <no. of k points per line> |
| x1 y1 z1 to x2 y2 z2 <to x3 y3 z3 .....> | |
| Units | x, y and z are fractions of reciprocal lattice vectors |
| Default | none |
| Use | Specifies the start and end points of lines through k space |
| along which the phonon dispersion will be calculated. | |
| Examples: | |
| dispersion 2 20 | |
| 0.0 0.0 0.0 to 0.5 0.5 0.5 to 0.5 0.0 0.0 | |
| 0.5 0.0 0.0 to 0.5 0.5 0.0 | |
| This would produce two plots, the first containing two parts | |
| and the second only one. Both plots would contain a total of | |
| 20 k points. | |
| See also | phonon shrink kpoints box kfull |
| Type | Option |
| Format | ditto <option_word> <configuration_no> |
| Units | none |
| Default | option_word = 'all' and configuration_no = last structure |
| Use | Copies the data from the previous configuration to this one |
| before options overwrite it. The option_word parameter is a | |
| string that states what is to be copied. Current valid words | |
| are; | |
| all - copy all of the below items | |
| conditions - copy temperature / pressure data | |
| md - copy all molecular dynamics related parameters | |
| solvent - copy solvent related data | |
| structure - copy structure related data | |
| The parameter, configuration_no, gives the configuration number | |
| to be copied when creating the present new structure. | |
| This option is useful when wanting to run a sequence of | |
| calculations on the same structure with different conditions. | |
| Note: The coordinates cannot be presently overwritten. |
| Type | Option |
| Format | dmaximum <x> <y> <z> |
| Default | 0.0 |
| Use | Part of genetic options section. Specifies the maximum value |
| used as a default in genetic optimisation. According to the | |
| dimensionality the arguments supplied should be: | |
| 2-D => z | |
| 1-D => y & z | |
| 0-D => x & y & z | |
| By specifying a maximum value, this allows GAs to be used for | |
| non-3D systems. | |
| See also | genetic |
| Type | Option |
| Format | dminimum <x> <y> <z> |
| Default | 0.0 |
| Use | Part of genetic options section. Specifies the minimum value |
| used as a default in genetic optimisation. According to the | |
| dimensionality the arguments supplied should be: | |
| 2-D => z | |
| 1-D => y & z | |
| 0-D => x & y & z | |
| By specifying a minimum value, this allows GAs to be used for | |
| non-3D systems. | |
| See also | genetic |
| Type | Option |
| Format | dump <every <n> noover> <channel> <cart> <connectivity> <generated> <filename a20> |
| Default | no dumpfile, n=1 if every is given |
| Use | Generates dumpfile after fitting or optimisation. |
| File is created on fortran channel 12. To change, specify either | |
| another channel number or a filename. If "every" is specified | |
| then a dumpfile will be written after every n cycles of fitting | |
| or optimisation. If "noover" is also specified then the dumpfile won't be | |
| overwritten every write, but labelled with a unique number. | |
| If "connectivity" is specified then the connectivity list will be | |
| written to the dump file. Note that this will only be done for the | |
| current configuration. | |
| If "generated" is specified then this will force the dumping of explicit | |
| potentials generated by automated rules (e.g. using uff1). | |
| NB: Although the filename can be anything you like it is proposed that | |
| the conventional extension be .grs (.res was being used but this | |
| conflicts with other software). | |
| NNB: During Monte Carlo and Molecular Dynamics calculations the use of | |
| a small value for the frequency of dumping may significantly lower the | |
| speed of the calculation. |
| Type | Option |
| Format | eam_alloy |
| atom scale <1 x flag> | |
| Units | None |
| Default | scale = 1.0 |
| Use | This option applies a scaling transformation to the EAM method. |
| While this has no effect on pure elements, it influences the | |
| results for alloys. The transformation is applied as; | |
| rho'(i) = scale(i)*rho(i) | |
| F'(sum(rho(i))) = F(sum(rho(i))/scale(i)) | |
| where F is the unscaled function of the density. | |
| See also | manybody eam_functional eam_density scmaxsearch |
| Type | option |
| Format | eam_density <power n/fpower/exponential n/gaussian n/cubic/quadratic/quartic/voter/glue/evoter/mei-davenport/baskes/vbo/spline> |
| atom1 <atom2> C (power law) <1 x flag > | |
| atom1 <atom2> C rn (fractional power law) <2 x flag > | |
| atom1 <atom2> A B r0 (exponential) <3 x flags> | |
| atom1 <atom2> A B r0 (gaussian) <3 x flags> | |
| atom1 <atom2> A r0 (quadratic) <2 x flags> | |
| atom1 <atom2> A r0 (cubic) <2 x flags> | |
| atom1 <atom2> A r0 (quartic) <2 x flags> | |
| atom1 <atom2> A beta (voter) <2 x flags> | |
| atom1 <atom2> A beta (evoter) <2 x flags> | |
| atom1 <atom2> c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags> | |
| atom1 <atom2> r1 r2 rm (glue) | |
| b1_3 b1_2 b1_1 b1_0 | |
| b2_3 b2_2 b2_1 b2_0 | |
| b3_3 b3_2 b3_1 b3_0 | |
| atom1 <atom2> A beta r0 (baskes) <3 x flags> | |
| atom1 <atom2> c sigma gamma r0 delta (vbo) <5 x flags> | |
| atom1 <atom2> A B C D rmin r0 (spline) <4 x flags> | |
| Units | Distances are in Angstrom |
| Use | Specifies the density due to a given atom1 at another |
| atomic centre (atom2) in the Embedded Atom Model (EAM). | |
| This density is only calculated for pairs of atoms | |
| where the "manybody" potential has been specified | |
| so that the user can control which atoms are part | |
| of the EAM. | |
| Where no atom2 is specified then the density is applied to | |
| all atoms allowed by the manybody potential, regardless of | |
| species type. | |
| The density can take one of several functional forms: | |
| Power Law: | |
| rho(i) = C*rij**(-n) | |
| e.g. eam_density power 6 | |
| Ni core 729.7 | |
| Fractional power Law: | |
| rho(i) = C*rij**(-rn) | |
| e.g. eam_density fpower | |
| Ni core 729.7 6.1 | |
| Exponential: | |
| rho(i) = A*(rij**n)*exp(-B(rij-r0)) | |
| e.g. eam_density exponential 0 | |
| Ni core 500.0 4.0 3.52 | |
| Gaussian: | |
| rho(i) = A*(rij**n)*exp(-B(rij-r0)**2) | |
| e.g. eam_density gaussian 2 | |
| Ni core 400.0 3.0 3.52 | |
| Quadratic: | |
| rho(i) = A*(rij-r0)**2 if r < r0, else = 0 | |
| Cubic: | |
| rho(i) = A*(rij-r0)**3 if r < r0, else = 0 | |
| Quartic: | |
| rho(i) = A*(rij-r0)**4 if r < r0, else = 0 | |
| Voter: | |
| rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r)) | |
| eVoter: | |
| rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))*exp(-1/(rmax - r)) | |
| Mei-Davenport: | |
| rho(i) = sum(l=0->5) (c_l/12)*(r/r0)**l | |
| In the above, rmax is the cutoff for the potential from the manybody | |
| option that controls the range of the density. | |
| Glue: | |
| if r < r1 | |
| rho(i) = b1_3*(r-r1)**3 + b1_2*(r-r1)**2 + b1_1*(r-r1) + b1_0 | |
| if r1 =< r < r2 | |
| rho(i) = b2_3*(r-r2)**3 + b2_2*(r-r2)**2 + b2_1*(r-r2) + b2_0 | |
| if r2 =< r < rm | |
| rho(i) = b3_3*(r-rm)**3 + b3_2*(r-rm)**2 + b3_1*(r-rm) + b3_0 | |
| Note that the cut-offs are set by the manybody potential except | |
| for the glue model where the maximum cutoff, rm, is a parameter | |
| of the model. | |
| Baskes: | |
| rho(i) = A*exp(-beta((rij/r0)-1)) | |
| VBO: | |
| rho(i) = c*sigma*N*exp(-gamma/(1 - sqrt(r/delta))) | |
| where N is a normalisation constant given by: | |
| N = exp(gamma/(1 - sqrt(r0/delta))) | |
| Spline: This is effectively one piece of a cubic spline. | |
| rho(i) = A*(rij-r0)**3 + B*(rij-r0)**2 + C*(rij-r0) + D if rmin < r < r0, else = 0 | |
| See also | manybody eam_functional scmaxsearch eam_alloy prt_eam meam_density |
| Type | option |
| Format | eam_functional <square_root> <power n> <banerjea_smith n> <johnson/glue/foiles/mei-davenport/baskes/vbo/igarashi/spline> |
| if square_root or power : | |
| atom1 A_1 <flag> | |
| atom2 A_2 <flag> etc... | |
| if banerjea_smith : | |
| atom1 F0_1 F1_1 rho0_1 <3*flags> | |
| atom2 F0_2 F1_2 rho0_2 <3*flags> etc... | |
| if johnson : | |
| atom1 F0_1 F1_1 rho0_1 alpha beta gamma <6*flags> | |
| atom2 F0_2 F1_2 rho0_2 alpha beta gamma <6*flags> etc... | |
| if glue : | |
| atom1 rho1 rho2 | |
| c1_4 c1_3 c1_2 c1_1 c1_0 | |
| c2_4 c2_3 c2_2 c2_1 c2_0 | |
| c3_3 c3_2 c3_1 c3_0 | |
| atom2 rho1 rho2 | |
| c1_4 c1_3 c1_2 c1_1 c1_0 | |
| c2_4 c2_3 c2_2 c2_1 c2_0 | |
| c3_3 c3_2 c3_1 c3_0 | |
| if foiles : | |
| atom1 F0_1 F1_1 F2_1 F3_1 <4*flags> | |
| atom2 F0_2 F1_2 F2_2 F3_2 <4*flags> etc... | |
| if mei-davenport : | |
| atom1 Ec_1 alpha_1 beta_1 gamma_1 delta_1 phi0_1 s_1_1 s_2_1 s_3_1 <9*flags> | |
| atom2 Ec_2 alpha_2 beta_2 gamma_2 delta_2 phi0_1 s_1_2 s_2_2 s_3_2 <9*flags> etc... | |
| if baskes : | |
| atom1 Ec_1 A_1 rho0_1 <2*flags> | |
| atom2 Ec_2 A_2 rho0_2 <2*flags> etc... | |
| if vbo : | |
| atom1 A_1 rn_1 <2*flags> | |
| atom2 A_2 rn_2 <2*flags> etc... | |
| if igarashi : | |
| atom1 A_1 B_1 <2*flags> | |
| atom2 A_2 B_2 <2*flags> etc... | |
| if spline : | |
| atom1 A_1 B_1 C_1 D_1 rho0_1 rho_max_1 <4 x flags> | |
| atom2 A_2 B_2 C_2 D_2 rho0_2 rho_max_2 <4 x flags> | |
| Units | A, B, C, D, AE0, F0, Ec, phi0 and F1 in eV, rho0/rho_max//alpha/beta/gamma/rn are dimensionless |
| Default | square_root, A = 1.0 |
| Use | specifies how the total energy contribution of an atom |
| in the Embedded Atom Model depends on the density at that | |
| site. The current possibilities are: | |
| Square_root: | |
| E = - sum(i) A(i)*(rho(i))**1/2 | |
| this is the most common functional, as used in the Sutton-Chen potential | |
| Power: | |
| E = - sum(i) A(i)*(rho(i))**1/n | |
| this is just a generalisation of the above case | |
| VBO: | |
| E = - sum(i) A(i)*(rho(i))**rn | |
| this is a further generalisation of the power case | |
| Banerjea_smith: | |
| E = - sum(i) F0 [1-ln(r)/n]*r**1/n + F1*r | |
| where r = rho(i)/rho0(i) | |
| this is the functional of Banerjea and Smith (Phys. Rev. B, | |
| 37, 6632 (1988)) - note that in this case that are atom | |
| dependent parameters also to be specified (F0, F1, rho0) | |
| where rho0 is the electron density at equilibrium. | |
| Johnson: | |
| E = - sum(i) F0 [1-ln(x)]*x + F1*y | |
| where x = (rho(i)/rho0(i))**(alpha/beta) | |
| and y = (rho(i)/rho0(i))**(gamma/beta) | |
| this functional is similar to that of Banerjea & Smith and is due | |
| to Johnson (PRB, 39, 12554 (1989)). | |
| Glue: | |
| if rho < rho1 | |
| E = c1_4*(rho-rho1)**4 + c1_3*(rho-rho1)**3 + c1_2*(rho-rho1)**2 + | |
| c1_1*(rho-rho1) + c1_0 | |
| if rho1 =< rho < rho2 | |
| E = c2_4*(rho-rho2)**4 + c2_3*(rho-rho2)**3 + c2_2*(rho-rho2)**2 + | |
| c2_1*(rho-rho2) + c2_0 | |
| if rho2 =< rho | |
| E = c3_3*(rho-rho2)**3 + c3_2*(rho-rho2)**2 + c3_1*(rho-rho2) + c3_0 | |
| this is the functional from Ercolessi et al, Phil. Mag. A, 58, 213 (1988). | |
| NB: At present there are no fitting parameters since there are constraints | |
| on the coefficients to ensure a smooth and continuous function. | |
| Foiles: | |
| E = sum(i) F0*rho(i)**2 + F1*rho(i) + F2*(rho(i)**(5/3)/(F3 + rho(i))) | |
| Mei-Davenport: | |
| E = sum(i) - Ec*[1-(alpha/beta)*ln(rho(i))]*rho(i)**(alpha/beta) + | |
| sum(m=1->3) 0.5*phi0*s_m*exp(-(sqrt(m)-1)*gamma)* | |
| [1+(sqrt(m)-1)*delta-sqrt(m)*delta*ln(rho(i))/beta]* | |
| rho(i)**(sqrt(m)*gamma/beta) | |
| Baskes: | |
| E = - sum(i) AE0*x*ln(x) | |
| where x = (rho(i)/rho0(i)) | |
| this functional is similar to that of Banerjea & Smith and Johnson, but | |
| is simplified to enable the parameters from the MEAM paper of Baskes to | |
| be input directly. AE0 is the combination of E0 and A from the above paper. | |
| Igarashi: | |
| E = - sum(i) A(i)*(rho(i)*(1 + B(i)*rho(i))**1/2 | |
| this functional form was proposed in Igarashi et al, Phil. Mag. B, 63, | |
| 603 (1991). | |
| Spline: | |
| if rho_max > rho > rho0: | |
| E = - sum(i) [A(i)*(rho(i)-rho0)**3 + B(i)*(rho(i)-rho0)**2 + C(i)*(rho(i)-rho0) + D(i)] | |
| else | |
| E = 0 | |
| See also | eam_density manybody scmaxsearch eam_alloy prt_eam |
| Type | Option |
| Format | eam_potential_shift <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <ener/grad> <kjmol/kcal/au> <scale14> |
| atom1 atom2 g beta <rmin> rmax <2*flags> | |
| Units | beta is in inverse Angstroms, g is nominally unit less as it is multiplied |
| by a conversion constant to place it in eV | |
| Default | None |
| Use | Specifies a two-body shift of the EAM potential energy component based on |
| the functional form of the Voter-Chen density. Needed to work with the | |
| embedding potential in the format used by Paradyn. | |
| The form of the potential is | |
| E = 2.0*g*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r)) | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | manybody eam_functional eam_density |
| Type | Option |
| Format | edip_accuracy accuracy1 accuracy2 |
| Units | None |
| Default | accuracy1 = 0.000001, accuracy2 = 0.0000000001 |
| Use | Controls the truncation of the exponential terms in the interaction energies of |
| EDIP. The parameter accuracy1 controls where the taper starts, while accuracy2 | |
| controls where the taper ends. Therefore accuracy1 must be greater than accuracy2. | |
| Although no taper is formally required, this option can reduce the cost of EDIP | |
| with negligible effect on the accuracy. | |
| See also | edip_coordination edip_twobody edip_threebody edip_zmax fastfd |
| Type | Option |
| Format | edip_coordination |
| species <core/shell> alpha flow fhigh <1 x flag> | |
| or | |
| edip_coordination pi | |
| species <core/shell> alpha flow fhigh Zdih Zrep c0 plow phigh <4 x flags> | |
| Units | flow, fhigh, plow, phigh, c0 in Angstroms |
| Default | None |
| Use | Specifies the parameters for the EDIP model coordination number. In the simplest |
| form the coordination number is just a spherical term that is given by: | |
| Z = sum f(r_ij) | |
| where f(r_ij) = 1 if r < flow, 0 if r > fhigh, and inbetween it is given by | |
| exp(alpha/(1-r_ij**-3)). | |
| If "pi" is specified as a sub-option then contributions for pi bonding are added. | |
| See also | edip_twobody edip_threebody edip_zmax edip_accuracy fastfd |
| Type | Option |
| Format | edip_threebody |
| species1 <core/shel> species2 <core/shel> species3 <core/shell> & | |
| lambda0 lambda' Z0 gamma gamma' q <6 x flags> | |
| or | |
| edip_threebody modified | |
| species1 <core/shel> species2 <core/shel> species3 <core/shell> & | |
| lambda0 lambda' Z0 gamma gamma' q kq <7 x flags> | |
| or | |
| edip_threebody original | |
| species1 <core/shel> species2 <core/shel> species3 <core/shell> & | |
| lambda mu eta gamma gamma' q <6 x flags> | |
| Default | None |
| Use | Specifies the parameters for the EDIP model threebody contribution. |
| Here the default form is that of Nigel Marks, whereas the original | |
| form follows the paper of Justo et al, PRB, 58, 2539 (1998). | |
| NB: Here the convention of N.A. Marks, J. Phys. Cond. Matter, 14, | |
| 2901-2927 (2002) is followed, where lambda0 = lambda0*gammap**2/q | |
| relative to the form in the earlier PRB, 63, 035401 (2000) paper. | |
| Note that the implementation here (optionally) includes a small modification | |
| that is not described in the papers in that there is an extra | |
| parameter, kq that can be included. When Zi < 2 then the form of h changes to be | |
| kq*(1 + cos(theta)) and so the extra value of kq is input. | |
| See also | edip_twobody edip_coordination edip_zmax edip_accuracy fastfd |
| Type | Option |
| Format | edip_twobody |
| species1 <core/shel> species2 <core/shel> epsilon B p beta sigma a a' <7 x flags> | |
| Default | None |
| Use | Specifies the parameters for the EDIP model twobody contribution. |
| The functional form of the term is: | |
| U2(r,Z) = epsilon*[(B/r)**p - exp(-beta*Z**2)].exp(sigma/(r - a -a'*Z)) | |
| NB In earlier versions the power p was not explicit given as it defaulted to the | |
| value used by Marks for carbon of 4 (Phys. Rev. B, 63, 035401 (2000)). Now the | |
| code has been generalised so that a value can be input. | |
| See also | edip_coordination edip_threebody edip_zmax edip_accuracy fastfd |
| Type | Option |
| Format | edip_zmax Zmax |
| Units | None |
| Default | 6.0 |
| Use | In the EDIP method, the interactions are truncated according to the following term; |
| exp(sigma/(r - a - a'*Z)) | |
| where a and a' are parameters. Here the cut-off is dependent on the coordination | |
| number, Z. While GULP iteratively tries to ensure that all atoms are found in the | |
| neighbour list based on the current cut-off, the Z value is approximated by the | |
| uncorrected value (i.e. no torsional corrections). In cases where discontinuities | |
| are found (should be rare) then the value of Zmax should be increased manually. | |
| See also | edip_coordination edip_twobody edip_threebody edip_accuracy fastfd |
| Type | Option |
| Format | einstein <cart> |
| atomnumber x y z k | |
| Units | x/y/z in fractional, unless "cart" specified, in which case |
| Angstroms; k in eV/Ang**2 | |
| Default | k = 0 for all atoms |
| Use | Specifies an Einstein model for the system. Here the atoms |
| are tied to lattice sites using a harmonic potential. In the | |
| input it is necessary to specify the lattice site for the | |
| atom and the force constant. | |
| Note: This option must be used with a fixed unit cell. | |
| See also | plane_lj |
| Type | Option |
| Format | elastic <n> <gpa> |
| i j elastic constant E(i,j) <weight> | |
| Units | GPa |
| Default | no elastic constants to be fitted |
| Use | Subsection of observables, used for specifying experimental |
| elastic constants for fitting. | |
| Only give unique elastic constants. Units are | |
| the same as THBREL and as output in GULP. | |
| See also | piezoelectric sdlc hfdlc srefractive hfrefractive weight |
| bornq young poisson |
| Type | Option |
| Format | electronegativity |
| <Atomic_symbol/atomic_number> chi <mu> <Q0> <E0> <2 x flags for fitting> | |
| or | |
| electronegativity <qrange/qmin/qmax> | |
| <Atomic_symbol/atomic_number> chi <mu> <Q0> <E0> <qmin> <qmax> <2 x flags for fitting> | |
| Units | Chi, mu, and E0 in eV, Q0, qmin, qmax in a.u. |
| Default | Q0 = 0.0, E0 = 0.0 |
| Use | Allows the user to specify the parameters needed for the |
| electronegativity equalisation method for determining | |
| charges. Note that if the flags are not specified they | |
| are assumed to be zero. | |
| Q0 is the charge about which the electronegativity equations | |
| are quadratic. In most methods this is zero, but need not be. | |
| For example, the EQeq method assigns values of Q0 not equal | |
| to zero. | |
| E0 is an additive constant for the energy of an atom. This is | |
| only really needed when using multiple q ranges to ensure | |
| energy matching. | |
| The sub-options qrange, qmin, and qmax control whether the | |
| values apply for a given value of charge. By default the values | |
| apply to all values of charge (q). If qmin is specified then | |
| they are only applied to charges larger than qmin, while if qmax | |
| is given the they are applied when q is less than qmax. When | |
| qrange is specified then the values apply for qmin =< q < qmax. | |
| NB: If no parameters are input then the default values will be | |
| used for all charge values. However, if parameters are input | |
| then this will override the default values and the user must | |
| set parameters for all relevant ranges of charge. | |
| See also | eem qelectronegativity smelectronegativity noqeem external_potential |
| eembond |
| Type | Option |
| Format | word |
| Default | data as in file eledata |
| Use | Section for changes in element properties. |
| See also | symbol mass covalent ionic vdw nmr |
| Type | Option |
| Format | end_field value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - default is time in picoseconds. |
| Default | 0.0 |
| Use | Specifies an end time for any time-dependent field |
| applied to the simulation. Can be used to stop the | |
| field being applied. | |
| See also | md production sample write temperature timestep |
| tscale nolist equilibration external_force | |
| td_external_force end_force td_field field delay_field |
| Type | Option |
| Format | end_force value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - default is time in picoseconds. |
| Default | 0.0 |
| Use | Specifies a time after which any external force is |
| removed from the simulation. | |
| See also | md production sample write temperature timestep |
| tscale nolist equilibration external_force | |
| td_external_force delay_force |
| Type | Option |
| Format | energy_of_configuration <ev/kcal/au/kjmol-1> <weight> |
| Default | energy in eV, weight = 1.0 |
| Use | Subsection of observables, assigns energy to successive |
| configurations for fitting. | |
| See also | fenergy |
| Type | option |
| Format | ensemble <NVE/NVT qnose/NPT qnose qpress/NPH> |
| Default | NVE |
| Use | Selects the ensemble to be use in molecular dynamics. |
| By default the program uses constant number, volume | |
| and energy. However, the canonical ensemble can be | |
| chosen if constant temperature is prefered to constant | |
| energy. If NVT is selected then the Nose-Hoover | |
| thermostat parameter must also be given. It is important | |
| to choose a suitable value such that the temperature | |
| fluctuations are minimised. For constant pressure, | |
| variable cell shape MD, the NPT ensemble can be used | |
| (keyword "conp" must be present). In this case it is | |
| necessary to supply the thermostat parameter and the | |
| barostat parameter. Both again need tuning to get the | |
| best performance for each system. NPT ensemble is | |
| implemented as a modified Nose-Hoover form based on | |
| Melchionna et al., Mol. Phys. 78 (1993) 533. | |
| See also | md integrator tau_barostat tau_thermostat |
| Type | Option within "observables" |
| Format | entropy |
| value <weight> <j/Kmol> | |
| Units | eV/(Kmol) (default) or J/(Kmol) |
| Default | Entropy not to be fitted |
| Use | Specifies the experimental vibrational entropy for |
| fitting. Remember that it is important to set the | |
| temperature for the structure otherwise the entropy | |
| will be zero. Also you should ensure that | |
| sufficient K points are sampled to give an accurate | |
| value. Remember that the value should be per mole of | |
| primitive unit cells, not just per mole when Z does | |
| not equal 1. | |
| See also | observables cv elastic sdlc hfdlc bulk shear |
| young poisson bornq weight |
| Type | Option |
| Format | epsilon <kcal/kjmol> <mm3> <bond/x12/x13/x14/mol/o14/g14> |
| <Atomic_symbol/atomic_number> epsilon sigma <2 x flags for fitting> | |
| Units | epsilon in eV and sigma in Angstroms |
| Use | Specifies epsilon and sigma values for each species type to be |
| used in combination rules to obtain Lennard-Jones potential | |
| parameters where specified. | |
| If the sub-option "mm3" is specified then the epsilon and sigma values | |
| are applied to mm3buck potentials rather than Lennard-Jones. | |
| If one of the bonding related sub-options is specified then the epsilon | |
| and sigma values are only applied to potentials with a matching bonding | |
| specification. An example of where this is needed is CHARMM, which has | |
| different values for 1-4 interactions as opposed to general VDW terms. | |
| See also | lennard atomab mm3buck |
| Type | Option |
| Format | equatorial <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K n beta r0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) | |
| <rmin(2-3)> rmax(2-3) <3*flag> | |
| Units | K in eV, r0, rmin and rmax in Angstroms and beta in inverse Angstroms |
| Default | none |
| Use | ESFF equatorial three-body form : |
| E(three) = (2K/n**2) * (1 - cos(n*theta)) + 2K*exp(-beta*(r13 - r0)) | |
| Here r13 is the distance between the atoms 1-3 in the triad. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2, 2-3 and 1-3 are bonded. | |
| See also | axilrod-teller angle stillinger-weber exponential bcross |
| urey-bradley murrell-mottram bacross three hydrogen-bond | |
| lin3 uff3 3coulomb bagcross |
| Type | Option |
| Format | equilibration value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - if integer, then value is by default |
| a multiple of the timestep or if non-integer then by | |
| default is the time in picoseconds. | |
| Use | Specifies the simulation time to be spent equilibrating |
| the kinetic and potential energy distributions prior to | |
| the production phase of the molecular dynamics run. | |
| See also | md production sample write temperature timestep |
| tscale nolist delay_force end_force momentum_correct |
| Type | Option |
| Format | erferfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> |
| atom1 atom2 A alpha beta <rmin> rmax <3 x flags> | |
| Units | A in eV, alpha and beta in Angs |
| Default | none |
| Use | Specifies the parameters of an erferfc potential, which has the form: |
| E_ij = A.erf(r/alpha).erfc(r/beta)/r | |
| See also | qerfc reperfc erfpot |
| Type | Option |
| Format | erfpot <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> |
| atom1 atom2 A alpha <rmin> rmax <2 x flags> | |
| Units | A in eV, alpha in Angs |
| Default | none |
| Use | Specifies the parameters of an erf potential, which has the form: |
| E_ij = A.erf(r/alpha)/r | |
| See also | qerfc reperfc erfpot |
| Type | Option |
| Use | Part of ignore/erongi pair. All lines of input after |
| "ignore" are treated as comments until the option | |
| "erongi" is found at the start of a line. Allows the | |
| user to comment out parts of an input file. Note | |
| any parts commented out will not be passed through | |
| to a restart file. | |
| See also | ignore keyword include |
| Type | Option |
| Format | ewaldrealradius value |
| Default | none |
| Use | Normally the Ewald sum real and reciprocal space radii are chosen |
| automatically to minimise the number of terms, subject to the value | |
| of the rspeed parameter. However, when using the spatial algorithm | |
| it is advantageous to control the real space extent of the Ewald | |
| sum to ensure that the system can be decomposed into sufficent regions. | |
| The value specified fixes the real space cut-off and the reciprocal | |
| space cut-off is calculated in order to achieve the target accuracy | |
| given by the accuracy option. | |
| See also | noexclude qwolf rspeed accuracy veck index_k |
| Type | Option |
| Format | exp2 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K rho2 r12_0 rho3 r13_0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) | |
| <rmin(2-3)> rmax(2-3) <5*flags> | |
| Units | K in eV, rho2/3 in Angstroms**-1, r12_0/r13_0/rmin/rmax in Angstroms |
| Use | Exponentially decaying three-body potential with 2 exponentials only: |
| E(three) = K*exp(-rho2*(r12-r12_0)).exp(-rho3*(r13-r13_0)) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2, 2-3 and 1-3 are bonded. | |
| See also | three-body angle axilrod-teller stillinger-weber bcross urey-bradley |
| murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb | |
| exponential bagcross |
| Type | Option |
| Format | exponential <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K rho1 rho2 rho3 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) | |
| <rmin(2-3)> rmax(2-3) <4*flags> | |
| Units | K in eV, rho1/2/3 in Angstroms**-1 |
| Use | Exponentially decaying three-body potential: |
| E(three) = K * exp(-rho1*r12).exp(-rho2*r13).exp(-rho3*r23) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2, 2-3 and 1-3 are bonded. | |
| See also | three-body angle axilrod-teller stillinger-weber bcross urey-bradley |
| murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb | |
| exp2 bagcross |
| Type | Option |
| Format | exppowers <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> |
| atom1 atom2 A B0 B1 B2 B3 <rmin> rmax <4*flags> | |
| Units | A in eV, B0 in appropriate power of Angstroms |
| Default | none |
| Use | Exp-powers potential - this potential has multiple powers of r in the |
| exponential form. | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A.exp(B0 + B1*r + B2*r**2 + B3*r**3) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | buckingham |
| Type | Option |
| Format | external_force |
| atomnumber force_X force_Y force_Z | |
| Units | eV/Angstrom |
| Default | 0.0 for all atoms and components |
| Use | Specifies a constant external force for the atoms specified. |
| Note that the atom number refers to the asymmetric unit and | |
| that the user must ensure that the force doesn't violate the | |
| symmetry of the system, otherwise any optimisation will fail. | |
| Example: | |
| external_force | |
| 1 0.2 0.0 0.0 | |
| 3 -0.2 0.0 0.0 | |
| See also | td_external_force |
| Type | Option |
| Format | external_potential |
| atomnumber V | |
| Units | V in eV/a.u. |
| Default | 0.0 for all atoms and components |
| Use | Specifies a constant external potential for the atoms specified. |
| Note that the atom number refers to the asymmetric unit and | |
| that the user must ensure that the potential doesn't violate the | |
| symmetry of the system. NB: Because the potential doesn't depend | |
| on the geometry this option is not recommend for runs that involve | |
| optimisation or use energy derivatives. The main use is intended | |
| to be for QM/MM coupling with charge equilibration schemes. | |
| Example: | |
| potential | |
| 1 0.4 | |
| 3 -0.1 | |
| See also | eem qeq sm |
| Type | Option |
| Format | extracutoff value |
| Units | Angstroms |
| Default | 0.0 |
| Use | When using the storevectors algorithm, this option specifies the extra |
| amount to be added to the global cutoff when deciding which vectors to | |
| store. It allows for atoms to move across the boundary between updates. | |
| See also | storevectors resetvectors |
| Type | Option |
| Format | factor theta |
| Default | theta=0.9 |
| Use | Temperature reduction factor. A larger factor implies a faster |
| decay of simulated temperature. |
| Type | Option |
| Format | fangle <n> |
| i j k theta <weight> | |
| Units | Degrees |
| Default | no bond angles to be fitted |
| Use | Subsection of observables, used for specifying values of |
| bond angles for fitting. Here i, j and k are the atom numbers | |
| whose bond angle is to be fitted and theta is the angle. The | |
| atom i is the pivot atom (i.e. the angle is j-i-k). | |
| NB For periodic systems the nearest image is taken. | |
| Example: | |
| fangle 1 | |
| 1 2 3 109.54 | |
| NB This option is intended for use with relax fitting. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq qreaxff fbond relax reaction |
| Type | Option |
| Format | fbond <n> |
| i j rij <weight> | |
| Units | Angstroms |
| Default | no bond lengths to be fitted |
| Use | Subsection of observables, used for specifying values of |
| bond lengths for fitting. Here i and j are the atom numbers | |
| whose bond is to be fitted and rij is the bond length. | |
| NB For periodic systems the nearest image is taken. | |
| Example: | |
| fbond 1 | |
| 1 2 0.96 | |
| NB This option is intended for use with relax fitting. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq qreaxff fangle relax reaction |
| Type | Option |
| Format | fc_supercell na nb nc |
| Default | na = nb = nc = 0 |
| Use | Build force constants separately for cells beyond the standard |
| unit cell. The number of cells either side of the central one | |
| is given by na, nb and nc in the respective directions. This will | |
| lead to a total of (2*na + 1)*(2*nb + 1)*(2*nc + 1) cells. | |
| The default algorithm for phonon calculations in gulp is to compute | |
| analytic force constants for each k point without storing force | |
| constants between k points. This option triggers GULP to use an | |
| alternative approach in which the unphased force constants are | |
| calculated for images of the central cell and stored separately. | |
| These are then later used to generate phonons as a function of k | |
| vector. This algorithm is potentially less expensive in CPU time | |
| than the default, but has the potential to use a lot more memory. | |
| This algorithm is particularly useful for force fields where | |
| analytical second derivatives are not yet available. | |
| NB: For some neighbour list based forces (usually bondorder, EDIP, | |
| ReaxFF) the finite difference calculation of force constants can | |
| contain errors where images of an atom have a non-zero interaction | |
| with each other. In such cases, the solution is run with a supercell | |
| specified and the ghostcell keyword that tells the code to compute | |
| the force constants for the supercell, but to construct the phonons | |
| as though they were for the original smaller cell. | |
| See also | kpoints dispersion shrink eigenvectors lower_symmetry |
| project_dos output nozeropt gamma_direction_of_approach omega | |
| dynamical_matrix meanke frequencies eckart box phonon | |
| numerical msd ghostcell ghost_supercell threshold |
| Type | Option |
| Format | fcartesian |
| x1 y1 z1 <r1> | |
| x2 y2 z2 <r2> | |
| .. .. .. | |
| xN yN zN <rN> | |
| Units | Angstroms |
| Default | None |
| Use | Specifies the coordinates of the final state for the nudged elastic |
| band method. The number of coordinates must match the number | |
| of atoms in the initial structure. The radii of the ions | |
| can be optionally given on the end of the line if a breathing | |
| shell model is being used. If not specified then they are | |
| assumed to be zero. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| rfractional ffractional rcell fcell neb fvectors |
| Type | Option |
| Format | fcell |
| a b c alpha beta gamma | |
| Units | Angstroms for a/b/c & degrees for alpha/beta/gamma |
| Default | None |
| Use | Specifies the final unit cell for the nudged elastic band method. |
| The number of cell parameters must match the dimensionality of the | |
| initial system. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell neb fvectors |
| Type | Option |
| Format | free_energy_of_configuration <ev/kcal/au/kjmol-1> <weight> |
| Default | free_energy in eV, weight = 1.0 |
| Use | Subsection of observables, assigns free energy to successive |
| configurations for fitting. | |
| See also | energy |
| Type | Option |
| Format | fermi-dirac <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> |
| atom1 atom2 a b r0 <rmin> rmax <3 x flags> | |
| Units | a in eV, b in Angs-1, r0 in Angs |
| Default | none |
| Use | Fermi-Dirac potential - optimisation flags for fitting. |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = a/(1+exp(b(r-r0))) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| Type | Option |
| Format | ffractional |
| x1 y1 z1 <r1> | |
| x2 y2 z2 <r2> | |
| .. .. .. | |
| xN yN zN <rN> | |
| Units | Fractional |
| Default | None |
| Use | Specifies the fractional coordinates of the final state for the |
| nudged elastic band method. The number of coordinates must match | |
| the number of atoms in the initial structure. The radii of the | |
| ions can be optionally given on the end of the line if a breathing | |
| shell model is being used. If not specified then they are | |
| assumed to be zero. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional rcell fcell neb fvectors |
| Type | Option |
| Format | field magnitude <direction> |
| Units | eV/(Ang.a.u.) |
| Use | Applies an electric field to a system, usually in a non-periodic direction. |
| Consequently, this option should really only be used for molecules, polymers and | |
| surfaces. The specification of the direction can either be given by the | |
| relevant axis (z, for a surface; y or z for a polymer; x, y or z for a | |
| molecule) or in the case of a 0-D system a general vector may be specified | |
| as 3 numbers in Cartesian space. Examples of valid input lines are: | |
| Surface: | |
| field 1.5 z | |
| Polymer: | |
| field 1.5 y | |
| Molecule: | |
| field 1.5 x | |
| OR | |
| field 1.5 0.2 0.3 0.4 | |
| If the direction is not specified then the default is to apply the | |
| field along the z axis. | |
| The possibility of applying an electric field within 3-D boundary | |
| conditions is also allowed for, in which case the field direction | |
| can also be set using a cell vector (a, b or c), as well as by a | |
| fractional or Cartesian vector: | |
| field 1.5 b | |
| field 1.5 0.2 0.3 0.4 | |
| field 1.5 cart 0.2 0.3 0.4 | |
| NB Be very careful if you do use 3-D boundary conditions as there | |
| are many things that can go wrong and the physical interpretation | |
| is complex since the Ewald sum will counter any induced dipole. | |
| Unless you really know what you are doing, it is very strongly | |
| suggested that you only apply an electric field in a non-periodic | |
| direction. You should definite use the "nomod" keyword when working | |
| with 3-D systems and an electric field. | |
| NB: Symmetry will be automatically turned off if this option is used | |
| for solids as the field will break the symmetry of the space group. | |
| Because the absolute energy is undefined, the energy relative to the | |
| initial state is used during minimisations. Note also that only one | |
| field can be defined per configuration. | |
| NB: You must fix at least one atom in the direction of field application | |
| otherwise the energy will head asymptotically for minus infinity!!! | |
| The units of the electric field are eV/Ang per unit charge in atomic units. | |
| This means an ion of charge +1.0 will experience a force equal to the electric | |
| field input. | |
| NB: The use of an electric field is presently incompatible with the ReaxFF model | |
| and analytic second derivatives for other variable charge models. | |
| See also | td_field dipole delta_dipole initial_coordinates |
| Type | Option |
| Format | finite <value> |
| Default | 0.0001 |
| Units | none (fractional) |
| Use | Requests that the first derivatives with respect to the energy (or |
| free energy if keyword "free" is present) are calculated numerically | |
| by central finite differences. If a value is specified after the | |
| option then this specifies the fractional change to be used as the | |
| step size. Note that if the value is too large then the gradients | |
| will be inaccurate. However, if the value is too small then numerical | |
| noise can lead to inaccuracies as well. | |
| This option is largely only of use for checking analytical derivatives | |
| during debugging and is intended for use with single point calculations. | |
| See also | gradients |
| Type | Option |
| Format | fix_atom <first/last/centre/none> <atom_no> |
| Units | none |
| Default | first (serial), last (parallel), centre (2-D) |
| Use | When optimising a structure using second derivatives it is necessary |
| to fix one atom in order to stop translational invariance and prevent | |
| the Hessian matrix from being singular. This option allows the user | |
| to specify which atom is fixed in several ways: | |
| 1) Fix the first atom in a structure: | |
| fix_atom first | |
| or | |
| fix_atom 1 | |
| This has generally been the default for GULP for most cases. | |
| 2) Fix the last atom in a structure: | |
| fix_atom last | |
| This is now the default for parallel second derivatives since it | |
| allows for more efficient generation of the Hessian matrix by allowing | |
| the same block cyclic distribution between the second derivatives and | |
| variables for an otherwise unconstrained system. Note here that last | |
| will fix the last core if shells are present, since fixing a shell | |
| would not make sense in the context of electronic polarisation. | |
| 3) Fix the most central atom: | |
| fix_atom centre | |
| Fix the most central atom. For a molecule this would be in the middle, | |
| while for a slab this is an atom furtherest from the surface. | |
| 4) Fix a general atom number: | |
| fix_atom 5 | |
| Here the atom number is given in the primitive cell | |
| 5) Don't fix any atom: | |
| fix_atom none | |
| This does what it says. However, this means that second derivatives should | |
| not be used since the Hessian cannot be inverted. | |
| See also | optimise gradient unfix unfreeze |
| Type | Option |
| Format | forceconstant <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <type_of_bond> |
| atom1 atom2 kL kT <rmin> rmax <2*flag> | |
| Units | kL and kT in eV*Angs**-2 |
| Use | Force constant potential - includes the force constants between a pair |
| of atoms, known as the longitudinal (kL) and transverse (kT) force | |
| constants. This is useful for vibrational calculations, but note that | |
| the energy and gradient are likely to be inconsistent. | |
| NB: Don't use this potential in an optimisation since it will go | |
| horribly wrong due to the above! | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| d2E/(da.db) = (kL - kT)*a.b/r^2 + delta_a.b*kT | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | harmonic |
| Type | Option |
| Format | fractional |
| at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> | |
| or | |
| at.sym. <species_type> x y z <charge> <occupancy> <radius> <3 x flags> | |
| Units | Fractional and electrons, except for radius in Angstroms |
| Use | Internal coordinates and charges for all species in the unit cell. |
| Either the atomic number or the symbol may be supplied, followed | |
| by the species type. If the species type is omitted then it is | |
| assumed to be a core. Individual charges may be supplied for each | |
| ion or the charges for each type of species given using the | |
| species option. If the charges are given, then optionally site | |
| occupancies may also be specified. Similarly, if the charge and | |
| occupancy are given, then the radius of a breathing shell may | |
| also be present. Optimisation flags are only needed if cellonly, | |
| conv, bulk, conp or shell are not specified. | |
| See also | cartesian ditto spacegroup cell |
| Type | Option |
| Format | frequency <n> |
| no. value <kpoint_number> <weight> (x n, on separate lines) | |
| Units | cm-1 |
| Use | Subsection of observables, used for specifying frequencies for |
| fitting to. The first number is the position of the mode required | |
| in order of increasing frequency. The third number is optionally | |
| the k point number to fit at with reference to the k point list | |
| for the present configuration. | |
| e.g. | |
| frequency 2 | |
| 1 0.0 | |
| 6 902.0 2 | |
| See also | observables elastic phonon piezoelectric sdlc hfdlc weight mode |
| frqtol |
| Type | Option |
| Format | frqtol value |
| Units | cm-1 |
| Default | 0.5 cm-1 |
| Use | When checking if there are imaginary modes through the use of the "lower" |
| keyword, the magnitude of the frequency is checked to see if it is smaller | |
| than this tolerance. | |
| See also | observables elastic phonon piezoelectric sdlc hfdlc weight mode |
| frequency |
| Type | Option |
| Format | ftol <opt/fit> real value |
| Units | fractional |
| Default | 0.00001 for both fitting and optimisation |
| Use | Function tolerance for optimisation/fitting. |
| Value may appear on same line as option or on the following line. | |
| If ftol > 1.0 => ftol=10**(-ftol) | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | gdcrit gtol gmax xtol |
| Type | Option |
| Format | fvectors <au> |
| x y z for vector 1 for 3D | |
| x y z for vector 2 for 3D | |
| x y z for vector 3 for 3D | |
| or | |
| x y z for vector 1 for 2D | |
| x y z for vector 2 for 2D | |
| or | |
| x y z for vector 1 for 1D | |
| Units | Angstroms |
| Default | None |
| Use | Specifies the final unit cell for the nudged elastic band method |
| using the cell vectors. The number of vectors must match the | |
| dimensionality of the system. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell neb fcell |
| Type | Option |
| Format | g3coulomb <intra/inter> <bond> <nbeq/nbne nbond> |
| atom1 atom2 atom3 A gamma <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 & | |
| <2 x flags> | |
| Units | A in a.u., gamma in Ang**3, distances in Angstroms |
| Default | rmin12 = rmin13 = rmin23 = 0.0 |
| Use | Coulomb subtraction between atoms that are connected by a three-body term: |
| E(three) = - A/(rij**3 + gamma)**(1/3) | |
| This potential is useful when subtracting the Coulomb term used in | |
| ReaxFF between fixed charges in order to mix a molecular mechanics | |
| force field with this form of reactive model. | |
| Here the term gamma represents 1/(gammai*gammaj)**3 where the gammai | |
| and gammaj are terms from the ReaxFF force field. The A term is the | |
| product of the two charges, A = q1*q2, in atomic units. The whole | |
| term is then converted internally from units of e2/Ang to eV. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2 and 1-3 are bonded. | |
| See also | gcoulomb 3coulomb |
| Type | Option |
| Format | gamma_angular_steps Nsteps |
| Units | none |
| Default | 0 |
| Use | Specifies the number of angular points for theta and phi to |
| be used in averaging the nonanalytic correction to the | |
| dynamical matrix over all possible approach directions. | |
| This leads to the polycrystalline powder average of the | |
| gamma point frequencies due to the LO/TO splittings in all | |
| directions. Note: the absolute magnitude does not matter - | |
| only the direction. | |
| See also | phonon nononanal gamma_direction_of_approach |
| Type | Option |
| Format | gamma_direction_of_approach Kx Ky Kz |
| Units | fractional |
| Default | 1.0 1.0 1.0 |
| Use | Specifies the direction of approach to the gamma point for the |
| calculation of the nonanalytic correction to the dynamical | |
| matrix due to the LO/TO splitting resulting from the electric | |
| field in the crystal. This option allows the frequencies to be | |
| calculated for a particular crystal orientation. Only used if | |
| gamma_angular_steps is set to zero. Note that the value is also | |
| ignored if a point is part of a dispersion curve, where the | |
| direction of the curve is taken. | |
| NB: Specification of this direction triggers the calculation of | |
| the non-analytic correction for a single k point. | |
| See also | phonon nononanal gamma_angular_steps |
| Type | Option |
| Format | gastdamping <original/fixed/accelerate> damping_factor |
| Units | None |
| Default | damping_factor = 0.5, original |
| Use | Controls the damping procedure during iterative solution |
| of the Gasteiger scheme. Here the damping factor is the | |
| fraction of the old and new electronativities that are | |
| used to propagate the charges. A small value of the damping | |
| factor implies slow, but stable, convergence whereas a | |
| large value can lead to fast convergence or oscillation. | |
| In the original Gasteiger method the damping factor is | |
| set to 1/2 and raised to the power of the iteration number. | |
| This means that the calculation becomes more damped as it | |
| progresses to guarantee convergence. The option to use | |
| either a fixed damping or accelerated damping is provided. | |
| However, this will yield different results from the original | |
| Gasteiger method. | |
| See also | eem gasteiger gastiter qeq gastparam gasttol noqeem |
| eembond |
| Type | Option |
| Format | gastiter maximum_number_iterations |
| Units | None |
| Default | 50 |
| Use | Sets the maximum number of iterations that are allowed |
| during the Gasteiger charge scheme. | |
| See also | eem gasteiger gasttol qeq gastparam gastdamping noqeem |
| eembond |
| Type | Option |
| Format | gastparam species A B C <Q0> <4*flags> |
| Units | A is in eV, B in eV/e, C in eV/e^2, Q0 in atomic units |
| Default | As per original paper, Tetrahedron, 36, 3219-3288 (1980), Q0=0 |
| Use | Sets a species specific set of parameters for use in a |
| Gasteiger charge calculation. For example to set the values | |
| for carbon type 4 with A = 7.98, B = 9.18 and C = 1.88, the | |
| input would be: | |
| gastparam C4 7.98 9.18 1.88 | |
| Q0 is the initial charge for the species, which is usually | |
| zero. Note that the Gasteiger algorithm is designed to guarantee | |
| convergence, but to a state that depends on the initial | |
| charges and so Q0 is used to initialise each charge solution | |
| rather than the values from the previous iteration. | |
| See also | eem gasteiger gasttol qeq gastiter gastdamping noqeem |
| eembond |
| Type | Option |
| Format | gasttol tolerance |
| Units | Electrons |
| Default | 0.000001 |
| Use | Sets the tolerance on the change in the charges between |
| iterations of the Gasteiger scheme. The value is set here | |
| for consistency with the original paper, which used 0.001 | |
| of an electron, but more converged values can be obtained | |
| by lowering the tolerance | |
| See also | eem gasteiger gastiter qeq gastparam gastdamping noqeem |
| eembond |
| Type | Option |
| Format | gcmcexistingmolecules mol1 mol2 mol3 ...etc.... |
| natmol1 atom1_1 atom1_2 atom1_3.... atom1_natmol1 | |
| natmol2 atom2_1 atom2_2 atom2_3.... atom2_natmol2 | |
| natmol3 atom3_1 atom3_2 atom3_3.... atom3_natmol3 | |
| etc... | |
| Default | No existing GCMC molecules in existing structure |
| Units | None |
| Use | Allows molecules in the current structure that are related to GCMC |
| molecules to be identified. The purpose of this option is to facilitate | |
| restarts of GCMC runs. For example, if a system contains 3 molecules | |
| where molecule numbers 2 and 3 were inserted by GCMC, while molecule 1 | |
| is a fixed framework into which the molecules are inserted then the | |
| input would be: | |
| gcmcexistingmolecules 2 3 | |
| 2 5 6 | |
| 2 7 8 | |
| Note that lines 2 and 3 identify that there are 2 atoms in molecule | |
| 2 numbered 5 & 6, while molecule 3 also has 2 atoms that are numbers | |
| 7 & 8 in the input for this structure. | |
| Where there are many molecules a range can also be specified as follows: | |
| gcmcexistingmolecules 4 to 8 | |
| See also | mccreate mcdestroy montecarlo gcmcspecies gcmcmolecules |
| Type | Option |
| Format | gcmcmolecule <number_of_atoms> <au> |
| AtomicSymbol <core/shell> x y z ( x number of atoms) | |
| Default | None |
| Units | Coordinates in Angstroms |
| Use | Specifies the coordinates for molecules that can be created |
| during a GCMC calculation trial step. The molecule will be | |
| inserted using the specified geometry at a random position | |
| and with a random orientation. Only used in GCMC calculations. | |
| Note that specifying the number of atoms is optional. | |
| Example | gcmcmolecule |
| N core 0.0 0.0 -0.6 | |
| N core 0.0 0.0 0.6 | |
| See also | mccreate mcdestroy montecarlo gcmcspecies gcmcexistingmolecules |
| Type | Option |
| Format | gcmcspecies <number_of_species> |
| AtomicSymbol <core/shell> x <number_of_species> | |
| Default | None |
| Units | None |
| Use | Specifies the species that can under go destruction/creation |
| operations in a trial MC step. Only used in GCMC calculations. | |
| Note that specifying the number of species is optional. | |
| Example | gcmcspecies 2 |
| H core | |
| O core | |
| See also | mccreate mcdestroy montecarlo gcmcmolecule |
| Type | Option |
| Format | gcoulomb <intra/inter> <bond/x12/x13/x14/o14/g14> <scale14> |
| atom1 atom2 A gamma <rmin> rmax <flag> | |
| Units | A in a.u., gamma in Ang**3, distances in Angstroms |
| Default | rmin = 0.0 |
| Use | Coulomb subtraction potential of ReaxFF form with gamma. This |
| potential is useful when mixing fixed charges in a ReaxFF calculation | |
| with a molecular mechanics force field between the fixed charges | |
| since it allows the ReaxFF charge term to be removed. | |
| E = - A/(rij**3 + gamma)**(1/3) | |
| Here the term gamma represents 1/(gammai*gammaj)**3 where the gammai | |
| and gammaj are terms from the ReaxFF force field. The A term is the | |
| product of the two charges, A = q1*q2, in atomic units. The whole | |
| term is then converted internally from units of e2/Ang to eV. | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction - this can also be achieved through the command molmec. | |
| o14 => only act between atoms which are 1-4, i.e. separated by | |
| 3 bonds | |
| When specified as bonded potential cutoffs are omitted from input. | |
| See also | molmec g3coulomb |
| Type | Option |
| Default | 4.0 |
| Use | Optimisation of defects involves a force balance |
| method, rather than direct minimisation of the | |
| energy. The method is implemented in GULP such that | |
| initially the energy is minimised until the gradient | |
| norm is sufficiently small, at which point the step | |
| length is based on -(H-1).g and no line search is | |
| used (where H = second derivative matrix and g = | |
| gradient vector). The criterion for switching | |
| between these minimisation methods is given by | |
| gdcrit/nvar, where nvar is the number of variables. | |
| See also | defect |
| Type | Option |
| Format | general <m> <n> <ener/grad> <intr/inte> <bon/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 A rho C <rmin> rmax <3*flags> | |
| Units | A in eV*Angs**m, rho in Angs, C in eV*Angs**n |
| Default | m=0 n=6 |
| Use | General potential - optimisation flags for fitting (0/1). |
| This potential is a combination of a Buckingham and Lennard-Jones. | |
| On the first line, general may be followed by m and n, which | |
| are the powers of r (12 6 => L-J potential). Rho=0.0 results in the | |
| exponential term being removed. The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. atom1 and atom2 may be specified either by atomic number or | |
| symbol, which in the latter case can be followed by a species type. | |
| If no species type is given then type is assumed to be core. | |
| E = A.exp(-r/rho)/r**m - C/r**n <-E(rmax) <+Grad correction term>> | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| See also | c6 zbl |
| Type | Option |
| Use | Start of genetic algorithm options section, closed by "end" |
| See also | tournament crossover mutation discrete |
| configurations best maximum minimum dmaximum dminimum |
| Type | Option |
| Default | Use tournament probability. |
| Use | Part of ga options section. If specified then probability of |
| success for a given configuration is weighted exponentially | |
| with respect to how good the configuration is compared with the | |
| other configurations within the present population. | |
| See also | tournament |
| Type | Option |
| Format | ghost_supercell (ncells in x) (ncells in y) (ncells in z) |
| Default | 1 1 1 (i.e. no underlying supercell) |
| Use | Tells GULP that the structure was generated by the supercell option |
| and so there is an underlying smaller unit cell. This is used for | |
| calculations where force constants between different cell images | |
| are needed. Main use is currently in generating files for ShengBTE, | |
| or for finite difference calculation of phonons with neighbour list | |
| based potentials. | |
| See also | supercell ghostcell fc_supercell |
| Type | Option |
| Format | gmax <opt/fit> real value |
| Units | fractional |
| Default | 0.001 for opt / 0.001 for fit |
| Use | Maximum allowed individual gradient for optimisation/fitting. |
| Value may appear on same line as option or on the following line. | |
| If gmax > 1.0 => gmax=10**(-gmax) | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | gdcrit gtol ftol xtol |
| Type | Option |
| Format | gradients <units> |
| atom_no. x y z <weight> | |
| Units | eV <eV/Angs or au/Angs or au> |
| Default | all fitted gradients are zero |
| Use | Subsection of observables, used for specifying the x, y and z |
| components of the derivatives on the atom number given for | |
| The atom number should refer to the order of the atoms | |
| in the asymmetric unit. Derivatives should be symmetry adapted | |
| if symmetry is being used (i.e. weighted by the number of | |
| symmetry related atoms of the type). | |
| Cartesian gradients may be supplied by specifying units. | |
| See also | observables elastic sdlc hfdlc piezo energy stress |
| Type | Option |
| Format | grid min <max> <iter> |
| Default | 64 by 64 by 64 fixed grid (i.e. min=max=6). |
| Use | Part of ga options section. Allows the grid size to change after |
| iter (default=20) iterations from (2^min)^3 to (2^min+1)^3 to a | |
| maximum number of grid points of (2^max)^3. | |
| Note that when optimisation stuck within a local minimum and this | |
| option word is used then grid size will begin changing again. | |
| See also | discrete |
| Type | Option |
| Format | grimme_c6 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 C6 d r0 <rmin> rmax <3*flags> | |
| Units | C6 in eV*Angs**6, r0 in Angs, d is unitless |
| Default | s_6 = 1, d = 20 |
| Use | Specifies potential parameters for the Grimme form of damped C6 term |
| (J. Comput. Chem., 27, 1787 (2006)). The energy is of the form: | |
| E = - C6*fdmp(r)/r**6 | |
| where the damping function, fdmp is given by: | |
| fdmp(r) = 1/[1 + exp(-d(r/r0 - 1))] | |
| NB: Here the s6 parameter of Grimme is subsumed into the C6 terms. | |
| See also | damped_dispersion becke_johnson_c6 |
| Type | Option |
| Format | gtol <opt/fit> real value |
| Units | fractional |
| Default | 0.0001 for opt / 0.0001 for fit |
| Use | Gradient tolerance for optimisation/fitting. |
| Value may appear on same line as option or on the following line. | |
| If gtol > 1.0 => gtol=10**(-gtol) | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | gdcrit gmax ftol xtol |
| Type | Option |
| Format | harmonic <k3> <k4> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> |
| atom1 atom2 k2 <k3> <k4> r0 <coul> <rmin> rmax <2-4*flags> | |
| Units | k2 in eV*Angs**-2, r0 in Angs, coul in none, k3 in eV*Angs**-3 |
| k4 in eV*Angs**-4 | |
| Defaults | k3 = k4 = 0.0, coul = 0.0 |
| Use | Harmonic potential - optimisation flags for fitting. |
| coul = 1.0 => Coulomb subtracted | |
| coul = 0.0 => not Coulomb subtracted | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = 1/2 K2*(r-r0)**2 + 1/6 K3*(r-r0)**3 + 1/24 K4*(r-r0)**4 | |
| -coul*qi*qj/r | |
| k3 and k4 terms can be included as follows: | |
| harm k3 | |
| atom1 atom2 k2 k3 r0 <coul> <rmin> rmax <3*flags> | |
| harm k4 | |
| atom1 atom2 k2 k4 r0 <coul> <rmin> rmax <3*flags> | |
| harm k3 k4 | |
| atom1 atom2 k2 k3 k4 r0 <coul> <rmin> rmax <4*flags> | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | spring squaredharmonic forceconstant mm3stretch |
| Type | Option |
| Format | hfdlc <n> |
| i j dielectric constand hfe(i,j) <weight> | |
| Units | none |
| Default | no high frequency dielectric constants to be fitted |
| Use | Subsection of observables, used for specifying experimental |
| high frequency dielectric constants for fitting. | |
| Only give unique high frequency dielectric constants. | |
| See also | elastic piezoelectric sdlc weight srefractive hfrefractive |
| bornq young poisson shear voigt bulk omega |
| Type | Option within "observables" |
| Format | i high_frequency_refractive_index(i) <weight> |
| Units | None |
| Default | No high frequency refractive indices to be fitted |
| Use | Specifies exptl high frequency refractive indices for fitting |
| along principal axes. | |
| See also | elastic piezoelectric sdlc hfdlc srefractive weight |
| Type | Option |
| Format | hfdlc <n> |
| i j dielectric constant hfe(i,j) <weight> | |
| Units | none |
| Default | no dielectric constants to be fitted |
| Use | Subsection of observables, used for specifying experimental |
| high frequency dielectric constants for fitting. | |
| Only give unique high frequency dielectric constants. | |
| See also | elastic piezoelectric sdlc weight srefractive hfrefractive |
| Type | Option |
| Format | hydrogen-bond <intra/inter> <kcal/kjmol> <m> <n> <p> <taper> <dreiding> |
| atom1 atom2 atom3 A B <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags> | |
| or if taper is specified: | |
| atom1 atom2 atom3 A B <theta_min theta_max> <rmin12> rmax12 <rmin13> rmax13 | |
| <rmin23> rmax23 <2*flags> | |
| Units | A in eV*Ang**m, B in eV*Ang**n |
| Defaults | m = 12, n = 10, p = 4 |
| Use | Specifies a three-body hydrogen bond potential of form: |
| If theta > 90 degrees : | |
| E(three) = (A/(r**m) - B/(r**n))*(cos(theta))**p | |
| If theta =< 90 degrees : | |
| E(three) = 0.0 | |
| where r is the distance between atoms 2 and 3, and theta is the angle | |
| between the 1-2 and 1-3 vectors. | |
| If the dreiding sub-option is specified then the rule that the | |
| potential will only be applied when H is bonded to one of the following | |
| donor atoms N, O, F, S, Cl, Br, I is used. | |
| Note that theta_min and theta_max are only input if the "taper" sub-option | |
| is specified. | |
| See also | three-body angle exponential axilrod-teller stillinger bcross |
| urey-bradley murrell-mottram bacross equatorial lin3 uff3 3coulomb | |
| bagcross |
| Type | Option |
| Format | igauss <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 A b r0 <rmin> rmax <3*flags> | |
| Units | A in eV, b in Angs**-2, r0, rmin and rmax in Angs |
| Default | none |
| Use | This option specifies the use of an inverted Gaussian potential |
| between two atoms. The form of the energy is: | |
| E = - A.exp(-b(r-r0)**2) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| Type | Option |
| Use | Part of ignore/erongi pair. All lines of input after |
| "ignore" are treated as comments until the option | |
| "erongi" is found at the start of a line. Allows the | |
| user to comment out parts of an input file. Note | |
| any parts commented out will not be passed through | |
| to a restart file. | |
| See also | erongi keyword include |
| Type | Option |
| Format | impurity symbol <core/shel> <symbol> <cart/frac> x y z <fix> |
| Use | Create an impurity (combined vacancy and interstitial) in a |
| defect calculation. The symbol for the impurity ion must be | |
| given first, optionally followed by a core/shell specification. | |
| If the type is not given then both will be added if appropriate. | |
| The position of the impurity can be specified in two ways: | |
| (a) atom symbol - replace the specified atom with the impurity. | |
| Takes the nearest image to the defect centre of the first | |
| atom of this type to be specified in the asymmetric unit. | |
| e.g. impurity Mg2 Ca | |
| (b) coordinates - any species within a given tolerance of the | |
| specified coordinates is to be replaced and the impurity | |
| is then placed at those coordinates. By default x y and z | |
| are taken to be fractional, unless "cart" is specified, | |
| in which case the image nearest the defect centre is taken. | |
| e.g. impurity Mg2 0.5 0.5 0.5 | |
| impurity Mg2 core cart 1.2 1.2 1.2 | |
| If "fix" is specified, then the impurity will be held fixed | |
| during the defect calculation. Partial fixing can also be achieved | |
| by specifying the directions to be fixed as well; | |
| e.g. impurity Mg2 core 1.2 1.2 1.2 fix xy | |
| would fix the Mg atom in the x and y directions. Allowed values | |
| are - x, y, z, xy, xz, yz and xyz. | |
| See also | defect vacancy interstitial size centre region_1 |
| Type | Option |
| Format | include filename |
| Use | Includes a separate file into the GULP input. This allows common input |
| for a series of runs to be placed in one file and then read into multiple | |
| inputs. | |
| See also | keyword ignore erongi |
| Type | Option |
| Format | index_k <integer_value> |
| Units | none |
| Default | 60 |
| Use | This specifies the limit on the looping indices for reciprocal lattice |
| vectors. If an error message appears that says that there are too many | |
| reciprocal lattice vectors then it means that this value has been | |
| exceeded. While the value can be increased, this may indicate that the | |
| unit cell of your system is becoming too small and thereby causing the | |
| volume of reciprocal space to become too large. | |
| See also | rspeed veck accuracy ewaldrealradius |
| Type | Option |
| Format | initial_coordinates |
| x1 y1 z1 | |
| x2 y2 z2 | |
| ..... | |
| xN yN zN | |
| Units | Angstroms |
| Use | Specifies the initial Cartesian coordinates of the atoms. Used for |
| restarting calculations that specify an electric field or the | |
| delta_dipole form of dipole energy. | |
| See also | md absolute_coordinates |
| Type | Option |
| Format | intconserved pr_cons |
| Units | eV |
| Default | 0.0 |
| Use | Specifies the integral of the conserved quantity so far for use in an MD run |
| for correct restarting. | |
| See also | md integrator conserved |
| Type | Option |
| Format | integrator <gear/velocity verlet/leapfrog verlet/stochastic> <iter> |
| Default | stochastic (note this is a change from earlier versions) |
| Use | Specifies the integration algorithm to be used in molecular |
| dynamics as being the Gear 5th order or either of the | |
| velocity or leapfrog methods of Verlet. Currently the Gear | |
| algorithm is only available in the NVE ensemble. | |
| Details of the stochastic integrator can be found in G. Bussi | |
| et al, J. Chem. Phys., 130, 074101 (2009). | |
| See also | md tau_barostat tau_thermostat p_isotropic p_flexible |
| Type | Option |
| Default | both |
| Use | All subsequent potentials to be treated as |
| intermolecular when molecule option is active. | |
| See also | molecule molq molmec intra both 14_scale |
| Type | Option |
| Format | interstitial symbol <core/shel> <cart/frac/bond> x y z <fix> |
| Use | Creates an interstitial in a defect calculation. The symbol |
| for the interstitial species must be given and optionally | |
| followed by the specification of core or shell. If core or | |
| shell is not specified then both will be added if appropriate. | |
| The coordinates for the interstitial must be given and by | |
| default are assumed to be fractional unless "cart" has been | |
| specified. If fractional coordinates are used then the image | |
| nearest to the defect centre will be used. | |
| e.g. interstitial Mg2 0.25 0.25 0.25 | |
| interstitial O1 shel cart 1.2 0.6 0.6 | |
| Alternatively the command "bond" may be used in place of frac or | |
| cart in which case the interstitial is added at the covalent | |
| bond length from an atom which is specified by either a symbol | |
| or the coordinates of the ion in the defective region 1. | |
| The program will attempt to place the bond to maximise the | |
| distance to any other atoms bonded to the specified centre. | |
| e.g. interstitial H bond O2 | |
| interstitial H1 core bond 0.1 0.4 0.24 | |
| interstitial H bond 1.2 3.4 2.7 | |
| If "fix" is specified, then the interstitial will be held fixed | |
| during the defect calculation. Partial fixing can also be achieved | |
| by specifying the directions to be fixed as well; | |
| e.g. interstitial H 1.2 3.4 2.7 fix xy | |
| would fix the H atom in the x and y directions. Allowed values | |
| are - x, y, z, xy, xz, yz and xyz. | |
| See also | defect vacancy impurity size centre region_1 |
| Type | Option |
| Default | both |
| Use | All subsequent potentials to be treated as |
| intramolecular when molecule option is active. | |
| See also | molecule molq molmec inter both and 14_scale |
| Type | Option |
| Format | inversion <squared> <intra/inter/bond/mol> <only3> <kcal/kjmol> |
| atom1 atom2 atom3 atom4 k <k0> rmax(1-2) rmax(1-3) rmax(1-4) <1 x flag> | |
| Units | k in eV, k0 in degrees |
| Default | none |
| Use | Out of plane energy - energy penalty for atom 1 lying |
| out of the plane of atoms 2, 3 and 4. This form uses the | |
| Dreiding planar expression: | |
| E = k.(1 - cos(phi)) | |
| where phi is the angle between the plane of the centre atom and two | |
| others with the bond from the centre atom to the third atom. | |
| Note that because phi depends on which of the 3 different angles is | |
| chosen, GULP computes the contribution for all 3 cases and takes the | |
| average. | |
| If the sub-option "squared" is specified then the modified form given | |
| below is used: | |
| E = 1/2 (k/sin(k0)**2).(cos(phi) - cos(k0))**2 | |
| and k0 must be input. | |
| If the only3 sub-option is specified then the potential applies where | |
| an atom has exactly 3 bonds present. | |
| See also | torsion ryckaert torangle torharm torexp xoutofplane outofplane |
| Type | Option |
| Format | ionic at.no. <radius> |
| Units | Angstroms |
| Default | value for most common oxidation state normally in octahedral |
| environment | |
| Use | Allows ionic radii to be changed. |
| To be used in breathing shell model eventually. | |
| Command is part of element section. | |
| See also | element |
| Type | Option |
| Format | iterations n <gradient_norm> <noextrapolate> <order_of_extrapolation> |
| Default | n = 100, gradient_norm = 1.0D-8, order of extrapolation = 8 |
| Use | Specifies that shell model molecular dynamics shall be performed with |
| massless shells. This is the default for molecular dynamics if shells | |
| are present. The shell positions are optimised in every time step for | |
| n iterations or until the specified gradient norm for the shells only | |
| is reached. Convergence of the shell gradients is crucial for the | |
| conservation of the momentum of the system. | |
| By default shell extrapolation using rational function interpolation | |
| is turned on, using a function of order 8. If "noextrapolate" is | |
| specified then this is turned off. Extrapolation usually greatly | |
| reduces the number of cycles for optimisation. | |
| See also | shellmass sopt md |
| Type | Option |
| Format | keyword <list of keywords> |
| Use | allows keywords to be specified anywhere in an input file |
| instead of just on the top line. | |
| e.g. | |
| keyword opti conp prop | |
| See also | include ignore erongi |
| Type | Option |
| Format | kim_model <number_of_models> |
| name_of_model1 | |
| name_of_model2 | |
| : | |
| name_of_modelN | |
| NB: To allow for the use of long model names this is given | |
| on the line after the option. | |
| Units | none |
| Default | No KIM model is to be used, number_of_models = 1 |
| Use | This option allows the user to select models from |
| the OpenKIM project for use with GULP. Note that the | |
| code must have been compiled with the -DKIM option in DEFS. | |
| See OpenKIM documentation for more details. | |
| If using multiple models then the number must be specified | |
| and then each model name will be read from a separate line. | |
| By default a single model name is expected. | |
| NB: From version 5.2 of GULP onwards only OpenKIM version | |
| 2.0 is supported. | |
| NB: At present KIM will only support a single type of each | |
| element and so species types are ignored when being passed | |
| to KIM. | |
| NB: If using KIM models then it is not currently possible | |
| to compute the attachment energy and so this will not be | |
| output. |
| Type | Option |
| Format | x y z <weight> |
| Units | x,y,z are fractions of reciprocal lattice vectors |
| Default | weight=1.0 |
| Use | Specifies the k points to be used in the phonon calculation / free |
| energy calculation explicitly. | |
| See also | phonon dispersion shrink kfull msd |
| Type | Option |
| Format | lbfgs_order <integer_value> |
| Units | None |
| Default | 10 |
| Use | Specifies the order of the limited memory BFGS algorithm. The |
| larger the value the more memory will be used, but the more | |
| rapid the convergence will be. Designed for use with large | |
| systems where the full Hessian cannot be stored. | |
| See also | numdiag dfp positive conjugate unit lbfgs |
| Type | Option |
| Format | lennard <epsilon> <zero> <esff> <combine/geometric/product> <m> <n> <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <type_of_bond> |
| <kcal/kjmol> <ener/grad> <all> <scale14> | |
| atom1 atom2 (A B/epsilon sigma) <rmin> rmax <2*flags> | |
| If combination rules are specified then the format is: | |
| atom1 atom2 <rmin> rmax | |
| If combination rules and "all" are specified then the format is: | |
| <rmin> rmax | |
| Units | A in ev*Angs**m, B in ev*Angs**n, epsilon in eV, sigma in Angs |
| Default | m=12, n=6 |
| Use | Lennard-Jones potential - optimisation flags for fitting. |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A/r**m - B/r**n | |
| The exponents are by default 12 and 6, but these can be changed | |
| by specifying values after the option word lennard. By specifying | |
| epsilon after lennard this means that the input is in terms of | |
| epsilon and sigma instead of A and B. | |
| E = epsilon*(c1*(sigma/r)**m - c2*(sigma/r)**n) | |
| Specifying "zero" allows the user to chose between sigma defined | |
| as the potential energy minimum distance (default) or the distance | |
| at which the potential energy goes to zero. | |
| r = sigma => E = epsilon | |
| c1 = (n/(m-n)) | |
| c2 = (m/(m-n)) | |
| r = sigma => E = zero | |
| c1 = (n/(m-n))*(m/n)**(m/(m-n)) | |
| c2 = (m/(m-n))*(m/n)**(n/(m-n)) | |
| If combine is specified as well as epsilon, then combination rules | |
| are used to obtain the epsilon and sigma parameters based on the | |
| values for individual species. The combination rules are as follows: | |
| epsilon = 2*sqrt(e1*e2)(s1**3.s2**3)/(s1**6+s2**6) | |
| sigma = ((s1**6+s2**6)/2)**1/6 | |
| where e1, e2, s1 and s2 are the atom related parameters. | |
| Alternatively, if geometric combination rules are specified then | |
| this becomes: | |
| epsilon = sqrt(e1*e2) | |
| sigma = (s1+s2)/2 | |
| As a further alternative, if product combination rules are specified | |
| then this becomes: | |
| epsilon = sqrt(e1*e2) | |
| sigma = sqrt(s1*s2) | |
| If combine is specified for a standard lennard-jones potential | |
| then the species values given in the "atomab" command are used | |
| to obtain potential parameters using the following rules: | |
| Aij = sqrt(Ai.Aj) | |
| Bij = sqrt(Bi.Bj) | |
| If esff is specified then this implies that the ESFF combination | |
| rules will be used to calculate the potential parameters. This | |
| automatically implies "combine" and that the functional form is | |
| 9/6. The parameters are then obtained from epsilon and sigma as | |
| follows: | |
| Aij = Ai.Bj + Aj.Bi | |
| Bij = 3 * Bi.Bj | |
| where Ai = sqrt(epsilon)*sigma**6 | |
| Bi = sqrt(epsilon)*sigma**3 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| If "all" is specified as a sub-option, then Lennard-Jones potentials | |
| will be automatically created and added for all combinations of A/B | |
| or epsilon/sigma, as appropriate. NB: This will be done based on the | |
| values that have been specified up to that point and so be sure to get | |
| the order right! In this case, the line following should only have the | |
| rmin and rmax to be used for all the potentials. | |
| e.g. | |
| lennard 12 6 combine all | |
| 0.0 12.0 | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | epsilon atomab c6 buffered_lj |
| Type | Option |
| Format | library name_of_library <nodump> |
| Use | Allows the user to access libraries of existing interatomic |
| potentials. If the word "nodump" is included then all the | |
| potentials selected from the library will be excluded | |
| from the dumpfile, otherwise they are included and the | |
| library call removed. | |
| NB If including a keyword line in the library file then this | |
| should precede the options to guarantee correct processing | |
| See also | libff libdump preserve_Q |
| Type | Option |
| Format | lin3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K isign n <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) | |
| <rmin(2-3)> rmax(2-3) <flag> | |
| Units | K in eV, rmin and rmax in Angstroms |
| Default | none |
| Use | ESFF linear three-body form : |
| E(three) = K * (1 + isign*cos(n*theta)) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2, 2-3 and 1-3 are bonded. | |
| See also | axilrod-teller angle stillinger-weber exponential bcross |
| urey-bradley murrell-mottram bacross three hydrogen-bond equatorial | |
| uff3 3coulomb bagcross |
| Type | Option |
| Format | integer number |
| Default | 10 |
| Use | Changes the maximum number of points in the line minimisation. |
| Number may appear on same line as command or the following line. |
| Type | Option |
| Format | ljbuffered <m> <n><intra/inter> <bond/x12/x13/x14/o14/g14/mol> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 A B r0 <rmin> rmax <3*flags> | |
| Units | A in eV*Angs**m, B in eV*Angs**n, r0 in Angs |
| Default | m = 12, n = 6, r0 = 0.0 |
| Use | Buffered Lennard-Jones potential, where r0 is added to the distance. |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A/(r + r0)**m - B/(r + r0)**n | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| Type | Option |
| Default | 0.01 |
| Use | This option controls the drop tolerance for the Lorentzian |
| broadening that is used during a thermal conductivity | |
| calculation. If the Lorentzian is below the input threshold | |
| then it is set to zero. | |
| e.g. lorent 0.001 | |
| See also | phonon thermalconductivity broaden_dos |
| Type | Option |
| Format | lowest_mode minimum_mode_number <maximum_mode_number> |
| Units | None |
| Use | Sets the lowest mode and optionally the highest mode |
| number to be used in the calculation of the free energy. | |
| Allows the user to select a band of frequencies whose | |
| value is to be used in the calculation of the vibrational | |
| component of the free energy. | |
| e.g. lowest 4 9 | |
| See also | free zsisa |
| Type | option |
| Format | manybody |
| atom1 atom2 <taper_range> <rmin> rmax | |
| Defaults | rmin = 0, taper_range = 0 |
| Use | Specifies that a manybody potential should act between this |
| pair of atoms. This implies that the density of each atom | |
| at the other will be calculated. The energy is subsequently | |
| calculated as a function of the total density at each site. | |
| This option is used as part of the Embedded Atom Model for | |
| metals and is based on the ideas of Finnis-Sinclair and | |
| subsequently other workers, such as Sutton-Chen. | |
| The densities at each site are determined by the "eam_density" | |
| option and the functional dependance on the total density | |
| by "eam_functional". | |
| Note that although for simplicity the manybody potential | |
| appears as part of the two-body potentials, it is infact | |
| many body at short-range, but tends to an effective pair | |
| potential at long range. Also note that this potential type | |
| is NOT compatible with <intra/inter/molmec> directives. | |
| The density can be smoothly tapered to zero over a distance | |
| which is input using the taper_range. Here the taper applies | |
| from (rmax - taper_range) to rmax. In most MEAM potentials | |
| the typical range used is 0.1 Angstroms. | |
| The form of the taper used for the density is chosen to be | |
| consistent with the MEAM literature: | |
| fcut(x) = 1, for x >= 1 | |
| = 0, for x =< 0 | |
| = [1 - (1-x)**4]**2, for 0 < x < 1 | |
| where x = (rmax - r)/taperrange | |
| See also | eam_density eam_functional scmaxsearch noquicksearch |
| Type | Option |
| Use | Allows a section of text to be inserted into a marvin input file |
| by surrounding text by "marvin" before the first line and "end" | |
| after the last line. | |
| See also | output |
| Type | Option |
| Format | mass symbol <mass> |
| Units | atomic units |
| Default | as per periodic table |
| Use | Allows atomic masses to be changed. Note that species symbols can |
| also be used for the mass to set different masses for different | |
| species of the same element: | |
| element | |
| mass O1 16.0 | |
| mass O2 17.0 | |
| end | |
| or the older form of using the atomic number can be used: | |
| element | |
| mass 8 16.0 | |
| end | |
| Command is part of element section. | |
| See also | element |
| Type | Option |
| Format | maths <eispack/lapack> <nodivide> |
| Default | lapack with divide and conquer |
| Use | Selects whether to use the Eispack or Lapack maths libraries |
| for finding the eigenvectors/eigenvalues of the dynamical | |
| matrix. When compiled from source the Eispack library appears | |
| to be significantly faster than straight Lapack, but if an | |
| optimised maths library is linked instead of lapack.o/blas.o | |
| then this may not be the case. However, the divide and conquer | |
| form of Lapack is faster than Eispack and so this is now the | |
| default. There is the chance of some loss of precision, and so | |
| the other options are there for validation purposes. | |
| See also | phonon matrix_format blocksize |
| Type | Option |
| Format | matrix_format <hessian/cosmo> <triangular/twodimensional> |
| Default | triangular in serial; twodimensional in parallel |
| Use | The Hessian matrix and the COSMO A matrix are symmetric matrices and |
| therefore can be stored and used in either triangular or two-dimensional | |
| form. For serial runs either format can be used with the more compact | |
| triangular form being the default. In parallel then the two-dimensional | |
| form must be used for compatibility with the parallel maths libraries used. | |
| This option is mainly for debugging and checking purposes. | |
| See also | hessian cosmo |
| Type | Option |
| Format | maxcyc <opt/fit> <integer value> |
| Units | none |
| Default | 1000 for optimisation |
| 500*(no. parameters) for fitting | |
| Use | Maximum number of function calls. |
| Value may appear on same line as option or on the following line. | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | stepmx optimise |
| Type | Option |
| Format | maximise <mode/order> n |
| secondary word, either "mode" or "order" followed by integer number | |
| Use | Controls the action of the rfo optimiser for transition state |
| calculations. | |
| mode n => find transition state along mode number <n> of Hessian | |
| order m => find transition state of order <m> | |
| Use of mode implies that the order must be one. | |
| See also | optimise rfo transition_state |
| Type | Option |
| Format | maximum <no._to_set>=N |
| <variables_to_be_set>xN | |
| <maximum_value>xN | |
| Default | Twice initial value. |
| Use | Part of genetic options section. Specifies the maximum allowed |
| value of a given parameter. | |
| See also | genetic |
| Type | Option |
| Format | mcchemicalpotential chemical_potential |
| Default | 0.0 |
| Units | eV |
| Use | Specifies the target chemical potential of the system for |
| a Grand Canonical Monte Carlo run. Controls the probability | |
| for creation and destruction moves being accepted. | |
| Example | mcchemicalpotential -1.00 |
| See also | mccreate mcdestroy mctrial montecarlo gcmcspecies mcvolume |
| Type | Option |
| Format | mccreate probability |
| Default | 0.0 |
| Units | None |
| Use | Specifies the relative probability of an atom being created |
| during a Monte Carlo simulation. Note all probabilities are | |
| renormalised at run time. A value of zero means that atoms | |
| will not be created. | |
| Example | mccreate 0.25 |
| See also | mcdestroy mcmove mcrotate mctrial montecarlo mcswap |
| Type | Option |
| Format | mcdestroy probability |
| Default | 0.0 |
| Units | None |
| Use | Specifies the relative probability of an atom being destroyed |
| during a Monte Carlo simulation. Note all probabilities are | |
| renormalised at run time. A value of zero means that atoms | |
| will not be destroyed. Note when an atom in a molecule is | |
| destroyed, then so is the whole molecule. | |
| Example | mcdestroy 0.25 |
| See also | mccreate mcmove mcrotate mcstrain mctrial montecarlo mcswap |
| Type | Option |
| Format | mclowest lowest_energy |
| Default | None |
| Units | lowest_energy in eV |
| Use | Specifies the running lowest value of the energy encountered |
| so far in the run. This value is only for restarting purposes. | |
| Example | mclowest -1140.6883129 |
| See also | mcstep mctrial montecarlo mcmeans |
| Type | Option |
| Format | mcmaxdisplacement <maxdisplacement> <target ratio <frequency>> |
| Default | 0.05 / no target ratio |
| Units | Angstroms |
| Use | Specifies the maximum Cartesian displacement that can be applied |
| in a translation trial step. If the "target" suboption is used | |
| then the maximum displacement is gradually adjusted to try to | |
| achieve the specified acceptance ratio for translation. The | |
| frequency of adjustment can also be specified. | |
| Examples | mcmaxdisplacement 0.1 |
| mcmaxdisplacement 0.05 target 0.5 20 | |
| See also | mcmove montecarlo |
| Type | Option |
| Format | mcmaxrotation <maxrotation> <target ratio <frequency>> |
| Default | 180 / no target ratio |
| Units | Degrees |
| Use | Specifies the maximum angle of rotation that can be applied |
| in a trial step. If the "target" suboption is used | |
| then the maximum rotation is gradually adjusted to try to | |
| achieve the specified acceptance ratio for rotation. The | |
| frequency of adjustment can also be specified. | |
| Examples | mcmaxrotation 90 |
| mcmaxrotation 180 target 0.5 20 | |
| See also | mcrotate montecarlo |
| Type | Option |
| Format | mcmaxstrain <maxstrain> <target ratio <frequency>> |
| Default | 0.1 / no target ratio |
| Units | Dimensionless |
| Use | Specifies the maximum strain that can be applied in a strain |
| trial step. Note that a strain step of more than 1.0 is not allowed | |
| since this would allow the cell to go to zero in a single step. | |
| Small values are more sensible. If the "target" suboption is used | |
| then the maximum strain is gradually adjusted to try to | |
| achieve the specified acceptance ratio for strain. The | |
| frequency of adjustment can also be specified. | |
| Examples | mcmaxstrain 0.01 |
| mcmaxstrain 0.15 target 0.5 30 | |
| See also | mcstrain montecarlo |
| Type | Option |
| Format | mcmeans mean_energy mean_number_of_atoms |
| Default | None |
| Units | mean_energy in eV |
| Use | Specifies the running mean of the energy and number of |
| atoms. This must be consistent with the number of MC | |
| steps so far given by mcstep and is used to restart a | |
| Monte Carlo job. | |
| Example | mcmeans -3.45155 4.059 |
| See also | mcstep mctrial montecarlo mclowest |
| Type | Option |
| Format | mcmove probability |
| Default | 1.0 |
| Units | None |
| Use | Specifies the relative probability of an atom being translated |
| during a Monte Carlo simulation. Note all probabilities are | |
| renormalised at run time. A value of zero means that atoms | |
| will not be translated. When an atom in a molecule is chosen | |
| for translation, then the whole molecule is translated. | |
| Example | mcmove 0.25 |
| See also | mccreate mcdestroy mcrotate mctrial montecarlo mcstrain mcswap |
| Type | Option |
| Format | mcoutfreq |
| Default | 100 |
| Units | None |
| Use | Specifies the frequency for printing the running averages to |
| the output. The value is specified as the number of trial | |
| operations between outputs. | |
| Example | mcoutfreq 1 |
| See also | mcsample montecarlo |
| Type | Option |
| Format | mcrotate <atom/line/centre> probability |
| Default | 0.0 / centre |
| Units | None |
| Use | Specifies the relative probability of a molecule being rotated |
| during a Monte Carlo simulation. Note all probabilities are | |
| renormalised at run time. A value of zero means that molecules | |
| will not be rotated. | |
| The sub-options atom, line and centre control the point about | |
| which the molecule will be rotated, and in the case of line the | |
| axis direction. For the default mode, centre, the molecule is | |
| rotated about the centre of the molecule based on the average | |
| coordinate. For atom, a random atom from within the molecule | |
| is chosen and then the rotation attempted about this. For line, | |
| two atoms are chosen at random and the rotation attempted about | |
| this axis. If more than one word is specified then all types of | |
| rotation specified will be tried according to a random choice. | |
| Example | mcrotate 0.25 |
| See also | mccreate mcdestroy mcmove mctrial mcmaxrotation montecarlo |
| mcstrain mcswap |
| Type | Option |
| Format | mcsample <frequency> <filename> <lowest> |
| Default | 10 / gulp.gmc |
| Units | None |
| Use | Specifies the frequency for outputting configuration data to |
| a binary file for post-run analysis. The value is specified | |
| as the number of accepted operations between writes. The | |
| filename can be anything with up to 60 characters. The | |
| extension ".gmc" is recommend as a convention. | |
| The format of the file is as follows. Each configuration is | |
| written as follows: | |
| write(31)numat | |
| write(31)energy | |
| write(31)(atomicno(i),i=1,numat) | |
| write(31)(atomictype(i),i=1,numat) | |
| write(31)(xcoordinate(i),i=1,numat) | |
| write(31)(ycoordinate(i),i=1,numat) | |
| write(31)(zcoordinate(i),i=1,numat) | |
| where the variables are as follows : | |
| integer(i4) numat = total number of atoms | |
| integer(i4) atomicno = atomic number of atom (1-maxele) | |
| integer(i4) atomictype = atomic type of atom (0-9999) | |
| real(dp) energy = total energy of system (eV) | |
| real(dp) xcoordinate = Cartesian coord in X direction (Angs) | |
| real(dp) ycoordinate = Cartesian coord in Y direction (Angs) | |
| real(dp) zcoordinate = Cartesian coord in Z direction (Angs) | |
| and the datatypes are given by : | |
| integer, parameter :: i4 = selected_int_kind(9) | |
| integer, parameter :: dp = kind(1.0d0) | |
| Example | mcsample 5 montesamples.gmc |
| See also | montecarlo mcoutfreq |
| Type | Option |
| Format | mcstep first_step number_of_accepted_steps_so_far |
| Default | 1 |
| Units | None |
| Use | Specifies the first step for a Monte Carlo restart and the |
| number of accepted steps so far. The former number must | |
| be consistent with the mean properties given and the second | |
| one must obviously be smaller than the first. | |
| Example | mcstep 50 24 |
| See also | mcmeans mctrial montecarlo mclowest |
| Type | Option |
| Format | mcstrain probability |
| Default | 0.0 |
| Units | None |
| Use | Specifies the relative probability of the cell being strained |
| during a Monte Carlo simulation. Note all probabilities are | |
| renormalised at run time. A value of zero means that the cell | |
| will not be strained. | |
| Example | mcstrain 0.25 |
| See also | mccreate mcdestroy mcrotate mctrial montecarlo mcmove |
| mcmaxstrain mcswap |
| Type | Option |
| Format | mcswap <any/only> probability <npair> <species list> |
| Default | 0.0 / any / 1 pair |
| Units | None |
| Use | Specifies the relative probability of ions being swapped during |
| a Monte Carlo simulation. Note all probabilities are renormalised | |
| at run time. A value of zero means that no swapping will be attempted. | |
| The suboptions control what species can be switched. If any is specified | |
| then all atoms can be swapped. However, if only is specified a list of | |
| species that can be swapped must be given. Note: Only swaps between | |
| different species will be considered since otherwise the energy is | |
| invariant. Furthermore, swaps involving atoms in molecules are not | |
| allowed. Swapping involving species with shells should also be avoided | |
| for now since the core/shell pair may get split. | |
| npair specifies the number of pairs of atoms to be swapped as part of | |
| a single attempted move. By default only 1 pair will be swapped. | |
| Multiple mcswap options are allowed so that different groups of atoms | |
| can be swapped in the same structure. | |
| Example | mcswap 0.25 |
| mcswap only 0.25 2 Mg Ca | |
| See also | mccreate mcdestroy mcrotate mctrial montecarlo mcmove |
| mcmaxstrain mcstrain |
| Type | Option |
| Format | mctrial number_of_trials |
| Default | 0 |
| Units | None |
| Use | Specifies the total number of attempted trial operations in a |
| Monte Carlo simulation. | |
| See also | montecarlo mccreate mcdestroy mcmove mcrotate mcstep mcswap |
| Type | Option |
| Format | mcvolume volume |
| Default | unit cell volume |
| Units | Angstroms**3 |
| Use | Specifies the volume that is used in a Grand Canonical Monte |
| Carlo calculation to determine the creation/destruction | |
| probability. If not specified, the volume of the unit cell is | |
| used. | |
| See also | montecarlo mcchemicalpotential |
| Type | Option |
| Format | mdarchive <unique> file_name |
| Use | Specifies name of archive file for molecular dynamics run. This file |
| is in MSI's archive file format and can be read by Insight II. | |
| If this option is given the current structure is written to the | |
| specified file with the frequency specified using 'write'. Note | |
| it is also necessary to specify the "output arc" option to trigger | |
| the writing of an arc file. | |
| If the "unique" sub-option is specified then the atom symbols will | |
| be appended with the atom number (within what is allowed by the | |
| archive file format) to create different labels for analysis. | |
| See also | md write output |
| Type | Option |
| Format | mdmaxtemp scale_factor |
| Default | 100.0 |
| Use | This option allows MD runs where the temperature is exploding |
| for one reason or another to be trapped and terminated. When | |
| the temperature exceeds the target temperature by a factor of | |
| greater than the number specified then the run will stop. | |
| If this occurs then common causes are that the timestep is | |
| too long, the structure was in a high energy state to start with | |
| and the potential can't be dissipated fast enough, the thermostat | |
| parameter is unsuitable, or that there are discontinuities or | |
| other flaws in the potential energy surface input. Another common | |
| cause is that the system size being used is too small leading to | |
| large fluctuations in the ensemble averages. | |
| See also | md temperature mdmaxvolchange |
| Type | Option |
| Format | mdmaxvolume scale_factor |
| Default | 100.0 |
| Use | This option allows MD runs where the unit cell volume is exploding |
| for one reason or another to be trapped and terminated. When | |
| the volume exceeds the initial volume by a factor of | |
| greater than the number specified then the run will stop. | |
| If this occurs then common causes are that the timestep is | |
| too long, the structure was in a high energy state to start with | |
| and the potential can't be dissipated fast enough, the barostat | |
| parameter is unsuitable, or that there are discontinuities or | |
| other flaws in the potential energy surface input. Another common | |
| cause is that the system size being used is too small leading to | |
| large fluctuations in the ensemble averages. | |
| See also | md temperature mdmaxtemp |
| Type | option |
| Format | meam_density order <power n/fpower/exponential n/gaussian n/cubic/quadratic/quartic/voter/glue/evoter/mei-davenport/baskes/vbo> |
| atom1 <atom2> C (power law) <1 x flag > | |
| atom1 <atom2> C rn (fractional power law) <2 x flag > | |
| atom1 <atom2> A B r0 (exponential) <3 x flags> | |
| atom1 <atom2> A B r0 (gaussian) <3 x flags> | |
| atom1 <atom2> A r0 (quadratic) <2 x flags> | |
| atom1 <atom2> A r0 (cubic) <2 x flags> | |
| atom1 <atom2> A r0 (quartic) <2 x flags> | |
| atom1 <atom2> A beta (voter) <2 x flags> | |
| atom1 <atom2> A beta (evoter) <2 x flags> | |
| atom1 <atom2> c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags> | |
| atom1 <atom2> A beta r0 (baskes) <3 x flags> | |
| atom1 <atom2> c sigma gamma r0 delta (vbo) <5 x flags> | |
| atom1 <atom2> A B C D rmin r0 (spline) <4 x flags> | |
| if order > 0 then there will be addition lines of the following form for each higher order | |
| C (power law) <1 x flag > | |
| A B r0 (exponential) <3 x flags> | |
| A B r0 (gaussian) <3 x flags> | |
| A r0 (quadratic) <2 x flags> | |
| A r0 (cubic) <2 x flags> | |
| A r0 (quartic) <2 x flags> | |
| A beta (voter) <2 x flags> | |
| A beta (evoter) <2 x flags> | |
| c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags> | |
| A beta r0 (baskes) <3 x flags> | |
| c sigma gamma r0 delta (vbo) <5 x flags> | |
| NB: The maximum value of order is currently 3 | |
| Units | Distances in Angstrom |
| Defaults | order = 3 |
| Use | specifies the density due a given atom1 at another |
| atomic centre (atom2) in the Modified Embedded Atom Model (MEAM). | |
| This density is only calculated for pairs of atoms | |
| where the "manybody" potential has been specified | |
| so that the user can control which atoms are part | |
| of the EAM. | |
| Where no atom2 is specified then the density is applied to | |
| all atoms allowed by the manybody potential, regardless of | |
| species type. | |
| In the MEAM formalism the density is a sum of contributions over | |
| a number of orders: | |
| rho_tot(i)**2 = sum(order = 0->3) t_order*rho_order(i)**2 | |
| where t is a coefficient for each order. | |
| The radial component of the density can take one of several functional forms: | |
| Power Law: | |
| rho(i) = C*rij**(-n) | |
| e.g. meam_density 3 power 6 | |
| Ni core 729.7 | |
| 429.2 | |
| 219.5 | |
| 106.2 | |
| Fractional power Law: | |
| rho(i) = C*rij**(-rn) | |
| e.g. meam_density 3 fpower | |
| Ni core 729.7 6.1 | |
| 429.2 | |
| 219.5 | |
| 106.2 | |
| Exponential: | |
| rho(i) = A*(rij**n)*exp(-B(rij-r0)) | |
| e.g. meam_density 0 exponential 0 | |
| Ni core 500.0 4.0 3.52 | |
| Gaussian: | |
| rho(i) = A*(rij**n)*exp(-B(rij-r0)**2) | |
| e.g. meam_density 1 gaussian 2 | |
| Ni core 400.0 3.0 3.52 | |
| 200.0 1.5 1.46 | |
| Quadratic: | |
| rho(i) = A*(rij-r0)**2 if r < r0, else = 0 | |
| Cubic: | |
| rho(i) = A*(rij-r0)**3 if r < r0, else = 0 | |
| Quartic: | |
| rho(i) = A*(rij-r0)**4 if r < r0, else = 0 | |
| Voter: | |
| rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r)) | |
| eVoter: | |
| rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))*exp(-1/(rmax - r)) | |
| Mei-Davenport: | |
| rho(i) = sum(l=0->5) (c_l/12)*(r/r0)**l | |
| Baskes: | |
| rho(i) = A*exp(-beta((rij/r0)-1)) | |
| e.g. meam_density 1 baskes | |
| N core 1.0 4.0 1.10 | |
| 1.0 4.0 1.10 | |
| NB: This form is a re-working of the exponential form for convenience for MEAM. | |
| In the above, rmax is the cutoff for the potential from the manybody | |
| option that controls the range of the density. | |
| VBO: | |
| rho(i) = c*sigma*N*exp(-gamma/(1 - sqrt(r/delta))) | |
| where N is a normalisation constant given by: | |
| N = exp(gamma/(1 - sqrt(r0/delta))) | |
| Note that the cut-offs are set by the manybody potential. | |
| Spline: This is effectively one piece of a cubic spline. | |
| rho(i) = A*(rij-r0)**3 + B*(rij-r0)**2 + C*(rij-r0) + D if rmin < r < r0, else = 0 | |
| See also | manybody meam_functional scmaxsearch eam_alloy prt_eam eam_density baskes meam_screening |
| meam_rhotype |
| Type | option |
| Format | meam_functional order <square_root/power n/banerjea_smith n/johnson/glue/foiles/mei-davenport/baskes/vbo/spline> |
| if square_root or power : | |
| atom1 A_1 <1*flag> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 A_2 <1*flag> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if banerjea_smith : | |
| atom1 F0_1 F1_1 rho0_1 <3*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 F0_2 F1_2 rho0_2 <3*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if johnson : | |
| atom1 F0_1 F1_1 rho0_1 alpha beta gamma <6*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 F0_2 F1_2 rho0_2 alpha beta gamma <6*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if glue : | |
| atom1 rho1 rho2 | |
| c1_4 c1_3 c1_2 c1_1 c1_0 | |
| c2_4 c2_3 c2_2 c2_1 c2_0 | |
| c3_3 c3_2 c3_1 c3_0 | |
| t_0 ... t_order <order+1*flags> | |
| atom2 rho1 rho2 | |
| c1_4 c1_3 c1_2 c1_1 c1_0 | |
| c2_4 c2_3 c2_2 c2_1 c2_0 | |
| c3_3 c3_2 c3_1 c3_0 | |
| t_0 ... t_order <order+1*flags> | |
| if foiles : | |
| atom1 F0_1 F1_1 F2_1 F3_1 <4*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 F0_2 F1_2 F2_2 F3_2 <4*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if mei-davenport : | |
| atom1 Ec_1 alpha_1 beta_1 gamma_1 delta_1 phi0_1 s_1_1 s_2_1 s_3_1 <9*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 Ec_2 alpha_2 beta_2 gamma_2 delta_2 phi0_1 s_1_2 s_2_2 s_3_2 <9*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if baskes : | |
| atom1 Ec_1 A_1 rho0_1 <3*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 Ec_2 A_2 rho0_2 <3*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if vbo : | |
| atom1 A_1 rn_1 <2*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 A_2 rn_2 <2*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if igarashi : | |
| atom1 A_1 B_1 <2*flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 A_2 B_2 <2*flags> etc... | |
| t_0 ... t_order <order+1*flags> | |
| if spline : | |
| atom1 A_1 B_1 C_1 D_1 rho0_1 rho_max_1 <4 x flags> | |
| t_0 ... t_order <order+1*flags> | |
| atom2 A_2 B_2 C_2 D_2 rho0_2 rho_max_2 <4 x flags> | |
| t_0 ... t_order <order+1*flags> | |
| Units | A, B, C, D, AE0, F0, Ec, phi0 and F1 in eV, rho0/rho_max/alpha/beta/gamma/t0... are dimensionless |
| Default | square_root, A = 1.0, order = 3 |
| Use | Specifies how the total energy contribution of an atom in the |
| Modified Embedded Atom Model depends on the density components at that | |
| site. The current possibilities are: | |
| Square_root: | |
| E = - sum(i) A(i)*(rho(i))**1/2 | |
| this is the most common functional, as used in the Sutton-Chen | |
| potential | |
| Power: | |
| E = - sum(i) A(i)*(rho(i))**1/n | |
| this is just a generalisation of the above case | |
| VBO: | |
| E = - sum(i) A(i)*(rho(i))**rn | |
| this is a further generalisation of the power case | |
| Banerjea_smith: | |
| E = - sum(i) F0 [1-ln(r)/n]*r**1/n + F1*r | |
| where r = rho(i)/rho0(i) | |
| this is the functional of Banerjea and Smith (Phys. Rev. B, | |
| 37, 6632 (1988)) - note that in this case that are atom | |
| dependent parameters also to be specified (F0, F1, rho0) | |
| where rho0 is the electron density at equilibrium. | |
| Johnson: | |
| E = - sum(i) F0 [1-ln(x)]*x + F1*y | |
| where x = (rho(i)/rho0(i))**(alpha/beta) | |
| and y = (rho(i)/rho0(i))**(gamma/beta) | |
| this functional is similar to that of Banerjea & Smith and is due | |
| to Johnson (PRB, 39, 12554 (1989)). | |
| Glue: | |
| if rho < rho1 | |
| E = c1_4*(rho-rho1)**4 + c1_3*(rho-rho1)**3 + c1_2*(rho-rho1)**2 + | |
| c1_1*(rho-rho1) + c1_0 | |
| if rho1 =< rho < rho2 | |
| E = c2_4*(rho-rho2)**4 + c2_3*(rho-rho2)**3 + c2_2*(rho-rho2)**2 + | |
| c2_1*(rho-rho2) + c2_0 | |
| if rho2 =< rho | |
| E = c3_3*(rho-rho2)**3 + c3_2*(rho-rho2)**2 + c3_1*(rho-rho2) + c3_0 | |
| this is the functional from Ercolessi et al, Phil. Mag. A, 58, 213 (1988). | |
| NB: At present there are no fitting parameters since there are constraints | |
| on the coefficients to ensure a smooth and continuous function. | |
| Foiles: | |
| E = sum(i) F0*rho(i)**2 + F1*rho(i) + F2*(rho(i)**(5/3)/(F3 + rho(i))) | |
| Mei-Davenport: | |
| E = sum(i) - Ec*[1-(alpha/beta)*ln(rho(i))]*rho(i)**(alpha/beta) + | |
| sum(m=1->3) 0.5*phi0*s_m*exp(-(sqrt(m)-1)*gamma)* | |
| [1+(sqrt(m)-1)*delta-sqrt(m)*delta*ln(rho(i))/beta]* | |
| rho(i)**(sqrt(m)*gamma/beta) | |
| Baskes: | |
| E = sum(i) A*Ec*x*ln(x) | |
| where x = (rho(i)/rho0(i)) | |
| this functional is similar to that of Banerjea & Smith and Johnson, but | |
| is simplified to enable the parameters from the MEAM paper of Baskes to | |
| be input directly. | |
| The value of order species the maximum order of the MEAM functional. Usually | |
| MEAM involves components from order 0 to 3 and values outside this range are | |
| not currently permitted. | |
| For all functionals, the values of t_0, t_1, ... t_order are the coefficients | |
| for the density contribution of each order. | |
| Igarashi: | |
| E = - sum(i) A(i)*(rho(i)*(1 + B(i)*rho(i))**1/2 | |
| this functional form was proposed in Igarashi et al, Phil. Mag. B, 63, | |
| 603 (1991). | |
| Spline: | |
| if rho_max > rho > rho0: | |
| E = - sum(i) [A(i)*(rho(i)-rho0)**3 + B(i)*(rho(i)-rho0)**2 + C(i)*(rho(i)-rho0) + D(i)] | |
| else | |
| E = 0 | |
| See also | meam_density manybody scmaxsearch eam_alloy prt_eam baskes meam_screening |
| meam_rhotype |
| Type | Option |
| Format | meam_rhotype <t21/t24> <sum/exponential/exphalf> |
| Units | none |
| Default | t24, exponential |
| Use | There are several different formulations of MEAM that have evolved according |
| to both the number of angular momentum terms and the way that they are | |
| combined. They can largely be broken down into the first, nearest-neighbour | |
| form (1NN), and the revised second nearest neighhbour form (2NN). | |
| In the original formulation there were 21 components of the density | |
| while later forms adopt 24 (3 extra terms for the order = 3 case). Which form | |
| is used can be selected using the sub-options: | |
| t21 = 1NN 21 term expression | |
| t24 = 2NN 24 term expression | |
| There are also two different ways that the total density, rho, can be assembled | |
| from the component density orders, rho_i. In the original version, 1NN, a simple | |
| sum of the densities squared, square rooted, was used and this can be selected | |
| by the sub-option, "sum": | |
| rho = sqrt[ sum (i=0->order) (t_i*rho_i**2) ] | |
| In later versions of the methodology (2NN) then a different form was proposed to | |
| avoid issues with the density becoming negative; | |
| rho = rho_0*G(gamma) | |
| where; | |
| G(gamma) = 2/(1 + exp(-gamma)) | |
| and; | |
| gamma = [ sum (i=1->order) (t_i*(rho_i/rho_0)**2) ] | |
| This second form, "exponential", is the default choice unless "sum" is given. | |
| There is also an alternative form of exponential that some papers have used | |
| that can be selected by "exphalf": | |
| G(gamma) = exp(gamma/2) | |
| See also | meam_density manybody scmaxsearch eam_alloy prt_eam baskes meam_screening |
| meam_functional |
| Type | Option |
| Format | meam_screening |
| atom1 <atom2 atom3> Cmin Cmax | |
| Units | none |
| Default | No screening (i.e. simple radial cut-offs applied), atom2 = atom3 = atom1 |
| Use | Controls the truncation of the MEAM density by applying a screening function to |
| the pairwise density between two atoms. For a pair of atoms, i-j, the screening | |
| function is given by: | |
| S_ij = Product(k=1,N,k.ne.i,k.ne.j) S_ikj | |
| where S_ikj is given by the construct described in M.I. Baskes, Mater. Chem. Phys., | |
| 50, 152-158 (1997): | |
| S_ikj = f_e(x) | |
| f_e(x) = 1 ; x >= 1 | |
| = [1 - (1-x)**4]**2 ; 1 > x > 0 | |
| = 0 ; x =< 1 | |
| x = (C - Cmin)/(Cmax - Cmin) | |
| C = [2(X_ik + X_jk) - (X_ik - X_jk)**2 - 1]/[1 - (X_ik - X_jk)**2] | |
| where X_ik = (r_ik/r_ij)**2 and X_jk = (r_jk/r_ij)**2 | |
| If only a single atom type is input then this is taken to be the | |
| self term. However, when atom2 and atom3 are given then the term | |
| becomes specific to a trio of atoms with the first atom being the | |
| one that is doing the screening. Note that the order of atoms 2 | |
| and 3 does not make any difference. | |
| NB: Analytic second derivatives are currently not available when | |
| screening is turned on. | |
| NB: Prior to version 4.3 there was only a single screening factor | |
| for all atoms where as it is now species specific. | |
| See also | meam_density meam_functional meam_rhotype |
| Type | Option |
| Format | mei-davenport <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 phi0 delta gamma r0 <rmin> rmax <4*flags> | |
| Units | phi0 in eV, r0 in Angs and delta & gamma are dimensionless. |
| Default | none |
| Use | Specifies the parameters for the two-body component of the Mei-Davenport |
| potential (PRB, 46, 21 (1992)): | |
| E_ij = - phi0*(1 + delta*(r/r0 - 1))*exp(-gamma*(r/r0 - 1)) | |
| See also | eam_density eam_functional |
| Type | Option |
| Format | mincell minimum_cell_parameter <au> |
| Units | Angstroms |
| Default | 0.5 Angstroms |
| Use | Stops an optimisation if the cell parameter falls below the |
| specified allowed value. This prevents the memory rapidly | |
| increasing due to the number of reciprocal lattice vectors | |
| tending to infinity as the cell parameter(s) go to zero. | |
| See also | rspeed optimise |
| Type | Option |
| Format | minimum <no._to_set>=N |
| <variables_to_be_set>xN | |
| <minimum_value>xN | |
| Default | 0.0 |
| Use | Part of genetic options section. Specifies the minimum value |
| allowed in the fitting procedure. | |
| See also | genetic |
| Type | Option |
| Format | mm3angle <nbeq/nbne nbond> <intra/inter> <bond/mol> <kcal/kjmol/degree> |
| atom1 atom2 atom3 k2 theta0 A B C D E <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) & | |
| <rmin(2-3)> rmax(2-3) <7 flags> | |
| Units | k2 in eVrad**-2, B in rad**-1, C in rad**-2, D in rad**-3, E in rad**-4 |
| A is unitless, theta0 in degrees, rmin & rmax in Angs | |
| Default | A = 0.021914, B = 0.014, C = 5.6, D = 7.0, E = 9.0 |
| Use | Three-body angle bending potential about atom1 in MM3 form. k2 is the force |
| constant and theta0 the equilibrium angle. The other constants control the | |
| higher order angular terms. Optional flags are for fitting. Atom 1 is | |
| the middle atom of the triad about which the force acts. | |
| E(three) = (A*k2*(theta-theta0)^2)*[1-B*(theta-theta0) + C*10^-5*(theta-theta0)^2 | |
| - D*10^-7*(theta-theta0)^3 + E*10^-10*(theta-theta0)^4] | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2 and 1-3 are bonded. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| The order of the bond type options matches the order of the pivot atom | |
| - end atom pairs. For example, if a potential acts for the triad | |
| S - C - O, where the C-S bond is a regular bond and the C-O is an | |
| exocyclic double bond then the input would look like: | |
| mm3angle bond single regular double exocyclic | |
| C core S core O core ...... etc | |
| Conditions can also be placed on a potential to check the number of bonds | |
| associated with the pivot atom (e.g. if a potential is designed for a 90 | |
| degree angle it might be necessary to check that the number of bonds is | |
| four or six for square planar or octahedral). The conditions are placed | |
| using one or more instances of "nbeq" or "nbne" followed by an integer. | |
| Here "nbeq" imples no. of bonds must equal and "nbne" number of bonds must | |
| not equal. Hence, "nbeq 4" would require the pivot to have 4 bonds. When | |
| multiple terms are used, the logic of nbeq is concatenated with "or", whereas | |
| that of nbne is joined by "and". Therefore "nbne 4 nbne 6" would apply to | |
| an atom with 3 bonds, but not one with 4 or 6. | |
| NB It's important to specify the first bond as being of "regular" type so | |
| that the "exocyclic" attribute is correctly assigned to the second bond | |
| since the first term is assumed to apply to the first bond, whereas the | |
| second applies to the second bond. | |
| See also | axilrod-teller angle stillinger-weber exponential bcross uff3 |
| urey-bradley murrell-mottram bacross lin3 hydrogen-bond equatorial | |
| 3coulomb exp2 bagcross three |
| Type | Option |
| Format | mm3buck <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> <all> |
| atom1 atom2 A B C epsilon rv <rmin> rmax <5*flags> | |
| or | |
| mm3buck combine <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> | |
| atom1 atom2 A B C <rmin> rmax <3*flags> | |
| or | |
| mm3buck combine all <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> | |
| A B C <rmin> rmax <3*flags> | |
| Units | A, B and C are unitless, epsilon in eV, rv in Angs |
| If kcal is given : epsilon in kcal, rv in Angs | |
| If kjmol is given: epsilon in kJmol-1, rv in Angs | |
| Default | none |
| Use | MM3 form of Buckingham potential |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = epsilon*[A.exp(-B*r/rv) - C*(rv/r)**6] | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| If "combine" is given as a sub-option then combination rules are used | |
| to compute the epsilon/sigma values based on the atomic values: | |
| epsilon = sqrt(e1*e2) | |
| sigma = (s1+s2)/2 | |
| If "all" is specified as a sub-option, then mm3buck potentials | |
| will be automatically created and added for all combinations of | |
| epsilon/sigma. NB: This will be done based on the values that | |
| have been specified up to that point and so be sure to get the | |
| order right! In this case, the line following should only have | |
| the rmin and rmax to be used for all the potentials. | |
| See also | c6 buckingham epsilon slater |
| Type | Option |
| Format | mm3stretch <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 k2 r0 <A B C> <coul> <rmin> rmax <5*flags> | |
| Units | k2 in eV*Angs**-2, r0 in Angs, A and coul are unitless, B and C in Angs**-1 |
| Defaults | coul = 0.0, A = 71.94, B = 2.55, C = 7/12 |
| Use | MM3 bond stretching potential |
| coul = 1.0 => Coulomb subtracted | |
| coul = 0.0 => not Coulomb subtracted | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A*(K2*(r-r0)**2)*[1 - B*(r-r0)*(1 - C*B*(r-r0))] | |
| For MM3 the values of A, B and C are constants equal to the default values. | |
| NB: The second B in the equation (to give B^2 in the quartic term) is missing | |
| in the original MM3 paper, but is added in the later literature. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | spring squaredharmonic forceconstant harm |
| Type | Option |
| Format | mode |
| value <kpoint_number> <weight> | |
| e1x e1y e1z | |
| e2x e2y e2z | |
| : : : | |
| eNx eNy eNz | |
| Units | cm-1 |
| Use | Subsection of observables, used for specifying vibrational modes for |
| fitting to. This option differs from frequency in that instead of | |
| supplying the mode number the eigenvectors for the modes are given. | |
| GULP will then project all modes on to the eigenvectors and fit the | |
| mode frequency with maximal overlap. This is mainly useful for fitting | |
| ab initio vibrational data. Here e1x denotes the x vibrational eigenvector | |
| component for atom 1, etc, up to the Nth atom. In the output of fitting | |
| the overlap with the mode is given in the comparison of initial and final | |
| values. | |
| The second number after the frequency is optionally the k point number | |
| to fit at with reference to the k point list for the present | |
| configuration. Only currently implemented for real eigenvectors at | |
| present and so only the gamma point should be used. | |
| NB: The number of atoms whose eigenvectors are input corresponds to the | |
| number of fully occupied core sites (as only these have vibrations). | |
| Care must be taken when using shells or sites with multiple partial | |
| occupancies. | |
| NB: It is NOT recommended to use this option with relaxed fitting. | |
| This is because optimisation will cause the frame of reference for the | |
| system to change and so the projection may not be valid. | |
| NB: It is important that the order of the atoms in the eigenvector list | |
| matches that the GULP uses after the input is read in. Note that GULP | |
| can sometimes change the order of the input atoms, though since usually | |
| this only involves placing cores at the start and shells at the end | |
| then this wouldn't alter the ordering of core eigenvector atoms. | |
| See also | observables elastic phonon piezoelectric sdlc hfdlc weight frequency |
| Type | Option |
| Default | 1 |
| Use | The displacements in region 2a can be calculated by a number of |
| different approximations to the force acting on the region 2a | |
| ions. Five modes are available at the moment for this purpose: | |
| 1 => use electrostatic force of region 1 screened by dielectric | |
| constant | |
| 2 => use electrostatic force of region 1 screened by dielectric | |
| constant, but neglecting contribution to derivatives of | |
| region 1 | |
| 3 => use electrostatic force of defects screened by dielectric | |
| constant | |
| 4 => use electrostatic force of defects screened by dielectric | |
| constant, but neglecting contribution to derivatives of | |
| region 1 | |
| 5 => consider interaction of region 2a only with defects | |
| By default the program uses method 4 for charged defects as this | |
| offers the best compromise between accuracy and computational effort. | |
| It is recommended that a comparison is made with mode2a=1 as a check. | |
| For optimisation the most efficient approach could be to optimise | |
| first with a higher mode and then restart in mode 1. | |
| See also | defect centre region_1 move_2a_to_1 noanisotropic_2b |
| vacancy interstitial impurity noanisotropic gdcrit | |
| bulk_noopt |
| Type | Option |
| Format | momentum_correct natom_equilibration <natom_production> |
| Default | All moving atoms to be corrected during both phases |
| Units | None |
| Use | By default linear momentum is removed during both equilibration |
| and production. This option allows the user to restrict the | |
| correction to a subset of atoms that come first in the input | |
| deck, either during equilibration or production, or both. | |
| For example, if the system consists of 100 atoms and all atoms | |
| should have their momenta corrected during equilibration, but | |
| only the first 10 atoms need to be corrected during production | |
| then the input would be: | |
| momentum_correct 100 10 | |
| See also | md timestep equilibration production temperature |
| tscale write nolist delay_force end_force sample |
| Type | Option |
| Format | monopoleq <n> |
| i Qi <weight> | |
| Units | atomic units |
| Default | no monopole charges to be fitted |
| Use | Subsection of observables, used for specifying values of |
| charges for fitting. Note that i is the | |
| atom number in the unit cell, not the asymmetric unit. | |
| Example: | |
| monopoleq 1 | |
| 1 1.95 | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq qreaxff |
| Type | Option |
| Format | morse <intra/inter> <bond/x12/x13/x14/o14/g14> <kcal/kjmol> <zero> <scale14> <etaper> <ener/grad> <type_of_bond> |
| atom1 atom2 De a r0 <coul> <rmin> rmax <3*flags> | |
| Units | De in eV, a in Angs-1, r0 in Angs, coul in none |
| Default | coul = 0.0 |
| Use | Morse potential - optimisation flags for fitting. |
| coul = 1.0 => Coulomb subtracted. | |
| coul = 0.0 => not Coulomb subtracted. | |
| The format of the data assumes that rmin is the least important | |
| entry. I.e., if one of the optional parameters, coul or rmin, | |
| is missing it is assumed that coul is present and rmin | |
| is set to zero. | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = De.((1-exp(-a(r-r0)))**2 - 1.0) - coul.qi.qj/r | |
| If "etaper" is specified then the potential is scaled by: | |
| exp(-1/(rmax-r)) | |
| to ensure that the potential (excluding the Coulomb subtraction) | |
| goes to zero at the cutoff. In this case, the energy/gradient | |
| options cannot be used. | |
| Note that the potential can also be written as: | |
| E = De.(exp(-2a(r-r0)) - 2exp(-a(r-r0))) - coul.qi.qj/r | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| The words energy or gradient may be given on the first line resulting | |
| in energy or gradient offsets being applied such that the specified | |
| quantity goes to zero at the cutoff distance. | |
| If the "zero" sub-option is specified then the energy of the potential | |
| is calculated relative to zero at the minimum rather than at dissociation. | |
| Type | Option |
| Format | move_2a_to_1 <radius> |
| Units | Angstroms |
| Default | none |
| Use | At the end of a defect calculation, region 2a ions within the |
| specified radius will be moved into region 1 for the dumpfile | |
| at their relaxed positions. This enables a better set of | |
| starting positions to be input for a restart with a larger | |
| region 1 as the ions will be approximately optimised to start | |
| with. If no radius is specified then all region 2a ions will | |
| be moved. The radius value must not be less than the region 1 | |
| radius and not greater than the region 2a value. | |
| See also | defect centre size region_1 vacancy interstitial |
| impurity bulk_noopt |
| Type | Option |
| Format | murrell-mottram <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K rho r012 r013 r023 <rmin(1-2)> rmax(1-2) <rmin(1-3)> | |
| rmax(1-3) <rmin(2-3)> rmax(2-3) <5*flags> | |
| c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 <11*flags> | |
| Units | K in eV, r012,r013,r023,rmin,rmax in Angstroms |
| Use | Specifies the Murrell-Mottram three-body potential; |
| E(three) = K.P(Q1,Q2,Q3).exp(-rho.Q1) | |
| P(Q1,Q2,Q3) = c0 + c1.Q1 + c2.Q1**2 + c3(Q2**2 + Q3**2) + c4.Q1**3 + | |
| c5.Q1(Q2**2 + Q3**2) + c6(Q3**3 - 3.Q3.Q2**2) + | |
| c7.Q1**4 + c8.Q1**2.(Q2**2+Q3**2) + c9.(Q2**2+Q3**2)**2 | |
| + c10.Q1(Q3**3 - 3.Q3.Q2**2) | |
| R1 = (r12-r012)/r012 R2 = (r13-r013)/r013 R3 = (r23-r023)/r023 | |
| Q1 = (R1+R2+R3)/sqrt(3) Q2 = (R2-R3)/sqrt(2) Q3 = (2*R1-R2-R3)/sqrt(6) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2, 2-3 and 1-3 are bonded. | |
| See also | three-body angle axilrod-teller stillinger-weber bcross urey-bradley |
| exponential bacross hydrogen-bond equatorial uff3 3coulomb | |
| bagcross |
| Type | Option |
| Format | mutation initial <final> <stepsize> |
| Default | 1/(sum of discretisation values) <initial> <0.0> |
| Use | Part of ga options section. Specifies the mutation probability |
| The higher the value, the more likely it is that mutations will | |
| occur. If <initial> value is less than <final> value then after | |
| 20 iterations tournament is incremented by <stepsize>. If the optimisation | |
| is stuck in a local minimum then either (i) if stepsize non-zero tournament | |
| is reset to <initial> OR (ii) grid fixed then mutation rate changed. | |
| See also | genetic anneal grid |
| Type | Option |
| Default | none |
| Use | Allows you to associate a one-word name with a particular |
| structure which is then displayed in the input banner for | |
| that structure. Helps in indentification when working | |
| with multiple structures in the same input file. | |
| This option must precede the geometry specification for | |
| a structure to avoid ambiguity in cases of multiple | |
| structures. | |
| Example: | |
| name alumina | |
| Type | Option |
| Format | nebiterations <maximum_number> |
| Default | 1000 |
| Use | Specifies the maximum number of iterations for minimization |
| of the force norm during the nudged elastic band run. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom neb rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nebrandom <random_weight> |
| Default | 0.0 |
| Units | Angstroms |
| Use | In the case where the initial pathway in the nudged elastic |
| band (formed by linear interpolation between the initial and | |
| final state) lies along a high symmetry direction it can be | |
| necessary to displace the replicas from the symmetric path. | |
| If this option is set to a non-zero value then a random | |
| displacement is applied to the initial coordinates of each | |
| replica. The input value is used to scale a random number | |
| between 0 and 1. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent neb nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nebreplica <nreplica> |
| Default | None |
| Use | Specifics the number of replicas to be used during a nudged elastic |
| band run, including the initial and final structure. Must be | |
| greater than 2 and controls how accurately the reaction path is | |
| discretised. | |
| See also | neb nebspring nebtolerance nodneb |
| nebtangent nebrandom nebiterations rcartesian fcartesian | |
| rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nebspring <vary> <maxspring> <minspring> |
| Default | maxspring = 1.0 - no varying |
| Units | eV/Angstroms**2 |
| Use | Specifies the spring constant between the replicas in the nudged |
| elastic band method. For a single spring value between all | |
| replicas the input would be; | |
| nebspring 10.0 | |
| For a spring constant that varies between 10.0 and 1.0 the input | |
| would be; | |
| nebspring vary 10.0 1.0 | |
| See also | neb nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nebtangent <option_number> |
| Default | 3 |
| Use | Specifies how the tangent to the reaction path is to be defined |
| in a nudged elastic band run. The following are valid options: | |
| 1 => central finite difference between replicas | |
| 2 => bisect vectors | |
| 3 => new algorithm favouring higher energy replica neighbour | |
| See also | nebspring nebtolerance nodneb |
| nebreplica neb nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nebtolerance <tolerance_value> |
| Default | 0.001 |
| Use | Specifies the convergence criteria for a nudged elastic band |
| run in terms of the residual force norm. | |
| See also | nebspring neb nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | nmr symbol chemical_shift_reference mean_shift fq |
| Units | ppm for chemical_shift_reference and mean_shift, unitless for fq |
| Default | None |
| Use | Allows species specific parameters to be set for use in the |
| calculation of NMR chemical shifts within the Pacha method. | |
| element | |
| nmr C2 185.4 155.95 1.0 | |
| end | |
| Command is part of element section. | |
| See also | element |
| Type | Option |
| Format | nobond species1 species2 |
| Use | Excludes bond formation between two species during molecule search. |
| See also | molecule molq molmec bond connect noautobond bondtype |
| Type | Option |
| Format | keyword |
| Default | only derivatives marked for optimisation |
| Use | Specifies fitting observables other than structure which use |
| derivatives. | |
| See also | elastic hfdlc sdlc energy bulk_modulus shear_modulus weight |
| gradients hfrefractive_index srefractive_index piezoelectric | |
| frequency gradient potential entropy bornq monopoleq cv | |
| stress qreaxff fbond fangle reaction young poisson coordno | |
| sqomega volume fenergy |
| Type | Option |
| Format | odirection <frac> x_in y_in z_in x_out y_out z_out |
| Units | dimensionless |
| Default | no directions |
| Use | If the frequency dependent properties are required for a |
| particular in/out direction combination then this option | |
| specifies the 2 directions. | |
| NOTE : This option only applies to a gamma point calculation | |
| By default the directions are assumed to be in Cartesian space | |
| unless the "frac" sub-option is given in which case they will | |
| be taken relative to the crystal axes. | |
| See also | phonon omega omega_damping |
| Type | Option |
| Format | omega frequency frequency_step no_of_steps |
| Units | cm-1 |
| Default | frequency = frequency_step = 0.0 no_of_steps = 0 |
| Use | Specifies that frequency dependent properties be calculated |
| over a given range. "frequency" represents the initial frequency | |
| while "frequency_step" is the interval between calculations. | |
| Example: | |
| omega 500.0 100.0 5 | |
| the above would calculate properties at a frequencies of 500, | |
| 600, 700, 800, 900 and 1000 cm-1. A no_of_steps = 0 implies a | |
| calculation at a single frequency. | |
| In the output of the frequency dependent dielectric constant | |
| the first line contains the real part of the dielectric | |
| function and the second one the complex part. | |
| NOTE : This option only applies to a gamma point calculation | |
| See also | phonon odirection omega_damping |
| Type | Option |
| Format | omega_af <rads> frequency <B> <v_s> <v_p> |
| Units | cm-1 for frequency, s/km**2 for B, m/s for v_s and v_p |
| If "rads" is specified as a sub-option then B is in 10^14 rads**2/s | |
| and frequency is in 10^12 rads/s. | |
| Default | 0.0 |
| Use | Specifies the minimum frequency to be used in a thermal conductivity |
| calculation in the Allen-Feldman contribution. If this option is | |
| included then the contribution from propagating modes will be added | |
| based on integrating the result for the Debye model from 0 to omega_af. | |
| This relies on finding an approximation to the phonon lifetime as a | |
| function of frequency based on the expression: | |
| tau = B*omega**-2 | |
| from which the propagating contribution to the thermal conductivity | |
| can be estimated by; | |
| kappa_pr = 4*pi*k_B*(c**3)*B*omega_af*(2/v_s + 1/v_p)/3 | |
| where k_B is Boltzmann's constant, c is the speed of light, omega_af | |
| is the frequency boundary between the propagating and Allen-Feldman | |
| contributions and v_s/v_p are the velocities of the propagating | |
| s- and p-waves, respectively. | |
| This expression for B/omega_af in rads is: | |
| kappa_pr = [k_B*B*omega_af/(2*pi**2)]*(2/v_s + 1/v_p)/3 | |
| If no value of v_s/v_p is input then these are approximated by the s- and | |
| p-wave velocities calculated in the properties according to the Reuss | |
| definition. If no value of B is input, then this is computed based | |
| on a simple approximation. Here the maximum peak in the Allen-Feldman | |
| mode diffusivity below omega_af is found and then this is used to | |
| determine the value of B via a one point fit using; | |
| D_pr(omega) = (1/3)*v_s**2*B*omega**-2 | |
| where D_pr(omega) is the mode diffusivity at the frequency of the | |
| maximum, omega, below the cutoff. If there are no modes below the | |
| value of omega_af specified then the propagating contribution can | |
| only be computed if B is input manually. A more accurate value of | |
| B could be found by fitting the low frequency Allen-Feldman region | |
| outside of GULP and then using this as input. | |
| See also | thermalconductivity broaden_dos temperature lorentzian_tolerance |
| Type | Option |
| Format | omega_damping damping_factor |
| Units | cm-1 |
| Default | 5.0 cm-1 |
| Use | Applies a damping factor to the frequency dependent optical |
| properties. This broads the peaks and prevents a singularity. | |
| Note that the value is constrained to be greater than 1 x 10^-6 | |
| to ensure numerical stability. | |
| See also | omega odirection phonon |
| Type | Option |
| Format | origin 1/2 or x y z or ix iy iz |
| Units | none |
| Default | origin 1 |
| Use | Allows the space group origin to be changed, either by selecting the |
| second setting in international tables by giving 2 on it's own, or | |
| specifying the desired origin shift either as three fractional | |
| coordinates or as three integers which represent 24 times the shift | |
| - e.g. a shift of 1/3 1/3 2/3 would be 8 8 16 thus avoiding precision | |
| problems with recurring decimals. |
| Type | Option |
| Format | outofplane <inter/intra> <bond> <only3> <kcal/kjmol> |
| atom1 atom2 atom3 atom4 k <k4> <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) <rmin(1-4)> rmax(1-4) <1-2 x flag> | |
| Units | k in eV*Angs**-2, k4 in eV*Angs**-4 |
| Default | rmin values = 0, k4 = 0 |
| Use | Out of plane energy - harmonic energy penalty for atom 1 lying |
| out of the plane of atoms 2, 3 and 4. Used for ring systems | |
| which should be planar: | |
| E = k.d**2 + k4.d**4, where d=distance to the plane | |
| If the only3 sub-option is specified then the potential applies where an atom has exactly | |
| 3 bonds present. | |
| See also | torsion ryckaert torangle torharm torexp xoutofplane inversion xangleangle |
| Type | Option |
| Format | output <filetype> <filename> |
| Default | no output files |
| Use | Write files suitable for other programs. |
| Available filetypes are marvin, thbrel, xtl, xr, cssr, arc | |
| xyz, trajectory, history, fdf, drv, frc, cif, str, pressure | |
| osc, phonon, pdf, qbo, cosmo, lammps, lammps_pots, dcd, eig | |
| cml, inertia, kpt, castep_phonon, shengBTE, dipole, xsf : | |
| marvin - generates a file suitable for input to Marvin for | |
| surface calculations. Index of surface plane needs to be | |
| added first, though this may be passed through GULP to the | |
| marvin input but using the "marvin" option. If the file | |
| extension ".mvn" is not given by the user it will be added | |
| by the program. | |
| e.g. output marvin alumina produces alumina.mvn | |
| If a file for Marvin2 is required, then use the sub-option | |
| marvin2 instead. | |
| e.g. output marvin2 alumina | |
| thbrel - converts the final bulk structure into a file format | |
| suitable for the THBREL suite of programs. Not all features | |
| are readily transferable between the programs so no guarantee | |
| is made that the input file is perfect and for similar reasons | |
| both programs may not always yield the same results unless the | |
| user is careful to make sure the files are equivalent. If a | |
| phonon run has been requested then the output is modified for | |
| THBPHON instead of THBREL. | |
| xtl - this is only applicable to crystal structures with a | |
| single structure per file. Produces a .xtl file for input | |
| into the BIOSYM software, though use of the archive file is | |
| better unless symmetry is present. If the filename input is | |
| not already terminated with ".xtl" then this will be added | |
| by the program. | |
| e.g. output xtl alumina produces alumina.xtl | |
| xr - this will output a modified CSSR file suitable for | |
| input into the Oxford Materials graphical interface | |
| program Crysalis. The file will have the extension ".xr" | |
| added. At the moment this is only applicable to 3D | |
| systems. | |
| e.g. output xr alumina produces alumina.xr | |
| cssr - this will output a CSSR file suitable for input | |
| into the MSI graphical interface Cerius2. The file will | |
| have the extension ".cssr" added. At the moment this | |
| is only applicable to 3D systems. | |
| e.g. output cssr alumina produces alumina.cssr | |
| arc - alternatively known as a ".car" file. This option produces | |
| archive files suitable for input into the BIOSYM Insight software | |
| and will handle bulk, cluster and defect calculations, all with | |
| multiple structures. The username should input a root name, | |
| e.g. output arc alumina | |
| The program will then produce archive file names with either | |
| "_3D", "_defe", or "_0D" appended to distinguish the files | |
| resulting from a particular section of the run. If multiple | |
| structures are present then an underscore followed by the | |
| structure number will be added, all followed by ".arc". | |
| e.g. if the above input for alumina contained two bulk structures | |
| then the files produced would be "alumina_bulk_1.arc" and | |
| "alumina_bulk_2.arc". | |
| If the word "movie" is specified then all structures during an | |
| optimisation will be included in the arcfile, rather than just | |
| the final one, so that the optimisation may be viewed. | |
| e.g. output movie arc alumina | |
| Note : for MD runs the name of the archive file is set by | |
| "mdarchive" to avoid overwriting the optimisation archive | |
| file if present. Also in the case of MD the file is only | |
| written during the production phase. | |
| It is also possible to specify a frequency for the output: | |
| e.g. output movie 5 arc alumina | |
| This would output an archive file frame every 5 steps during the | |
| movie. The default is to output at every step. | |
| NB: The residue field has now been changed to contain the molecule | |
| number, rather than the atom number or a dummy string. | |
| xyz - this will output an xyz file suitable for | |
| input into programs such as Molden and with slight | |
| modification Unichem. The file will have the extension ".xyz" | |
| At the moment this is only applicable to non-periodic | |
| systems. When called with a periodic case just the Cartesian | |
| coordinates will be output, without the unit cell. | |
| e.g. output xyz cluster produces cluster.xyz | |
| If the word "movie" is specified then all structures during an | |
| optimisation will be included in the xyz file, rather than just | |
| the final one, so that the optimisation may be viewed. | |
| e.g. output movie xyz cluster | |
| trajectory - this is a binary file which stores the coordinates | |
| and velocities from a molecular dynamics run, as well as some | |
| of the system properties. This file is used by the Cerius interface | |
| to generate a .trj file for analysis in Cerius. Note that this | |
| file is only written during the production phase by default. | |
| e.g. output trajectory alumina | |
| For this sub-option the further option "ascii" may be specified | |
| in order to obtain an ASCII format trajectory file. Note that | |
| this is less efficient for disk space usage! | |
| e.g. output trajectory ascii alumina | |
| Furthermore, the sub-option "equil" may be added to force writing | |
| during the equilibration phase of the simulation. | |
| The default extension for this file type is .trg | |
| history - this is a text file in the DLPOLY HISTORY file format | |
| containing the structure and velocities sampled from a MD run. | |
| This file can be used for post-MD analysis using the same | |
| programs as for DLPOLY such as "After". | |
| fdf - this is a text file in the Flexible Data Format of Alberto | |
| Garcia and Jose M. Soler. This file can then form the basis of | |
| an input deck for the program SIESTA. | |
| drv - this is a text file containing the energy and appropriate | |
| derivatives calculated by GULP at the last function evaluation. | |
| This can be used for QM/MM schemes. Note that if freezing is | |
| being used then second derivatives may not be output since not | |
| all derivatives may be calculated. To turn off freezing then | |
| specify the keyword "noexclude". | |
| frc - this is a text file containing the energy and appropriate | |
| force constants for cores only calculated by GULP during a phonon | |
| calculation. This can be used for QM/MM schemes, such as in the | |
| program QMPOT. A phonon calculation must be specified otherwise | |
| no file will be output. NB: Force constant matrices can also be | |
| output in a format suitable for ShengBTE and Phonopy using the | |
| output shengbte option. | |
| cif - this is only applicable to crystal structures with a | |
| single structure per file. Produces a .cif file for input | |
| into a variety of programs. If the filename input is | |
| not already terminated with ".cif" then this will be added | |
| by the program. Note that at present the files are output | |
| in P1 regardless of symmetry for simplicity. | |
| e.g. output cif alumina produces alumina.cif | |
| Strictly speak a cif file is only valid for 3-D systems, but | |
| files can be output from GULP for 0-D, 1-D and 2-D with the | |
| addition of a dummy cell parameter. This value can be set | |
| from the option: | |
| e.g. output cif 12.0 surface | |
| will create a 3-D cif file with a dummy lattice parameter of | |
| 12 Angstroms for directions that are non-periodic. The default | |
| dummy lattice parameter is 0 which implies that a cif file | |
| shouldn't be written for the wrong periodicity. | |
| str - this is a file in the CRYSTAL98 format, suitable for | |
| reading by DLV. If the filename input is not already | |
| terminated with ".str" then this will be added. If multiple | |
| structures are specified then the filename will be modified | |
| so that a separate file can be written for each structure. | |
| phonon - this option leads to the density of states from a | |
| phonon calculation and any dispersion curve points being | |
| output to the files <filename>.dens and <filename>.disp, | |
| respectively, in a format suitable for input into a curve | |
| plotting program. If the sub-option "ir" is specified then | |
| the density of states will be weighted by the IR intensities | |
| e.g. output phonon ir alumina | |
| frequency - this option produces a list of frequencies over all | |
| k points for use in an analysis program. A typical application | |
| might be in the calculation of the Gruneisen parameter by | |
| differencing of the frequencies with respect to the cell volume. | |
| The file can either be output in binary format (to maintain | |
| precision - the default): | |
| e.g. output freq binary <filename> <ndecimal> | |
| or as ordinary text: | |
| e.g. output freq text <filename> <ndecimal> | |
| Here the optional value of ndecimal specifies how many decimal | |
| places you get (up to a maximum of 12 since going further than | |
| this would be non-sensical in double precision!). | |
| pressure - this option outputs a file containing the pressure | |
| tensor during a molecular dynamics run, both instanteously and | |
| as an average. File is output as <filename>.pre using units of | |
| GPa. | |
| osc - this is a text file containing the oscillator strengths | |
| for the phonon modes so that the frequency dependent data can | |
| be handled in post processing. In this file the frequencies | |
| are in wavenumbers, while the oscillator strengths are in cm^-2 | |
| pdf - this option sets the name for the .wid and .pdf files | |
| created by the pdf keyword. The .wid file can be suppressed by | |
| the nowidth keyword. | |
| cosmo - this outputs a COSMO file in the Accelrys format for | |
| visualisation of information relating to solvation an the | |
| solvent accessible surface | |
| lammps - this outputs a LAMMPS input files for a system based on | |
| the information available to GULP. This includes a .lmp file | |
| containing the structure and bonding information. If followed by | |
| "var" then variable names will be used in the output. | |
| lammps_pots - this outputs a LAMMPS file containing a tabulation | |
| of any twobody potentials. There are 3 addition pieces of information | |
| that can be provided which are the start of the range, r0, the end | |
| of the range, rend, and the number of points, np. | |
| e.g. output lammps_pots 0.1 9.0 1000 myfile | |
| This would create a table from 0.1 to 9.0 Angstroms with 1000 points | |
| and write it to a file called myfile. | |
| cml - this is a Chemical Markup Language output file which | |
| contains all the important information about the calculation | |
| in an XML format. This output is suitable for various database | |
| tools and for data transfer between CML-enabled applications. | |
| eig - this outputs the eigenvectors for each K point as a file. | |
| qbo - this file contains the charges and bond orders, as appropriate, | |
| for a potential model. | |
| e.g. output qbo myfile | |
| The above command would produce a file myfile.qbo containing the | |
| charges and bond orders for the final configuration. If the | |
| values for all structures are required then the sub-option "append" | |
| can be used: | |
| e.g. output qbo append myfile | |
| dcd - this file contains the coordinates from an MD trajectory and | |
| can be used by programs such as VMD for analysis and visualisation. | |
| inertia - output information on the moment of inertia tensor for | |
| molecules at the final structure for each configuration | |
| castep_phonon - this file contains the phonon information from multiple | |
| K points in the same format as used for the program CASTEP. The default | |
| extension for this is ".csp": | |
| e.g. output castep_phon myfile.csp | |
| kpt - this file list the k points within the asymmetric unit of the | |
| Brillouin zone along with the symmetry unique images of the k point. | |
| shengBTE - this causes the files needed to perform a ShengBTE run to be | |
| output. This usually comprises the files CONTROL, FORCE_CONSTANTS_2ND, | |
| FORCE_CONSTANTS_3RD that contain the system information and control | |
| parameters, the second order force constants, and the third order force | |
| constants, respectively. Note that the FORCE_CONSTANTS_2ND file is also | |
| suitable for use with Phonopy. | |
| NB: Since the calculation of the third order force constants is | |
| potentially expensive expect this option to substantially increase | |
| the computational cost of a run!!! The use of the keyword nod3 allows | |
| the ShengBTE output to be restricted to second derivatives only. | |
| NB: The option "threshold" controls the minimum size for force constants | |
| to be output as non-zero | |
| dipole - this causes GULP to output a text file that contains the | |
| dipole of the system for each time step of a molecular dynamics run. | |
| If the delta_dipole keyword is specifed then the dipole is computed | |
| relative to the initial value. The units of the dipoles for this file | |
| are Debye and the format has the current time in ps follow by the | |
| three Cartesian components in the order x, y and z. | |
| xsf - output a file in XCrySDen format. When performing MD it is possible | |
| to output either a single XSF file or a sequence of files for single | |
| frames with a number appended to differentiate them. The format is: | |
| output xsf <seq/sym> myfile | |
| where seq (sequential) is optional but if specified will result in multiple | |
| files being output during molecular dynamics. Here myfile is the root name | |
| for the file. For example; | |
| output xsf seq myfile | |
| would produce myfile000001.xsf, myfile000002.xsf, etc. If "sym" is specified | |
| then atomic symbols are used instead of atomic numbers in the files. This | |
| is relevant if using Aenet which expects symbols, whereas XCrySDen specifies | |
| atomic numbers for the format. | |
| See also | marvin dump ghost_supercell num3 numerical shopt threshold nod3 |
| Type | Option |
| Format | p_flexible |
| p_flx(1,1) p_flx(2,1) p_flx(3,1) | |
| p_flx(1,2) p_flx(2,2) p_flx(3,2) | |
| p_flx(1,3) p_flx(2,3) p_flx(3,3) | |
| Use | Used only for restarting a molecular dynamics simulation with the |
| stochastic integrator. Not intended for user input. | |
| See also | integrator |
| Type | Option |
| Format | p_isotropic <value> |
| Use | Used only for restarting a molecular dynamics simulation with the |
| stochastic integrator. Not intended for user input. | |
| See also | integrator |
| Type | Option |
| Format | parallel <avoid_communication> |
| Units | none |
| Default | Use communication. |
| Use | This option controls various settings that relate to the |
| parallel algorithms used, where choices exist. | |
| avoid_communication - if specified then communication is | |
| minimised by recalculating on each node for some parts of | |
| the code. | |
| See also | maths matrix_format blocksize |
| Type | Option |
| Format | pcell <angs/au> |
| a <1 x optimisation flag> | |
| Units | Angstrom (default) or au for a |
| Use | Polymer unit cell. Either "pvector" or "pcell" |
| must be given for a polymer. For optimisations or fitting, | |
| flags must be set unless cellonly, conp or conv are specified. | |
| See also | pvector twist |
| Type | Option |
| Format | pdf <all> |
| <further options> | |
| end | |
| Use | Opens pdf input block. This is used for the input of options used by pdf |
| calculations. Specifically, it should be used for the pdf options | |
| rmax, rbins, wmax, wmin, units. | |
| The block is opened with the word pdf and all further options read are | |
| treated as pdf-related until the word end. | |
| When working with multiple configurations, one pdf input block is needed | |
| per configuration, unless the option all is given, when the options act on all | |
| configurations. This allows PDF output to be comparable between configurations. | |
| See also | PDFcut PDFkeep nowidth nofreq rmax rbins wmax wmin units bbar siginc |
| Type | Option |
| Format | pfinite delta |
| Default | 0.00001 |
| Units | Angstroms |
| Use | Sets the finite difference intervals to be used for the numerical |
| evaluation of phonons by central finite differencing of the | |
| analytic first derivatives. | |
| See also | numerical sfinite |
| Type | Option |
| Format | pfractional <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> |
| at.sym. <species_type> x y z <charge> <occupancy> <radius> <3 x flags> | |
| Units | Fractional for x Angstroms for y and z, and electrons, radius in |
| Angstroms | |
| Use | Internal coordinates and charges for all species in the polymer cell. |
| Either the atomic number or the symbol may be supplied, followed | |
| by the species type. If the species type is omitted then it is | |
| assumed to be a core. Individual charges may be supplied for each | |
| ion or the charges for each type of species given using the | |
| species option. If the charges are given, then optionally site | |
| occupancies may also be specified. Similarly, if the charge and | |
| occupancy are given, then the radius of a breathing shell may | |
| also be present. Optimisation flags are only needed if cellonly, | |
| conv, bulk, conp or shell are not specified. | |
| See also | pcell |
| Type | Option |
| Format | piezoelectric <n> <stress/strain> |
| i <x/y/z> piezoelectric constant p(i,alpha) <weight> | |
| Units | C/m**2 for piezoelectric strain constants |
| 10**-9 C/N for piezoelectric stress constants | |
| Default | no piezoelectric constants to be fitted - constants are strains |
| Use | Subsection of observables, used for specifying values of |
| piezoelectric stress and strain constants for fitting. | |
| Units are the same as output from the program and it is | |
| only necessary to give unique piezoelectric constants. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive bornq |
| young poisson shear voigt bulk |
| Type | Option |
| Format | plane_lj m n |
| atom1 plane zcoord A B rmin rmax <2xflags> | |
| Units | zcoord, rmin and rmax in Angstroms, A & B in |
| eV/Angstroms**m and eV/Angstroms**n, respectively. | |
| Default | m = 10, n = 4 |
| Use | Specifies a Lennard-Jones potential between atom1 and a plane. |
| Because the method is only applicable to 2-D systems the plane | |
| is assumed to be parallel to xy. The absolute position in z | |
| is given by zcoord. For example to include an integrated L-J | |
| 12-6 potential (which would give m=10 and n=4) that acts on carbon | |
| positioned at -0.75 Ang the input would look like: | |
| plane_lj 10 4 | |
| C core -0.75 1000.0 14.0 0.0 12.0 | |
| See also | lennard einstein |
| Type | Option |
| Format | plumed_input <plumed_file_name> |
| Units | none |
| Default | plumed_file_name = plumed.dat |
| Use | By specifying this option GULP tried to use the plumed |
| plug-in with the input for this coming from an external | |
| file. | |
| See also | md plumed_log |
| Type | Option |
| Format | plumed_log <plumed_log_name> |
| Units | none |
| Default | plumed_log_name = plumed.log |
| Use | Specifies the name for the log file from Plumed |
| See also | md plumed_input |
| Type | Option |
| Format | pointsperatom <no. of points per atom> |
| Default | 1082 (for dodecahedron) / (974 for octahedron) |
| Units | None |
| Use | Specifies the number of points per atom for the basic |
| sphere used to construct the solvent-accessible surface | |
| in a COSMO calculation. The value must conform to the | |
| following formula : | |
| Dodecahedron | |
| pointsperatom = 10*(3**k)*(4**l)+2 | |
| Octahedron | |
| pointsperatom = 4*(3**k)*(4**l)+2 | |
| where k and l are integers. The larger the value of | |
| this parameter, the more precise and expensive the | |
| calculation will be. | |
| See also | cosmo segmentsperatom solventepsilon solventradius |
| solventrmax vdw cosmoshape rangeforsmooth |
| Type | Option |
| Format | poisson_ratio <n> |
| <xy/xz/yz> poissons_ratio <weight> | |
| Units | Dimensionless |
| Default | no Poissons ratios to be fitted |
| Use | Subsection of observables, used for specifying values of |
| Poisson's ratios for fitting. | |
| Example | To fit a Poisson's ratio of 0.23 for the x-z component |
| with a weight of 0.01: | |
| poisson 1 | |
| xz 0.23 0.01 | |
| NB: The Poisson ratios are computed assuming that the | |
| material is linear elastic orthotropic. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive bornq |
| piezoelectric young shear voigt bulk |
| Type | Option |
| Format | polarisability |
| atom_symbol <core/shell> dipolar_polarisability | |
| Units | dipolar_polarisability in Angs**3 |
| Default | Polarisability is equal to zero, except for shell contribution |
| Use | Allows the inclusion of point ion polarisability in a calculation. |
| At the moment this is non-self consistent, i.e. induced moments on | |
| different centres do not interact. |
| Type | Option |
| Format | polynomial <harmonic> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| norder | |
| atom1 atom2 (norder+1)*coeff <r0> <rmin> rmax <(norder+1)*flags> | |
| order of coefficients = lowest to highest | |
| Units | eV and Angstroms |
| Default | r0 = 0 |
| Use | Polynomial potential, order = 1-8: |
| E = c0 + c1*(r-r0) + c2*(r-r0)**2 + ... + cn*(r-r0)**n | |
| If sub-option harmonic is specified, then the polynomial is premultiplied | |
| by a harmonic term: | |
| E = (r - r0)**2 * (c0 + c1*r + c2*r**2 + ... + cn*r**n) for r < r0 | |
| E = 0 for r > r0 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) |
| Type | Option |
| Format | potential <reverse> <au> |
| x y z V <weight> | |
| If "reverse" is specified then order is: | |
| V x y z <weight> | |
| Units | V is in eV per electron charge in a.u., x, y and z are |
| the fractional coordinates of the site for a 3D system | |
| or the cartesian coordinates for an isolated molecule. | |
| Use | Specifies the electrostatic potential at a given point |
| in space for use in fitting of electrostatic potential | |
| surfaces as a means of deriving charges. This option is | |
| a sub-option of the observables section. | |
| See also | zero_potential potsites pot potgrid |
| Type | Option |
| Format | potential_interpolation number_of_points |
| Units | None |
| Default | Do not use interpolation |
| Use | Requests that linear interpolation of potentials is used to |
| accelerate the calculation where possible at the expense of | |
| numerical precision. The larger the number of points the greater | |
| will be the precision (values of 100,000 & larger are typical). | |
| Currently this technique is only used in MD. |
| Type | Option |
| Format | potgrid <xmin xmax ymin ymax zmin zmax> nx ny nz |
| Units | fractional (3D) / fractional/Angstroms (2D) / Angstroms (cluster) |
| Use | Calculates the electrostatic potential at a grid of points. The |
| limits of the grid are given by xmin,xmax,ymin,ymax,zmin and zmax | |
| in fractional units for a periodic system and in cartesian coordinates | |
| for a cluster. These values can be omitted for a periodic system, | |
| in which case they default to 0 for the minimum and 1 for the | |
| maximum (ie the whole unit cell). The integer values nx, ny, nz | |
| control how many points are calculated in each direction. The | |
| number of points will be one greater than the number input. For | |
| example, a value of nx=5 will generate 6 points at 0.0, 0.2, 0.4, | |
| 0.6, 0.8 and 1.0. | |
| NB: If symmetry is turned off using the "nosym" option then the | |
| fractional range will apply to the new cell that is generated. | |
| See also | pot potential potsites |
| Type | Option |
| Format | potsites <cart> <au> |
| x1 y1 z1 | |
| x2 y2 z2 | |
| etc..... | |
| Units | fractional/Cartesian as appropriate to dimensionality |
| Default | none |
| Use | Allows the user to specify points in space at which the electrostatic |
| potential should be calculated. Note that it is necessary to also | |
| specify the "pot" keyword to trigger the calculation of the potential. | |
| NB: If the potential sites are specified using fractional coordinates | |
| for a centred cell (e.g. hexagonal) then they will be transformed to | |
| the primitive setting automatically for consistency. In other words | |
| the fractional coordinates are taken to be in the same frame of reference | |
| as for the atomic coordinates input. | |
| NB: If symmetry is turned off using the "nosym" option then the | |
| fractional coordinates will be transformed as per the atomic fractional | |
| coordinates. | |
| See also | pot potential potgrid |
| Type | Option |
| Format | pressure value_of_pressure <GPa/kPa/MPa/Pa/atm/Nm-2/kbar> |
| Units | Gigapascals, kilopascals, megapascals, pascals, atmospheres, kbar (Default = GPa) |
| Default | 0 GPa |
| Use | Specifies pressure to be applied to structure. Causes energy to be |
| replaced by enthalpy in calculations. |
| Type | Option |
| Format | n = integer no. |
| Use | Prints out current parameters during fitting whenever cycle number is |
| exactly divisable by n. | |
| See also | dump |
| Type | Option |
| Format | production value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - if integer, then value is by default |
| a multiple of the timestep or if non-integer then by | |
| default is the time in picoseconds. | |
| Use | Specifies the simulation time to be spent collecting |
| production data for subsequent analysis. | |
| See also | md equilibration sample write temperature timestep |
| tscale nolist delay_force end_force momentum_correct |
| Type | Option |
| Format | project_dos <n> |
| For each <n> there should be a line listing the atoms in the | |
| asymmetric unit onto which to project the density of states, or | |
| alternatively atomic symbols and types may be given. | |
| Use | Projects the phonon density of states onto given sets of atoms. |
| Note that this requires the explicit calculation of the eigenvectors | |
| for each k point. Atoms for projection must be cores and not | |
| shells as the shells have no component in the DOS. Projections | |
| will also be output to the .dens file if requested. | |
| Examples: | |
| To project on to atoms 4, 7 and 10: | |
| project_dos 1 | |
| 4 7 10 | |
| To project on to all species C1 and O3: | |
| project_dos 1 | |
| C1 O3 | |
| See also | phonon eigenvectors output |
| Type | Option |
| Format | pvector <angs/au> |
| x for vector | |
| <1 x optimisation flags> | |
| Units | Angstrom (default) or au |
| Use | Specifies the cartesian component of the polymer vector. |
| Either "pvector" or "pcell" must be included for a polymer. | |
| Strain optimsation flags appear on last line. | |
| See also | pcell |
| Type | Option |
| Format | qelectronegativity |
| <Atomic_symbol/atomic_number> chi <mu> <radius> <Q0> <E0> <3 x flags for fitting> | |
| or | |
| qelectronegativity <qrange/qmin/qmax> | |
| <Atomic_symbol/atomic_number> chi <mu> <radius> <Q0> <E0> <qmin> <qmax> <3 x flags for fitting> | |
| Units | Chi, mu, and E0 in eV, radius in Ang, Q0, qmin, qmax in a.u. |
| Default | Q0 = 0.0, E0 = 0.0 |
| Use | Allows the user to specify the parameters needed for the |
| QEq electronegativity equalisation method for determining | |
| charges. Note that if the flags are not specified they | |
| are assumed to be zero. | |
| Q0 is the charge about which the electronegativity equations | |
| are quadratic. In most methods this is zero, but need not be. | |
| For example, the EQeq method assigns values of Q0 not equal | |
| to zero. | |
| E0 is an additive constant for the energy of an atom. This is | |
| only really needed when using multiple q ranges to ensure | |
| energy matching. | |
| The sub-options qrange, qmin, and qmax control whether the | |
| values apply for a given value of charge. By default the values | |
| apply to all values of charge (q). If qmin is specified then | |
| they are only applied to charges larger than qmin, while if qmax | |
| is given the they are applied when q is less than qmax. When | |
| qrange is specified then the values apply for qmin =< q < qmax. | |
| NB: If no parameters are input then the default values will be | |
| used for all charge values. However, if parameters are input | |
| then this will override the default values and the user must | |
| set parameters for all relevant ranges of charge. | |
| See also | eem electronegativity qeq smelectronegativity noqeem external_potential |
| eembond |
| Type | Option |
| Format | qeqiter maximum_number_iterations |
| Units | None |
| Default | 20 |
| Use | Sets the maximum number of iterations that are allowed |
| during the QEq electronegativity equalisation scheme. | |
| Only applies to systems where hydrogen is present. | |
| See also | eem qeq qeqtol qeqradius dcharge noqeem |
| Type | Option |
| Format | qeqradius radius |
| Units | Angstroms |
| Default | 15.0 |
| Use | Sets the maximum radius for the calculation of the |
| Coulomb term using the formula for two Slater s | |
| type orbitals in the QEq electronegativity equalisation | |
| scheme. Beyond this radius the terms are calculated | |
| using just the inverse distance. Generally the default | |
| value should be large enough for convergence. However, | |
| the user may wish to try smaller values to achieve a | |
| faster calculation. Note that failure to achieve | |
| satisfactory convergence in an optimisation may be | |
| due to this value being too small. | |
| See also | eem qeq qeqiter qeqtol dcharge noqeem |
| Type | Option |
| Format | qeqtol tolerance |
| Units | Electrons |
| Default | 0.000001 |
| Use | Sets the tolerance on the change in the charges between |
| iterations of the QEq electronegativity equalisation | |
| scheme. This only applies to systems which contain | |
| hydrogen. | |
| See also | eem qeq qeqiter qeqradius dcharge noqeem |
| Type | Option |
| Format | qerfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <au/nm/pm> <ener/grad> <type_of_bond> |
| atom1 atom2 rho rmax <1*flag> | |
| Units | rho and rmax in Angstroms |
| Default | none |
| Use | Screened Coulomb interaction using the complementary error function. |
| E = [qi.qj/r].erfc(r/rho) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| NOTE : The keyword "noelectrostatics" should be included when using | |
| this potential to turn off the normal Ewald sum, otherwise the | |
| Coulomb interaction will be double counted. | |
| See also | noelectrostatics |
| Type | Option |
| Format | qgrid nqx nqy nqz |
| Units | none |
| Default | nqx = nqy = nqz = 24 |
| Use | Specifies the grid dimensions for use in SPME. It is important that the |
| user checks that the energy is converged with respect to this grid. The | |
| size will depend on the system and weighting between real/reciprocal | |
| space chosen. The grid dimension must be large than or equal to the B spline | |
| order (default = 8) | |
| See also | rspeed veck accuracy ewaldrealradius spme bspline |
| Type | Option |
| Format | qincrement |
| atom1 atom2 delta <1*flag> | |
| Default | delta = 0.0 |
| Use | If the keyword qbond is given then the charges on the atoms are |
| determined by bond increments given by this option. An example | |
| of the input is: | |
| qincrement | |
| O2 core C core -0.24 | |
| O3 core C core 0.15 | |
| NB: The order of the atoms is important in that the sign of delta | |
| changes if the order is reversed. Consequently if atom1 and atom2 | |
| are of the same type then delta must be zero. Hence, the value of | |
| delta is applied with the input sign to atom1 and the negative of | |
| this to atom2. | |
| See also | qeq eem gasteiger qbond noqeem eembond |
| Type | Option |
| Format | qiterations n <convergence_tolerance> |
| Default | n = 200, convergence_tolerance = 0.00000001 |
| Use | Allows the user to change the default number of iterations and |
| convergence tolerance for iterative charge solves triggered by | |
| the qiteration keyword | |
| See also | qiterative |
| Type | Option |
| Format | qmmm <mechanical/electronic> |
| Units | None |
| Default | No QM/MM scheme |
| Use | Controls whether a QM/MM scheme is used to modify the energy in |
| GULP, and if so which scheme. The two options are: | |
| mechanical: This implies that the interactions within the MM | |
| regions and between the QM and MM regions are calculated, but | |
| not within the QM region. | |
| electronic: This implies the same as mechanical embedding, except | |
| that the Coulomb interactions between the QM and MM regions are | |
| also excluded since these are assumed to be accounted for by the | |
| QM portion of the calculation. | |
| NB: At present there are restrictions on which facilities will | |
| work in combination with this option. Only 0-D calculations with | |
| up to first derivatives are generally enabled for all models. |
| Type | Option |
| Format | qonsas total_charge |
| Units | Atomic units (i.e. electrons) |
| Default | 0.0 |
| Use | Specifies the total charge on the SAS for the COSMIC method. |
| Note that for charged systems the SAS will be constructed so | |
| that the charge is neutralised. This option adds to the | |
| default charge on the SAS due to any net charge of the atoms. | |
| See also | cosmo cosmic qsas |
| Type | Option |
| Format | qoverr2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <au/nm/pm> <ener/grad> |
| atom1 atom2 rmax <1*flag> | |
| Units | rmax in Angstroms |
| Default | none |
| Use | Computes the charge interaction as a local one based on: |
| E = [qi.qj/r**2] | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| NOTE : The keyword "noelectrostatics" should be included when using | |
| this potential to turn off the normal Ewald sum, otherwise the | |
| Coulomb interaction will be double counted. | |
| NOTE : This expression is used for the Coulomb term in Accelrys's | |
| implementation of Dreiding. | |
| See also | noelectrostatics |
| Type | Option |
| Format | qreaxff <n> |
| i Qi <weight> | |
| Units | atomic units |
| Default | no ReaxFF charges to be fitted |
| Use | Subsection of observables, used for specifying values of |
| ReaxFF charges for fitting. Note that i is the | |
| atom number in the unit cell, not the asymmetric unit. | |
| Example: | |
| qreaxff 1 | |
| 1 1.95 | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq |
| Type | Option |
| Format | qsolver <itpack/lapack/bcg> |
| Units | none |
| Default | itpack (serial) / bcg (parallel) |
| Use | Selects the algorithm for iterative charge solution in COSMO. |
| Note that itpack can only be used in serial. | |
| See also | qiterative parallel matrix_format |
| Type | Option |
| Format | qtaper <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 C rmax <1*flag> | |
| Units | C in eV, rmax in Angs |
| Default | none |
| Use | Tapers the Coulomb interaction to a constant value, C, at short |
| distances. Currently implemented crudely as an interatomic | |
| potential to stop Coulomb collapse. However, this won't avoid | |
| numerical errors if atoms are started too close in the first | |
| place. The potential uses a taper from rmax to 0.0 to match the | |
| Coulomb potential using the charges of the species to the constant | |
| value at the nucleus. This potential mimics the fact that at | |
| short range the Coulomb term becomes damped by being an integral | |
| rather than just a 1/r potential. | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = [qi.qj/r].f(r) + C.(1-f(r)), where f(r) = polynomial taper | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential cutoffs are omitted from input. | |
| Type | Option |
| Format | qwolf <original/fennell> <eta> <rmax> |
| Units | eta in inverse Angstroms and rmax in Angstroms |
| Default | none |
| Use | Calculates the electrostatic energy using the approximation to the Ewald |
| sum due to Wolf et al (J. Chem. Phys., 110, 8254, 1999): | |
| Eij = [qi.qj/r].erfc(eta*r) - lim{r->rmax}([qi.qj/rmax].erfc(eta*rmax)) | |
| Ei = - (erfc(eta*rmax)/(2*rmax) + eta/sqrt(pi))*qi**2 | |
| Note: it is up to the user to set the eta and rmax values such that the | |
| Ewald limit is recovered. At present the Wolf sum cannot be used with a | |
| defect calculation. | |
| NB: The original Wolf sum has energy and forces that are inconsistent | |
| with each other (i.e. the forces are not the negative first derivative of the | |
| energy). Hence GULP uses forces that are based on the Wolf energy by default. | |
| If you want to force the use of the original Wolf sum then you can use the | |
| "original" sub-option, but don't expect optimisations to converge properly. | |
| You have been warned! | |
| The "fennell" sub-option specifies that the alternative form of the Wolf | |
| sum due to Fennell and Gezelter (J. Chem. Phys., 124, 234104 (2006)) be | |
| used. The advantage of their method is that the potential and force are | |
| consistent while neither is discontinuous at the cut-off radius. The only | |
| downside is that the potential is different from the Ewald result. However, | |
| potential differences (and therefore energetics) should be well-described. | |
| The energy expression for this form is: | |
| Eij = qi*qj*[erfc(eta*r)/r - erfc(eta*rmax)/rmax + (r - rmax)* | |
| (erfc(eta*rmax)/rmax**2 + | |
| (2*eta/sqrt(pi))*exp(-(eta*rmax)**2)/rmax) | |
| See also | noelectrostatics |
| Type | Option |
| Format | radial_force K x y z |
| Units | K in eV/Ang, x, y, z in Ang |
| Default | No radial force |
| Use | This option allows a radial harmonic force to be applied |
| to a system with a force constant K and origin of force | |
| at (x,y,z). Because of the point nature of the force it | |
| can only be applied to finite systems. The energy of the | |
| contribution is given by: | |
| E = sum(i) 1/2 K*[(x_i - x)**2 + (y_i - y)**2 + (z_i - z)**2] | |
| where the sum is over all atoms, i. |
| Type | Option |
| Format | random ncall1 ncall2 ncall3 <G> |
| Units | None |
| Default | ncall1 = ncall2 = ncall3 = 0 |
| Use | This option is used for consistent restarting of runs that utilise |
| random numbers by keeping track of how many calls were made during | |
| the previous run so that the position in the sequence of numbers | |
| can be recreated on restart. There are three types of random number | |
| generated in GULP at present and so the three numbers are to track the | |
| number of calls for each generator. | |
| The optional letter G at the end indicates that the Gaussian number | |
| generator was called last; this is important in obtaining the proper | |
| sequence going forward in some cases. | |
| NB: This option is not intended for user setting and is included to | |
| explain why this line is present in the restart file. | |
| See also | md |
| Type | Option |
| Format | rangeforsmooth <range> |
| Units | Angstroms |
| Default | 0.0 |
| Use | Smooths the inclusion of points on the solvent-accessible |
| surface to make the energy surface more continuous. | |
| See also | cosmo pointsperatom segmentsperatom |
| Type | Option |
| Format | rbins <n> |
| Default | 100 |
| Use | Used within the pdf input block for PDF calculations. |
| Sets the number of bins to be used for PDF correlation function output | |
| See also | PDFkeep PDFcut |
| Type | Option |
| Format | rcartesian replica_number |
| x1 y1 z1 <r1> | |
| x2 y2 z2 <r2> | |
| .. .. .. | |
| xN yN zN <rN> | |
| Units | Angstroms |
| Default | None |
| Use | Specifies the coordinates of a replica for the nudged elastic |
| band method. The number of coordinates must match the number | |
| of atoms in the initial structure. This option is primarily | |
| useful for restarting. If the coordinates of the replicas are | |
| not given then the values are initialised based on a linear | |
| interpolation between the initial and final states. The radii | |
| of the ions can be optionally given on the end of the line if | |
| a breathing shell model is being used. If not specified then | |
| they are assumed to be zero. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations neb | |
| fcartesian rfractional ffractional rcell fcell fvectors |
| Type | Option |
| Format | rcell replica_number |
| a b c alpha beta gamma (for 3-D) | |
| a b alpha (for 2-D) | |
| a (for 1-D) | |
| Units | Angstroms for a/b/c & degrees for alpha/beta/gamma |
| Default | None |
| Use | Specifies the unit cell of a replica for the nudged elastic band |
| method. This option is primarily useful for restarting. If the | |
| unit cells of the replicas are not given then the values are | |
| initialised based on a linear interpolation between the initial | |
| and final states. The number of cell parameters must match the | |
| dimensionality of the initial system. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian rfractional ffractional fcell neb fvectors |
| Type | Option |
| Format | rcspatial rcspatial_value <rcspatial_BO_value> |
| rcspatial anisotropic rcspatial_x rcspatial_y rcspatial_z <rcspatial_BO_x rcspatial_BO_y rcspatial_BO_z> | |
| Units | Angstroms |
| Default | Set equal to the largest potential cutoff in real space. |
| Use | Can be used to set the domain size in the spatial decomposition to make |
| it smaller than the potential cutoff. In this case looping over multiple | |
| cells is needed. | |
| If the anisotropic suboption is used then a different domain size is applied along each axis. | |
| See also | spatial |
| Type | Option |
| Format | rdirection <frac> x_in y_in z_in x_out y_out z_out |
| Units | dimensionless |
| Default | x_in = y_in = z_in = x_out = y_out = z_out = 1 |
| Use | If the Raman susceptibilites are calculated then this |
| option specifies in the directions of the incident and | |
| outgoing photons. | |
| NOTE : This option only applies to a gamma point calculation | |
| By default the directions are assumed to be in Cartesian space | |
| unless the "frac" sub-option is given in which case they will | |
| be taken relative to the crystal axes. In all cases, the | |
| directions will be normalised, such that the absolute | |
| magnitude does not influence the result. | |
| See also | phonon raman |
| Type | Option |
| Format | reaction <n> |
| ncfg energy <weight> (icfg fcfg) x ncfg | |
| Units | eV |
| Default | no reaction energies to be fitted |
| Use | Subsection of observables, used for specifying reaction energies |
| in terms of configuration energies. | |
| In the input line, ncfg is the number of configurations to be | |
| used in the reaction (which must be less than or equal to the | |
| number specified in the input so far), and then for each ncfg | |
| case the configuration number and scale factor is given, followed | |
| by the target energy and optionally a weight. | |
| Example: | |
| If configuration 1 is H2O, configuration 2 is CO and configuration | |
| 3 is the 2H2O...CO complex whose heat of formation is -0.21 eV and | |
| a weight of 10.0 is desired then the input for this would be like: | |
| reaction 1 | |
| 3 -0.21 10.0 1 -2.0 2 -1.0 3 1.0 | |
| i.e. The coefficients are negative for the left-hand side and positive | |
| for the RHS. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq qreaxff fbond relax reaction |
| Type | Option |
| Format | reaxff0_bond p_boc1 p_boc2 <2 x flags> |
| Type | Option |
| Format | reaxff0_lonepair p_lp1 <1 x flag> |
| Type | Option |
| Format | reaxff0_over p_ovun3 p_ovun4 p_ovun6 p_ovun7 p_ovun8 <5 x flags> |
| Type | Option |
| Format | reaxff0_penalty p_pen2 p_pen3 p_pen4 <3 x flags> |
| Type | Option |
| Format | reaxff0_torsion p_tor2 p_tor3 p_tor4 p_cot2 <4 x flags> |
| Type | Option |
| Format | reaxff0_valence p_val7 p_val8 p_val9 p_val10 <4 x flags> |
| Type | Option |
| Format | reaxff0_vdw p_vdw1 <1 x flag> |
| Type | Option |
| Format | reaxff1_angle |
| species <core/shell> p_val3 p_val5 <2 x flags> | |
| Default | None |
| Use | Specifies the parameters for the species-wise angle parameters. |
| p_val3 is used in the calculation of the ReaxFF function f7 (eqn 13b). | |
| p_val5 is used in the calculation of the ReaxFF function f8 (eqn 13c). | |
| See also | reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_morse |
| reaxff1_morse |
| Type | Option |
| Format | reaxff1_include_under |
| species <0/1> | |
| Default | 1 (yes) for 1st row elements and 0 (no) for everything else |
| Use | In the ReaxFF formalism the under coordination formalism due to pi bonding |
| is modified for elements with a mass greater than 21 amu. This option | |
| allows the user to select which form of the under coordination correction | |
| is applied for each element. Here a value of 1 => first row formula and 0 | |
| implies the 2nd row form. No other values are allowed. | |
| See also | reaxff1_under |
| Type | Option |
| Format | reaxff1_lonepair |
| species <core/shell> n_lp_opt p_lp2 <2 x flags> | |
| Default | None |
| Use | Specifies the parameters for the species-wise lone pair energy parameters. |
| n_lp_opt is the optimal number of lone pairs used to construct delta_lp (eqn 9). | |
| p_lp2 is the parameter that scales the lone pair energy for each atom (eqn 10). | |
| See also | reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_angle |
| reaxff1_morse |
| Type | Option |
| Format | reaxff1_morse <au/kcal/kjmol> |
| species <core/shell> alpha Dij rvdw gamma_w <4 x flags> | |
| Default | None |
| Use | Specifies the parameters for the species-wise morse parameters for the |
| VDW energy (eqns 21a and 21b). In the final morse potential, | |
| Dij = sqrt(Dij(i)*Dij(j)), alpha_ij = sqrt(alpha(i)*alpha(j)), | |
| r_vdw = 2*sqrt(rvdw(i)*rvdw(j)) | |
| See also | reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_angle |
| reaxff2_bo reaxff2_bond |
| Type | Option |
| Format | reaxff1_over |
| species <core/shell> p_boc3 p_boc4 p_boc5 p_ovun2 <4 x flags> | |
| Default | None |
| Use | Specifies the parameters for the species wise overcoordination parameters. |
| Parameters p_boc3, p_boc4, p_boc5 are used to compute the functions f4 & f5 | |
| that correct the bond order (eqns 4e & 4f). The final parameter, p_ovun2, is | |
| part of the overcoordination energy (eqn 11a). | |
| See also | reaxff1_radii reaxff1_valence reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse |
| Type | Option |
| Format | reaxff1_radii |
| species <core/shell> r_sigma r_pi r_pipi <3 x flags> | |
| Default | None |
| Use | Specifies the radii for a species that are to be used in the ReaxFF bond order |
| calculation. Here the uncorrected bond order is given by: | |
| BO' = exp(p_bo1*(r/r_sigma)**p_bo2) + exp(p_bo3*(r/r_pi)**p_bo4) + | |
| exp(p_bo5*(r/r_pipi)**p_bo6) | |
| The remaining parameters, p_bo1 - p_bo6, are input via the reaxff2_bo option. | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff2_bo |
| Type | Option |
| Format | reaxff1_under |
| species <core/shell> p_ovun5 <1 x flag> | |
| Default | None |
| Use | Specifies the parameter for the species-wise undercoordination parameters. |
| p_ovun5 scales the undercoordination energy (eqn 12). | |
| See also | reaxff1_radii reaxff1_valence reaxff1_over reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_include_under |
| Type | Option |
| Format | reaxff1_valence |
| species <core/shell> Val_normal Val_boc Val_lp Val_angle <4 x flags> | |
| Default | None |
| Use | Specifies the valence states for a species that are to be used in the ReaxFF |
| calculation of delta values. The value of delta' (eqn 3a) is given by: | |
| delta'(i) = - Val_normal(i) + sum(j=1->neigh(i)) BO_ij' | |
| There is a second valence used for delta'_boc (eqn 3b): | |
| delta'_boc(i) = - Val_boc(i) + sum(j=1->neigh(i)) BO_ij' | |
| There is a third valence used for delta_e (eqn 7) as part of the lone pair | |
| energy: | |
| delta_e(i) = - Val_lp(i) + sum(j=1->neigh(i)) BO_ij | |
| There is a fourth valence used for delta_angle (eqn 13e): | |
| delta_angle(i) = - Val_angle(i) + sum(j=1->neigh(i)) BO_ij | |
| See also | reaxff1_radii reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse |
| Type | Option |
| Format | reaxff2_bo <over> <bo13> |
| species1 <core/shell> species2 <core/shell> p_bo1 p_bo2 p_bo3 p_bo4 p_bo5 p_bo6 <6xflags> | |
| Default | None |
| Use | Specifies the pairwise parameters between species that are to be used in the |
| ReaxFF bond order calculation. Here the uncorrected bond order is given by: | |
| BO' = exp(p_bo1*(r/r_sigma)**p_bo2) + exp(p_bo3*(r/r_pi)**p_bo4) + | |
| exp(p_bo5*(r/r_pipi)**p_bo6) | |
| The remaining parameters, r_sigma, r_pi, r_pipi, are input via the reaxff1_radii option. | |
| The two sub-option words control if the bond order is corrected: | |
| reaxff2_bo over => correct for overcoordination using f1 | |
| reaxff2_bo bo13 => correct for 1-3 terms using f4 and f5 | |
| reaxff2_bo over bo13 => correct for overcoordination using f1 and 1-3 terms using f4 and f5 | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bond reaxff2_over reaxff2_morse reaxff2_pen |
| Type | Option |
| Format | reaxff2_bond |
| species1 <core/shell> species2 <core/shell> De_sigma De_pi De_pipi p_be1 p_be2 <5xflags> | |
| Default | None |
| Use | Specifies the pairwise parameters between species that are to be used in the |
| ReaxFF bond order energy. Here the bond order energy is given by: | |
| E_bond = - De_sigma*BO_sigma*exp(p_be1*(1-(BO_sigma)**p_be2)) - De_pi*BO_pi | |
| - De_pipi*BO_pipi | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_over reaxff2_morse reaxff2_pen |
| Type | Option |
| Format | reaxff2_morse |
| species1 <core/shell> species2 <core/shell> De alpha r0 r_sigma r_pi r_pipi <6 x flags> | |
| Default | None |
| Use | Specifies pairwise Morse potential parameters for ReaxFF |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff2_pen |
| Type | Option |
| Format | reaxff2_over |
| species1 <core/shell> species2 <core/shell> p_ovun1 <1 x flag> | |
| Default | None |
| Use | Specifies the pairwise parameters between species that are to be used in the |
| ReaxFF overcoordination energy. Here the overcoordination energy is given by: | |
| E_over_i = (sum(j=>neigh(i)) p_ovun1(ij).De_sigma.BO_ij).delta_lpcorr(i) | |
| ------------------------------------------------------------- | |
| (delta_lpcorr(i) + Val_i) * (1 + exp(p_ovun2*delta_lpcorr(i)) | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_morse reaxff2_pen |
| Type | Option |
| Format | reaxff2_pen |
| species1 <core/shell> species2 <core/shell> p_pen1 p_pen2 p_pen3 <3 x flags> | |
| Default | None |
| Use | Specifies pairwise penalty energy parameters for ReaxFF. The penalty energy is |
| given by: | |
| Epen = sum [ p_pen1 * (BO_ij - delta_i - p_pen2*delta**4 - p_pen3)**2] | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff2_morse |
| Type | Option |
| Format | reaxff3_angle <au/kcal/kjmol> |
| species1 <core/shell> species2 <core/shell> species3 <core/shell> & | |
| theta_00 p_val1 p_val2 p_val4 p_val7 <p_val6> <6 x flags> | |
| Default | None |
| Use | Specifies the parameters that determine the angular valence energy that depend |
| on a triad of species in the ReaxFF force field. Here species1 is the pivot | |
| atom of the three-body like term. Here the valence energy is given by: | |
| E_val = f7(BO_12)*f7(BO_13)*f8(delta(1))*p_val1*(1-exp(-p_val2*(theta_0 - theta)**2)) | |
| The function f7 is given by: | |
| f7(BO) = 1 - exp(-p_val3*BO**p_val4) | |
| If not explicitly given, the value of p_val6 is taken from the global value. | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_pen | |
| reaxff3_conjugation |
| Type | Option |
| Format | reaxff3_conjugation <au/kcal/kjmol> |
| species1 <core/shell> species2 <core/shell> species3 <core/shell> & | |
| p_coa1 p_coa2 p_coa3 p_coa4 <4 x flags> | |
| Default | None |
| Use | Specifies the parameters that determine the three-body conjugation energy that depend |
| on a triad of species in the ReaxFF force field. Here species1 is the pivot | |
| atom of the three-body like term. Here the valence energy is given by: | |
| E_val = p_coa1*(1/(1+exp(p_coa2*delta_1_val)))* | |
| exp(-p_coa3*(-BO_12 + sum(n=1->neighbours of 2) BO_2n))* | |
| exp(-p_coa3*(-BO_13 + sum(n=1->neighbours of 3) BO_3n))* | |
| exp(-p_coa4*(BO_12 - 1.5)**2)*exp(-p_coa4*(BO_13 - 1.5)**2) | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle | |
| reaxff3_hbond reaxff3_angle reaxff4_torsion |
| Type | Option |
| Format | reaxff3_hbond <au/kcal/kjmol> |
| species1 <core/shell> species2 <core/shell> species3 <core/shell> r0_hb p_hb1 & | |
| p_hb2 p_hb3 <4 x flags> | |
| Default | None |
| Use | Specifies the parameter that determines the hydrogen bonding energy that depends |
| on a triad of species in the ReaxFF force field (eqn 18). Here species1 is the pivot | |
| atom of the three-body like term and is usually hydrogen. | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle | |
| reaxff3_pen reaxff4_torsion |
| Type | Option |
| Format | reaxff3_pen <au/kcal/kjmol> |
| species1 <core/shell> species2 <core/shell> species3 <core/shell> p_pen1 <1 x flag> | |
| Default | None |
| Use | Specifies the parameter that determines the angular penalty energy that depends |
| on a triad of species in the ReaxFF force field (eqn 14a). Here species1 is the pivot | |
| atom of the three-body like term. | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle | |
| reaxff3_hbond reaxff3_conjugation reaxff4_torsion |
| Type | Option |
| Format | reaxff4_torsion <au/kcal/kjmol> |
| spec1 <core/shell> spec2 <core/shell> spec3 <core/shell> spec4 <core/shell> & | |
| V1 V2 V3 p_tor1 p_cot1 <5 x flags> | |
| Default | None |
| Use | Specifies the parameters that determine the torsional energy that depends |
| on a quartet of species in the ReaxFF force field (eqn 16a). Here the species | |
| are connected 1-2-3-4 to yield the relevant torsional angle. | |
| V1, V2, V3 are the barrier heights for different powers of the cosine of phi. | |
| p_tor1 is a scaling factor for an exponent in the V2 contribution. | |
| p_cot1 is a scaling factor for the conjugation energy (eqn 17a). | |
| See also | reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle |
| reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle | |
| reaxff3_pen reaxff4_torsion |
| Type | Option |
| Format | reaxff_chi |
| species <core/shell> chi <1 x flag> | |
| Default | None |
| Use | Specifies the electronegativity for the species in the ReaxFF charge equilibration |
| scheme. | |
| See also | reaxff_mu reaxff_gamma qiterative reaxff_qshell norxQ reaxff_q0 |
| Type | Option |
| Format | reaxff_gamma |
| species <core/shell> gamma <1 x flag> | |
| Default | None |
| Use | Specifies the shielding parameter gamma for the species in the ReaxFF charge equilibration |
| scheme. | |
| See also | reaxff_chi reaxff_mu qiterative reaxff_qshell norxQ reaxff_q0 |
| Type | Option |
| Format | reaxff_mu |
| species <core/shell> mu <1 x flag> | |
| Default | None |
| Use | Specifies the hardness for the species in the ReaxFF charge equilibration |
| scheme. | |
| See also | reaxff_chi reaxff_gamma qiterative reaxff_qshell norxQ reaxff_q0 |
| Type | Option |
| Format | reaxff_q0 |
| species <core/shell> q0 | |
| Default | 0.0 |
| Use | Specifies the equilibrium isolated species charge in the ReaxFF charge equilibration |
| scheme. | |
| See also | reaxff_chi reaxff_gamma qiterative reaxff_qshell norxQ reaxff_mu |
| Type | Option |
| Format | reaxff_qshell |
| species <core/shell> dMu Qs beta <3 x flags> | |
| Default | dMu = 0.0, Qs & beta no default |
| Use | Specifies the optional shell structure modifier for the ReaxFF charges. |
| This term adds an extra energy term to the electronegativity equalisation | |
| scheme that suppresses charges above a value Qs. This can often occur due | |
| to shell structure that breaks the validity of the harmonic charge expansion. | |
| The energy penalty takes the form of a fourth-order polynomial: | |
| E_shell(q) = dMu*(q - Qs)**4 for q > Qs ; 0 for q < Qs | |
| See also | reaxff_chi reaxff_mu qiterative reaxff_gamma |
| Type | Option |
| Format | reaxff_r12 |
| species <core/shell> r12 <1 x flag> | |
| Default | None |
| Use | Test modification option at present. |
| See also | reaxff_chi reaxff_mu qiterative reaxff_qshell reaxff_r12 |
| Type | Option |
| Format | reaxfftol bomin <anglemin> <angleprod> <hbondmin> <hbonddist> <torsionprod> |
| Use | This command sets a number of tolerances that control the behaviour of ReaxFF. |
| bomin - the general threshold for bond orders in pairwise terms | |
| anglemin - the threshold for bond orders in valence, penalty and 3-body conjugation | |
| angleprod - a threshold for the product of bond orders (1-2 x 2-3, where 2 = pivot) | |
| Hard coded in original program to 0.001, but this leads to discontinuities | |
| hbondmin - threshold for A-H bond order in a hydrogen bond. Hard coded to 0.01 in | |
| original code. | |
| hbonddist - threshold for A...B distance in A-H...B hydrogen bond. Hard coded to | |
| 7.5 Ang in original code. | |
| torsionprod- a threshold for the product of bond orders (1-2 x 2-3 x 3-4) for torsion | |
| interactions. | |
| See also | reaxffcutoff |
| Type | Option |
| Format | region_1 |
| atomic_symbol x y z <charge> <occupancy> <radius> <mol no> .... | |
| <mol_cell_index> <3*flags> for each ion | |
| Units | coordinates in Angstroms and charges in electrons |
| Use | Specifies an explicit region 1. Primarily used for restarts |
| from previous runs, but can be used to allow the user to generate | |
| complicated defects. | |
| See also | defect centre size regi_before bulk_noopt |
| Type | Option |
| Format | reldef |
| nreg1 x atom numbers | |
| Use | Used by the program to enable restarts when performing |
| defect calculations involving bond specifications. This | |
| command lists the perfect atom number that each defect | |
| atom started life as. A zero indicates an interstitial | |
| species. Normally this list should only need to be | |
| written by the program rather than the user. | |
| See also | defect deflist centre region restore save size |
| Type | Option |
| Format | reperfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> |
| atom1 atom2 A beta <rmin> rmax <3*flags> | |
| Units | A in eV and beta in Angs |
| Default | none |
| Use | Specifies the parameters of an reperfc potential, which has the form: |
| E_ij = A.erfc(r/beta)/r | |
| See also | qerfc erferfc erfpot |
| Type | Option |
| Format | resetvectors no_of_steps |
| Units | None |
| Default | 1 |
| Use | Specifies the frequency with which the interatomic vector table is |
| updated if using the storevectors keyword. | |
| See also | storevectors extracutoff |
| Type | Option |
| Format | rfractional replica_number |
| x1 y1 z1 <r1> | |
| x2 y2 z2 <r2> | |
| .. .. .. | |
| xN yN zN <rN> | |
| Units | Fractional |
| Default | None |
| Use | Specifies the fractional coordinates of a replica for the nudged |
| elastic band method. The number of coordinates must match the number | |
| of atoms in the initial structure. This option is primarily | |
| useful for restarting. If the coordinates of the replicas are | |
| not given then the values are initialised based on a linear | |
| interpolation between the initial and final states. The radii | |
| of the ions can be optionally given on the end of the line if | |
| a breathing shell model is being used. If not specified then | |
| they are assumed to be zero. | |
| See also | nebspring nebtolerance nodneb |
| nebreplica nebtangent nebrandom nebiterations rcartesian | |
| fcartesian ffractional rcell fcell neb fvectors |
| Type | Option |
| Format | rmax <n> |
| Units | Angstroms |
| Default | 5.0 |
| Use | Used within the pdf input block for PDF calculations. |
| Sets the maximum radius for atomic pairs to be generated. | |
| See also | PDFkeep PDFcut |
| Type | Option |
| Format | rspeed rspeed_value |
| Default | 1.0 |
| Use | Relative speed for reciprocal and real space terms to be calculated. |
| Formulae for determining optimum eta value assume rspeed=1.0. However, | |
| calculations can be speeded up by using larger values for small | |
| systems (e.g. 2.0) or small values for large systems (0.25) | |
| as reciprocal space calculation is generally faster. | |
| See also | noexclude qwolf ewaldrealradius accuracy veck index_k |
| Type | Option |
| Format | rtol scale_factor |
| Units | none |
| Default | 1.2 |
| Use | Bond length tolerance when deciding if two atoms are bonded. |
| Number multiplies the sum of the covalent radii. |
| Type | Option |
| Format | ryckaert (or torsion ryck) norder <type_of_bond> |
| atom1 atom2 atom3 atom4 k0 rmax(1-2) rmax(2-3) rmax(3-4) rmax(1-4) <flags*norder+1> | |
| norder*coefficients | |
| Units | k0 in eV, rmax in Angstroms, coefficients in eV |
| Default | none |
| Use | Torsional potential about atoms 2 and 3. Polynomial expansion in |
| cos(phi) up to fifth order maximum. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion outofplane torangle torharm torexp uff4 |
| Type | Option |
| Format | rydberg <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 A B r0 <rmin> rmax <3*flags> | |
| Units | A in eV, r0 in Angs |
| Use | Rydberg potential also found in the following article |
| Rose/Smith/Guinea/Ferrante potential (Phys. Rev. B, | |
| 29, 2963 (1984)) - used in modelling metals. | |
| E = -A.[1+B*((r/r0)-1)].exp(-B*((r/r0)-1)) | |
| Type | Option |
| Format | sample value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - if integer, then value is by default |
| a multiple of the timestep or if non-integer then by | |
| default is the time in picoseconds. | |
| Use | Controls how often the properties of the molecular |
| dynamics run are to be sampled and output to the | |
| standard output channel. Averaged properties are also | |
| based on these samples. | |
| See also | md timestep equilibration production temperature |
| tscale write nolist delay_force end_force |
| Type | Option |
| Format | sasexclude natom_min <natom_max> |
| Default | Include all particles as specified by sasparticles option |
| Use | Allows the user to specifically exclude a range of atoms |
| from being involved in determining the solvent accessible | |
| surface. | |
| e.g. | |
| sasexclude 10 | |
| would exclude atom 10 from contributing to the SAS, while | |
| sasexclude 10 20 | |
| would exclude atoms from 10 to 20 from the SAS. Note that | |
| the atom numbers are those in the full cell rather than | |
| the asymmetric unit. | |
| See also | sasparticles |
| Type | Option |
| Format | sasparticles <cores_only/both_cores_and_shells> |
| Default | cores_only |
| Use | In all calculations the cores define the position of the |
| solvent accessible surface. This option controls whether | |
| the potential is determined by the sum of the core and | |
| shell charges at the core position (cores_only) or by | |
| the explicit potential due to both the core and shell | |
| (both) | |
| See also | cosmo sasexclude |
| Type | Option |
| Format | sbulkenergy <bulk energy of surface region 1> |
| Units | eV |
| Use | Specifies the energy that the atoms of a surface region 1 would |
| have had in the bulk material. This value is determined when | |
| building the surface slab and is required to calculate the | |
| surface energy. | |
| As an example, consider a surface region 1 of formula Mg24O24 - | |
| here the value would be 24 times the value of the bulk MgO energy | |
| for the primitive cell as calculated by GULP. | |
| See also | sregion2 |
| Type | Option |
| Format | scale <real_number> |
| Units | none |
| Default | 1.0 |
| Use | Scales subsequent cell vectors and cartesian coordinates by the |
| scale factor. |
| Type | Option |
| Format | scan_cell d_a d_b d_c d_alpha d_beta d_gamma nstep (for 3-D) |
| scan_cell d_a d_b d_alpha nstep (for 2-D) | |
| scan_cell d_a nstep (for 1-D) | |
| scan_cell strain e1 e2 e3 e4 e5 e6 nstep (for 3-D) | |
| scan_cell strain e1 e2 e3 nstep (for 2-D) | |
| scan_cell strain e1 nstep (for 1-D) | |
| Units | Angstrom for d_a, d_b, d_c and degrees for d_alpha, d_beta, d_gamma |
| Use | Allows a scan over cell parameters to be performed. Here d_a, d_b |
| and d_c are the changes in cell lengths, while d_alpha, d_beta and | |
| d_gamma are the changes in cell angles. It is recommend that this | |
| option be only used for either constant volume calculations or that | |
| it is used in conjunction with the ocell keyword when the cell is | |
| being varied. The number of steps is given by nstep (each step | |
| will change cell parameter a by d_a/nstep, for example) | |
| Note that the translate and scan_cell options are mutually exclusive. | |
| NB A value for the change in cell parameters that causes the cell | |
| to go negative is not allowed. | |
| If strain is specified after the option then the input values will | |
| be taken as strains (e1-e6) rather than angles. Here zero means | |
| that no strain will be applied to that component. | |
| See also | cell vectors ocell translate strain |
| Type | Option |
| Format | scell <angs/au> |
| a b alpha <3 x optimisation flags> | |
| Units | Angstrom (default) or au for a, b and degrees for angle |
| Use | Surface unit cell. Either "svectors" or "scell" |
| must be given for a surface. For optimisations or fitting, | |
| flags must be set unless cellonly, conp or conv are specified. | |
| See also | svectors sfrac sregion2 |
| Type | Option |
| Format | scmaxsearch <value> |
| Units | None |
| Default | 2.0 |
| Use | For free energy minimisation, this parameter sets the maximum |
| search range for pairs of atoms interacting via the same many | |
| body term that gives a contribution to the third derivatives. | |
| The value is a multiple of the density cut-off value for the | |
| EAM model. In principle, the range can be up to 3 times the | |
| density pairwise cut-off. However, this makes free energy | |
| minimisation very expensive. In practice, a value of around | |
| 2 will give almosts identical results, depending on the system, | |
| with a dramatic increase in speed. However, if precise gradients | |
| are needed then a value of 3.0 should be used to check | |
| the influence. Negative values and values greater than 3.0 are | |
| disallowed as being stupid! | |
| See also | free zsisa manybody eam_functional eam_density lowest_mode |
| Type | Option |
| Format | sdlc <n> |
| i j dielectric constant se(i,j) <weight> | |
| Units | none |
| Default | no static dielectric constants to be fitted |
| Use | Subsection of observables, used for specifying experimental |
| static dielectric constants for fitting. | |
| Only give unique static dielectric constants. | |
| See also | elastic piezoelectric hfdlc weight srefractive hfrefractive |
| bornq young poisson shear voigt bulk omega |
| Type | Option |
| Format | seed q |
| Default | -1 |
| Use | Initial pointer used in random number generation wherever random numbers are used. |
| Input value is an integer. |
| Type | Option |
| Format | segmentsperatom <no. of segments per atom> <no. per H atom> |
| Default | 92 (dodecahedron) / 110 (octahedron) |
| Units | None |
| Use | Specifies the number of segments per atom for the |
| solvent-accessible surface in a COSMO calculation. | |
| The points per atom are grouped together to form | |
| the segments. Note it is possible to specify a | |
| different value for H. However, if this is omitted | |
| then it defaults to the same value as for other atoms. | |
| See also | cosmo pointsperatom solventepsilon solventradius |
| solventrmax vdw cosmoshape rangeforsmooth |
| Type | Option |
| Format | sfinite deltaC deltaS |
| Default | 0.00001 / 0.00001 |
| Units | Angstroms and none for deltaC and deltaS, respectively. |
| Use | Sets the finite difference intervals to be used for the numerical |
| evaluation of properties by central finite differencing of the | |
| analytic first derivatives. deltaC is used for the Cartesian | |
| displacements while deltaS controls the change in strain. | |
| See also | numerical pfinite |
| Type | Option |
| Format | sfractional <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> |
| at.sym. <species_type> x y z <charge> <occupancy> <radius> <3 x flags> <T/%> | |
| Units | Fractional for x and y, Angstroms for z and radius, and electrons |
| Default | For region 2, rigid is the default. |
| Use | Internal coordinates and charges for all species in the surface cell. |
| Either the atomic number or the symbol may be supplied, followed | |
| by the species type. If the species type is omitted then it is | |
| assumed to be a core. Individual charges may be supplied for each | |
| ion or the charges for each type of species given using the | |
| species option. If the charges are given, then optionally site | |
| occupancies may also be specified. Similarly, if the charge and | |
| occupancy are given, then the radius of a breathing shell may | |
| also be present. Optimisation flags are only needed if cellonly, | |
| conv, bulk, conp or shell are not specified. | |
| If the "region" sub-option is specified, then this tells the program | |
| the region number for the following atoms. In a surface calculation | |
| region 2 is held fixed. If the "rigid" sub-option is also specified | |
| after "region" then the region is created as a rigid body so that | |
| all atoms are constrained with respect to each other. By specifying | |
| a string after this containing x, y and/or z, the region may be | |
| allowed to move in particular directions. For example, in an interface | |
| calculation, a region could be specified that is allowed to only relax | |
| in the z direction by using: | |
| sfrac region 3 rigid z | |
| NB: The "region" sub-option must come before any of the other related | |
| sub-options. | |
| If a "T" is specified then the atom is marked for the translate option | |
| If a "%" is specified then the atom is part of a growth slice if it | |
| is in region 1 of a surface calculation. | |
| See also | scell sregion2 |
| Type | Option |
| Format | shear_modulus <weight> |
| Units | GPa |
| Default | shear modulus not to be fitted |
| Use | Subsection of observables, used for specifying the experimental |
| shear modulus for fitting. By default, the Reuss definition of | |
| the bulk modulus is used. However, the Voigt and Hill definitions | |
| can be used by specifying the appropriate keyword. | |
| See also | observables elastic sdlc hfdlc bulk_modulus srefractive |
| hfrefractive weight bornq hill voigt young poisson |
| Type | Option |
| Format | shellmass |
| species_symbol ratio | |
| Default | ratio = 0.0 |
| Use | Specifies that shells will get assigned masses in shell model |
| molecular dynamics. If shells have a mass their equations of motion | |
| are integrated as for a core. "ratio" is the fraction of the total | |
| mass of an ion which will be assigned to the shell. It has to be | |
| selected so that the shell motions are significantly faster than | |
| the motions of the cores. GULP calculates "wave numbers" for the | |
| core/shell relative motion if this option is specified to assist | |
| in the selection of a suitable ratio. Note that the finite mass | |
| algorithm is not compatible with breathing shells - the iterations | |
| option should be used instead in this case. | |
| The shellmass ratio should be specified for each species, unlike | |
| previous versions. | |
| e.g. | |
| shellmass | |
| Al 0.25 | |
| O 0.12 | |
| See also | iterations md |
| Type | Option |
| Format | shift energy_shift <ev/au/kcal/kjmol-1> |
| Units | eV (default), au, kcal or kJmol-1 |
| Default | 0.0 eV |
| Use | Shifts energy by this amount - mainly for use in fitting |
| ab initio energy surfaces. Shift is applied to all subsequent | |
| configurations until the value of shift is changed by another | |
| shift directive. Shift can also appear in the variables section | |
| as a command to cause the shift to be fitted. | |
| See also | sshift ashift |
| Type | Option |
| Format | shrink ix <iy> <iz> |
| Units | ix, iy and iz are dimensionless integers |
| Default | 1 1 1 |
| Use | Specifies the shrinking factors in reciprocal space. The higher the |
| shrinking factor the more extensively k space is sampled. One value | |
| may be given, in which case the shrinking factor is used isotropically | |
| or three anisotropic values can be given. | |
| In theory an isotropic shrinking factor n will generate n**3 k points. | |
| However, GULP by default uses some of the symmetry of the Patterson | |
| group to reduce this number. This can be turned off using "noksym". | |
| Remember that if anisotropic values are given that do not conform | |
| to the symmetry of the unit cell then the symmetry adapted sampling | |
| will give slightly different results to the P -1 sampling - beware! | |
| N.B. If phonon properties are required the user must make sure that | |
| convergence has been achieved with respect to the number of k points. | |
| See also | phonon dispersion kpoints noksym msd |
| Type | Option |
| Format | siginc atomic_nnumber <siginc> |
| Units | Angstrom2 (=108 Barns) |
| Use | Used within element option input block, overwrites the default bound |
| incoherent neutron scattering cross-section (siginc) for a specified element. | |
| (at. no. or symbol may be used) | |
| See also | coreinfo element bbar |
| Type | Option |
| Format | size radius_region_1 <radius_region_2a> <old_radius_region_1> |
| Units | Angstroms |
| Default | none |
| Use | Specifies the region 1 and 2a radii for use in defect calculations. |
| If no value is specified for region 2 then it is set equal to the | |
| region 1 radius. When restarting from a dumpfile containing | |
| an explicit region 1 specification, but with a larger region 1 | |
| radius, then the old region 1 radius from the previous run must | |
| also be given to ensure a correct restart. | |
| See also | defect centre region_1 vacancy interstitial impurity |
| bulk_noopt |
| Type | Option |
| Format | slater <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> |
| atom1 atom2 A B <rmin> rmax <2*flags> | |
| Units | A in eV, B in Angs**-1 |
| If kcal is given : A in kcal, B in Angs**-1 | |
| If kjmol is given: A in kJmol-1, B in Angs**-1 | |
| Default | none |
| Use | Specifies a Slater two-body potential that arises from the overlap of |
| two spherical atomic densities that decay exponentially. | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = A.[((B*r)**2/3) + B*r + 1]*exp(-B*r) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| The words energy or gradient may be | |
| given on the first line resulting in energy or gradient offsets being | |
| applied such that the specified quantity goes to zero at the cutoff | |
| distance. | |
| See also | c6 mm3buck buckingham |
| Type | Option |
| Format | slower <value> |
| Units | None |
| Default | 0.001 |
| Use | This is the scale factor by which the eigenvectors will be |
| multiplied when attempting to lower the symmetry along an | |
| imaginary mode direction. | |
| See also | lower_symmetry |
| Type | Option |
| Format | smelectronegativity |
| <Atomic_symbol/atomic_number> chi mu zeta Znuc <Q0> <E0> <4 x flags> | |
| or | |
| smelectronegativity <qrange/qmin/qmax> | |
| <Atomic_symbol/atomic_number> chi mu zeta Znuc <Q0> <E0> <qmin> <qmax> <4 x flags> | |
| Units | Chi, mu, and E0 in eV, Znuc in a.u., zeta in Angstroms**-1, Q0, qmin, qmax in a.u. |
| Default | Q0 = 0.0, E0 = 0.0 |
| Use | Allows the user to specify the parameters needed for the |
| Streitz and Mintmire electronegativity equalisation method | |
| for determining charges. Note that if the flags are not | |
| specified they are assumed to be zero. | |
| Q0 is the charge about which the electronegativity equations | |
| are quadratic. In most methods this is zero, but need not be. | |
| For example, the EQeq method assigns values of Q0 not equal | |
| to zero. | |
| E0 is an additive constant for the energy of an atom. This is | |
| only really needed when using multiple q ranges to ensure | |
| energy matching. | |
| The sub-options qrange, qmin, and qmax control whether the | |
| values apply for a given value of charge. By default the values | |
| apply to all values of charge (q). If qmin is specified then | |
| they are only applied to charges larger than qmin, while if qmax | |
| is given the they are applied when q is less than qmax. When | |
| qrange is specified then the values apply for qmin =< q < qmax. | |
| NB: If no parameters are input then the default values will be | |
| used for all charge values. However, if parameters are input | |
| then this will override the default values and the user must | |
| set parameters for all relevant ranges of charge. | |
| See also | sm eem electronegativity qeq qelectronegativity noqeem external_potential |
| eembond |
| Type | Option |
| Format | solventepsilon <dielectric constant OR solvent_name> |
| Default | 1.0 |
| Units | None |
| Use | Specifies the dielectric constant of the solvent to |
| be used in a COSMO solvation energy calculation. Note | |
| that values must be greater than 1.0! | |
| The values of the dielectric constant for use in | |
| COSMO are known for the following solvents : | |
| solvent_name dielectric_constant | |
| ------------ ------------------- | |
| water 78.400 | |
| acetone 20.700 | |
| benzene 2.274 | |
| chlorobenzene 5.621 | |
| chloroform 4.806 | |
| cyclohexane 2.015 | |
| ethylether 4.335 | |
| methanol 32.630 | |
| tetrachloromethane 2.228 | |
| conductor 1000.000 | |
| See also | cosmo pointsperatom segmentsperatom solventradius |
| solventrmax vdw |
| Type | Option |
| Format | solventradius <Rsolv> <deltaRsolv> |
| Defaults | 1.0 / 0.1 Angstroms |
| Units | Angstroms |
| Use | Specifies the radius of the solvent molecule, Rsolv, |
| and the distance of the screening centre from the | |
| molecular centre, deltaRsolv, for use in a COSMO | |
| screening calculation. Note that these two values | |
| are the parameters for each solvent that must be | |
| determined in order to obtain accurate solvation | |
| energies. | |
| See also | cosmo pointsperatom segmentsperatom solventepsilon |
| solventrmax vdw |
| Type | Option |
| Format | solventrmax <maximum distance> <smoothing range> |
| Defaults | 10.0 / 1.0 Angstroms |
| Units | Angstroms |
| Use | Maximum distance parameter used by COSMO solvation |
| model. Below this value, elements of the A matrix | |
| are evaluated at the level of sub-points, while | |
| beyond this they are evaluated between segments, | |
| which is more approximate. The smoothing range | |
| is used to taper the two sides of the cut-off | |
| together continuously to avoid problems during | |
| optimisation. | |
| See also | cosmo pointsperatom segmentsperatom solventepsilon |
| solventradius vdw |
| Type | Option |
| Format | space group no. or Hermann-Maugain symbol |
| Note: symbol must be in capital letters with spaces between them | |
| e.g. for MgO => 225 or F M -3 M | |
| Units | none |
| Default | no symmetry => P1 |
| Use | Specifies symmetry information by space group. Either the standard |
| symbol may be used or the extended symbol for specifying alternative | |
| settings. When giving extended symbols only the first line in | |
| International Tables should be given i.e. the 4th operator/qualifier | |
| after the centring symbol should be omitted. For example, in order | |
| specify the non-standard P 21/A setting of P 21/C the input should be: | |
| space | |
| P 1 21/A 1 | |
| See also | origin valid_spacegroups symmetry_operator |
| Type | Option |
| Format | atomic_symbol <core/shell> charge <radius> <library symbol> |
| Default | charge and radius both equal to zero |
| Use | Specify charges and radius by species and type, rather than for each |
| ion separately. The library symbol is a symbolic name to be assigned | |
| to this species for referencing libraries of interatomic potentials, | |
| otherwise the atomic symbol will try to be used. See library for | |
| more details. | |
| NB: The species command will overwrite the charges of ions that | |
| are specified individually on the coordinate input line unless the | |
| preserve_Q keyword is specified. | |
| See also | library preserve_Q |
| Type | Option |
| Format | spline <cubic> <reverse> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <type_of_bond> |
| atom1 atom2 <shift> <rmin> rmax <1*flag> | |
| energy_1 distance_1 | |
| energy_2 distance_2 | |
| : : | |
| energy_n distance_n | |
| Units | Energies in eV, distances in Angs |
| Default | rational function spline, shift = 0.0 |
| Use | Spline potential - flag for fitting (0/1) of shift. |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| If the option "reverse" is specified then the spline information | |
| will be read as distance then energy, ie the reverse order to | |
| normal. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded, potential cutoffs are omitted from input. | |
| Type | Option |
| Format | split <number of species to be varied> |
| list of cores whose charges are to be varied | |
| Units | none |
| Default | charges fixed |
| Use | Allows split of core-shell to be varied during fitting while |
| maintaining the initial total charge. | |
| This directive must be part of the variables section. | |
| NB: DO NOT specify charges on the coordinate line for the atoms | |
| that you wish to be influenced by this option since they will be | |
| held fixed as they are NOT overwritten by the species option. |
| Type | Option |
| Format | spring <kcal/kjmol> |
| atom1 k2 <k4> <flags> | |
| Eqn | E = (1/2)*k2*r**2 + (1/24)*k4*r**4 |
| Units | k2 in eV/Angs*2, k4 in eV/Angs**4 |
| Default | k4 = 0.0 |
| Use | Core-shell spring potential - optimisation flags for fitting. |
| Spring potential does not need cutoffs as the maximum is set by cuts | |
| and the minimum is zero. | |
| Only atom1 needs to be specified as this potential is specifically | |
| for core shell pairs. Atom1 can be given either by atomic number | |
| or symbol which in the latter case can be followed by a species | |
| type. If no species type is given then type is assumed to be core. | |
| See also | cosh-spring |
| Type | Option |
| Format | sqomega filename.sqw <weight> |
| Units | Arbitrary |
| Default | No S(Q,omega) data to be fitted |
| Use | This option enables fitting of S(Q,omega) data. The S(Q,omega) |
| data is read from a .sqw file specified on this line. | |
| The parameters that control the grid for S(Q,omega) are | |
| specified by the commands for scattering and must match those | |
| present in the .sqw file. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive piezo |
| bornq monopoleq qreaxff fbond fangle relax reaction |
| Type | Option |
| Format | squaredharmonic <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <grad> <scale14> <type_of_bond> |
| atom1 atom2 k2 r0 <coul> <rmin> rmax <2*flags> | |
| Units | k2 in eV*Angs**-4, r0 in Angs, coul in none |
| Use | GROMOS bonded potential - optimisation flags for fitting. |
| coul = 1.0 => Coulomb subtracted | |
| atom1 and atom2 may be specified either by atomic number or symbol | |
| which in the latter case can be followed by a species type. If | |
| no species type is given then type is assumed to be core. | |
| E = 1/4 K2*(r**2 - r0**2)**2 - coul*qi*qj/r | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| When specified as bonded potential, cutoffs are omitted from input. | |
| See also | spring harmonic |
| Type | Option within "observables" |
| Format | i static_refractive_index(i) <weight> |
| Units | None |
| Default | No static refractive indices to be fitted |
| Use | Specifies exptl static refractive indices for fitting |
| along principal axes. | |
| See also | elastic piezoelectric sdlc hfdlc hfrefractive weight |
| Type | Option |
| Format | sregion2 atom_number |
| Units | none |
| Use | Specifies the first atom in the slab that is in region 2. Region 2 |
| is the region that contains the fixed atoms that represent the | |
| bulk in a surface calculation. Atoms in region 2 will automatically | |
| be fixed during geometry optimisation and the self-energy of the | |
| region will be excluded from the surface energy of the slab - i.e. | |
| the surface energy calculated will be for one side, that of region 1. | |
| See also | sfrac scell sbulkenergy |
| Type | Option |
| Format | srglue <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 d rmin rmax | |
| a14 a13 a12 a11 a10 | |
| a26 a25 a24 a23 a22 a21 a20 | |
| Units | eV and Angstroms |
| Default | none |
| Use | Input for the Short-Range part of the Glue model: |
| if r < d: | |
| E = a14*(r-d)**4 + a13*(r-d)**3 + a12*(r-d)**2 + a11*(r-d) + a10 | |
| if d < r =< rmax: | |
| E = a26*(r-d)**6 + a25*(r-d)**5 + a24*(r-d)**4 + a23*(r-d)**3 + | |
| a22*(r-d)**2 + a21*(r-d) + a20 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then potential will only act between bonded | |
| atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3 | |
| interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions) | |
| See also | eam_functional eam_density |
| Type | Option |
| Format | sshift scale_factor |
| Units | none |
| Default | 1.0 |
| Use | Scales the shift value for the present configuration. Allows |
| energies of structures with different numbers of formula units | |
| to be fitted. | |
| See also | shift |
| Type | Option |
| Use | Causes program to skip the rest of the input file and begin execution. |
| Type | Option |
| Format | sdlc <n> |
| i j dielectric constant se(i,j) <weight> | |
| Units | none |
| Default | no static dielectric constants to be fitted |
| Use | Subsection of observables, used for specifying experimental |
| static dielectric constants for fitting. | |
| Only give unique static dielectric constants. | |
| See also | elastic piezoelectric hfdlc weight srefractive hfrefractive |
| Type | Option |
| Format | stepmx <opt/fit/rfo> <real value> |
| Units | fractional |
| Default | 1.0 for opt / 1000.0 for fit / 100.0 for rfo |
| Use | Maximum step size in optimisation/fitting/rfo. |
| Value may appear on same line as option or on the following line. | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | maxcyc optimise fit rfo switch_stepmx |
| Type | Option |
| Use | Causes program to stop execution at that point in the input file. Use |
| is mainly for locating problems in input files. |
| Type | Option |
| Format | strain_derivative |
| strain_no strain_derivative_value <weight> | |
| Units | GPa |
| Default | all fitted strain derivatives are zero |
| Use | Subsection of observables, used for specifying the strain derivative |
| components for fitting to. Here the strain_no is as follows: | |
| 1 => xx 2 => yy 3 => zz 4 => yz 5 => xz 6 => xy | |
| Note that strains are dependent on the cell orientation | |
| and so take care when specifying. | |
| See also | observables gradients stress |
| Type | Option |
| Format | stress |
| stress_no stress_value <weight> | |
| Units | GPa |
| Default | all fitted stresses are zero |
| Use | Subsection of observables, used for specifying the stress |
| components for fitting to. Here the stress_no is as follows: | |
| 1 => xx 2 => yy 3 => zz 4 => yz 5 => xz 6 => xy | |
| Note that stresses are dependent on the cell orientation | |
| and so take care when specifying. | |
| See also | observables gradients strain_derivative |
| Type | Option |
| Format | supercell (ncells in x) (ncells in y) (ncells in z) |
| Default | 1 1 1 (i.e. no supercell) |
| Use | Expands the input unit cell by the three factors given to create a |
| supercell. This implies that symmetry is removed from the structure | |
| at the moment. | |
| See also | ghost_supercell |
| Type | Option |
| Format | svectors <angs/au> |
| x y for vector 1 | |
| x y for vector 2 | |
| <2 x optimisation flags> | |
| Units | Angstrom (default) or au |
| Use | Specifies the cartesian components of the surface vectors. |
| Either "svectors" or "scell" must be included for a surface. | |
| Strain optimsation flags appear on last line. | |
| See also | scell |
| Type | Option |
| Format | sw2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
| atom1 atom2 A rho B rmin rmax <3*flags> | |
| Units | A in eV, B in Angs**4, rho in Angs |
| Use | Stillinger-Weber's two-body potential with cutoff smoothing |
| such that potential goes to zero at rmax: | |
| E = A.exp(rho/(r-rmax)).(B/r**4 - 1) | |
| See also | sw3 sw2jb sw3jb |
| Type | Option |
| Format | sw2jb <intra/inter> <bond/x12/x13/x14/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 A rho B Q <rmin> rmax <4*flags> | |
| Units | A in eV, B in Angs**4, rho in Angs, Q in a.u. |
| Use | Jiang and Brown's variant of Stillinger-Weber's two-body potential |
| which includes charge dependent bond softening | |
| E = A.exp(rho/(r-rmax)).(B/r**4 - 1)*F(qi,qj) | |
| F(qi,qj) = exp(1/Q)exp(1/(qi + qj - Q)) if qi+qj < Q | |
| F(qi,qj) = 0 if qi+qj > Q | |
| See Chem. Eng. Sci., 49, 2991 (1994) for more details. | |
| See also | sw3 sw2 sw3jb |
| Type | Option |
| Format | sw3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> | |
| rmax23 <4*flags> | |
| or | |
| sw3 modified <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> | |
| atom1 atom2 atom3 K theta0 rho1 rho2 C <rmin12> rmax12 <rmin13> rmax13 <rmin23> | |
| rmax23 <5*flags> | |
| or | |
| sw3 garofalini <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> | |
| atom1 atom2 atom3 K theta0 rho1 rho2 C <rmin12> rmax12 <rmin13> rmax13 <rmin23> | |
| rmax23 <5*flags> | |
| Units | K in eV, theta in degrees, rho1 and rho2 in Angstroms |
| Use | Stillinger-Weber's three-body potential with cutoff smoothing |
| E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*(cos-ct0)**2 | |
| where cos = cos(theta(jik)) and ct0 = cos(theta0) | |
| If "modified" is specified then the functional form given in J. Appl. Phys. | |
| 101, 103515 (2007) is given: | |
| E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*(cos-ct0)**2/(1 + C*(cos-ct0)**2) | |
| If "garofalini" is specified then the functional form given in J. Phys. Chem. | |
| 100, 2201 (1996) is given: | |
| E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*[(cos-ct0)*sin*cos]**2 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. Note that unlike most potentials, the specification of the | |
| cut-off distances is still required when using the "bond" sub-option | |
| since the values act as parameters to the model. | |
| See also | three-body angle exponential axilrod-teller bcross sw2 sw2jb urey-bradley |
| murrell-mottram bcoscross bacross hydrogen-bond equatorial sw3jb uff3 | |
| lin3 3coulomb bagcross |
| Type | Option |
| Format | sw3jb <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K theta0 rho1 rho2 Q <rmin12> rmax12 <rmin13> rmax13 <rmin23> | |
| rmax23 <5*flags> | |
| Units | K in eV, theta in degrees, rho1 and rho2 in Angstroms, Q in a.u. |
| Use | Jiang and Brown's variant of Stillinger-Weber's three-body potential with |
| charge-dependent softening | |
| E(three) = K*F12*F13*exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))(cos-ct0)**2 | |
| where cos = cos(theta(jik)) and ct0 = cos(theta0) | |
| F12(q1,q2) = exp(1/Q)exp(1/(q1 + q2 - Q)) if q1+q2 < Q | |
| F12(q1,q2) = 0 if q1+q2 > Q | |
| F13(q1,q3) = exp(1/Q)exp(1/(q1 + q3 - Q)) if q1+q3 < Q | |
| F13(q1,q3) = 0 if q1+q3 > Q | |
| See Chem. Eng. Sci., 49, 2991 (1994) for more details. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. Note that unlike most potentials, the specification of the | |
| cut-off distances is still required when using the "bond" sub-option | |
| since the values act as parameters to the model. | |
| See also | three-body angle exponential axilrod-teller bcross sw2 sw2jb urey-bradley |
| murrell-mottram bcoscross bacross hydrogen-bond equatorial sw3 lin3 | |
| uff3 bagcross |
| Type | Option |
| Format | switch_minimiser <minimiser> <cycle/gnorm/lower> <criterion> |
| Use | This option allows the minimiser to be changed part |
| way through an optimisation when the given criterion | |
| is satisfied. The criterion can be either the number | |
| of cycles of optimisation or when the gradient norm | |
| drops below a certain value. This option is particularly | |
| useful for cases where the RFO minimiser is needed to | |
| accelerate the end game convergence. However it is | |
| inefficient and unstable a long way from the minimum. | |
| Valid minimisers are: | |
| bfgs (default) | |
| rfo (rational function optimisation) | |
| unit (bfgs, but starting from a unit Hessian) | |
| nume (bfgs, but starting from numerical diagonal Hessian) | |
| conj (conjugate gradients) | |
| Examples: | |
| switch rfo cycle 10 | |
| => Change to rfo method after 10 cycles of optimisation. | |
| Note that the order of words after switch is irrelevant | |
| and additional words can be inserted to make the line more | |
| readable. For example this line could be written as: | |
| switch to rfo method after 10 cycles of optimisation | |
| switch conj gnorm 0.123 | |
| => Change to conjugate gradient method when Gnorm is less | |
| than 0.123. Note that if cycle and gnorm are omitted then | |
| GULP assumes gnorm as a default. | |
| switch rfo lower | |
| => Change to rfo method if restarting optimisation after | |
| the lower option has been applied. | |
| See also | optimise rfo unit conj optlower switch_stepmx |
| Type | Option |
| Format | switch_stepmx new_step_max <cycle/gnorm> <criterion> |
| Use | This option allows the minimiser to change the maximum |
| step size to a value new_step_max from the current one | |
| when a given criterion is met. | |
| Examples: | |
| switch_stepmx 0.1 cycle 10 | |
| => Change to a maximum step size of 0.1 after 10 cycles | |
| of optimisation. | |
| switch 0.1 gnorm 0.123 | |
| => Change to maximum step size of 0.1 when Gnorm is less | |
| than 0.123. Note that if cycle and gnorm are omitted then | |
| GULP assumes gnorm as a default. | |
| See also | stepmx switch_minimiser |
| Type | Option |
| Format | symbol at.no. <symbol(a2)> |
| Default | as per periodic table |
| Use | Allows atomic symbols to be changed. |
| Command is part of element section. | |
| See also | element |
| Type | Option |
| Format | symmetry_cell <cell_type> |
| Default | Triclinic |
| Use | When specifying the symmetry manually, this allows the user to set the |
| cell type. Allowed values are triclinic, monoclinic, orthorhombic, | |
| tetragonal, hexagonal, rhombohedral and cubic. | |
| See also | symmetry_operator |
| Type | Option |
| Format | symmetry_number value |
| Default | 1 |
| Use | This option allows the user to specify the symmetry number for use |
| in calculating the rotational partition function. | |
| See also | property temperature pressure |
| Type | Option |
| Format | symmetry_operator |
| r(1,1) r(1,2) r(1,3) t(1) | |
| r(2,1) r(2,2) r(2,3) t(2) | |
| r(3,1) r(3,2) r(3,3) t(3) | |
| Units | None / Fractional |
| Use | Specifies the symmetry operators for a 3-D system manually. The |
| matrix r specifies the rotational matrix and the vector t specifies | |
| the translational component of the roto-translational operator. Note | |
| that the identity operator is always present and should not be given | |
| again. If specified, this option causes any spacegroup specified to | |
| be ignored. | |
| See also | spacegroup origin symmetry_cell |
| Type | Option |
| Format | synciterations <maximum_number> |
| Default | 1000 |
| Use | Specifies the maximum number of iterations for minimization |
| of the force norm during each step of a syncrhonous transit run. | |
| See also | neb syncsteps synctolerance |
| nebreplica fcartesian ffractional fcell fvectors |
| Type | Option |
| Format | syncsteps <maximum_number> |
| Default | 1000 |
| Use | Specifies the maximum number of steps during a syncrhonous |
| transit run. Each consists of a move of one image towards the other | |
| followed by minimisation of that image while the force remains | |
| orthogonal to the vector between the images. | |
| See also | neb syncsteps synctolerance |
| nebreplica fcartesian ffractional fcell fvectors |
| Type | Option |
| Format | synctolerance <tolerance_value> |
| Default | 0.0001 |
| Use | Specifies the convergence criteria for a synchronous transit |
| run in terms of the residual force norm. | |
| See also | neb syncsteps synciterations |
| nebreplica fcartesian ffractional fcell |
| Type | Option |
| Format | tau_barostat tau <s/ns/ps/fs> |
| Units | s, ns, ps or fs; default is ps |
| Default | 1 ps |
| Use | Specifies the relaxation time for the barostat if the integrator is |
| set to type "stochastic". | |
| See also | integrator md tau_thermostat |
| Type | Option |
| Format | tau_thermostat tau <s/ns/ps/fs> |
| Units | s, ns, ps or fs; default is ps |
| Default | 1 ps |
| Use | Specifies the relaxation time for the thermostat if the integrator is |
| set to type "stochastic". | |
| See also | integrator md tau_barostat |
| Type | Option |
| Format | td_external_force |
| atomnumber direction forceA forceB forceC | |
| Units | forceA in eV/Angstrom, forceB in 1/ps, & forceC in fraction |
| of 2*pi | |
| Default | No time dependent force |
| Use | Specifies that a time-dependent force is applied to selected |
| atoms during a molecular dynamics simulation. This force can | |
| be specified separately for each Cartesian direction and takes | |
| the form of; | |
| F = forceA*cos[2*pi*(t*forceB + forceC)] | |
| where t is the time within the simulation. | |
| Example 1: | |
| 1 z 3.5 0.5 0.5 | |
| 3 z 3.5 0.5 0.0 | |
| Example 2: | |
| 1 z -3.5 0.5 0.0 | |
| 3 z 3.5 0.5 0.0 | |
| Note: both of the other examples would cause the atoms to | |
| oscillate exactly out of phase with each other and are | |
| equivalent. The maximum force experienced would be +/- | |
| 3.5 eV/Angstrom | |
| See also | external_force |
| Type | Option |
| Format | td_field magnitude <direction> B C |
| Units | magnitude in eV/(Ang.a.u.), B in 1/ps, & C in fraction of 2*pi |
| Default | No time dependent force |
| Use | Specifies that a time-dependent field is applied to the system. |
| For details of how to specify the field direction see the time-independent | |
| field option. The time-dependence is then given by: | |
| F = magnitude*cos[2*pi*(t*B + C)] | |
| where t is the time within the simulation. | |
| Multiple time-dependent fields can be applied to each configuration. | |
| NB: This option only influences MD simulations. | |
| See also | field delay_field end_field dipole delta_dipole initial_coordinates |
| Type | Option |
| Format | temperature value_of_temperature <C/F/K> <step> <no. of steps> <step0> |
| Units | Kelvin (or Centigrade if C added, or Fahrenheit if F added) |
| Default | 0 K, no steps (for phonons) 100 K for simulated annealing. |
| Use | Specifies temperature of a structure for use in the calculation of |
| phonon properties, such as the entropy, free energy and heat capacity. | |
| Also specifies the temperature for molecular dynamics and Monte Carlo | |
| runs, including annealing. | |
| Temperature can optionally be followed by an increment, a number of steps, | |
| (and a first step for MD). | |
| Phonons | |
| If a range is given, then the phonon properties will be calculated at each | |
| temperature value over the range. Note that if present during a free energy | |
| calculation this will result in the last temperature being used for the | |
| run. For CPU time reasons a range should not be used during a free energy | |
| minimisation. | |
| Molecular dynamics / Monte Carlo | |
| Here the option is used to set the temperature of the run or the schedule | |
| of temperatures for an anneal. For example, if the initial temperature is | |
| to be 298 K for the first 300 steps and then is to increase to 398 K over | |
| a 1000 steps, the input would look like: | |
| temperature 298 0.1 1000 300 | |
| See also | phonon free predict anneal ftol factor ttol |
| Type | Option |
| Format | terse <in/out/inout> <cell/coordinates/structure/potentials/derivatives> |
| Default | All appropriate quantities are output in full. |
| Use | Offers the user the option of making the output more terse - i.e. to not |
| print out so much. The first word should control whether the sub-options | |
| refer to the input information, the output information or both, while the | |
| second refers to the quantity not to be printed: | |
| cell => don't output the unit cell parameters for vectors | |
| coordinates => don't output the coordinates of the atoms | |
| structure => don't output the structure (i.e. cell & coordinates) | |
| potentials => don't output the interatomic potentials | |
| derivatives => don't output the final derivatives | |
| Type | Option |
| Format | tether n1-n2 or n1,n2, ... or any combination of both |
| Use | Specifies atoms to keep fixed during a molecular dynamics calculation. |
| These atoms create forces on other atoms, but do not move themselves. | |
| n1, n2 ... is the number of the atom in the input file, e. g. if | |
| atoms 2, 3, 4, and 7 shall be kept fixed tether 2-4,7 will do that. | |
| NB: The line continuation character should not be used with the tether | |
| option. Instead multiple tether lines can be used. | |
| e.g. | |
| tether 1-3, 121- 123, 127 - 129 | |
| tether 143 - 146, 150, 152, 181 - 183, 10, 11, 12 | |
| See also | md |
| Type | Option |
| Format | three <exponential/vessal/cosine> <k3> <k4> <nbeq/nbne nbond> <intra/inter> <bond/mol> <kcal/kjmol/degree> |
| atom1 atom2 atom3 k <k3> <k4> theta0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) & | |
| <rmin(2-3)> rmax(2-3) <2-4 flags> | |
| Units | k in eVrad**-2, k3 in eVrad**-3, k4 in eVrad**-4 (for standard) |
| k in eVrad**-2 (for exponential/vessal) | |
| k, k3 and k4 in eV (for cosine) | |
| theta0 in degrees, rmin & rmax in Angs | |
| Default | none |
| Use | Three-body potentials about atom1. k is force constant and theta0 |
| the equilibrium angle. Optional flags are for fitting. Atom 1 is | |
| the middle atom of the triad about which the force acts. | |
| E(three) = 1/2 * k * (theta-theta0)**2 | |
| Exponentially decaying form is also available: | |
| E(three) = 1/2 * k * (theta-theta0)**2.exp(-r12/rho1).exp(-r13/rho2) | |
| Format: | |
| three exponential | |
| atom1 atom2 atom3 k theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags> | |
| Exponentially decaying form is also available in Vessal form: | |
| E(three) = 1/4*A*(B**2).exp(-r12/rho1).exp(-r13/rho2) | |
| A = k/(2*(theta0-pi)**2) | |
| B = (theta0-pi)**2 - (theta-pi)**2 | |
| Format: | |
| three vessal | |
| atom1 atom2 atom3 k theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags> | |
| k3 and k4 terms can also be included: | |
| E(three) = 1/2*k*(theta-theta0)**2 + 1/6*k3*(theta-theta0)**3 | |
| + 1/24*k4*(theta-theta0)**4 | |
| Formats: | |
| three k3 | |
| atom1 atom2 atom3 k k3 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <3xflags> | |
| three k4 | |
| atom1 atom2 atom3 k k4 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <3xflags> | |
| three k3 k4 | |
| atom1 atom2 atom3 k k3 k4 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags> | |
| NB: k3 and k4 terms can only be specified with the standard threebody or cosine forms | |
| Cosine of theta can also be used instead of theta, if the cosine | |
| option is used : | |
| E(three) = 1/2*k*(cos(theta)-cos(theta0))**2 | |
| k3 and k4 terms can also be included for the cosine form: | |
| E(three) = 1/2*k*(cos(theta)-cos(theta0))**2 + 1/6*k3*(cos(theta)-cos(theta0))**3 | |
| + 1/24*k4*(cos(theta)-cos(theta0))**4 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2 and 1-3 are bonded. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| The order of the bond type options matches the order of the pivot atom | |
| - end atom pairs. For example, if a potential acts for the triad | |
| S - C - O, where the C-S bond is a regular bond and the C-O is an | |
| exocyclic double bond then the input would look like: | |
| three bond single regular double exocyclic | |
| C core S core O core ...... etc | |
| Conditions can also be placed on a potential to check the number of bonds | |
| associated with the pivot atom (e.g. if a potential is designed for a 90 | |
| degree angle it might be necessary to check that the number of bonds is | |
| four or six for square planar or octahedral). The conditions are placed | |
| using one or more instances of "nbeq" or "nbne" followed by an integer. | |
| Here "nbeq" imples no. of bonds must equal and "nbne" number of bonds must | |
| not equal. Hence, "nbeq 4" would require the pivot to have 4 bonds. When | |
| multiple terms are used, the logic of nbeq is concatenated with "or", whereas | |
| that of nbne is joined by "and". Therefore "nbne 4 nbne 6" would apply to | |
| an atom with 3 bonds, but not one with 4 or 6. | |
| NB It's important to specify the first bond as being of "regular" type so | |
| that the "exocyclic" attribute is correctly assigned to the second bond | |
| since the first term is assumed to apply to the first bond, whereas the | |
| second applies to the second bond. | |
| See also | axilrod-teller angle stillinger-weber exponential bcross uff3 |
| urey-bradley murrell-mottram bacross lin3 hydrogen-bond equatorial | |
| 3coulomb exp2 bagcross mm3angle |
| Type | Option |
| Format | threshold min_fc3_ij min_fc3 |
| Default | 0.0000001 / 0.00001 |
| Units | eV/Angs**3 |
| Use | Sets thresholds for the smallest values of third order force constants that |
| are considered non-zero. Because third order force constants can contain | |
| numerical error, especially when using finite differences, many of the | |
| resulting force constants contain noise. This allows some of this to be | |
| removed. There are two threshold values: | |
| min_fc3_ij: If an individual force constant is below this value then it is set | |
| to zero. | |
| min_fc3 : If all force constants within a block are below this value then the | |
| : whole block is set to zero. | |
| See also | num3 output |
| Type | Option |
| Format | time time_limit <seconds/minutes/hours> |
| Units | seconds (default), minutes or hours |
| Default | Infinity! |
| Use | Specifies time limit for calculation. |
| Type | Option |
| Format | timestep value <s/ns/ps/fs> |
| Units | s, ns, ps or fs; default is ps |
| Use | Specifies the timestep for integration in a molecular |
| dynamics simulation. A value must be supplied for an | |
| MD run. | |
| See also | md equilibration production sample write nolist |
| tscale temperature delay_force end_force momentum_correct |
| Type | Option |
| Format | a72 |
| Default | none |
| Use | Adds title lines to output |
| This option can now handle multiple title lines and they can be | |
| input via either of the two following formats: | |
| title N (where N=no of title lines) | |
| <line 1> | |
| <line 2> | |
| : : | |
| <line N> | |
| OR | |
| title | |
| <line 1> | |
| <line 2> | |
| : : | |
| <line N> | |
| end | |
| Type | Option |
| Format | torangle <intra/bond/improper> <kcal/kjmol> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 K theta0 theta0' rmax(1-2) rmax(2-3) rmax(3-4) <3 x flags> | |
| Units | K in eV/rad**2, theta0 & theta0' in degrees |
| Default | none |
| Use | Specifies a torsional - angle cross potential. The form of the potential is: |
| E = K.cos(phi).(theta - theta0).(theta' - theta0') | |
| where theta is the angle between 1-2-3 & theta' is between 2-3-4 | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torharm torexp outofplane uff4 torcosangle |
| Type | Option |
| Format | torcosangle <intra/bond/improper> <kcal/kjmol> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 K theta0 theta0' rmax(1-2) rmax(2-3) rmax(3-4) <3 x flags> | |
| Units | K in eV/rad**2, theta0 & theta0' in degrees |
| Default | none |
| Use | Specifies a torsional - cosine angle cross potential. The form of the potential is: |
| E = K.cos(phi).(cos(theta) - cos(theta0)).(cos(theta') - cos(theta0')) | |
| where theta is the angle between 1-2-3 & theta' is between 2-3-4 | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torharm torexp outofplane uff4 torangle |
| Type | Option |
| Format | torexp <bond/improper/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 k <+/->nphase <phi0> rho12 rho23 rho34 rmax(1-2) | |
| rmax(2-3) rmax(3-4) rmax(4-1) <4 x flags> | |
| or if esff option is specified | |
| atom1 atom2 atom3 atom4 k1 k2 <+/->nphase rho12 rho23 rho34 rmax(1-2) rmax(2-3) | |
| rmax(3-4) rmax(4-1) <5 x flags> | |
| Units | k/k1/k2 in eV, isign is +1 or -1 according to the sign of nphase, |
| rho12/23/34 and rmax in Angstroms, phi0 in degrees | |
| Default | if phi0 is not given it is assumed to be zero |
| Use | Specifies an exponentially decaying torsional potential of the form: |
| E = k*(1+isign*cos(nphase*phi-phi0))*exp(-r12/rho12)*exp(-r23/rho23)*exp(-r34/rho34) | |
| ESFF : | |
| E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)]* | |
| *exp(-r12/rho12)*exp(-r23/rho23)*exp(-r34/rho34) | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torharm outofplane torexp uff4 |
| Type | Option |
| Format | torharm <bond/improper/intra/inter> <kcal/kjmol> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 K <phi0> rmax(1-2) rmax(2-3) rmax(3-4) <rmax(1-4)> <2 x flags> | |
| Units | K in eV/rad**2, phi0 in degrees |
| Default | none, phi0 = 0 if omitted, rmax(1-4) = 0.0 |
| Use | Specifies a harmonic torsional potential. Note that this is not a sensible |
| choice for a convenientional torsional potential, but is used by some | |
| forcefields for an improper torsional angle. The form of the potential is: | |
| E = 1/2 K(phi - phi0)**2 | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torangle torexp outofplane uff4 |
| Type | Option / Keyword |
| Format | torsion <intra/inter> <bond/improper> <esff> <dreiding> <kcal/kjmol> <type_of_bond> |
| atom1 atom2 atom3 atom4 k <+/->n <phi0> rmax(1-2) rmax(2-3) | |
| rmax(3-4) rmax(4-1) <1 x flag> | |
| or if esff option is specified | |
| atom1 atom2 atom3 atom4 k1 k2 <+/->n rmax(1-2) rmax(2-3) | |
| rmax(3-4) rmax(4-1) <2 x flags> | |
| Eqn | Normal : |
| E = k*(1+isign*cos(n*phi-phi0)) | |
| ESFF : | |
| E = k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi) | |
| Units | k/k1/k2 in eV, isign is +1 or -1 according to the sign of n, |
| rmax in Angstroms, phi0 in degrees | |
| Default | if phi0 is not given it is assumed to be zero |
| Use | Torsional potential about atoms 2 and 3. k is half the barrier |
| and nphase is the periodicity. The optional flag is for fitting of k. | |
| If rmax(4-1) is input as zero then rmax(4-1) is set to infinity. | |
| Note that when rmax(4-1) is not zero then atoms 1 and 4 cannot be | |
| the same atom for a valid torsional term. | |
| When used as a keyword, torsion causes a list of valid torsion terms | |
| to be output before and after any optimisation/calculation. | |
| See also Ryckaert for an alternative form of torsion potential. | |
| four is an alternative valid name for this potential type. | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given then no cutoffs are required as the potential | |
| will act only when i-j, j-k and k-l are bonded. If improper is given | |
| then again no cutoffs are required, but the atoms must now be bonded | |
| i-j, j-k, j-l to make an improper torsion about atom j. | |
| if the option esff is specified after torsion then the potential takes | |
| the ESFF form. Here the potential becomes dependent on the two angles | |
| involved in the torsional angle so that it smoothly goes to zero when | |
| the torsional angle becomes indeterminate. Strictly the two coefficients | |
| k1 and k2 should be related by : | |
| k1 = K / (sin10**2.sin20**2) k2 = K / (sin10**n.sin20**n) | |
| where sin10 and sin20 are the sines of the equilibrium values of angles | |
| 1 and 2 respectively. Here they are just input as coefficients for | |
| generality. | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | ryckaert outofplane torexp tortaper torangle uff4 |
| Type | Option |
| Format | tortaper <bond/improper/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 k <+/->nphase <phi0> rtaper rmax(1-2) | |
| rmax(2-3) rmax(3-4) rmax(4-1) <1 x flags> | |
| or if esff option is specified | |
| atom1 atom2 atom3 atom4 k1 k2 <+/->nphase rtaper rmax(1-2) rmax(2-3) | |
| rmax(3-4) rmax(4-1) <2 x flags> | |
| Units | k/k1/k2 in eV, isign is +1 or -1 according to the sign of nphase, |
| rtaper and rmax in Angstroms, phi0 in degrees | |
| Default | if phi0 is not given it is assumed to be zero |
| Use | Specifies a torsional potential with tapering of the cut-offs over rtaper of the form: |
| E = k*(1+isign*cos(nphase*phi-phi0))*f(r12)*f(r23)*f(r34) | |
| ESFF : | |
| E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)] | |
| *f(r12)*f(r23)*f(r34) | |
| where f(r) is a cosine tapering function. | |
| If the sub-option dreiding is specified then the force constant is divided | |
| by the number of torsional interactions for each central j-k pair to | |
| ensure a constant torsional barrier for the j-k bond. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torharm outofplane torexp torangle uff4 |
| Type | Option |
| Format | totalenergy <total energy of bulk unit cell> |
| Units | eV |
| Use | This option is written out by GULP as information for the generation |
| of a surface calculation input by GDIS based on a restart file. | |
| See also | sbulkenergy |
| Type | Option |
| Format | tournament initial <final> <stepsize> |
| Default | 0.8 <0.8> <0.0> |
| Use | Part of ga options section. Specifies the tournament selection |
| probability. The higher the value, the more likely it is that | |
| the better configuration will be selected. If <initial> value | |
| is less than <final> value then after 20 iterations tournament | |
| incremented by <stepsize>. If the optimisation is stuck in a local minimum | |
| then, if stepsize non-zero, tournament is reset to <initial>. | |
| See also | genetic anneal gexp |
| Type | Option |
| Default | Use one point crossover |
| Use | Part of ga options section. |
| See also | crossover |
| Type | Option |
| Default | none |
| Units | dmax in Angstroms |
| Use | Repeats the requested calculation type automatically for |
| a series of points in which a subset of atoms are shifted | |
| by a translation vector. This option is useful for mapping | |
| out energy surfaces at the moment in one dimension. | |
| The input format is: | |
| translate x y z nstep <noise fmax> <thermal dmax> | |
| where x, y, z are the components of the vector between the | |
| the initial and final positions of the atoms. If the | |
| system is three-dimensional then x, y and z are assumed | |
| to be in fractional units. If the system is a cluster | |
| then they are assumed to be in angstroms. nstep is the | |
| number of points to be sampled along the translation | |
| vector (this leads to nstep+1 calculations including | |
| the first and last points). | |
| The subset of atoms to which the translation is to be | |
| applied is defined by adding a "T" flag to the end of the | |
| coordinate lines of these atoms. If the flag "T-" is used | |
| then the atoms are translated in the opposite direction to | |
| the vector input. | |
| If "noise" is also specified with a value then random displacements | |
| are added to the coordinates of the atoms in non-rigid regions | |
| after each translation step to prevent trapping in local high | |
| symmetry states. The magnitude of the displacement is given by a | |
| random number between -1 and 1 times the step size during translate | |
| scaled by fmax. Therefore fmax should usually be a small value << 1. | |
| If "thermal" is specified with a value then random displacements | |
| are added to the coordinates of all atoms in non-rigid regions, | |
| regardless of whether they were displaced or not in the translation. | |
| The magnitude of the displacement is given by a Gaussian random value with | |
| mean of zero and a standard deviation of dmax (in Angstroms). | |
| Note that the translate and scan_cell options are mutually exclusive. | |
| See also | nofirst_point scan_cell |
| Type | Option |
| Format | tscale value <freq> <s/ns/ps/fs> |
| Units | s, ns, ps or fs; default is ps. |
| Use | Controls how long in simulation time the temperature |
| scaling is to be applied for. By default this is set | |
| equal to the length of the equilibration phase of | |
| the run. Optionally the frequency of scaling can be | |
| specified, which normally defaults to the timestep. | |
| See also | md equilibration production timestep sample write |
| nolist temperature delay_force end_force momentum_correct |
| Type | Option |
| Format | tsuneyuki <form2> <inter/intra/bond> <x12/x13/x14/mol/o14/g14> <type_of_bond> |
| atom1 atom2 Q1 Q2 zeta <rmin> rmax <1*flag> | |
| Units | Q1 & Q2 in a.u., zeta in Angstroms**-1 |
| Defaults | form1 |
| Use | Specifies the short-range Coulomb correction described by Tsuneyuki et al |
| PRL, 61, 869 (1988). Note that the role of the charges is inverted relative | |
| to the paper in order that charge neutrality is achieved in the long-range | |
| limit. It is assumed that this was a typo. The correction to the Coulomb | |
| term is given by: | |
| U = [Q1.Q2 - q1.q2]g(r)/r | |
| where q1 & q2 are the regular charges specified elsewhere, and g(r) is: | |
| Form1: g(r) = (1+z.r)exp(-2z.r) | |
| Form2: g(r) = (1 + 11(z.r)/8 + 3(z.r)**2/4 + (z.r)**3/6)exp(-2z.r) | |
| where z is used as a short-hand for zeta | |
| Type | Option |
| Format | ttol Tmin |
| Default | Tmin=0.01 |
| Use | Temperature tolerence for simulated annealing routine. |
| Type | Option |
| Format | twist <+/->n |
| Units | None |
| Defaults | n = 0, or if twist is specified then +1 |
| Use | Takes the coordinates of a 1-D periodic system and introduces |
| a twist angle about the central axis in the repeat direction. | |
| The periodicity will be set so that the twist completes over | |
| a single cell. Longer periods can be created by first creating | |
| a supercell, while n specifies the number of complete twists | |
| in a single cell. By specifying -n then the phase is reversed. | |
| See also | pcell |
| Type | Option |
| Format | uff1 <intra/inter> <bond> <kcal/kjmol> |
| atom1 r theta x D zeta Zeff type tor Koop Thetaoop Chi <10 x flags> | |
| Units | r & x in Ang, theta & thetaoop in degrees, D, Koop, chi and tor in eV, Zeff in a.u. |
| Default | none |
| Use | Specifies the species parameters for UFF force field generation by |
| combination rules. | |
| See also | umorse |
| Type | Option |
| Format | uff3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K theta0 rmin(1-2) rmax(1-2) rmin(1-3) rmax(1-3) | |
| rmin(2-3) rmax(2-3) <flag> | |
| Units | K in eV, theta0 in degrees, rmin and rmax in Angstroms |
| Default | none |
| Use | UFF non-linear three-body form : |
| E(three) = K * (C0 + C1*cos(theta) + C2*cos(2*theta)) | |
| Here the coefficients are related to theta0 by: | |
| C2 = 1/(2*sin(theta0))**2 | |
| C1 = - 4*C2*cos(theta0) | |
| C0 = C2*(2*(cos(theta0))**2 + 1) | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species were 1-2, 2-3 and 1-3 are bonded. | |
| See also | axilrod-teller angle stillinger-weber exponential bcross lin3 |
| urey-bradley murrell-mottram bacross three hydrogen-bond equatorial | |
| 3coulomb bagcross |
| Type | Option |
| Format | uff4 <bond/improper/intra/inter> <kcal/kjmol> <dreiding> <type_of_bond> |
| atom1 atom2 atom3 atom4 K n <phi0> rmax(1-2) rmax(2-3) rmax(3-4) rmax(4-1) <1 x flag> | |
| Units | K in eV, phi0 in degrees |
| Default | none, phi0 = 0 if omitted |
| Use | Specifies a torsional potential of the UFF form: |
| E = 1/2 K*(1 - cos(n.phi0)*cos(n.phi)) | |
| n is an integer and there is only a flag for K | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion torangle torexp outofplane torharm |
| Type | Option |
| Format | uff_bondorder bond_type bond_order |
| Units | None |
| Default | |
| double => bond_order = 2.0 | |
| treble => bond_order = 3.0 | |
| quadruple => bond_order = 4.0 | |
| resonant => bond_order = 1.5 | |
| amide => bond_order = 1.41 | |
| half => bond_order = 0.5 | |
| quarter => bond_order = 0.25 | |
| third => bond_order = 1/3 | |
| custom => bond_order = 1.0 | |
| Use | Allows the user to change the default bond orders for use in UFF. |
| NB: The single bond order is fixed at 1.0 and cannot be changed. | |
| See also | connect |
| Type | Option |
| Format | uffoop <intra/inter/bond/mol> <only3> <kcal/kjmol> |
| atom1 atom2 atom3 atom4 k C0 C1 C2 rmax(1-2) rmax(1-3) rmax(1-4) <4 x flags> | |
| Units | k in eV, C0, C1, C2 are unitless |
| Default | none |
| Use | Out of plane energy - energy penalty for atom 1 lying |
| out of the plane of atoms 2, 3 and 4. This form uses the | |
| Universal Force Field expression: | |
| E = k.(C0 + C1*cos(phi) + C2*cos(2*phi)) | |
| where phi is the angle between the plane of the centre atom and two | |
| others with the bond from the centre atom to the third atom. | |
| Note that because phi depends on which of the 3 different angles is | |
| chosen, GULP computes the contribution for all 3 cases and takes the | |
| average. | |
| If the only3 sub-option is specified then the potential applies where | |
| an atom has exactly 3 bonds present. | |
| See also | torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane |
| Type | Option |
| Format | either: atom_no. radius |
| or x y z radius | |
| Units | fractional for x, y, z and Angstroms for radius |
| Default | none |
| Use | Atoms with no variables marked for optimisation are frozen out of the |
| derivative calculations to save cpu time. This can be done either by | |
| setting the appropriate flags or running a "cello" calculation in | |
| which only the strains are marked for optimisation, but no internal | |
| variables. Unfreeze causes atoms within a spherical region about | |
| either a given atom or a given origin to be marked for optimisation. | |
| This option cannot be used with conp or conv for obvious reasons! | |
| This option is primarily designed for large unit cell situations | |
| where in effect a defect calculation is being performed. | |
| See also | optimise transition_state cello noexclude fix_atom |
| Type | Option |
| Format | unique d |
| Default | d=0.0d0 |
| Use | Part of ga options section. Any 2 candidates to be optimised must |
| have a cost function difference of at least d. |
| Type | Option |
| Format | units <kcaltoev/evtoangs> value |
| Default | The default values for unit conversion factors are: |
| kcaltoev = 4.3364432032d-2 | |
| angstoev = 14.3997584 | |
| Use | The default values of unit conversion factors can be changed either |
| by editing the values in modules.f90 before compilation or by setting | |
| this value in the input. | |
| NB: This should be placed after the keyword line otherwise any use | |
| of the conversion factor before this command will use the default | |
| value. | |
| See also |
| Type | Option |
| Format | integer number |
| Default | 10 |
| Use | Changes the maximum number of cycles of Hessian updating before exact |
| calculation is performed. Number may appear on same line as command | |
| or the following line. |
| Type | Option |
| Format | urey-bradley <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
| atom1 atom2 atom3 K r0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags> | |
| Units | K in eV/Angs**2, r0 in Angstroms |
| Use | Harmonic distance potential between atoms which are 1-3 |
| E(three) = 1/2 * K * (r - r0)**2 | |
| intra/inter can also be specified for molecular calculations, as can | |
| bond. If bond is given no cutoff is required as the potential will | |
| only act between species where 1-2 and 1-3 are bonded. | |
| See also | three-body angle exponential axilrod-teller stillinger bcross lin3 |
| murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb |
| Type | Option |
| Format | vacancy <cartesian/fractional/molecule> <number> <symbol> <x y z> |
| Use | Creates a vacancy in a defect calculation. The vacancy site may |
| be specified in the following ways: | |
| (a) atom number - removes the nearest image to the defect centre | |
| of the asymmetric unit site of that number. | |
| e.g. vacancy 2 | |
| (b) atom symbol - removes the first atom in the asymmetric unit | |
| with the symbol matching that given. The nearest image to | |
| to the defect centre is removed. | |
| e.g. vacancy Mg2 | |
| (c) molecule number - removes a complete molecule. Takes the | |
| nearest image of the molecule number given to the defect | |
| centre. Remember that when molecular defects are being | |
| run the energy of the molecule at infinite separation | |
| must be corrected for. | |
| e.g. vacancy molecule 3 | |
| (d) coordinates - removes any ions within a tolerance of that | |
| position. By default fractional coordinates are assumed in | |
| which case the nearest image to the defect centre is taken. | |
| If "cartesian" is specified then x y z are taken as being | |
| absolute cartesian coordinates. | |
| e.g. vacancy 0.5 0.5 0.5 | |
| vacancy cart 1.2 1.2 1.2 | |
| See also | defect intersitial impurity size centre region_1 |
| Type | Option |
| Format | keyword |
| Default | none |
| Use | Specifies fitting variables associated with |
| different species - valid options are charge, split, | |
| and shift. Also allows constraints to be applied. | |
| See also | constrain charge split shift |
| Type | Option |
| Format | vbo_twobody |
| atom1 atom2 c gamma R0 delta <4xflags> | |
| Units | c in eV; R0 and delta in Angstroms; gamma is unitless |
| Default | None |
| Use | Twobody potential of a form suitable for use as part of VBO model of Truhlar et al. |
| E = N.exp(-gamma/(1-sqrt(r/delta))) for r < delta & E = 0 for r >= delta | |
| NB: Because the potential goes to zero at delta there is no rmax or rmin for this | |
| potential (i.e. rmax = delta). | |
| The normalisation constant N is given by: | |
| N = 2*exp(gamma/(1-sqrt(R0/delta))) | |
| NB: The factor of two in N comes from the translation of how the two-body sum is | |
| expressed in the papers by Truhlar to how it is implemented in GULP. | |
| See also | eam_functional eam_density |
| Type | Option |
| Format | vdw at.no. <radius> |
| Units | Angstroms |
| Default | standard literature value |
| Use | Allows VDW radii to be changed. |
| Command is part of element section. | |
| Can be species specific for use with COSMO/COSMIC | |
| e.g. to change the VDW radius of all oxygens to 1.5 Ang: | |
| element | |
| vdw O 1.5 | |
| end | |
| e.g. to change the VDW radius of 2 different types of oxygen: | |
| element | |
| vdw O2 1.3 | |
| vdw O4 1.5 | |
| end | |
| See also | element |
| Type | Option |
| Format | vectors <angs/au> |
| x y z for vector 1 | |
| x y z for vector 2 | |
| x y z for vector 3 | |
| <6 x optimisation flags> | |
| Units | Angstrom (default) or au |
| Use | Specifies the cartesian components of the lattice vectors. |
| Either "vectors" or "cell" must be included. | |
| Strain optimisation flags appear on last line. |
| Type | Option |
| Format | velocities <angs/ps> |
| atom_no velocity_x velocity_y velocity_z | |
| Units | Angstroms / ps |
| Default | None |
| Use | Specifies the current Cartesian velocities in an MD simulation and |
| can be used for restarting such a run. Can also be used to set the | |
| initial velocities. | |
| See also | md accelerations |
| Type | Option |
| Format | volume vol <weight> |
| Units | Angstroms**3 |
| Default | Volume is not fitted, weight = 1 |
| Use | Subsection of observables, used for specifying that the volume |
| is fitted. Usually the cell parameters of a system are fitted | |
| and so this constrains the volume. This option allows the | |
| volume to be targetted instead. | |
| See also | observables elastic sdlc hfdlc piezo energy stress |
| Type | Option |
| Format | weight <number of weights to be changed> |
| list of observables whose weights are to be changed | |
| list of new weights in order | |
| Units | none |
| Default | 1.0 |
| Use | Subsection of observables, allows weighting factors to changed. |
| Number of weights = 0 causes default to be | |
| changed for subsequent observables. | |
| See also | default_weight |
| Type | Option |
| Format | wmax <n> |
| Units | THz |
| Default | None: must be specified. |
| Use | Used within the "pdf" input block for "PDFcut" or "PDFkeep" calculations. |
| Sets the maximum phonon frequency to be used in calculating PDFs. | |
| Units can be changed using 'unit freq' | |
| See also | PDFkeep PDFcut units wmin |
| Type | Option |
| Format | wmin <n> |
| Units | THz |
| Default | None: must be specified. |
| Use | Used within the "pdf" input block for "PDFcut" or "PDFkeep" calculations. |
| Sets the minimum phonon frequency to be used in calculating PDFs. | |
| Units can be changed using 'unit freq' | |
| See also | PDFkeep PDFcut units wmax |
| Type | Option |
| Format | write value <s/ns/ps/fs> |
| Units | s, ns, ps or fs - if integer, then value is by default |
| a multiple of the timestep or if non-integer then by | |
| default is the time in picoseconds. | |
| Use | Determines how often the program writes to the molecular |
| dynamics dumpfile during the production phase of the | |
| run for subsequent analysis. | |
| See also | md timestep equilibration production temperature |
| tscale sample nolist delay_force end_force |
| Type | Option |
| Format | xangleangle <inter/intra> <bond> <kcal/kjmol> |
| atom1 atom2 atom3 atom4 k(213/4) k(312/4) k(412/3) theta0(213) theta0(214) theta0(314) & | |
| rmax(1-2) rmax(1-3) rmax(1-4) <6 x flag> | |
| Units | All k in eV*rad**-2 and all theta0 in degrees |
| Default | none |
| Use | Angle-angle cross potential for all angles about a central atom, atom 1: |
| E = k(213/4)*(theta(213) - theta0(213))*(theta(214) - theta0(214)) + | |
| k(312/4)*(theta(312) - theta0(312))*(theta(314) - theta0(314)) + | |
| k(412/3)*(theta(412) - theta0(412))*(theta(413) - theta0(413)) | |
| See also | torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane |
| uffoop xcosangleangle |
| Type | Option |
| Format | xcosangleangle <inter/intra> <bond> <kcal/kjmol> |
| atom1 atom2 atom3 atom4 k(213/4) k(312/4) k(412/3) theta0(213) theta0(214) theta0(314) & | |
| rmax(1-2) rmax(1-3) rmax(1-4) <6 x flag> | |
| Units | All k in eV and all theta0 in degrees |
| Default | none |
| Use | Angle cosine - angle cosine cross potential for all angles about a central atom, atom 1: |
| E = k(213/4)*(cos(theta(213)) - cos(theta0(213)))*(cos(theta(214)) - cos(theta0(214))) + | |
| k(312/4)*(cos(theta(312)) - cos(theta0(312)))*(cos(theta(314)) - cos(theta0(314))) + | |
| k(412/3)*(cos(theta(412)) - cos(theta0(412)))*(cos(theta(413)) - cos(theta0(413))) | |
| See also | torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane |
| uffoop xangleangle |
| Type | Option |
| Format | xoutofplane <intra/inter/bond/mol> <kcal/kjmol> <type_of_bond> |
| atom1 atom2 atom3 atom4 atom5 atom6 k rmax(1-2) rmax(1-3) rmax(1-4) rmax(2-5) rmax(2-6) <1 x flag> | |
| Units | k in eV*Angs**-2 |
| Default | none |
| Use | Specifies an cross - out of plane potential of form: |
| E = k.d1.d2 | |
| where d1 is the out of plane distance of atom 1 from the plane of atoms 2/3/4 | |
| and d2 is the out of plane distance of atom 2 from the plane of atoms 1/5/6. This | |
| functional form is used in the CVFF forcefield. This is a six-body potential. | |
| The type of bond sub-option can be used to control which bonded atoms the | |
| potential applies to. For a three-body potential, the bond type for the | |
| two bonds connected to the pivot atom can be supplied and then checked | |
| before applying the potential. Valid type of bond options are: single, | |
| double, triple, quadruple, resonant, amide, custom, half, quarter, and third. | |
| In addition a bond may specified as regular (default), cyclic or exocyclic. | |
| See also | torsion ryckaert torangle torharm torexp outofplane uffoop |
| Type | Option |
| Format | xtol <opt/fit> <real value> |
| Units | fractional |
| Default | 0.00001 for opt / 0.00001 for fit |
| Use | Parameter tolerance for optimisation/fitting. |
| Value may appear on same line as option or on the following line. | |
| If xtol > 1.0 => xtol=10**(-xtol) | |
| If opt/fit is not supplied then value is applied to both. | |
| See also | gdcrit gtol gmax ftol |
| Type | Option |
| Format | youngs_modulus <n> |
| <x/y/z> youngs_modulus <weight> | |
| Units | GPa |
| Default | no Youngs moduli to be fitted |
| Use | Subsection of observables, used for specifying values of |
| Young's moduli for fitting. | |
| Example | To fit a Young's modulus of 240.0 GPa in the x direction |
| with a weight of 1.0: | |
| young 1 | |
| x 240.0 1.0 | |
| NB: The Young's moduli are computed assuming that the | |
| material is linear elastic orthotropic. | |
| See also | elastic sdlc hfdlc weight srefractive hfrefractive bornq |
| piezoelectric poisson shear voigt bulk |
| Type | Option |
| Format | zbl <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> |
| atom1 atom2 <b1 c1 b2 c2 b3 c3 b4 c4 d n> <rmin> rmax <9*flags> | |
| Units | d, n, b1-4 are unitless, c1-4 are in Ang**-1 |
| Default | d = 0.46850, n=0.23, b1=0.18175, b2=0.50986, b3=0.28022, b4=0.02817 |
| c1=3.19980, c2=0.94229, c3=0.40290, c4=0.20162 | |
| Use | Specifies the use of the ZBL potential, as widely used in simulations |
| of radiation cascades. | |
| E = (1/(4*pi*epsilon0)) * Zi*Zj*e**2*phi(rij/a)/rij | |
| where Zi & Zj are the atomic numbers of the elements. The constant a | |
| is given by; | |
| a = d/(Zi**n + Zj**n) | |
| and phi(x) by: | |
| phi(x) = sum(i=1,4) bi*exp(-ci*x) | |
| See also | general |
| Type | Information |
| Info | Many organic forcefields require the scaling of 1-4 two body |
| interactions. Typically a factor of a 1/2 is used. This can | |
| be achieved in GULP. Nearly all two-body potentials allow a | |
| scale factor to be specified on the same line as the potential | |
| option word which has this effect. Similarly Coulomb interactions | |
| can be scaled by using the Coulomb subtract potential which | |
| already has a coefficient and can be specified to act only for | |
| 1-4 interactions. |
| Type | Information |
| Use | The control C key sequence can be used to exit a fitting |
| process or optimisation cleanly at the end of the current | |
| cycle. If control C is executed twice then the program | |
| will terminate. |
| Type | Information |
| Info | To continue a line onto further lines the character |
| "&" can be given at the end of the line. | |
| e.g. the following input could be given in the two | |
| following ways: | |
| buck | |
| Si core O shel 1280.0 0.3 0.0 0.0 12.0 1 0 0 | |
| or | |
| buck | |
| Si core O shel & | |
| 1280.0 0.3 0.0 0.0 12.0 & | |
| 1 0 0 |
| Type | Information |
| Info | Many organic forcefields require the scaling of 1-4 two body |
| interactions. Typically a factor of a 1/2 is used. This can | |
| be achieved in GULP. Nearly all two-body potentials allow a | |
| scale factor to be specified on the same line as the potential | |
| option word which has this effect. Similarly Coulomb interactions | |
| can be scaled by using the Coulomb subtract potential which | |
| already has a coefficient and can be specified to act only for | |
| 1-4 interactions. |
| Type | Information |
| Info | The 2 and 3 body potentials of Stillinger-Weber are |
| available using the potential types sw2 and sw3, | |
| respectively. | |
| See also | sw2 sw2jb sw3 sw3jb |