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 |
Default | Do not output eigenvalues and eigenvectors of elastic constants |
Use | If present then the eigenvalues and eigenvectors of the elastic |
constant tensor will be output. These can provide information | |
regarding the elastic stability of the system. | |
See also | piezoelectric sdlc hfdlc srefractive hfrefractive weight |
bornq young poisson elastic |
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 cstrain |
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 |
Default | properties calculated with infinitesimal strains |
Use | Specifies that properties should be computed using derivatives |
computed for finite strain. | |
By default all derivatives are evaluated based on the assumption | |
of infinitesimal strain relative to the current structure. If the | |
strain keyword is specified then the strains are taken relative | |
to the initial cell parameters as a reference point. This causes | |
the strain derivatives to be changed as they are at finite strain. | |
If the keyword property is given with the keyword strain then the | |
use of finite strain derivatives is turned off during property | |
evaluation to yield the standard property values. If this keyword | |
is specified then properties are computed using derivatives at | |
finite strain which will alter the values. | |
See also | strain property numerical |
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 |
Use | If specified, then duplication of torsions by potentials with wildcards is |
removed. This means the wildcard potential will only act where there is no | |
other potential with fewer wildcard elements for the end terms. As an example, | |
if the torsions H-C1-C2-H and X-C1-C2-X were specified then the second torsion | |
would be excluded for the case where the end atoms were both H, but would act | |
for H-C1-C2-C3. Currently only applies to standard torsions and not impropers. | |
See also | torsion |
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 |
Default | Shell coordinates can be zero in simultaneous fit |
Use | This keyword causes GULP to displace shell coordinates away from zero |
during a simultaneous fit (by 0.01). This used to be the default but | |
was turned off to make the fitting of energy surfaces with shells | |
easier. | |
See also | relax fit breathe noflags simultaneous |
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 fsprop |
ceigen |
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 rfo_eig rfo_grad |
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 noshellzero |
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 cstrain |
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. | |
NB: When using the strain keyword and cstrain option, then | |
the stress is defined with respect to the reference cell and | |
accordingly the volume of this cell is used. | |
See also | atomic_stress strain cstrain |
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 j3 |
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 j3 |
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 j3 |
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 j3 |
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 j3 |
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 j3 |
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 j3 |
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 j3 |
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 | 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 | cstrain 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 | 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. | |
NB: The attachment energy cannot currently be computed if using KIM models. | |
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> <old> <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). | |
If "old" is used then the line length for restarts is restricted to 80 | |
characters for backward compatibility. | |
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/numeric> |
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> | |
if numeric : | |
atom1 filename | |
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 | |
Numeric: | |
If this sub-option is specified then the EAM functional is read from a numeric tabulation | |
in an external file. This file is in the "funcfl" format from ParaDyn / DYNAMO 86. | |
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 ceigen |
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 spin |
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 j3 |
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 j3 |
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 <first/second/all> <value> |
Default | Finite differences not to be used, but 0.0001 / all if finite is given |
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 pfinite sfinite |
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 e2pot |
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 j3 |
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 | j2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond> |
atom1 atom2 J2 <rmin> rmax <1*flag> | |
Units | J2 in eV |
Defaults | None |
Use | Adds an energy term to the two-body energy if an interaction is found. |
Value of energy doesn't depend on distance between the atoms, as long as the | |
interaction is valid (i.e. less than the cutoff or according to the bonding criteria) | |
However, it is does depend on the "spin" assigned to each species involved: | |
E = - J2*spin_1*spin_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. | |
See also | harmonic spring squaredharmonic forceconstant mm3stretch spin j2 |
Type | Option |
Format | j3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> |
atom1 atom2 atom3 J3 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 | |
Units | J3 in eV, distances in Angstroms |
Use | Adds an energy to the three-body contribution if a valid 3-body term |
is found. The value does not depend on the distances or angle, just | |
the "spin" of the atoms involved: | |
E(three) = - J3*spin_1*spin_2*spin_3 | |
This is used for addition of an Ising Hamiltonian to the energy. | |
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 3coulomb spin j2 |
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 j3 |
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 j3 |
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 <damp> <bdamp> |
atom_symbol <core/shell> dipolar_polarisability | |
Units | dipolar_polarisability in Angs**3, bdamp in inverse Angstroms |
Default | Polarisability is equal to zero, except for shell contribution |
bdamp = 0.0 | |
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. | |
If "damp" is specified as a sub-option then short-range damping is | |
applied to the charge-dipole interaction using the Tang-Toennies | |
form as proposed by Madden and Wilson. The range of the damping is | |
controlled by the factor bdamp. | |
See also | spin |
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 | reaxffsmooth k <lone/over/both> |
Units | k is unitless |
Default | No smoothing; k = 80.0; if specified then both |
Use | This option controls whether a smoothing factor is used for the lone pair terms |
in ReaxFF. The original formalism has a discontinuity due to rounding to the integer | |
below a value. If specified, this option changes this to a smooth approximation to | |
the Heaviside function such that the discontinuity is removed, at the expense of | |
deviating from the original model. The smoothing uses the expression; | |
f(x) = 1/(1+exp(-k*(x-x0))) | |
where x0 is the nearest integer value and x is the actual value. As k tends to infinity | |
the function tends toward the original discontinuous form. However, if k is too small | |
then the smoothing function will not decay to 0/1 before (x-x0) reaches a half causing | |
problems. Therefore care is necessary if changing the default value of k. | |
There are two main energy terms that are influenced by this change - the over coordination | |
and lone pair energies. The sub-options "lone", "over" or "both" control which of the | |
energies the smoothing is applied to. | |
See also | reaxffcutoff reaxfftol |
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 reaxffsmooth |
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 | rfo_eig value |
Units | eV/Ang**2 |
Default | -0.001 eV/Ang**2 |
Use | Tolerance on eigenvalues of the Hessian matrix to be labelled as |
negative during RFO optimisation. | |
NB: The value can be input as positive since it is enforced that | |
it will be less than or equal to zero. | |
See also | rfo rfo_grad |
Type | Option |
Format | rfo_grad value |
Units | eV/Ang |
Default | 1.0 x 10**-8 eV/Ang |
Use | Tolerance on the projected gradient onto the Hessian mode for |
the mode to be included in the active space for optimisation. | |
NB: If a value greater than 1 is input then it is assumed to | |
be the exponent (e.g. 2 -> 10**-2) | |
See also | rfo rfo_eig |
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 no4duplicates |
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_force F fx fy fz vx vy vz |
Units | F in eV/Ang**2, fx, fy, fz, vx, vy, vz Cartesian vector components |
Default | F = 0, i.e. no shear force |
Use | Specifies a shear force on system. The magnitude of the force is given by F multiplied |
by the initial distance from the plane containing the fixed atom for the system. The direction | |
of the force is given by (fx,fy,fz) in Cartesian space where the components are normalised. | |
The normal to the plane of shear is given by the Cartesian vector (vx,vy,vz) | |
NB: The distance used to scale the force constant is based on the initial coordinates and | |
then held fixed. Otherwise the force would have a perpendicular component. | |
NB: If the vectors input are not normalised then GULP will enforce this automatically. | |
NB: This option forces the turning off of symmetry and wrapping of coordinates | |
See also | force_minimisation optimise td_external_force external_force nowrap nosymmetry |
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> <+1/-1> |
Units | None |
Default | 0.001 +1 |
Use | This is the scale factor by which the eigenvectors will be |
multiplied when attempting to lower the symmetry along an | |
imaginary mode direction. When applying the lower operation | |
the phonon eigenvectors can be applied in one of two directions | |
depending on the sign. By specifying "-1" this change the direction | |
of displacement. | |
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 polarisability spin |
Type | Option |
Format | spin symbol <spin> |
Units | None |
Default | Spin is equal to zero. |
Use | Allows species spins to be set. Note that species symbols can |
also be used for the spin to set different spins for different | |
species of the same element: | |
element | |
spin O1 0.5 | |
spin O2 -0.5 | |
end | |
or the older form of using the atomic number can be used: | |
element | |
spin 8 0.5 | |
end | |
The spin can then contribute to an Ising Hamiltonian via the | |
j2 and j3 potentials. NB: This is currently not implemented | |
for the Mott-Littleton method. | |
Command is part of element section. | |
See also | element j2 j3 |
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 | eV |
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. | |
NB: This keyword currently implies that symmetry will be turned off | |
since there is no guarantee that the strains or cell orientation will | |
be compatible with the symmetry-adapted algorithms. | |
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 j3 |
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 j3 |
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 <multi> 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 | |
If the "multi" sub-option is specified then a more complex temperature | |
profile can be created using multiple variable temperature steps. For example, | |
to hold the temperature at 398 K in the above example for 500 steps and then | |
increase it by a further 100 K using the same rate the input would be: | |
temperature multi 298 0.1 1000 300 | |
0.1 1000 500 | |
As many temperature ramps as necessary can be included. | |
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 j3 |
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 no4duplicates |
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 no4duplicates |
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 no4duplicates |
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 no4duplicates |
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 no4duplicates |
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 no4duplicates |
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 j3 |
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 no4duplicates |
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 j3 |
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 |
Type : Information Written once only for each run : write(31)version write(31)numat,ndimensions Written for every configuration : Version = 3.4: write(31)timesofar,ekin,fc,temp write(31)(xalat(i),i=1,numat) write(31)(yalat(i),i=1,numat) write(31)(zalat(i),i=1,numat) write(31)(velx(i),i=1,numat) write(31)(vely(i),i=1,numat) write(31)(velz(i),i=1,numat) if (lconp) then write(31)(xcell(i),i=1,9) write(31)(velc(i),i=1,nstrains) endif Version = 4.0 onwards: write(31)timesofar,ekin,fc,temp write(31)(xalat(i),i=1,numat) write(31)(yalat(i),i=1,numat) write(31)(zalat(i),i=1,numat) write(31)(velx(i),i=1,numat) write(31)(vely(i),i=1,numat) write(31)(velz(i),i=1,numat) write(31)(xdrv(i),i=1,numat) write(31)(ydrv(i),i=1,numat) write(31)(zdrv(i),i=1,numat) write(31)(esite(i),i=1,numat) if (lconp) then write(31)(xcell(i),i=1,9) write(31)(velc(i),i=1,nstrains) endif Meaning of variables : version (real*8) = version number of GULP numat (integer*4) = total number of atoms including shells timesofar (real*8) = elapsed time of simulation for this frame (ps) ekin (real*8) = kinetic energy for this frame (eV) fc (real*8) = potential energy for this frame (eV) temp (real*8) = temperature for this frame (Kelvin) xalat (real*8) = x Cartesian coordinates of atoms (Angstroms) yalat (real*8) = y Cartesian coordinates of atoms (Angstroms) zalat (real*8) = z Cartesian coordinates of atoms (Angstroms) velx (real*8) = x component of velocities (Angstroms/ps) vely (real*8) = y component of velocities (Angstroms/ps) velz (real*8) = z component of velocities (Angstroms/ps) xdrv (real*8) = x component of first derivatives (eV/Angstroms) -> negative force ydrv (real*8) = y component of first derivatives (eV/Angstroms) -> negative force zdrv (real*8) = z component of first derivatives (eV/Angstroms) -> negative force esite (real*8) = energy contribution of each atom (eV) lconp (logical) = .true. for NPT calculation, otherwise .false. xcell (real*8) = Cartesian components of cell vectors (Angstroms) velc (real*8) = velocities of cell components (Angstroms)
Valid space groups for GULP: _______________________________________________________________________________ Number Label Number Label Number Label _______________________________________________________________________________ 1 P 1 2 P -1 3 P 2 4 P 21 5 C 2 6 P M 7 P C 8 C M 9 C C 10 P 2/M 11 P 21/M 12 C 2/M 13 P 2/C 14 P 21/C 15 C 2/C 16 P 2 2 2 17 P 2 2 21 18 P 21 21 2 19 P 21 21 21 20 C 2 2 21 21 C 2 2 2 22 F 2 2 2 23 I 2 2 2 24 I 21 21 21 25 P M M 2 26 P M C 21 27 P C C 2 28 P M A 2 29 P C A 21 30 P N C 2 31 P M N 21 32 P B A 2 33 P N A 21 34 P N N 2 35 C M M 2 36 C M C 21 37 C C C 2 38 A M M 2 39 A B M 2 40 A M A 2 41 A B A 2 42 F M M 2 43 F D D 2 44 I M M 2 45 I B A 2 46 I M A 2 47 P M M M 48 P N N N 49 P C C M 50 P B A N 51 P M M A 52 P N N A 53 P M N A 54 P C C A 55 P B A M 56 P C C N 57 P B C M 58 P N N M 59 P M M N 60 P B C N 61 P B C A 62 P N M A 63 C M C M 64 C M C A 65 C M M M 66 C C C M 67 C M M A 68 C C C A 69 F M M M 70 F D D D 71 I M M M 72 I B A M 73 I B C A 74 I M M A 75 P 4 76 P 41 77 P 42 78 P 43 79 I 4 80 I 41 81 P -4 82 I -4 83 P 4/M 84 P 42/M 85 P 4/N 86 P 42/N 87 I 4/M 88 I 41/A 89 P 4 2 2 90 P 4 21 2 91 P 41 2 2 92 P 41 21 2 93 P 42 2 2 94 P 42 21 2 95 P 43 2 2 96 P 43 21 2 97 I 4 2 2 98 I 41 2 2 99 P 4 M M 100 P 4 B M 101 P 42 C M 102 P 42 N M 103 P 4 C C 104 P 4 N C 105 P 42 M C 106 P 42 B C 107 I 4 M M 108 I 4 C M 109 I 41 M D 110 I 41 C D 111 P -4 2 M 112 P -4 2 C 113 P -4 21 M 114 P -4 21 C 115 P -4 M 2 116 P -4 C 2 117 P -4 B 2 118 P -4 N 2 119 I -4 M 2 120 I -4 C 2 121 I -4 2 M 122 I -4 2 D 123 P 4/M M M 124 P 4/M C C 125 P 4/N B M 126 P 4/N N C 127 P 4/M B M 128 P 4/M N C 129 P 4/N M M 130 P 4/N C C 131 P 42/M M C 132 P 42/M C M 133 P 42/N B C 134 P 42/N N M 135 P 42/M B C 136 P 42/M N M 137 P 42/N M C 138 P 42/N C M 139 I 4/M M M 140 I 4/M C M 141 I 41/A M D 142 I 41/A C D 143 P 3 144 P 31 145 P 32 146 R 3 147 P -3 148 R -3 149 P 3 1 2 150 P 3 2 1 151 P 31 1 2 152 P 31 2 1 153 P 32 1 2 154 P 32 2 1 155 R 3 2 156 P 3 M 1 157 P 3 1 M 158 P 3 C 1 159 P 3 1 C 160 R 3 M 161 R 3 C 162 P -3 1 M 163 P -3 1 C 164 P -3 M 1 165 P -3 C 1 166 R -3 M 167 R -3 C 168 P 6 169 P 61 170 P 65 171 P 62 172 P 64 173 P 63 174 P -6 175 P 6/M 176 P 63/M 177 P 6 2 2 178 P 61 2 2 179 P 65 2 2 180 P 62 2 2 181 P 64 2 2 182 P 63 2 2 183 P 6 M M 184 P 6 C C 185 P 63 C M 186 P 63 M C 187 P -6 M 2 188 P -6 C 2 189 P -6 2 M 190 P -6 2 C 191 P 6/M M M 192 P 6/M C C 193 P 63/M C M 194 P 63/M M C 195 P 2 3 196 F 2 3 197 I 2 3 198 P 21 3 199 I 21 3 200 P M 3 (P M -3) 201 P N 3 (P N -3) 202 F M 3 (F M -3) 203 F D 3 (F D -3) 204 I M 3 (I M -3) 205 P A 3 (P A -3) 206 I A 3 (I A -3) 207 P 4 3 2 208 P 42 3 2 209 F 4 3 2 210 F 41 3 2 211 I 4 3 2 212 P 43 3 2 213 P 41 3 2 214 I 41 3 2 215 P -4 3 M 216 F -4 3 M 217 I -4 3 M 218 P -4 3 N 219 F -4 3 C 220 I -4 3 D 221 P M 3 M 222 P N 3 N 223 P M 3 N 224 P N 3 M 225 F M 3 M 226 F M 3 C 227 F D 3 M 228 F D 3 C 229 I M 3 M 230 I A 3 D Non-standard space groups: C 1 / C -1 Alternative settings of the above space groups should also be valid _______________________________________________________________________________