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GULP help file
Keywords and options in alphabetical order
14_scale,
absolute_coordinates, accelerations, accuracy, angle, anneal, atomab, aver, average, axilrod-teller,
bacross, bcoscross, bcross, best, boattractive, bocharge, bond, borepulsive, bornq, boselfenergy, both, botwobody, box, breathe, brenner, broaden_dos, bsm, buck4, buckingham, bulk_modulus, bulk_noopt,
c6, cartesian, caver, cell, cellonly, centre, cfaver, charge, cmm, compare, configurations, conjugate, connect, conp, conserved, constrain, contents, conv, cosh-spring, cost, coulomb, covalent, covexp, crossover, current_time, cutd, cutp, cuts, cv, cvec,
damped_dispersion, dcharge, debug, defect, deflist, delayforce, delf, delta, dfp, dhkl, dipole, discrete, dispersion, distance, ditto, dmaximum, dminimum, dump,
eam_alloy, eam_density, eam_functional, eam_potential_shift, eem, efg, eigenvectors, einstein, elastic, electronegativity, element, endforce, energy, ensemble, entropy, epsilon/sigma, equilibration, erongi, ewaldrealradius, exponential_three_body, external_force, extracutoff,
factor, fbfgs, fermi-dirac, finite, fit, fix_molecule, fractional, free_energy, frequency, ftol, full,
gamma_angular_steps, gamma_direction_of_approach, gcmcmolecule, gcmcspecies, gdcrit, general, genetic, gexp, global, gmax, gradient, gradients, grid, gtol,
harmonic, hessian, hexagonal, hfdlc, hfrefractive_index, high-fq, hill,
igauss, ignore, impurity, integrator, intensity, inter, interstitial, intra, ionic, isotropic, iterations,
keyword, kfull, kpoints,
lbfgs, lbfgs_order, lennard_jones, library, lin3, line, line_continuation, linmin, ljbuffered, lower_symmetry, lowest_mode,
manybody, marvin, marvinSE, mass, maxcyc, maximise, maximum, mcchemicalpotential, mccreate, mcdestroy, mcmaxdisplacement, mcmaxrotation, mcmeans, mcmove, mcoutfreq, mcrotate, mcsample, mcstep, mctrial, mcvolume, md, mdarchive, mdconstraint, mincell, minimum, minimum_image, mode2a, molecule, molmec, molq, momentum_correct, monopoleq, montecarlo, morse, move_2a_to_1, murrell-mottram, mutation,
name, newda, noanisotropic_2b, nobond, nobreathe, nod2sym, nodensity_out, nodpsym, nodsymmetry, noelectrostatics, noenergy, noexclude, nofirst_point, noflags, nofrequency, nokpoints, noksymmetry, nolist_md, nomodcoord, nomolecularinternalke, nononanal, noquick, noreal, norecip, norepulsive_cutoff, nosderv, nosymmetry, nozeropt, numdiag,
observables, odirection, oldelastic, oldunits, omega, omega_damping, operators, optimise, origin, outcon, outofplane, output,
pcell, pfractional, phonon, piezoelectric, polarisability, polynomial, positive, pot, potential, potential_interpolation, potgrid, potsites, predict, pressure, print, production, project_dos, property, pvector,
qelectronegativity, qeq, qeqiter, qeqradius, qeqtol, qerfc, qok, qtaper, qwolf,
regi2a, regi_before, region_1, relax, reldef, resetvectors, restore, rfo, rspeed, rtol, ryckaert, rydberg,
sample, save, sbulkenergy, scale, scell, scmaxsearch, sdlc, seed, sfractional, shear_modulus, shell, shellmass, shift, shrink, simultaneous, single, size, slower, sm, smelectronegativity, spacegroup, spatial, species, spline, split, spring, squaredharmonic, srefractive_index, sregion2, sshift, start, static, static_first, stepmx, stillinger-weber, stop, storevectors, supercell, svectors, sw2, sw2jb, sw3, sw3jb, switch_minimiser, symbol, symmetry_cell, symmetry_operator,
td_external_force, temperature, terse, tether, three-body, time, timestep, title, torangle, torexp, torharm, torsion, tortaper, totalenergy, tournament, tpxo, trajectory_format, transition_state, translate, tscale, tsuneyuki, ttol,
unfreeze, unique, unit, update, urey-bradley,
vacancy, valid_spacegroups, variables, vdw, vectors, velocities, voigt,
weight, write,
xtol,
zero_potential, zsisa
Topic: | terse |
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
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Topic: | oldunits |
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.
|
Topic: | nomodcoord |
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.
|
Topic: | brenner |
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.
The option REBO is a synonym for this option.
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See also: | spatial.
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Topic: | spatial |
Type: | Keyword |
Use: | Requests that a spatial decomposition algorithm is used whereever possible to try to achieve linear scaling with system size.
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Topic: | nomolecularinternalke |
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.
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Topic: | einstein |
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.
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Topic: | external_force |
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:
force
1 0.2 0.0 0.0
3 -0.2 0.0 0.0
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See also: | td_external_force.
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Topic: | td_external_force |
Type: | Option |
Format: | td_external_force atomnumber direction forceA forceB forceC
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Units: | forceA in eV/Angstrom, forceB in 1/seconds, & 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
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See also: | external_force.
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Topic: | mincell |
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.
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See also: | rspeed, optimise.
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Topic: | ditto |
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.
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Topic: | omega |
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.
NOTE : This option only applies to a gamma point calculation
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See also: | phonon, odirection, omega_damping.
|
Topic: | omega_damping |
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.
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See also: | omega, odirection, phonon.
|
Topic: | odirection |
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.
|
Topic: | nononanal |
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.
Note: The Born effective charges are not presently available
with electronegativity equalisation and therefore this keyword
will automatically be set.
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See also: | phonon, gamma_direction_of_approach, gamma_angular_steps.
|
Topic: | 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.
|
See also: | phonon, nononanal, gamma_angular_steps.
|
Topic: | gamma_angular_steps |
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.
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See also: | phonon, nononanal, gamma_direction_of_approach.
|
Topic: | zero_potential |
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.
|
Topic: | mccreate |
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.
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See also: | mcdestroy, mcmove, mcrotate, mctrial, montecarlo.
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Topic: | mcdestroy |
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.
|
See also: | mccreate, mcmove, mcrotate, mctrial, montecarlo.
|
Topic: | mcmove |
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.
|
See also: | mccreate, mcdestroy, mcrotate, mctrial, montecarlo.
|
Topic: | mcrotate |
Type: | Option |
Format: | mcrotate probability |
Default: | 0.0 |
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.
|
See also: | mccreate, mcdestroy, mcmove, mctrial, mcmaxrotation, montecarlo.
|
Topic: | mctrial |
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.
|
Topic: | mcoutfreq |
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.
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See also: | mcsample, montecarlo.
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Topic: | mcsample |
Type: | Option |
Format: | mcsample <frequency> <filename> |
Default: | 10 / gulp.gmc |
Units: | None |
Use: | Specifies the frequency for outputing 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)
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See also: | montecarlo, mcoutfreq.
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Topic: | mcmaxdisplacement |
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.
mcmaxdisplacement 0.1
mcmaxdisplacement 0.05 target 0.5 20
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See also: | mcmove, montecarlo.
|
Topic: | mcmaxrotation |
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.
mcmaxrotation 90
mcmaxrotation 180 target 0.5 20
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See also: | mcrotate, montecarlo.
|
Topic: | mcchemicalpotential |
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.
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See also: | mccreate, mcdestroy, mctrial, montecarlo, gcmcspecies, mcvolume.
|
Topic: | mcvolume |
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.
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See also: | montecarlo, mcchemicalpotential.
|
Topic: | gcmcspecies |
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.
H core
O core
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See also: | mccreate, mcdestroy, montecarlo, gcmcmolecule.
|
Topic: | gcmcmolecule |
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.
N core 0.0 0.0 -0.6
N core 0.0 0.0 0.6
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See also: | mccreate, mcdestroy, montecarlo, gcmcspecies.
|
Topic: | mcstep |
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 constitent with the mean properties given and the second
one must obviously be smaller than the first.
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See also: | mcmeans, mctrial, montecarlo.
|
Topic: | mcmeans |
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.
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See also: | mcstep, mctrial, montecarlo.
|
Topic: | trajectory_format |
Type: | Information |
Topic: | scmaxsearch |
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!
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See also: | free, zsisa, manybody, eam_functional, eam_density.
|
Topic: | lowest_mode |
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
|
Topic: | srefractive_index |
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, and weight.
|
Topic: | hfrefractive_index |
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.
|
Topic: | finite |
Type: | Option |
Format: | finite <value> |
Default: | 0.0001 |
Units: | none (fractional) |
Use: | Requests that the first derivatives with respect to the energy (or free energy if keyword "free" is present) are calculated numerically
by central finite differences. If a value is specified after the
option then this specifies the fractional change to be used as the
step size. Note that if the value is too large then the gradients
will be inaccurate. However, if the value is too small then numerical
noise can lead to inaccuracies as well.
This option is largely only of use for checking analytical derivatives
during debugging and is intended for use with single point calculations.
|
See also: | gradients.
|
Topic: | marvinSE |
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)
|
Topic: | noelectrostatics |
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.
|
Topic: | zsisa |
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.
|
Topic: | keyword |
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
|
Topic: | ignore |
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.
|
Topic: | erongi |
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.
|
Topic: | dcharge |
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.
|
Topic: | qeq |
Type: | Keyword |
Use: | Calculate charges by Rappe and Goddards QEq scheme. This differs from Mortiers 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 EEM and fixed
charges will be taken for region 2.
|
See also: | eem, qeqtol, qeqiter, qeqradius, dcharge, sm.
|
Topic: | qeqtol |
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.
|
Topic: | qeqiter |
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.
|
Topic: | qeqradius |
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.
|
Topic: | minimum_image |
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.
|
See also: | md.
|
Topic: | integrator |
Type: | Option |
Format: | integrator <gear/velocity verlet/leapfrog verlet> <iter> |
Default: | leapfrog verlet |
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.
|
See also: | md.
|
Topic: | rydberg |
Type: | Option |
Format: | rydberg <intra/inter> <bond/x12/x13/o14> <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))
|
Topic: | manybody |
Type: | option |
Format: | manybody atom1 atom2 <rmin> rmax
|
Default: | = 0 rmin = 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.
|
See also: | eam_density, eam_functional, scmaxsearch, noquicksearch.
|
Topic: | noquicksearch |
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!
|
Topic: | eam_functional |
Type: | option |
Format: | eam_functional <square_root> <power n> <banerjea_smith n> if square_root or power :
atom1 A_1
atom2 A_2 etc...
if banerjea_smith :
atom1 F0_1 F1_1 rho0_1
atom2 F0_2 F1_2 rho0_2 etc...
|
Units: | A, F0 and F1 in eV, rho0 is 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. Currently there are 3 possibilities:
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
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
dependant parameters also to be specified (F0, F1, rho0)
where rho0 is the electron density at equilibrium.
|
See also: | eam_density, manybody, scmaxsearch, eam_alloy.
|
Topic: | eam_density |
Type: | option |
Format: | eam_density <power/exponential/gaussian/cubic/quadratic/quartic> <n> atom C (power law) <1 x flag >
atom A B r0 (exponential) <3 x flags>
atom A B r0 (gaussian) <3 x flags>
atom A r0 (quadratic) <2 x flags>
atom A r0 (cubic) <2 x flags>
atom A r0 (quartic) <2 x flags>
atom A beta (voter) <2 x flags>
|
Units: | depends on density functional chosen, but energies are in eV and distances in Angstroms
|
Use: | specifies the density due a given atom at another atomic centre 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.
The density can take one of three functional forms:
Power Law:
rho(i) = C*rij**(-n)
e.g. eam_density power 6
Ni core 729.7
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))
Note that the cut-offs are set by the manybody potential
|
See also: | manybody, eam_functional, scmaxsearch, eam_alloy.
|
Topic: | eam_alloy |
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 unscale function of the density.
|
See also: | manybody, eam_functional, eam_density, scmaxsearch.
|
Topic: | eam_potential_shift |
Type: | Option |
Format: | eam_potential_shift <kjmol/kcal/au> 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))
|
See also: | manybody, eam_functional, eam_density.
|
Topic: | newda |
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.
|
Topic: | qok |
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.
|
Topic: | dipole |
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 however
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.
|
Topic: | oldelastic |
Type: | keyword |
Use: | It has recently been found that there was a term missing from the original published expressions for some of the
elastic constants as coded in all known programs in this
area. Because the missing term is the first strain derivative
there will only have been an error in elastic constants
calculated away from the equilibrium geometry (where they
are not particularly meaningful). Hence most results will
still be correct despite this missing term, except where
complex structures have been fitted to elastic constants
without the relax option.
|
See also: | prop.
|
Topic: | ensemble |
Type: | option |
Format: | ensemble <NVE/NVT qnose/NPT qnose qpress> |
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.
|
See also: | md.
|
Topic: | tether |
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.
|
See also: | md.
|
Topic: | shellmass |
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.
|
Topic: | mdarchive |
Type: | Option |
Format: | mdarchive 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.
|
See also: | md, write, output.
|
Topic: | mdconstraint |
Type: | Option |
Format: | mdconstraint atom_1 atom_2 distance |
Units: | Angstroms |
Use: | Specifies that two atoms are constrained to a given distance during an MD simulation. Currently only one constraint is allowed per MD
run. This allows the direct solution for the constraint force, rather
than use of the Rattle algorithm.
|
See also: | md.
|
Topic: | velocities |
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.
|
Topic: | accelerations |
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.
|
Topic: | absolute_coordinates |
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.
|
Topic: | cvec |
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.
|
Topic: | caver |
Type: | Option |
Format: | aver 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.
|
Topic: | aver |
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.
|
Topic: | cfaver |
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.
|
Topic: | current_time |
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.
|
Topic: | iterations |
Type: | Option |
Format: | iterations n <gradient norm> <noextrapolate> <order_of_extrapolation> |
Default: | n = 10, gradient norm = 1.0D-10, 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.
|
Topic: | conserved |
Type: | Keyword |
Use: | Causes the conserved quantity for the MD ensemble to be output where applicable.
|
Topic: | hexagonal |
Type: | Keyword |
Use: | Causes a rhombohedral structure to be output in hexagonal form in the dumpfile.
|
Topic: | potgrid |
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.
|
See also: | pot, potential, potsites.
|
Topic: | 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.
|
See also: | pot, potential, potgrid.
|
Topic: | accuracy |
Type: | Option |
Format: | accuracy <exponent> < |
Units: | none |
Default: | 8.0 < 4 20 > |
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 same precision by searching for the number of
neutral cells that must be included in each direction in the sum. The last
parameter 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.
|
Topic: | c6 |
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.
|
Topic: | name |
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
|
Topic: | translate |
Type: | Option |
Default: | none |
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
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.
|
See also: | nofirst_point.
|
Topic: | nofirst_point |
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.
|
Topic: | gdcrit |
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). gdcrit sets the criterion for
switching between these minimisation methods.
|
See also: | defect.
|
Topic: | fix_molecule |
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.
|
Topic: | cmm |
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.
|
Topic: | norepulsive_cutoff |
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.
|
Topic: | switch_minimiser |
Type: | Option |
Format: | switch_minimiser <minimiser> <cycle/gnorm> <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.
|
See also: | optimise, rfo, unit, conj.
|
Topic: | potential |
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.
|
Topic: | library |
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.
|
Topic: | line_continuation |
Type: | Information |
Use: | 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
|
Topic: | bsm |
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
|
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.
|
Topic: | save |
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.
|
Topic: | restore |
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.
|
Topic: | deflist |
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.
|
Topic: | reldef |
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.
|
Topic: | nod2sym |
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.
|
Topic: | tscale |
Type: | Option |
Format: | tscale value <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.
|
See also: | md, equilibration, production, timestep, sample, write.
nolist, temperature, delayforce, endforce, momentum_correct.
|
Topic: | timestep |
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, delayforce, endforce, momentum_correct.
|
Topic: | equilibration |
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, delayforce, endforce, momentum_correct.
|
Topic: | production |
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, delayforce, endforce, momentum_correct.
|
Topic: | sample |
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, delayforce, endforce.
|
Topic: | momentum_correct |
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, delayforce, endforce, sample.
|
Topic: | write |
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, delayforce, endforce.
|
Topic: | delayforce |
Type: | Option |
Format: | delayforce 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, endforce.
|
Topic: | endforce |
Type: | Option |
Format: | endforce 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, delayforce.
|
Topic: | md |
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.
|
Topic: | nolist_md |
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, four, md.
|
Topic: | frequency |
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.
|
Topic: | epsilon/sigma |
Type: | Option |
Format: | epsilon <kcal/kjmol> <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.
|
See also: | lennard, atomab.
|
Topic: | atomab |
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.
|
Topic: | electronegativity |
Type: | Option |
Format: | <Atomic symbol/atomic number> chi <mu> <2 x flags for fitting> |
Units: | Chi and mu in eV |
Use: | Allows the user to specify the parameters need for the electronegativity equalisation method for determining
charges. Note that if the flags are not specified they
are assumed to be zero.
|
See also: | eem, qelectronegativity, smelectronegativity.
|
Topic: | qelectronegativity |
Type: | Option |
Format: | <Atomic symbol/atomic number> chi <mu> <2 x flags for fitting> |
Units: | Chi and mu in eV |
Use: | Allows the user to specify the parameters need for the QEq electronegativity equalisation method for determining
charges. Note that if the flags are not specified they
are assumed to be zero.
|
See also: | eem, electronegativity, qeq, smelectronegativity.
|
Topic: | smelectronegativity |
Type: | Option |
Format: | <Atomic symbol/atomic number> chi mu zeta Znuc <4 x flags> |
Units: | Chi and mu in eV, Znuc in a.u., zeta in Angstroms**-1 |
Use: | Allows the user to specify the parameters need 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.
|
See also: | sm, eem, electronegativity, qeq, qelectronegativity.
|
Topic: | sm |
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.
|
Topic: | bulk_noopt |
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.
|
Topic: | move_2a_to_1 |
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. Should the number of ions exceed the maximum
allowed for region 1 then the ions will be moved up to the
final shell of ions that will fit. The radius value must
not be less than the region 1 radius.
|
See also: | defect, centre, size, region_1, vacancy, interstitial,.
impurity, bulk_noopt.
|
Topic: | noanisotropic_2b |
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.
|
Topic: | mode2a |
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.
|
Topic: | size |
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.
|
Topic: | centre |
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.
|
See also: | defect, size, region_1, region_before,.
impurity, vacancy, impurity, interstitial, frequency, bulk_noopt.
|
Topic: | defect |
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, region_before, vacancy,.
impurity, interstitial, frequency, noanisotropic, save.
restore, gdcrit, and bulk_noopt.
|
Topic: | region_1 |
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, region_before, bulk_noopt.
|
Topic: | regi_before |
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.
|
Topic: | vacancy |
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.
|
Topic: | interstitial |
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.
|
Topic: | impurity |
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.
|
Topic: | optimise |
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, trans, rfo.
|
Topic: | gradients |
Type: | Option |
Format: | gradients <units> atom_no. x y z
|
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.
|
Topic: | transition_state |
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: | opti, rfo.
|
Topic: | rfo |
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: | opti, trans.
|
Topic: | maximise |
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: | opti, rfo, trans.
|
Topic: | distance |
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".
|
Topic: | eem |
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.
|
Topic: | pot |
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.
|
Topic: | nodpsym |
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.
|
Topic: | conv |
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.
|
Topic: | conp |
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.
|
Topic: | noflags |
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.
|
Topic: | shell |
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.
|
Topic: | breathe |
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.
|
Topic: | cellonly |
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.
|
Topic: | isotropic |
Type: | Keyword |
Use: | Only allow isotropic cell expansion and contraction during optimisation.
|
Topic: | free_energy |
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.
|
See also: | phonon, nozeropt, static_first, zsisa, scmaxsearch.
|
Topic: | static_first |
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, and zsisa.
|
Topic: | nozeropt |
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.
|
Topic: | noenergy |
Type: | Keyword |
Use: | Do not calculate energy. |
Topic: | nodensity_out |
Type: | Keyword |
Use: | Do not write phonon density of states curve to output channel. |
Topic: | broaden_dos |
Type: | Keyword and option |
Default: | 0.2 |
Use: | An approximation to the delta function is used in order to line Lorenzian 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 smaller the factor, the greater the broadening.
|
See also: | phonon, project, output.
|
Topic: | unfreeze |
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: | opti, trans, cello, and noexclude.
|
Topic: | debug |
Type: | Keyword |
Use: | Could do anything! For programmers' use only. |
Topic: | efg |
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.
|
Topic: | single |
Type: | Keyword |
Use: | Calculate energy only - default calculation. |
Topic: | ftol |
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.
|
Topic: | gmax |
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 gtol > 1.0 => gtol=10**(-gtol)
If opt/fit is not supplied then value is applied to both.
|
See also: | gdcrit, gtol.
|
Topic: | gtol |
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.
|
Topic: | bond |
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.
|
Topic: | angle |
Type: | Keyword |
Use: | Print out all valid three-body angles found for the three-body potentials.
|
Topic: | linmin |
Type: | Keyword |
Default: | no printing |
Use: | Print out details of line minimisations. |
Topic: | both |
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.
|
Topic: | scale |
Type: | Option |
Format: | scale <real number> |
Units: | none |
Default: | 1.0 |
Use: | Scales subsequent cell vectors and cartesian coordinates by the scale factor.
|
Topic: | vectors |
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 optimsation flags appear on last line.
|
Topic: | svectors |
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.
|
Topic: | pvector |
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.
|
Topic: | cell |
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.
|
Topic: | scell |
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.
|
Topic: | pcell |
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.
|
Topic: | cartesian |
Type: | Option |
Format: | cartesian <region <n> <rigid <xyz>>> <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
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.
|
Topic: | fractional |
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.
|
Topic: | sregion2 |
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.
|
Topic: | sbulkenergy |
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.
|
Topic: | totalenergy |
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.
|
Topic: | dhkl |
Type: | Option |
Format: | dhkl <width of growth slice> <au> |
Units: | eV |
Use: | This specifies the spacing of the hkl planes which is equivalent to the width of the growth slice for the calculation of the attachment energy.
This should only be specified for an unrelaxed surface. For a general
surface the growth slice can be marked by adding a "%" sign to the end
of the coordinate line.
|
See also: | sfractional, cartesian.
|
Topic: | sfractional |
Type: | Option |
Format: | sfractional <region <n> <rigid <xyz>>> 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
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.
|
Topic: | pfractional |
Type: | Option |
Format: | pfractional <region <n> <rigid <xyz>>> 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.
|
Topic: | cutd |
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.
|
Topic: | cutp |
Type: | Option |
Format: | cutp cutoff_distance <polynomial/cosine/voter> <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). Either a polynomial or cosine taper form can be used.
The form of the Voter taper is:
E_smooth(r) = E(r) - E(rcut) + (rcut/m)*(1 - (r/rcut)**m)*(dE(rcut)/dR)
Note that in the case of the Voter taper form there is no taper range
since it applies over the whole range.
|
Topic: | bocharge |
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.
|
Topic: | boselfenergy |
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.
|
Topic: | botwobody |
Type: | Option |
Format: | botwobody <kcal/kjmol> atom1 atom2 A B za zb rtaper rmax <4*flags>
or
botwobody combine
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 |
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.
|
See also: | borepulsive, boattractive, bocharge, boselfenergy.
|
Topic: | borepulsive |
Type: | Option |
Format: | borepulsive atom1 alpha m n lamba <3*flags>
or
borepulsive theta
atom1 alpha m n lambda c d h <6*flags>
|
Units: | lambda in 1/Angstroms All other quantities are unitless.
|
Default: | none |
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.
|
See also: | botwobody, boattractive, bocharge, boselfenergy.
|
Topic: | boattractive |
Type: | Option |
Format: | boattractive atom1 alpha m n lamba <3*flags>
or
boattractive theta
atom1 alpha m n lambda c d h <6*flags>
|
Units: | lambda in 1/Angstroms All other quantities are unitless.
|
Default: | none |
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.
|
See also: | botwobody, borepulsive, bocharge, boselfenergy.
|
Topic: | potential_interpolation |
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.
|
Topic: | buckingham |
Type: | Option |
Format: | buckingham <inter/intra> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential, cutoffs are omitted from input.
|
See also: | c6.
|
Topic: | spline |
Type: | Option |
Format: | spline <rational/cubic> <reverse> <intra/inter> <bond/x12> <kcal/kjmol> 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.
When specified as bonded, potential cutoffs are omitted from input.
|
Topic: | buck4 |
Type: | Option |
Format: | buck4 <inter/intra> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential, cutoffs are omitted from input.
|
Topic: | tsuneyuki |
Type: | Option |
Format: | tsuneyuki <form1/form2> atom1 atom2 Q1 Q2 zeta <rmin> rmax <1*flag>
|
Units: | Q1 & Q2 in a.u., zeta in Angstroms**-1 |
Default: | 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
limited. 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
|
Topic: | lennard |
Type: | Option |
Format: | lennard <epsilon> <zero> <esff> <combine/geometric> <m> <n> <inter/intra> <kcal/kjmol> <all> <scale14>
atom1 atom2 (A B/epsilon sigma) <rmin> rmax <2*flags>
|
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
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.
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, based on the values that have been
specified up to that point. 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.
|
See also: | epsilon, atomab, c6.
|
Topic: | igauss |
Type: | Option |
Format: | igauss <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | covexp |
Type: | Option |
Format: | covexp <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | morse |
Type: | Option |
Format: | morse <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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: | none |
Use: | Morse 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 = De.((1-exp(-a(r-r0)))**2 - 1.0) -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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | fermi-dirac |
Type: | Option |
Format: | fermi-dirac <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> atom1 atom2 a b r0 <rmin> rmax <3*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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | ljbuffered |
Type: | Option |
Format: | ljbuffered <m> <n> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | qtaper |
Type: | Option |
Format: | qtaper <intra/inter> <bond/x12/x13/o14> <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.
When specified as bonded potential cutoffs are omitted from input.
|
Topic: | qerfc |
Type: | Option |
Format: | qerfc <intra/inter> <bond/x12/x13/o14> <au/nm/pm> 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.
When specified as bonded potential cutoffs are omitted from input.
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.
|
Topic: | qwolf |
Type: | Option |
Format: | qwolf <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.
|
See also: | noelectrostatics.
|
Topic: | delta |
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.
|
Topic: | maxcyc |
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.
|
Topic: | stepmx |
Type: | Option |
Format: | stepmx <opt/fit> <real value> |
Units: | fractional |
Default: | 1.0 for opt / 1000.0 for fit |
Use: | Maximum step size in optimisation/fitting. 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.
|
Topic: | xtol |
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.
|
Topic: | spacegroup |
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.
|
Topic: | nosymmetry |
Type: | Keyword |
Use: | Switches off symmetry after generating unit cell. For non-primitive systems the final unit cell is primitive.
|
Topic: | nodsymmetry |
Type: | Keyword |
Use: | Switches off the use of symmetry in defect calculations. |
Topic: | fbfgs |
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.
|
Topic: | genetic |
Type: | Keywrd |
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, and cost.
| Topic: | genetic |
Type: | Option |
Use: | Start of genetic algorithm options section, closed by "end" | See also: | tournament, crossover, mutation, discrete,.
configurations, best, maximum, minimum, dmaximum, dminimum.
|
Topic: | tournament |
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 optimisation stuck in local min
then if stepsize non-zero tournament is reset to <initial>.
|
See also: | genetic, anneal, option, and gexp.
|
Topic: | crossover |
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 incremented by <stepsize>. If optimisation
stuck in local min then if stepsize non-zero tournament is reset
to <initial>.
|
See also: | genetic, anneal, option, and tpxo.
|
Topic: | mutation |
Type: | Option |
Format: | mutation initial <final> <stepsize> |
Default: | 1/(sum of discretation 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 incremented by <stepsize>. If optimisation
stuck in local min then either (i) if stepsize non-zero tournament
is reset to <initial> OR (ii) grid fixed then mutation rate changed.
|
See also: | genetic, anneal, option, and grid.
|
Topic: | configurations |
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
greater than n then population will expand by stepsize (default
2) every iteration until <n=max> afterwhich <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, and predict.
|
Topic: | unique |
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.
|
Topic: | best |
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, and predict.
|
Topic: | discrete |
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.
|
Topic: | minimum |
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.
|
Topic: | maximum |
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.
|
Topic: | dminimum |
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.
|
Topic: | dmaximum |
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.
|
Topic: | time |
Type: | Option |
Format: | time time_limit <seconds/minutes/hours> |
Units: | seconds (default), minutes or hours |
Default: | Infinity! |
Use: | Specifies time limit for calculation. |
Topic: | variables |
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.
|
Topic: | shift |
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.
|
Topic: | sshift |
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.
|
Topic: | three-body |
Type: | Option |
Format: | three <exponential/vessal/cosine> <k3> <k4> <intra/inter> <bond> <kcal/kjmol> 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) <2xflags>
|
Units: | k in eVrad**-2, theta0 in degrees, rmin & rmax in Angs, k3 in eVrad**-3 k4 in eVrad**-4
|
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 rmax12 rmax13 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 rmax12 rmax13 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 rmax12 rmax13 rmax23 <3xflags>
three k4
atom1 atom2 atom3 k k4 theta0 rmax12 rmax13 rmax23 <3xflags>
three k3 k4
atom1 atom2 atom3 k k3 k4 theta0 rmax12 rmax13 rmax23 <4xflags>
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
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: | axilrod-teller, angle, stillinger-weber, exponential, bcross.
urey-bradley, murrell-mottram, bacross, lin3.
|
Topic: | lin3 |
Type: | Option |
Format: | lin3 <intra/inter> <bond> <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 * (isign*cos(n*theta) + 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.
urey-bradley, murrell-mottram, bacross, three.
|
Topic: | axilrod-teller |
Type: | Option |
Format: | axilrod-teller <intra/inter> <bond> <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, angle, exponential, stillinger-weber, bcross, urey-bradley,.
murrell-mottram, bacross.
|
Topic: | murrell-mottram |
Type: | Option |
Format: | murrell-mottram <intra/inter> <bond> <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, angle, axilrod-teller, stillinger-weber, bcross, urey-bradley,.
exponential, bacross.
|
Topic: | exponential |
Type: | Option |
Format: | exponential <intra/inter> <bond> <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, angle, axilrod-teller, stillinger-weber, bcross, urey-bradley,.
murrell-mottram, bacross.
|
Topic: | stillinger-weber |
Type: | Information 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.
|
Topic: | sw2 |
Type: | Option |
Format: | sw2 <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
|
Topic: | sw2jb |
Type: | Option |
Format: | sw2jb <intra/inter> <bond/x12/x13/o14> <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 (2000) for more details.
|
See also: | sw3, sw2, sw3jb.
|
Topic: | sw3 |
Type: | Option |
Format: | sw3 <intra/inter> <bond> <kcal/kjmol> atom1 atom2 atom3 K theta0 rho1 rho2 rmin12 rmax12 rmin13 rmax13 rmin23
rmax23 <4*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)
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, angle, exponential, axilrod-teller, bcross, sw2, sw2jb, urey-bradley,.
murrell-mottram, bcoscross, bacross, sw3jb.
|
Topic: | sw3jb |
Type: | Option |
Format: | sw3jb <intra/inter> <bond> <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 (2000) 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, angle, exponential, axilrod-teller, bcross, sw2, sw2jb, urey-bradley,.
murrell-mottram, bcoscross, bacross, sw3.
|
Topic: | bcoscross |
Type: | Option |
Format: | bcoscross <intra/inter> <bond> <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, angle, exponential, axilrod-teller, stillinger, urey-bradley,.
murrell-mottram, bacross, bcross.
|
Topic: | bcross |
Type: | Option |
Format: | bcross <intra/inter> <bond> <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, angle, exponential, axilrod-teller, stillinger, urey-bradley,.
murrell-mottram, bacross.
|
Topic: | bacross |
Type: | Option |
Format: | bacross <intra/inter> <bond> <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**2, 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, angle, exponential, axilrod-teller, stillinger, urey-bradley,.
murrell-mottram, bcross.
|
Topic: | urey-bradley |
Type: | Option |
Format: | urey-bradley <intra/inter> <bond> <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, angle, exponential, axilrod-teller, stillinger, bcross,.
urey-bradley, murrell-mottram, bacross.
|
Topic: | rtol |
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.
|
Topic: | title |
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
|
Topic: | species |
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.
|
See also: | library.
|
Topic: | polarisability |
Type: | Option |
Format: | polarisability atom_symbol <core/shell> dipolar_polarisability
|
Units: | dipolar_polarisability in Angs**3 |
Default: | Polarisability is equal to zero, except for shell contribution |
Use: | Allows the inclusion of point ion polarisability in a calculation. At the moment this is non-self consistent, i.e. induced moments on
different centres do not interact.
|
Topic: | dump |
Type: | Option |
Format: | dump <every <integer n>> <channel> <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.
|
Topic: | harmonic |
Type: | Option |
Format: | harmonic <k3> <k4> <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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
|
Use: | Harmonic 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 = 1/2 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.
When specified as bonded potential, cutoffs are omitted from input.
|
See also: | spring, squaredharmonic.
|
Topic: | squaredharmonic |
Type: | Option |
Format: | squaredharmonic <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential, cutoffs are omitted from input.
|
See also: | spring, harmonic.
|
Topic: | cuts |
Type: | Option |
Format: | cuts cutoff_distance <angs/au> |
Units: | Angstrom (default) or au |
Default: | 0.6 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.
|
Topic: | simultaneous |
Type: | Keyword |
Default: | no relaxation |
Use: | Allows simultaneous relaxation of shells during fitting, including both position and radius.
|
See also: | relax, fit, breathe, noflags.
|
Topic: | charge |
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.
|
Topic: | Cv |
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,.
bornq, and weight.
|
Topic: | entropy |
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,.
bornq, and weight.
|
Topic: | bulk_modulus |
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.
|
Topic: | shear_modulus |
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.
|
Topic: | hill |
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.
|
Topic: | voigt |
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.
|
Topic: | elastic |
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.
|
Topic: | piezoelectric |
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.
|
Topic: | hfdlc |
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.
|
Topic: | sdlc |
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.
|
Topic: | bornq |
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
Note: Born effective charges cannot currently be calculated
with electronegativity equalisation.
|
See also: | elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo.
monopoleq.
|
Topic: | monopoleq |
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.
|
Topic: | weight |
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.
|
Topic: | property |
Type: | Keyword |
Default: | properties not calculated |
Use: | Causes properties to be calculated and output. |
Topic: | energy |
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.
|
Topic: | hfdlc |
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.
|
Topic: | sdlc |
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.
|
Topic: | polynomial |
Type: | Option |
Format: | polynomial <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> order of polynomial
atom1 atom2 (norder+1)*coeff rmin rmax <(norder+1)*flags>
order of coefficients = lowest to highest
|
Units: | eV and Angstroms |
Default: | none |
Use: | Polynomial potential, order = 1-5:
E = c0 + c1*r + c2*r**2 + ... + cn*r**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.
|
Topic: | print |
Type: | Option |
Format: | n = integer no. |
Use: | Prints out current parameters during fitting whenever cycle number is exactly divisable by n.
|
See also: | dump, .
|
Topic: | split |
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.
|
Topic: | element |
Type: | Option |
Format: | word |
Default: | data as in file eledata |
Use: | Section for changes in element properties. | See also: | symbol, mass, covalent, ionic, vdw.
|
Topic: | symbol |
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.
|
Topic: | mass |
Type: | Option |
Format: | mass at.no. <mass> |
Units: | atomic units |
Default: | as per periodic table |
Use: | Allows atomic masses to be changed. Command is part of element section.
|
Topic: | covalent |
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.
|
Topic: | vdw |
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.
|
Topic: | ionic |
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.
|
Topic: | general |
Type: | Option |
Format: | general <m> <n> <ener/grad> <intr/inte> <bon/x12/x13/o14> <kcal/kjmol> <scale14> 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.
When specified as bonded potential, cutoffs are omitted from input.
|
See also: | c6.
|
Topic: | damped_dispersion |
Type: | Option |
Format: | damped <intra/inter> <bond/x12/x13/o14> <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.
When specified as bonded potential cutoffs are omitted from input.
Note that this potential cannot yet be used with the c6 keyword.
|
See also: | also:.
|
Topic: | molecule |
Type: | Keyword |
Default: | no molecules |
Use: | Program locates molecules 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,.
and 14_scale.
|
Topic: | inter |
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, and 14_scale.
|
Topic: | intra |
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.
|
Topic: | constrain |
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 the 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.
|
Topic: | outcon |
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.
|
Topic: | output |
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 and phonon:
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.
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.
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.
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.
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
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.
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>
or as ordinary text:
e.g. output freq text <filename>
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.
|
See also: | marvin, dump.
|
Topic: | rspeed |
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.
|
Topic: | ewaldrealradius |
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.
|
Topic: | compare |
Type: | Keyword |
Default: | no comparison |
Use: | Causes a table comparing the initial and final structures to printed out both for bulk and defects.
|
Topic: | torsion |
Type: | Option / Keywrd |
Format: | torsion <intra/inter> <bond> <esff> <kcal/kjmol> 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>
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 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.
|
See also: | ryckaert, outofplane, torexp, tortaper, torangle.
|
Topic: | tortaper |
Type: | Option |
Format: | tortaper <bond/intra/inter> <kcal/kjmol> <esff> 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.
|
See also: | torsion, torharm, outofplane, torexp, torangle.
|
Topic: | torexp |
Type: | Option |
Format: | torexp <bond/intra/inter> <kcal/kjmol> <esff> 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)
|
See also: | torsion, torharm, outofplane, torexp.
|
Topic: | torharm |
Type: | Option |
Format: | torharm <bond> <kcal/kjmol> atom1 atom2 atom3 atom4 K phi0 rmax(1-2) rmax(2-3) rmax(3-4) <2 x flags>
|
Units: | K in eV/rad**2, phi0 in degrees |
Default: | none |
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
|
See also: | torsion, torangle, torexp, outofplane.
|
Topic: | torangle |
Type: | Option |
Format: | torangle <bond> <kcal/kjmol> 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
|
See also: | torsion, torharm, torexp, outofplane.
|
Topic: | ryckaert |
Type: | Option |
Format: | ryckaert (or torsion ryck) norder atom1 atom2 atom3 atom4 k0 rmax(1-2) rmax(2-3) rmax(3-4) rmax(1-4) <flags*n+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.
|
See also: | torsion, outofplane, torangle, torharm, torexp.
|
Topic: | outofplane |
Type: | Option |
Format: | outofplane <intra> <bond> <kcal/kjmol> atom1 atom2 atom3 atom4 k <k4> rmax(1-2) rmax(1-3) rmax(1-4) <1 x flag>
|
Units: | k in eV*Angs**-2, k4 in eV*Angs**-4 |
Default: | none |
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
|
See also: | torsion, ryckaert, torangle, torharm, torexp.
|
Topic: | update |
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.
|
Topic: | line |
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.
|
Topic: | unit |
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.
|
Topic: | lbfgs |
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.
|
Topic: | lbfgs_order |
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.
|
Topic: | numdiag |
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.
|
Topic: | positive |
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.
|
Topic: | conjugate |
Type: | Keyword |
Use: | Use conjugate gradients to optimise geometry, instead of second derivative based methods.
|
See also: | dfp, numdiag, unit, positive, lbfgs.
| Topic: | conjugate |
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.
|
Topic: | hessian |
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.
|
Topic: | spring |
Type: | Option |
Format: | spring <kcal/kjmol> atom1 k2 <k4> <flags>
|
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 potl 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.
|
Topic: | cosh-spring |
Type: | Option |
Format: | cosh-spring <kcal/kjmol> atom1 k2 d <2 x flags>
|
Units: | k2 in eV/Angs*2, d in Angs |
Default: | None |
Use: | Core-shell spring potential with cosh functional form. Cosh-spring potl 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.
|
Topic: | coulomb |
Type: | Option |
Format: | coulomb <intra/inter> <bond/x12/x13/o14> <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 potl 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.
|
Topic: | delf |
Type: | Option |
Format: | delf energy change |
Units: | eV |
Default: | none |
Use: | Maximum change per step of minimisation of the function before Hessian is recalculated.
|
Topic: | marvin |
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.
|
Topic: | nosderv |
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.
|
Topic: | nobond |
Type: | Option |
Format: | nobond species1 species2 |
Use: | Excludes bond formation between two species during molecule search. | See also: | molecule, molq, molmec, bond, and connect.
|
Topic: | connect |
Type: | Option |
Format: | connect atom1 atom2 <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 -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
|
See also: | molecule, molq, molmec, nobond, and bond.
|
Topic: | start |
Type: | Option |
Use: | Causes program to skip the rest of the input file and begin execution. |
Topic: | stop |
Type: | Option |
Use: | Causes program to stop execution at that point in the input file. Use is mainly for locating problems in input files.
|
Topic: | molq |
Type: | Keyword |
Default: | no molecules |
Use: | Program locates molecules 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.
and 14_scale.
|
Topic: | molmec |
Type: | Keyword |
Default: | no molecules |
Use: | Program locates molecules 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.
and 14_scale.
|
Topic: | 14_scale |
Type: | Information 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 affect. 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.
|
Topic: | relax |
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.
|
Topic: | supercell |
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.
|
Topic: | eigenvectors |
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. The maximum
number of atoms is reduced by 7/10 when generating eigenvectors.
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, and intensity.
|
Topic: | lower_symmetry |
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 keyword "eigenvectors" is
implicit.
|
See also: | phonon, eigenvectors, slower.
|
Topic: | slower |
Type: | Option |
Format: | slower <value> |
Units: | None |
Default: | 0.001 |
Use: | This is the scale factor by which the eigenvectors will be multiplied when attempting to lower the symmetry along an
imaginary mode direction.
|
See also: | lower_symmetry.
|
Topic: | intensity |
Type: | Information have been calculated using "eigen". 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).
|
Topic: | project_dos |
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: | Project 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.
|
See also: | phonon, eigenvectors, output.
|
Topic: | kpoints |
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.
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See also: | phonon, dispersion, shrink, kfull.
|
Topic: | nokpoints |
Type: | Keyword |
Use: | Prevents output of list of k points for each configuration. |
Topic: | dispersion |
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 calcluated.
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.
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See also: | phonon, shrink, kpoints, box, kfull.
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Topic: | kfull |
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.
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See also: | kpoints, dispersion.
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Topic: | shrink |
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.
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See also: | phonon, dispersion, kpoints, noksym.
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Topic: | box |
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 outputing the phonon density of states or/and phonon dispersion
curves.
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See also: | phonon, dispersion, shrink.
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Topic: | origin |
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.
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Topic: | nofrequency |
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.
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See also: | kpoints, dispersion, shrink, phonon.
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Topic: | temperature |
Type: | Option |
Format: | temperature value_of_temperature <C/F/K> <step> <no. of steps> <step0> |
Units: | Kelvin (or Centigrade if C added, or Fahrenheit if F added) |
Default: | 0 K, no steps (for phonons) 100 K for simulated annealing |
Use: | Specifies temperature of a structure for use in the calculation of phonon properties, such as the entropy, free energy and heat capacity.
Also specifies the temperature for molecular dynamics runs, including
annealling.
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
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
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See also: | phonon, free, predict, anneal, ftol, factor, and ttol.
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Topic: | pressure |
Type: | Option |
Format: | value_of_pressure <GPa/kPa/Pa/atm/Nm-2/kbar> |
Units: | Gigapascals, kilopascals, 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.
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Topic: | full |
Type: | Keyword |
Use: | Causes the nosymmetry option to produce the full, instead of the primitive, unit cell.
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See also: | nosymmetry.
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Topic: | noksymmetry |
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.
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See also: | phonon, shrink.
|
Topic: | average |
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.
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Topic: | norecip |
Type: | Keyword |
Use: | Do not calculate reciprocal space contributions to the energy and derivatives.
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See also: | noreal.
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Topic: | noreal |
Type: | Keyword |
Use: | Do not calculate real space contributions to the energy and derivatives.
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See also: | norecip.
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Topic: | noexclude |
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.
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See also: | unfreeze.
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Topic: | storevectors |
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.
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See also: | resetvectors, extracutoff.
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Topic: | resetvectors |
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.
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See also: | storevectors, extracutoff.
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Topic: | extracutoff |
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.
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See also: | storevectors, resetvectors.
|
Topic: | operators |
Type: | Keyword |
Use: | Causes the program to print out the rotation matrix and shifts for all bulk symmetry operators. Primarily a debugging keyword.
|
Topic: | symmetry_cell |
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.
|
Topic: | symmetry_operator |
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.
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See also: | spacegroup, origin, symmetry_cell.
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Topic: | predict |
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).
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See also: | genetic, anneal, contents, global, and cost.
| Topic: | predict |
Type: | Option |
Use: | Start of global optimiser options section, closed by "end" | See also: | minimum, maximum, discrete, configurations, conjugate,.
tournament, crossover, mutation, seed, grid.
|
Topic: | anneal |
Type: | Keyword |
Use: | Given contents of unit cell find possible atomic coordinates by implementing an algorithm which simulates annealing.
Generally a local minimisation is proformed on the best configuration
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See also: | predict, cost, global, and temperature.
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Topic: | contents |
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 oberserved 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.
|
Topic: | global |
Type: | Keyword |
Use: | After finding possible crystal coordinates (because keyword predict specified) dump out restart files before proforming local
minimisation of the best structures.
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See also: | predict, genetic, and anneal.
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Topic: | grid |
Type: | Genetic 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.
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See also: | discrete.
|
Topic: | seed |
Type: | Genetic Option |
Format: | seed q |
Default: | -1.0 |
Use: | Part of ga options section. Initial pointer used in random number generation.
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Topic: | Two |
Type: | Genetic Option |
Default: | One Point Crossover |
Use: | Part of ga options section. | See also: | crossover.
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Topic: | Exponential |
Type: | Genetic Option |
Default: | Use tournament probability. |
Use: | Part of ga options section. If specified then probability of successs for a given configuartion is weighted exponentially
with respect to how good the configuration is compared with the
other configurations within the present population.
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See also: | tournament.
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Topic: | Minimum |
Type: | Option |
Format: | ttol Tmin |
Default: | Tmin=0.01 |
Use: | Temperature tolerence for simulated annealing routine. |
Topic: | Temperature |
Type: | Option |
Format: | factor theta |
Default: | theta=0.9 |
Use: | Temperature reduction factor. A larger factor implies a faster decay of simulated temperature.
|
Topic: | Cost |
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.
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See also: | predict, genetic, and anneal.
| Topic: | Cost |
Type: | Genetic Option |
Format: | cost k q |
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.
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Topic: 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
|