GULP help file

(HTML version generated from help.txt, see also GULP plain text file)

Keywords in alphabetical order


14_scale,
accuracy, angle, anneal, atomab, average, axilrod-teller,
bacross, bcross, best, bond, both, box, breathe, broaden_dos, bsm, buck4, buckingham, bulk_modulus, bulk_noopt,
c6, cartesian, cell, cellonly, centre, charge, cmm, compare, configurations, conjugate, conp, constrain, contents, conv, cost, coulomb, covalent, covexp, crossover, cutd, cutp, cuts, cv,
damped_dispersion, dcharge, debug, defect, deflist, delf, delta, dfp, dipole, discrete, dispersion, distance, dump,
eam_density, eam_functional, eem, efg, eigenvectors, elastic, electronegativity, element, energy, ensemble, entropy, epsilon/sigma, equilibration, erongi, exponential_three_body,
factor, finite, fit, fix_molecule, fractional, free_energy, frequency, ftol, full,
gdcrit, general, genetic, gexp, global, gradient, gradients, grid, gtol,
harmonic, hessian, hexagonal, hfdlc, hfrefractive_index, high-fq,
ignore, impurity, integrator, intensity, inter, interstitial, intra, ionic, isotropic, iterations,
keyword, kpoints,
lennard_jones, library, lin3, line, line_continuation, linmin, lower_symmetry, lowest_mode,
manybody, marvin, mass, maxcyc, maximise, maximum, maxone, md, mdarchive, minimum, minimum_image, mode2a, molecule, molmec, molq, 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, noreal, norecip, norepulsive_cutoff, nosderv, nosymmetry, nozeropt, numdiag,
observables, oldelastic, operators, optimise, origin, outcon, outofplane, output,
phonon, piezoelectric, polynomial, positive, pot, potential, potgrid, predict, pressure, print, production, project_dos, property,
qeq, qeqiter, qeqradius, qeqtol, qerfc, qok, qtaper,
regi2a, regi_before, region_1, relax, reldef, restore, rfo, rspeed, rtol, ryckaert, rydberg,
sample, save, scale, scmaxsearch, sdlc, seed, shear_modulus, shell, shellmass, shift, shrink, simultaneous, single, size, spacegroup, species, spline, split, spring, srefractive_index, start, static, static_first, stepmx, stillinger-weber, stop, supercell, sw2, sw3, switch_minimiser, symbol,
temperature, tether, three-body, time, timestep, title, torsion, tournament, tpxo, trajectory_format, transition_state, translate, tscale, ttol,
unfreeze, unique, unit, update, urey-bradley,
vacancy, valid_spacegroups, variables, vectors,
weight, write,
xtol,
zsisa,
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!
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.
See also:gradients.
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.
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. Note that it is important to investigate the effect of qeqradius on the degree of convergence and CPU time.

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.

See also:eem, qeqtol, qeqiter, qeqradius, dcharge.
Topic:qeqtol
Type:Option
Format:qeqtol tolerance
Units:Electrons
Default:0.0001
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.
Topic:eam_functional
Type:option
Format:eam_functional <square_root> <power n> <banerjea_smith n> if banerjea_smith: atom1 F0_1 F1_1 rho0_1 atom2 F0_2 F1_2 rho0_2 etc...
Units:F0 and F1 in eV, rho0 is dimensionless
Default:square_root
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) (rho(i))**1/2

this is the most common functional, as used in the Sutton-Chen potential

Power:

E = - sum(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.
Topic:eam_density
Type:option
Format:eam_density <power/exponential/gaussian/cubic> <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 (cubic) <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

Cubic:

rho(i) = A*(r0-rij)**3

Note that the cut-offs are set by the manybody potential

See also:manybody, eam_functional, scmaxsearch.
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 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.
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'.
See also:md, write.
Topic:iterations
Type:Option
Format:iterations n <gradient norm>
Default:n = 10, gradient norm = 1.0D-10
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.
See also:shellmass.
Topic:hexagonal
Type:Keyword
Use:Causes a rhombohedral structure to be output in hexagonal form in the dumpfile.
Topic:maxone
Type:Option
Format:maxone <integer number>
Units:none
Use:Controls the maximum size of the second derivative matrix that GULP can use, when dynamic memory is available. Normally this value will default to 3 x the number of atoms, or 4 if breathing shells are present. Setting this parameter to a lower value will force the program to use less memory, which may mean that some calculation types are no longer possible and that an optimisation may chose a different default algorithm.
Topic:potgrid
Type:Option
Format:potgrid <xmin xmax ymin ymax zmin zmax> nx ny nz
Units:fractional (3D) / 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.
Topic:accuracy
Type:Option
Format:real number on same or next line
Units:none
Default:8.0
Use:Controls the accuracy of Ewald summation. Value is used as an exponent.
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:1.0
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.
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> <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>

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))]

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.
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.
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.
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.
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.
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.
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, and minimum_image.
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 <weight> (x n, on separate lines)
Units:cm-1
Use:Subsection of observables, used for specifying frequencies for fitting to. The number is the position of the mode required in order of increasing frequency. For three-dimensional solids only one k point may be fitted at once, and if none is specified then the gamma point is assumed. e.g. frequency 2 1 0.0 6 902.0
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>
Units:Chi and mu in eV
Use:Allows the user to specify the parameters need for the electronegativity equilisation method for determining charges.
See also:eem.
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_2> <old_radius_region_1>
Units:Angstroms
Default:none
Use:Specifies the region 1 and 2 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:regi2a
Type:keyword
Use:print out region 2a in the output
See also:region_1, regi_before, defect.
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:gradient
Type:Keyword
Use:Calculate gradients but do not optimise
See also:conp, conv, cellonly, isotropic, finite, and shell.
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.

See also:qeq, dcharge.
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.
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:nobreathe
Type:Keyword
Use:Excludes radii from the optimisation variables.
See also:conp, conv, noflags, shell, breathe, 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.
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:gtol
Type:Option
Format:gtol <opt/fit> real value
Units:fractional
Default:0.00001 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.
Topic:bond
Type:Keyword
Use:Print out bond length analysis at beginning and end of run. Standard covalent radii are used with a 10% tolerance. To change radii see element and covalent.
See also:distance, average.
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.
See also:cell.
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:cartesian
Type:Option
Format:cartesian <angs/au> at no. x y z <charge> <occupancy> <3 x optimisation flags> or at no. x y z <charge> <occupancy> <3 x optimisation flags> or at.sym. <species type> x y z <charge> <occupancy> <3 x flags>
Units:Angstrom (default) or au for coordinates and electrons for charge
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.
See also:fractional, spacegroup.
Topic:fractional
Type:Option
Format:fractional at no. x y z <charge> <occupancy> <3 x optimisation flags> or at no. x y z <charge> <occupancy> <3 x optimisation flags> or at.sym. <species type> x y z <charge> <occupancy> <3 x flags>
Units:Fractional and electrons
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, and space.
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 <taper range> <angs/au>
Units:Angstrom (default) or au
Default:Use individual potential values
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).
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:lennard
Type:Option
Format:lennard <epsilon> <zero> <esff> <combine> <m> <n> <inter/intra> <kcal/kjmol> 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.

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. When specified as bonded potential, cutoffs are omitted from input.

See also:epsilon, atomab, c6.
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: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: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.
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:fit
Type:Keyword
Use:Perform fitting run using BFGS method.
See also:simul, relax, genetic.
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.
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:observables
Type:Option
Format:keyword
Default:only derivatives marked for optimisation
Use:Specifies fitting observables other than structure which use derivatives.
See also:elastic, hfdlc, sdlc, energy, bulk_modulus, shear_modulus, weight.
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: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:torsion, ryckaert.
Topic:three-body
Type:Option
Format:three <exponential/vessal/cosine> <k3> <k4> <intra/inter> <bond> <kcal/kjmol> atom1 atom2 atom3 k <k3> <k4> theta0 rmax(1-2) rmax(1-3) rmax(2-3) <2xflags>
Units:k in eVrad**-2, theta0 in degrees, 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 theta 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 rmax(1-2) rmax(1-3) rmax(2-3) <flag>
Units:K in eV
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 rmax(1-2) rmax(1-3) rmax(2-3) <flag>
Units:k in eV*Angstroms**9
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 rmax12 rmax13 rmax23 <5*flags> c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 <11*flags>
Units:K in eV, r012,r013,r023 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)

Q1 = (r12-r012)/r012 Q2 = (r13-r013)/r013 Q3 = (r23-r023)/r023

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 rmax12 rmax13 rmax23 <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, sw3.
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.
Topic:sw3
Type:Option
Format:sw3 <intra/inter> <bond> <kcal/kjmol> atom1 atom2 atom3 K theta0 rho rmax12 rmax13 rmax23 <3*flags>
Units:K in eV, theta in degrees, rho in Angstroms
Use:Stillinger-Weber's three-body potential with cutoff smoothing

E(three) = K * exp(rho/(r12-rmax12) + rho/(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.

See also:three, angle, exponential, axilrod-teller, bcross, sw2, urey-bradley,. murrell-mottram, and bacross.
Topic:bcross
Type:Option
Format:bcross <intra/inter> <bond> <kcal/kjmol> atom1 atom2 atom3 K r1 r2 rmax12 rmax13 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 rmax12 rmax13 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 rmax12 rmax13 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: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.
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, 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, and weight.
Topic:bulk_modulus
Type:Option
Format:bulk_modulus <weight> <gpa>
Units:dyne/cm**2 x 10**11 (default) or GPa
Default:bulk modulus not to be fitted
Use:Subsection of observables, used for specifying the experimental bulk modulus for fitting.
See also:observables, elastic, sdlc, hfdlc, shear_modulus, weight.
Topic:shear_modulus
Type:Option
Format:shear_modulus <weight> <gpa>
Units:dyne/cm**2 x 10**11 (default) or GPa
Default:shear modulus not to be fitted
Use:Subsection of observables, used for specifying the experimental shear modulus for fitting.
See also:observables, elastic, sdlc, hfdlc, bulk_modulus, srefractive,. hfrefractive, weight.
Topic:elastic
Type:Option
Format:elastic <n> <gpa> i j elastic constant E(i,j) <weight> <gpa>
Units:dyne/cm**2 x 10**11 (default) or 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.
Topic:piezoelectric
Type:Option
Format:piezoelectric <n> <stress/strain> i j piezoelectric constant p(i,j) <weight>
Units:C/m**2 for piezoelectric stress constants 10**-7 C/dyne for piezoelectric strain constants
Default:no piezoelectric constants to be fitted - constants are stresses
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.
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.
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: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.
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: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 linear fit: constrain <fit> <no. of constraints> nvari nfix coefficient <offset>

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

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.

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 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

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 "_bulk", "_defe", or "_clus" 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.

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 e.g. output trajectory alumina

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.

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>

See also:marvin, dump.
Topic:rspeed
Type:Option
Format:rspeed rspeed0 <rspeed1> <rspeed2>
Default:1.0 / 1.0 / 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. Three separate parameters are possible where rspeed0 applies to an energy only calculation, rspeed1 applies to an energy and gradient calculation and rspeed2 applies when the second derivatives are being calculated. This enables different types of function call to be tuned separately - for example large systems are much faster in second derivative calcs with very small rspeed values. If only one value is input then it will be used to set all three rspeed values. Note that if freezing is being used then a common value of rspeed must be used for all levels of derivative calculation.
See also:noexclude.
Topic:compare
Type:Keyword
Default:no comparison
Use:Causes a table comparing the initial and final structures to printed out.
Topic:torsion
Type:Option / Keywrd
Format:torsion <intra/inter> <bond> <esff> <kcal/kjmol> atom1 atom2 atom3 atom4 k <+/->nphase <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 <+/->nphase rmax(1-2) rmax(2-3) rmax(3-4) rmax(4-1) <2 x flags>

E = k*(1+isign*cos(nphase*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 nphase, 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.
Topic:ryckaert
Type:Option
Format:ryckaert (or torsion ryck) norder atom1 atom2 atom3 atom4 k0 rmax(1-2) rmax(2-3) rmax(3-4) <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.
Topic:outofplane
Type:Option
Format:outofplane <intra/inter> <bond> <kcal/kjmol> atom1 atom2 atom3 atom4 k rmax(1-2) rmax(1-3) rmax(1-4) <1 x flag>
Units:k in eV*Angs**-2
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, where d=distance to the plane

See also:torsion, ryckaert.
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.
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.
Topic:dfp
Type:Keyword
Use:Use the Davidon-Fletcher-Powell updating formula instead of BFGS.
See also:unit, numdiag, positive, conjugate.
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.
Topic:conjugate
Type:Keyword
Use:Use conjugate gradients to optimise geometry, instead of second derivative based methods.
See also:dfp, numdiag, unit, positive.
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.
Topic:coulomb
Type:Option
Format:coulomb <intra/inter> <bond/x12/x13/o14> <scale14> atom1 atom2 <scale> <rmin> rmax
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.
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:phonon
Type:Keyword
Use:Causes the phonon frequencies to be calculated for each structure with k points specified at the end of each run. If no k points are explicitly given the phonons are calculated at the gamma point. ******************************************************************* * Phonon option causes scratch files to be written - large jobs * * should be executed on a scratch disk. * *******************************************************************
See also:kpoints, dispersion, shrink, eigenvectors, lower_symmetry,. project_dos, output, nozeropt.
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.
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.
See also:phonon, dispersion, shrink.
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.

See also:phonon, shrink, kpoints, box.
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.
See also:phonon, dispersion, kpoints, noksym.
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.
See also:phonon, dispersion, shrink.
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.
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.
See also:kpoints, dispersion, shrink, phonon.
Topic:temperature
Type:Option
Format:temperature value_of_temperature <C/F/K> <step> <no. of steps>
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. Temperature can optionally be followed by an increment and a number of steps. In this case the phonon properties will be calculated at a range of temperatures for each phonon calculation. Note that this range is ignored by molecular dynamics runs and that if present during a free energy calculation will result in the last temperature being used for the calculation instead of the average of all temper- -atures. For CPU time reasons a range should not be used during a free energy minimisation. Also acts as initial temperature to be used in simulated annealing routine
See also:phonon, free, predict, anneal, ftol, factor, and ttol.
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.
Topic:full
Type:Keyword
Use:Causes the nosymmetry option to produce the full, instead of the primitive, unit cell.
See also:nosymmetry.
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.
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.
Topic:norecip
Type:Keyword
Use:Do not calculate reciprocal space contributions to the energy and derivatives.
See also:noreal.
Topic:noreal
Type:Keyword
Use:Do not calculate real space contributions to the energy and derivatives.
See also:norecip.
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.
See also:unfreeze.
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: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).
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
See also:predict, cost, global, and temperature.
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.
See also:predict, genetic, and anneal.
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.
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.
Topic:Two
Type:Genetic Option
Default:One Point Crossover
Use:Part of ga options section.
See also:crossover.
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.
See also:tournament.
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.
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.
Valid space groups for GULP:
NumberLabelNumberLabelNumberLabel
1P 1 2P -1 3P 2
4P 21 5C 2 6P M
7P C 8C M 9C C
10P 2/M 11P 21/M 12C 2/M
13P 2/C 14P 21/C 15C 2/C
16P 2 2 2 17P 2 2 21 18P 21 21 2
19P 21 21 21 20C 2 2 21 21C 2 2 2
22F 2 2 2 23I 2 2 2 24I 21 21 21
25P M M 2 26P M C 21 27P C C 2
28P M A 2 29P C A 21 30P N C 2
31P M N 21 32P B A 2 33P N A 21
34P N N 2 35C M M 2 36C M C 21
37C C C 2 38A M M 2 39A B M 2
40A M A 2 41A B A 2 42F M M 2
43F D D 2 44I M M 2 45I B A 2
46I M A 2 47P M M M 48P N N N
49P C C M 50P B A N 51P M M A
52P N N A 53P M N A 54P C C A
55P B A M 56P C C N 57P B C M
58P N N M 59P M M N 60P B C N
61P B C A 62P N M A 63C M C M
64C M C A 65C M M M 66C C C M
67C M M A 68C C C A 69F M M M
70F D D D 71I M M M 72I B A M
73I B C A 74I M M A 75P 4
76P 41 77P 42 78P 43
79I 4 80I 41 81P -4
82I -4 83P 4/M 84P 42/M
85P 4/N 86P 42/N 87I 4/M
88I 41/A 89P 4 2 2 90P 4 21 2
91P 41 2 2 92P 41 21 2 93P 42 2 2
94P 42 21 2 95P 43 2 2 96P 43 21 2
97I 4 2 2 98I 41 2 2 99P 4 M M
100P 4 B M 101P 42 C M 102P 42 N M
103P 4 C C 104P 4 N C 105P 42 M C
106P 42 B C 107I 4 M M 108I 4 C M
109I 41 M D 110I 41 C D 111P -4 2 M
112P -4 2 C 113P -4 21 M 114P -4 21 C
115P -4 M 2 116P -4 C 2 117P -4 B 2
118P -4 N 2 119I -4 M 2 120I -4 C 2
121I -4 2 M 122I -4 2 D 123P 4/M M M
124P 4/M C C 125P 4/N B M 126P 4/N N C
127P 4/M B M 128P 4/M N C 129P 4/N M M
130P 4/N C C 131P 42/M M C 132P 42/M C M
133P 42/N B C 134P 42/N N M 135P 42/M B C
136P 42/M N M 137P 42/N M C 138P 42/N C M
139I 4/M M M 140I 4/M C M 141I 41/A M D
142I 41/A C D 143P 3 144P 31
145P 32 146R 3 147P -3
148R -3 149P 3 1 2 150P 3 2 1
151P 31 1 2 152P 31 2 1 153P 32 1 2
154P 32 2 1 155R 3 2 156P 3 M 1
157P 3 1 M 158P 3 C 1 159P 3 1 C
160R 3 M 161R 3 C 162P -3 1 M
163P -3 1 C 164P -3 M 1 165P -3 C 1
166R -3 M 167R -3 C 168P 6
169P 61 170P 65 171P 62
172P 64 173P 63 174P -6
175P 6/M 176P 63/M 177P 6 2 2
178P 61 2 2 179P 65 2 2 180P 62 2 2
181P 64 2 2 182P 63 2 2 183P 6 M M
184P 6 C C 185P 63 C M 186P 63 M C
187P -6 M 2 188P -6 C 2 189P -6 2 M
190P -6 2 C 191P 6/M M M 192P 6/M C C
193P 63/M C M 194P 63/M M C 195P 2 3
196F 2 3 197I 2 3 198P 21 3
199I 21 3 200P M 3 (P M -3) 201P N 3 (P N -3)
202F M 3 (F M -3) 203F D 3 (F D -3) 204I M 3 (I M -3)
205P A 3 (P A -3) 206I A 3 (I A -3) 207P 4 3 2
208P 42 3 2 209F 4 3 2 210F 41 3 2
211I 4 3 2 212P 43 3 2 213P 41 3 2
214I 41 3 2 215P -4 3 M 216F -4 3 M
217I -4 3 M 218P -4 3 N 219F -4 3 C
220I -4 3 D 221P M 3 M 222P N 3 N
223P M 3 N 224P N 3 M 225F M 3 M
226F M 3 C 227F D 3 M 228F D 3 C
229I M 3 M 230I A 3 D

Non-standard space groups:

C 1

Alternative settings of the above space groups should also be valid