Topic:  terse 
Type:  Option 
Format:  terse <in/out/inout> <cell/coordinates/structure/potentials/derivatives> 
Default:  All appropriate quantities are output in full. 
Use:  Offers the user the option of making the output more terse  i.e. to not print out so much. The first word should control whether the suboptions
refer to the input information, the output information or both, while the
second refers to the quantity not to be printed:
cell => don't output the unit cell parameters for vectors coordinates => don't output the coordinates of the atoms structure => don't output the structure (i.e. cell & coordinates) potentials => don't output the interatomic potentials derivatives => don't output the final derivatives

Topic:  neb 
Type:  Keyword 
Use:  Invokes a Nudged Elastic Band run to map out the minimum energy pathway between two structures. A limited memory BFGS run is used to converge the replicas to the path. See the papers of G. Henkelman and H. Jonsson (e.g. J. Chem. Phys., 113, 9978 (2000)). By default the Doubly Nudged Elastic Band form is used. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nodneb 
Type:  Keyword 
Use:  Turns off the doubly nudged elastic band method and uses the singly nudged formalism. 
See also:  nebspring, nebtolerance, neb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nebreplica 
Type:  Option 
Format:  nebreplica <nreplica> 
Default:  None 
Use:  Specifics the number of replicas to be used during a nudged elastic band run, including the initial and final structure. Must be at least greater than 2 and controls how accurately the reaction path is discretised. 
See also:  neb, nebspring, nebtolerance, nodneb,. nebtangent, nebrandom, nebiterations, rcartesian, fcartesian,. rfractional, ffractional, rcell, fcell. 
Topic:  nebspring 
Type:  Option 
Format:  nebspring <vary> <maxspring> <minspring> 
Default:  maxspring = 1.0  no varying 
Units:  eV/Angstroms**2 
Use:  Specifies the spring constant between the replicas in the nudged elastic band method. For a single spring value between all
replicas the input would be;
nebspring 10.0 For a spring constant that varies between 10.0 and 1.0 the input would be; nebspring vary 10.0 1.0

See also:  neb, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nebtolerance 
Type:  Option 
Format:  nebtolerance <tolerance_value> 
Default:  0.001 
Use:  Specifies the convergence criteria for a nudged elastic band run in terms of the residual force norm. 
See also:  nebspring, neb, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nebtangent 
Type:  Option 
Format:  nebtangent <option_number> 
Default:  3 
Use:  Specifies how the tangent to the reaction path is to be defined in a nudged elastic band run. The following are valid options:
1 => central finite difference between replicas 2 => bisect vectors 3 => new algorithm favouring higher energy replica neighbour

See also:  nebspring, nebtolerance, nodneb,. nebreplica, neb, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nebrandom 
Type:  Option 
Format:  nebrandom <random_weight> 
Default:  0.0 
Units:  Angstroms 
Use:  In the case where the initial pathway in the nudged elastic band (formed by linear interpolation between the initial and final state) lies along a high symmetry direction it can be necessary to displace the replicas from the symmetric path. If this option is set to a nonzero value then a random displacement is applied to the initial coordinates of each replica. The input value is used to scale a random number between 0 and 1. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, neb, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  nebiterations 
Type:  Option 
Format:  nebiterations <maximum_number> 
Default:  1000 
Use:  Specifies the maximum number of iterations for minimization of the force norm during the nudged elastic band run. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, neb, rcartesian,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  rcartesian 
Type:  Option 
Format:  rcartesian replica_number x1 y1 z1 <r1> x2 y2 z2 <r2> .. .. .. xN yN zN <rN> 
Units:  Angstroms 
Default:  None 
Use:  Specifies the coordinates of a replica for the nudged elastic band method. The number of coordinates must match the number of atoms in the initial structure. This option is primarily useful for restarting. If the coordinates of the replicas are not given then the values are initialised based on a linear interpolation between the initial and final states. The radii of the ions can be optionally given on the end of the line if a breathing shell model is being used. If not specified then they are assumed to be zero. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, neb,. fcartesian, rfractional, ffractional, rcell, fcell. 
Topic:  fcartesian 
Type:  Option 
Format:  fcartesian x1 y1 z1 <r1> x2 y2 z2 <r2> .. .. .. xN yN zN <rN> 
Units:  Angstroms 
Default:  None 
Use:  Specifies the coordinates of the final state for the nudged elastic band method. The number of coordinates must match the number of atoms in the initial structure. The radii of the ions can be optionally given on the end of the line if a breathing shell model is being used. If not specified then they are assumed to be zero. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. rfractional, ffractional, rcell, fcell, neb. 
Topic:  rfractional 
Type:  Option 
Format:  rfractional replica_number x1 y1 z1 <r1> x2 y2 z2 <r2> .. .. .. xN yN zN <rN> 
Units:  Fractional 
Default:  None 
Use:  Specifies the fractional coordinates of a replica for the nudged elastic band method. The number of coordinates must match the number of atoms in the initial structure. This option is primarily useful for restarting. If the coordinates of the replicas are not given then the values are initialised based on a linear interpolation between the initial and final states. The radii of the ions can be optionally given on the end of the line if a breathing shell model is being used. If not specified then they are assumed to be zero. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, ffractional, rcell, fcell, neb. 
Topic:  ffractional 
Type:  Option 
Format:  ffractional x1 y1 z1 <r1> x2 y2 z2 <r2> .. .. .. xN yN zN <rN> 
Units:  Fractional 
Default:  None 
Use:  Specifies the fractional coordinates of the final state for the nudged elastic band method. The number of coordinates must match the number of atoms in the initial structure. The radii of the ions can be optionally given on the end of the line if a breathing shell model is being used. If not specified then they are assumed to be zero. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, rcell, fcell, neb. 
Topic:  rcell 
Type:  Option 
Format:  rcell replica_number a b c alpha beta gamma (for 3D) a b alpha (for 2D) a (for 1D) 
Units:  Angstroms for a/b/c & degrees for alpha/beta/gamma 
Default:  None 
Use:  Specifies the unit cell of a replica for the nudged elastic band method. This option is primarily useful for restarting. If the unit cells of the replicas are not given then the values are initialised based on a linear interpolation between the initial and final states. The number of cell parameters must match the dimensionality of the initial system. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, fcell, neb. 
Topic:  fcell 
Type:  Option 
Format:  fcell a b c alpha beta gamma 
Units:  Angstroms for a/b/c & degrees for alpha/beta/gamma 
Default:  None 
Use:  Specifies the final unit cell for the nudged elastic band method. The number of cell parameters must match the dimensionality of the initial system. 
See also:  nebspring, nebtolerance, nodneb,. nebreplica, nebtangent, nebrandom, nebiterations, rcartesian,. fcartesian, rfractional, ffractional, rcell, neb. 
Topic:  oldunits 
Type:  Keyword 
Use:  The default units of elastic constants have now changed to GPa in order to be consistent and modern. This keyword is included to maintain backwards compatibility. 
Topic:  nomodcoord 
Type:  Keyword 
Use:  Prevents the use of mod on the input coordinates for most purposes. The mod function is used to place fractional coordinates into the central unit cell. Note that this option applies to all steps of a calculation. 
Topic:  brenner 
Type:  Option 
Format:  brenner 
Use:  Specifies that the REBO forcefield of Brenner et al (2002 variant) be included in the energy calculation. Note that this is only available for the elements C, H, and O. The parameters for O are from the work of Ni, Lee and Sinnott (J. Phys.: Condens. Matter, 16, 7261 (2004), but with some changes from the authors that lead to improvements. The option REBO is a synonym for this option. If the model number is given as 1 (i.e. "brenner 1") then the original Brenner model will be used. This option has parameters for C, H and Si using the extended parameter set given in Dyson and Smith, Surf. Sci., 355, 140 (1996) 
See also:  spatial. 
Topic:  spatial 
Type:  Keyword 
Use:  Requests that a spatial decomposition algorithm is used whereever possible to try to achieve linear scaling with system size. 
See also:  rcspatial. 
Topic:  rcspatial 
Type:  Option 
Format:  rcspatial rcspatial_value <rcspatial_BO_value> 
Units:  Angstroms 
Default:  Set equal to the largest potential cutoff in real space. 
Use:  Can be used to set the domain size in the spatial decomposition to make it smaller than the potential cutoff. In this case looping over multiple cells is needed. 
See also:  spatial. 
Topic:  nomolecularinternalke 
Type:  Keyword 
Use:  Causes the initial velocites of atoms within a molecule to be initialised to the same average value thereby resulting in no internal kinetic energy. 
See also:  md. 
Topic:  plane_lj 
Type:  Option 
Format:  plane_lj m n atom1 plane zcoord A B rmin rmax <2xflags> 
Units:  zcoord, rmin and rmax in Angstroms, A & B in eV/Angstroms**m and eV/Angstroms**n, respectively. 
Default:  m = 10, n = 4 
Use:  Specifies a LennardJones potential between atom1 and a plane. Because the method is only applicable to 2D systems the plane
is assumed to be parallel to xy. The absolute position in z
is given by zcoord. For example to include an integrated LJ
126 potential (which would give m=10 and n=4) that acts on carbon
positioned at 0.75 Ang the input would look like:
plane_lj 10 4 C core 0.75 1000.0 14.0 0.0 12.0

See also:  lennard, einstein. 
Topic:  einstein 
Type:  Option 
Format:  einstein <cart> atomnumber x y z k 
Units:  x/y/z in fractional, unless "cart" specified, in which case Angstroms; k in eV/Ang**2 
Default:  k = 0 for all atoms 
Use:  Specifies an Einstein model for the system. Here the atoms are tied to lattice sites using a harmonic potential. In the input it is necessary to specify the lattice site for the atom and the force constant. Note: This option must be used with a fixed unit cell. 
See also:  plane_lj. 
Topic:  random 
Type:  Option 
Format:  random ncall1 ncall2 
Units:  None 
Default:  ncall1 = ncall2 = 0 
Use:  This option is used for consistent restarting of runs that utilise random numbers by keeping track of how many calls were made during the previous run so that the position in the sequence of numbers can be recreated on restart. There are two types of random number generate in GULP at present and so the two numbers are to track the number of calls for each generator. 
See also:  md. 
Topic:  radial_force 
Type:  Option 
Format:  radial_force K x y z 
Units:  K in eV/Ang, x, y, z in Ang 
Default:  No radial force 
Use:  This option allows a radial harmonic force to be applied to a system with a force constant K and origin of force
at (x,y,z). Because of the point nature of the force it
can only be applied to finite systems. The energy of the
contribution is given by:
E = sum(i) 1/2 K*[(x_i  x)**2 + (y_i  y)**2 + (z_i  z)**2] where the sum is over all atoms, i. 
Topic:  external_force 
Type:  Option 
Format:  external_force atomnumber force_X force_Y force_Z 
Units:  eV/Angstrom 
Default:  0.0 for all atoms and components 
Use:  Specifies a constant external force for the atoms specified. Note that the atom number refers to the asymmetric unit and that the user must ensure that the force doesn't violate the symmetry of the system otherwise any optimisation will fail. Example: force 1 0.2 0.0 0.0 3 0.2 0.0 0.0 
See also:  td_external_force. 
Topic:  td_external_force 
Type:  Option 
Format:  td_external_force atomnumber direction forceA forceB forceC 
Units:  forceA in eV/Angstrom, forceB in 1/seconds, & forceC in fraction of 2*pi 
Default:  No time dependent force 
Use:  Specifies that a timedependent force is applied to selected atoms during a molecular dynamics simulation. This force can
be specified separately for each Cartesian direction and takes
the form of;
F = forceA*cos[2*pi*(t*forceB + forceC)] where t is the time within the simulation. Example 1: 1 z 3.5 0.5 0.5 3 z 3.5 0.5 0.0 Example 2: 1 z 3.5 0.5 0.0 3 z 3.5 0.5 0.0 Note: both of the other examples would cause the atoms to oscillate exactly out of phase with each other and are equivalent. The maximum force experienced would be +/ 3.5 eV/Angstrom 
See also:  external_force. 
Topic:  mincell 
Type:  Option 
Format:  mincell minimum_cell_parameter <au> 
Units:  Angstroms 
Default:  0.5 Angstroms 
Use:  Stops an optimisation if the cell parameter falls below the specified allowed value. This prevents the memory rapidly increasing due to the number of reciprocal lattice vectors tending to infinity as the cell parameter(s) go to zero. 
See also:  rspeed, optimise. 
Topic:  ditto 
Type:  Option 
Format:  ditto <option_word> <configuration_no> 
Units:  none 
Default:  option_word = 'all' and configuration_no = last structure 
Use:  Copies the data from the previous configuration to this one before options overwrite it. The option_word parameter is a
string that states what is to be copied. Current valid words
are;
all  copy all of the below items conditions  copy temperature / pressure data md  copy all molecular dynamics related parameters solvent  copy solvent related data structure  copy structure related data The parameter, configuration_no, gives the configuration number to be copied when creating the present new structure. This option is useful when wanting to run a sequence of calculations on the same structure with different conditions. Note: The coordinates cannot be presently overwritten. 
Topic:  omega 
Type:  Option 
Format:  omega frequency frequency_step no_of_steps 
Units:  cm1 
Default:  frequency = frequency_step = 0.0 no_of_steps = 0 
Use:  Specifies that frequency dependent properties be calculated over a given range. "frequency" represents the initial frequency
while "frequency_step" is the interval between calculations.
Example : omega 500.0 100.0 5 the above would calculate properties at a frequencies of 500, 600, 700, 800, 900 and 1000 cm1. A no_of_steps = 0 implies a calculation at a single frequency. NOTE : This option only applies to a gamma point calculation

See also:  phonon, odirection, omega_damping. 
Topic:  omega_damping 
Type:  Option 
Format:  omega_damping damping_factor 
Units:  cm1 
Default:  5.0 cm1 
Use:  Applies a damping factor to the frequency dependent optical properties. This broads the peaks and prevents a singularity. Note that the value is constrained to be greater than 1 x 10^6 to ensure numerical stability. 
See also:  omega, odirection, phonon. 
Topic:  odirection 
Type:  Option 
Format:  odirection <frac> x_in y_in z_in x_out y_out z_out 
Units:  dimensionless 
Default:  no directions 
Use:  If the frequency dependent properties are required for a particular in/out direction combination then this option
specifies the 2 directions.
NOTE : This option only applies to a gamma point calculation By default the directions are assumed to be in Cartesian space unless the "frac" suboption is given in which case they will be taken relative to the crystal axes. 
See also:  phonon, omega, omega_damping. 
Topic:  nononanal 
Type:  Keyword 
Use:  If present, then the nonanalytic correction to the phonons at the gamma point is excluded. This was always true for versions of GULP prior to 1.4 and so this keyword allows backwards compatability while leading to an incorrect LO/TO splitting. Note: The Born effective charges are not presently available with electronegativity equalisation and therefore this keyword will automatically be set. 
See also:  phonon, gamma_direction_of_approach, gamma_angular_steps. 
Topic:  gamma_direction_of_approach 
Type:  Option 
Format:  gamma_direction_of_approach Kx Ky Kz 
Units:  fractional 
Default:  1.0 1.0 1.0 
Use:  Specifies the direction of approach to the gamma point for the calculation of the nonanalytic correction to the dynamical matrix due to the LO/TO splitting resulting from the electric field in the crystal. This option allows the frequencies to be calculated for a particular crystal orientation. Only used if gamma_angular_steps is set to zero. Note that the value is also ignored if a point is part of a dispersion curve, where the direction of the curve is taken. 
See also:  phonon, nononanal, gamma_angular_steps. 
Topic:  gamma_angular_steps 
Type:  Option 
Format:  gamma_angular_steps Nsteps 
Units:  none 
Default:  0 
Use:  Specifies the number of angular points for theta and phi to be used in averaging the nonanalytic correction to the dynamical matrix over all possible approach directions. This leads to the polycrystalline powder average of the gamma point frequencies due to the LO/TO splittings in all directions. Note: the absolute magnitude does not matter  only the direction. 
See also:  phonon, nononanal, gamma_direction_of_approach. 
Topic:  zero_potential 
Type:  Keyword 
Use:  Sets the average potential across all lattice sites to be zero. This allows comparison of the site potentials to be made more readily between the bulk and molecular/surface situations. 
See also:  potential. 
Topic:  montecarlo 
Type:  Keyword 
Use:  Specifies that a Monte Carlo calculation is to be performed. 
See also:  mccreate, mcdestroy, mcmove, mcrotate, mctrial, mcoutfreq,. mcsample, gcmcspecies, gcmcmolecule, mcstrain, nomcediff. 
Topic:  nomcediff 
Type:  Keyword 
Use:  Controls the algorithm used for calculating the energy difference during a trial move. By default, GULP will try to use the energy change associated only with the atoms that are affected by the trial step, where possible. Specifying this keyword forces the full calculation of the total energy at each step, which is more expensive. This option is mainly for debug checking. 
See also:  montecarlo. 
Topic:  mccreate 
Type:  Option 
Format:  mccreate probability 
Default:  0.0 
Units:  None 
Use:  Specifies the relative probability of an atom being created during a Monte Carlo simulation. Note all probabilities are renormalised at run time. A value of zero means that atoms will not be created. 
See also:  mcdestroy, mcmove, mcrotate, mctrial, montecarlo. 
Topic:  mcdestroy 
Type:  Option 
Format:  mcdestroy probability 
Default:  0.0 
Units:  None 
Use:  Specifies the relative probability of an atom being destroyed during a Monte Carlo simulation. Note all probabilities are renormalised at run time. A value of zero means that atoms will not be destroyed. Note when an atom in a molecule is destroyed, then so is the whole molecule. 
See also:  mccreate, mcmove, mcrotate, mcstrain, mctrial, montecarlo. 
Topic:  mcmove 
Type:  Option 
Format:  mcmove probability 
Default:  1.0 
Units:  None 
Use:  Specifies the relative probability of an atom being translated during a Monte Carlo simulation. Note all probabilities are renormalised at run time. A value of zero means that atoms will not be translated. When an atom in a molecule is chosen for translation, then the whole molecule is translated. 
See also:  mccreate, mcdestroy, mcrotate, mctrial, montecarlo, mcstrain. 
Topic:  mcrotate 
Type:  Option 
Format:  mcrotate <atom/line/centre> probability 
Default:  0.0 / centre 
Units:  None 
Use:  Specifies the relative probability of a molecule being rotated during a Monte Carlo simulation. Note all probabilities are renormalised at run time. A value of zero means that molecules will not be rotated. The suboptions atom, line and centre control the point about which the molecule will be rotated, and in the case of line the axis direction. For the default mode, centre, the molecule is rotated about the centre of the molecule based on the average coordinate. For atom, a random atom from within the molecule is chosen and then the rotation attempted about this. For line, two atoms are chosen at random and the rotation attempted about this axis. If more than one word is specified then all types of rotation specified will be tried according to a random choice. 
See also:  mccreate, mcdestroy, mcmove, mctrial, mcmaxrotation, montecarlo,. mcstrain. 
Topic:  mcstrain 
Type:  Option 
Format:  mcstrain probability 
Default:  0.0 
Units:  None 
Use:  Specifies the relative probability of the cell being strained during a Monte Carlo simulation. Note all probabilities are renormalised at run time. A value of zero means that the cell will not be strained. 
See also:  mccreate, mcdestroy, mcrotate, mctrial, montecarlo, mcmove,. mcmaxstrain. 
Topic:  mctrial 
Type:  Option 
Format:  mctrial number_of_trials 
Default:  0 
Units:  None 
Use:  Specifies the total number of attempted trial operations in a Monte Carlo simulation. 
See also:  montecarlo, mccreate, mcdestroy, mcmove, mcrotate, mcstep. 
Topic:  mcoutfreq 
Type:  Option 
Format:  mcoutfreq 
Default:  100 
Units:  None 
Use:  Specifies the frequency for printing the running averages to the output. The value is specified as the number of trial operations between outputs. 
See also:  mcsample, montecarlo. 
Topic:  mcsample 
Type:  Option 
Format:  mcsample <frequency> <filename> <lowest> 
Default:  10 / gulp.gmc 
Units:  None 
Use:  Specifies the frequency for outputing configuration data to a binary file for postrun analysis. The value is specified
as the number of accepted operations between writes. The
filename can be anything with up to 60 characters. The
extension ".gmc" is recommend as a convention.
The format of the file is as follows. Each configuration is written as follows: write(31)numat write(31)energy write(31)(atomicno(i),i=1,numat) write(31)(atomictype(i),i=1,numat) write(31)(xcoordinate(i),i=1,numat) write(31)(ycoordinate(i),i=1,numat) write(31)(zcoordinate(i),i=1,numat) where the variables are as follows : integer(i4) numat = total number of atoms integer(i4) atomicno = atomic number of atom (1maxele) integer(i4) atomictype = atomic type of atom (09999) real(dp) energy = total energy of system (eV) real(dp) xcoordinate = Cartesian coord in X direction (Angs) real(dp) ycoordinate = Cartesian coord in Y direction (Angs) real(dp) zcoordinate = Cartesian coord in Z direction (Angs) and the datatypes are given by : integer, parameter :: i4 = selected_int_kind(9) integer, parameter :: dp = kind(1.0d0)

See also:  montecarlo, mcoutfreq. 
Topic:  mcmaxdisplacement 
Type:  Option 
Format:  mcmaxdisplacement <maxdisplacement> <target ratio <frequency>> 
Default:  0.05 / no target ratio 
Units:  Angstroms 
Use:  Specifies the maximum Cartesian displacement that can be applied in a translation trial step. If the "target" suboption is used then the maximum displacement is gradually adjusted to try to achieve the specified acceptance ratio for translation. The frequency of adjustment can also be specified. mcmaxdisplacement 0.1 mcmaxdisplacement 0.05 target 0.5 20 
See also:  mcmove, montecarlo. 
Topic:  mcmaxstrain 
Type:  Option 
Format:  mcmaxstrain <maxstrain> <target ratio <frequency>> 
Default:  0.1 / no target ratio 
Units:  Dimensionless 
Use:  Specifies the maximum strain that can be applied in a strain trial step. Note that a strain step of more than 1.0 is not allowed since this would allow the cell to go to zero in a single step. Small values are more sensible. If the "target" suboption is used then the maximum strain is gradually adjusted to try to achieve the specified acceptance ratio for strain. The frequency of adjustment can also be specified. mcmaxstrain 0.01 mcmaxstrain 0.15 target 0.5 30 
See also:  mcstrain, montecarlo. 
Topic:  mcmaxrotation 
Type:  Option 
Format:  mcmaxrotation <maxrotation> <target ratio <frequency>> 
Default:  180 / no target ratio 
Units:  Degrees 
Use:  Specifies the maximum angle of rotation that can be applied in a trial step. If the "target" suboption is used then the maximum rotation is gradually adjusted to try to achieve the specified acceptance ratio for rotation. The frequency of adjustment can also be specified. mcmaxrotation 90 mcmaxrotation 180 target 0.5 20 
See also:  mcrotate, montecarlo. 
Topic:  mcchemicalpotential 
Type:  Option 
Format:  mcchemicalpotential chemical_potential 
Default:  0.0 
Units:  eV 
Use:  Specifies the target chemical potential of the system for a Grand Canonical Monte Carlo run. Controls the probability for creation and destruction moves being accepted. 
See also:  mccreate, mcdestroy, mctrial, montecarlo, gcmcspecies, mcvolume. 
Topic:  mcvolume 
Type:  Option 
Format:  mcvolume volume 
Default:  unit cell volume 
Units:  Angstroms**3 
Use:  Specifies the volume that is used in a Grand Canonical Monte Carlo calculation to determine the creation/destruction probability. If not specified, the volume of the unit cell is used. 
See also:  montecarlo, mcchemicalpotential. 
Topic:  gcmcspecies 
Type:  Option 
Format:  gcmcspecies <number_of_species> AtomicSymbol <core/shell> x <number_of_species> 
Default:  None 
Units:  None 
Use:  Specifies the species that can under go destruction/creation operations in a trial MC step. Only used in GCMC calculations. Note that specifying the number of species is optional. H core O core 
See also:  mccreate, mcdestroy, montecarlo, gcmcmolecule. 
Topic:  gcmcmolecule 
Type:  Option 
Format:  gcmcmolecule <number_of_atoms> <au> AtomicSymbol <core/shell> x y z ( x number of atoms) 
Default:  None 
Units:  Coordinates in Angstroms 
Use:  Specifies the coordinates for molecules that can be created during a GCMC calculation trial step. The molecule will be inserted using the specified geometry at a random position and with a random orientation. Only used in GCMC calculations. Note that specifying the number of atoms is optional. N core 0.0 0.0 0.6 N core 0.0 0.0 0.6 
See also:  mccreate, mcdestroy, montecarlo, gcmcspecies, gcmcexistingmolecules. 
Topic:  gcmcexistingmolecules 
Type:  Option 
Format:  gcmcexistingmolecules mol1 mol2 mol3 ...etc.... 
Default:  No existing GCMC molecules in existing structure 
Units:  None 
Use:  Allows molecules in the current structure that are related to GCMC molecules to be identified. The purpose of this option is to facilitate
restarts of GCMC runs. For example, if a system contains 3 molecules
where molecule numbers 2 and 3 were inserted by GCMC, while molecule 1
is a fixed framework into which the molecules are inserted then the
input would be:
gcmcexistingmolecules 2 3 Where there are many molecules a range can also be specified as follows: gcmcexistingmolecules 4 to 8

See also:  mccreate, mcdestroy, montecarlo, gcmcspecies, gcmcmolecules. 
Topic:  mcstep 
Type:  Option 
Format:  mcstep first_step number_of_accepted_steps_so_far 
Default:  1 
Units:  None 
Use:  Specifies the first step for a Monte Carlo restart and the number of accepted steps so far. The former number must be constitent with the mean properties given and the second one must obviously be smaller than the first. 
See also:  mcmeans, mctrial, montecarlo, mclowest. 
Topic:  mcmeans 
Type:  Option 
Format:  mcmeans mean_energy mean_number_of_atoms 
Default:  None 
Units:  mean_energy in eV 
Use:  Specifies the running mean of the energy and number of atoms. This must be consistent with the number of MC steps so far given by mcstep and is used to restart a Monte Carlo job. 
See also:  mcstep, mctrial, montecarlo, mclowest. 
Topic:  mclowest 
Type:  Option 
Format:  mclowest lowest_energy 
Default:  None 
Units:  lowest_energy in eV 
Use:  Specifies the running lowest value of the energy encountered so far in the run. This value is only for restarting purposes. 
See also:  mcstep, mctrial, montecarlo, mcmeans. 
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 cutoff value for the EAM model. In principle, the range can be up to 3 times the density pairwise cutoff. 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 and is intended for use with single point calculations. 
See also:  gradients. 
Topic:  marvinSE 
Type:  Keyword 
Use:  Changes the way that many body terms are apportioned between regions 1 and 2 to match the convention that Marvin adopts (i.e. all 3/4 body interactions involving a region 1 atom are assigned to the region 1 energy) 
Topic:  noelectrostatics 
Type:  Keyword 
Use:  Turns off the Ewald summation/Coulomb interaction even when charges are present in the input. This is mainly used when a screened Coulomb potential is being used, such as "qerfc", which requires the charges to be present but replaces the normal energy term. 
See also:  qerfc, qwolf. 
Topic:  zsisa 
Type:  Keyword 
Use:  perform free energy minimisation in the Zero Static Internal Stress Approximation (ZSISA)  this implies that only the strain derivatives with respect to the free energy are used while the internal derivatives neglect the free energy contribution. This approach is equivalent to the old numerical method of free energy minimisation. Note this keyword does not apply to molecules! 
See also:  free. 
Topic:  keyword 
Type:  Option 
Format:  keyword <list of keywords> 
Use:  allows keywords to be specified anywhere in an input file instead of just on the top line.
e.g. keyword opti conp prop

Topic:  ignore 
Type:  Option 
Use:  Part of ignore/erongi pair. All lines of input after "ignore" are treated as comments until the option "erongi" is found at the start of a line. Allows the user to comment out parts of an input file. Note any parts commented out will not be passed through to a restart file. 
See also:  erongi. 
Topic:  erongi 
Type:  Option 
Use:  Part of ignore/erongi pair. All lines of input after "ignore" are treated as comments until the option "erongi" is found at the start of a line. Allows the user to comment out parts of an input file. Note any parts commented out will not be passed through to a restart file. 
See also:  ignore. 
Topic:  dcharge 
Type:  Keyword 
Use:  Calculate the first derivatives of the atomic charges with respect to the coordinates of the atoms (and strain) as calculated according to either the EEM or QEq electronegativity equalisation schemes. 
See also:  eem, qeq. 
Topic:  qeq 
Type:  Keyword 
Use:  Calculate charges by Rappe and Goddard's QEq scheme. This differs from Mortier's scheme in that the Coulomb
interaction is replaced by the integral over two s
type Slater orbitals for small distances. It is also
available for the whole periodic table up to Lr (103).
If specified with optimise then the charges will be
recalculated at every point of the optimisation.
NB Electronegativity equalisation schemes should NOT be used in combination with Coulomb subtraction of any form otherwise the calculation of the charges and the energy will not be selfconsistent. This leads to all derivatives being incorrect as dE/dQ is no longer zero. If Coulomb subtracted potentials are to be used then charges must be calculated for the initial geometry and then frozen. Note: it is important to investigate the effect of qeqradius on the degree of convergence and CPU time. Note: Phonon calculations are limited with the QEq keyword to the gamma point without the LO/TO splitting. Note: Only region 1 atoms are included in QEq and fixed charges will be taken for region 2. 
See also:  eem, qeqtol, qeqiter, qeqradius, dcharge, sm, qelectronegativity,. gasteiger. 
Topic:  qeqtol 
Type:  Option 
Format:  qeqtol tolerance 
Units:  Electrons 
Default:  0.000001 
Use:  Sets the tolerance on the change in the charges between iterations of the QEq electronegativity equalisation scheme. This only applies to systems which contain hydrogen. 
See also:  eem, qeq, qeqiter, qeqradius, dcharge. 
Topic:  qeqiter 
Type:  Option 
Format:  qeqiter maximum_number_iterations 
Units:  None 
Default:  20 
Use:  Sets the maximum number of iterations that are allowed during the QEq electronegativity equalisation scheme. Only applies to systems where hydrogen is present. 
See also:  eem, qeq, qeqtol, qeqradius, dcharge. 
Topic:  qeqradius 
Type:  Option 
Format:  qeqradius radius 
Units:  Angstroms 
Default:  15.0 
Use:  Sets the maximum radius for the calculation of the Coulomb term using the formula for two Slater s type orbitals in the QEq electronegativity equalisation scheme. Beyond this radius the terms are calculated using just the inverse distance. Generally the default value should be large enough for convergence. However, the user may wish to try smaller values to achieve a faster calculation. Note that failure to achieve satisfactory convergence in an optimisation may be due to this value being too small. 
See also:  eem, qeq, qeqiter, qeqtol, dcharge. 
Topic:  minimum_image 
Type:  Keyword 
Use:  Requests that the real space components of the energy for a solid are calculated using the minimum image convention during a molecular dynamics or conjugate gradient simulation. For large unit cells this can accelerate the real space calculation of the program by reducing the work done in searching for interactions, especially for right angled unit cells. 
See also:  md. 
Topic:  integrator 
Type:  Option 
Format:  integrator <gear/velocity verlet/leapfrog verlet/stochastic> <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, tau_barostat, tau_thermostat. 
Topic:  rydberg 
Type:  Option 
Format:  rydberg <intra/inter> <bond/x12/x13/mol/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 FinnisSinclair and
subsequently other workers, such as SuttonChen.
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 twobody potentials, it is infact many body at shortrange, but tends to an effective pair potential at long range. Also note that this potential type is NOT compatible with <intra/inter/molmec> directives. 
See also:  eam_density, eam_functional, scmaxsearch, noquicksearch. 
Topic:  noquicksearch 
Type:  Keyword 
Use:  Turns off some timesaving changes to the searching algorithm for pairs of distances. Should have no effect, but this is still under evaluation! 
Topic:  srglue 
Type:  Option 
Format:  srglue <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 d rmin rmax a14 a13 a12 a11 a10 a26 a25 a24 a23 a22 a21 a20 
Units:  eV and Angstroms 
Default:  none 
Use:  Input for the ShortRange part of the Glue model: if r < d: E = a14*(rd)**4 + a13*(rd)**3 + a12*(rd)**2 + a11*(rd) + a10 if d < r =< rmax: E = a26*(rd)**6 + a25*(rd)**5 + a24*(rd)**4 + a23*(rd)**3 + a22*(rd)**2 + a21*(rd) + a20 intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. 
See also:  eam_functional, eam_density. 
Topic:  eam_functional 
Type:  option 
Format:  eam_functional <square_root> <power n> <banerjea_smith n> <johnson> <glue> <foiles> <meidavenport> if square_root or power : atom1 A_1 <flag> atom2 A_2 <flag> etc... if banerjea_smith : atom1 F0_1 F1_1 rho0_1 <3*flags> atom2 F0_2 F1_2 rho0_2 <3*flags> etc... if johnson : atom1 F0_1 F1_1 rho0_1 alpha beta gamma <6*flags> atom2 F0_2 F1_2 rho0_2 alpha beta gamma <6*flags> etc... if glue : atom1 rho1 rho2 c1_4 c1_3 c1_2 c1_1 c1_0 c2_4 c2_3 c2_2 c2_1 c2_0 c3_3 c3_2 c3_1 c3_0 atom2 rho1 rho2 c1_4 c1_3 c1_2 c1_1 c1_0 c2_4 c2_3 c2_2 c2_1 c2_0 c3_3 c3_2 c3_1 c3_0 if foiles : atom1 F0_1 F1_1 F2_1 F3_1 <4*flags> atom2 F0_2 F1_2 F2_2 F3_2 <4*flags> etc... if meidavenport : atom1 Ec_1 alpha_1 beta_1 gamma_1 delta_1 phi0_1 s_1_1 s_2_1 s_3_1 <9*flags> atom2 Ec_2 alpha_2 beta_2 gamma_2 delta_2 phi0_1 s_1_2 s_2_2 s_3_2 <9*flags> etc... 
Units:  A, F0, Ec, phi0 and F1 in eV, rho0/alpha/beta/gamma are dimensionless 
Default:  square_root, A = 1.0 
Use:  specifies how the total energy contribution of an atom in the Embedded Atom Model depends on the density at that
site. The currently possibilities are:
Square_root: E =  sum(i) A(i)*(rho(i))**1/2 this is the most common functional, as used in the SuttonChen potential Power: E =  sum(i) A(i)*(rho(i))**1/n this is just a generalisation of the above case Banerjea_smith: E =  sum(i) F0 [1ln(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. Johnson: E =  sum(i) F0 [1ln(x)]*x + F1*y where x = (rho(i)/rho0(i))**(alpha/beta) and y = (rho(i)/rho0(i))**(gamma/beta) this functional is similar to that of Banerjea & Smith and is due to Johnson (PRB, 39, 12554 (1989)). Glue: if rho < rho1 E = c1_4*(rhorho1)**4 + c1_3*(rhorho1)**3 + c1_2*(rhorho1)**2 + c1_1*(rhorho1) + c1_0 if rho1 =< rho < rho2 E = c2_4*(rhorho2)**4 + c2_3*(rhorho2)**3 + c2_2*(rhorho2)**2 + c2_1*(rhorho2) + c2_0 if rho2 =< rho E = c3_3*(rhorho2)**3 + c3_2*(rhorho2)**2 + c3_1*(rhorho2) + c3_0 this is the functional from Ercolessi et al, Phil. Mag. A, 58, 213 (1988). NB: At present there are no fitting parameters since there are constraints on the coefficients to ensure a smooth and continuous function. Foiles: E = sum(i) F0*rho(i)**2 + F1*rho(i) + F2*(rho(i)**(5/3)/(F3 + rho(i))) MeiDavenport: E = sum(i)  Ec*[1(alpha/beta)*ln(rho(i))]*rho(i)**(alpha/beta) + sum(m=1>3) 0.5*phi0*s_m*exp((sqrt(m)1)*gamma)* [1+(sqrt(m)1)*deltasqrt(m)*delta*ln(rho(i))/beta]* rho(i)**(sqrt(m)*gamma/beta)

See also:  eam_density, manybody, scmaxsearch, eam_alloy, prt_eam. 
Topic:  eam_density 
Type:  option 
Format:  eam_density <power/exponential/gaussian/cubic/quadratic/quartic/voter/glue/evoter/meidavenport> <n> atom1 <atom2> C (power law) <1 x flag > atom1 <atom2> A B r0 (exponential) <3 x flags> atom1 <atom2> A B r0 (gaussian) <3 x flags> atom1 <atom2> A r0 (quadratic) <2 x flags> atom1 <atom2> A r0 (cubic) <2 x flags> atom1 <atom2> A r0 (quartic) <2 x flags> atom1 <atom2> A beta (voter) <2 x flags> atom1 <atom2> A beta (evoter) <2 x flags> atom1 <atom2> c0 c1 c2 c3 c4 c5 r0 (meidavenport) <7 x flags> atom1 <atom2> r1 r2 rm (glue) b1_3 b1_2 b1_1 b1_0 b2_3 b2_2 b2_1 b2_0 b3_3 b3_2 b3_1 b3_0 
Units:  Distances in Angstroms 
Use:  specifies the density due a given atom1 at another atomic centre (atom2) in the Embedded Atom Model (EAM).
This density is only calculated for pairs of atoms
where the "manybody" potential has been specified
so that the user can control which atoms are part
of the EAM.
Where no atom2 is specified then the density is applied to
all atoms allowed by the manybody potential, regardless of
species type.
The density can take one of several functional forms:
Power Law: rho(i) = C*rij**(n) e.g. eam_density power 6 Ni core 729.7 Exponential: rho(i) = A*(rij**n)*exp(B(rijr0)) e.g. eam_density exponential 0 Ni core 500.0 4.0 3.52 Gaussian: rho(i) = A*(rij**n)*exp(B(rijr0)**2) e.g. eam_density gaussian 2 Ni core 400.0 3.0 3.52 Quadratic: rho(i) = A*(rijr0)**2 if r < r0, else = 0 Cubic: rho(i) = A*(rijr0)**3 if r < r0, else = 0 Quartic: rho(i) = A*(rijr0)**4 if r < r0, else = 0 Voter: rho(i) = A*r**6*(exp(beta*r) + 2**9*exp(2*beta*r)) eVoter: rho(i) = A*r**6*(exp(beta*r) + 2**9*exp(2*beta*r))*exp(1/(rmax  r)) MeiDavenport: rho(i) = sum(l=0>5) (c_l/12)*(r/r0)**l In the above, rmax is the cutoff for the potential from the manybody option that controls the range of the density. Glue: if r < r1 rho(i) = b1_3*(rr1)**3 + b1_2*(rr1)**2 + b1_1*(rr1) + b1_0 if r1 =< r < r2 rho(i) = b2_3*(rr2)**3 + b2_2*(rr2)**2 + b2_1*(rr2) + b2_0 if r2 =< r < rm rho(i) = b3_3*(rrm)**3 + b3_2*(rrm)**2 + b3_1*(rrm) + b3_0 Note that the cutoffs are set by the manybody potential except for the glue model where the maximum cutoff, rm, is a parameter of the model.

See also:  manybody, eam_functional, scmaxsearch, eam_alloy, prt_eam. 
Topic:  eam_alloy 
Type:  Option 
Format:  eam_alloy atom scale <1 x flag> 
Units:  None 
Default:  scale = 1.0 
Use:  This option applies a scaling transformation to the EAM method. While this has no effect on pure elements, it influences the
results for alloys. The transformation is applied as;
rho'(i) = scale(i)*rho(i) F'(sum(rho(i))) = F(sum(rho(i))/scale(i)) where F is the unscale function of the density.

See also:  manybody, eam_functional, eam_density, scmaxsearch. 
Topic:  eam_potential_shift 
Type:  Option 
Format:  eam_potential_shift <inter/intra> <bond/x12/x13/mol/o14> <ener/grad> <kjmol/kcal/au> <scale14> atom1 atom2 g beta <rmin> rmax <2*flags> 
Units:  beta is in inverse Angstroms, g is nominally unit less as it is multiplied by a conversion constant to place it in eV 
Default:  None 
Use:  Specifies a twobody shift of the EAM potential energy component based on the functional form of the VoterChen density. Needed to work with the
embedding potential in the format used by Paradyn.
The form of the potential is E = 2.0*g*r**6*(exp(beta*r) + 2**9*exp(2*beta*r)) The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

See also:  manybody, eam_functional, eam_density. 
Topic:  prt_eam 
Type:  Keyword 
Use:  Output the density and energy associated with atoms during an EAM calculation. 
See also:  eam_functional, eam_density, prt_two. 
Topic:  prt_two 
Type:  Keyword 
Use:  Output the real space twobody energy contributions. 
See also:  prt_eam. 
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 nondefective 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 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/NPH> 
Default:  NVE 
Use:  Selects the ensemble to be use in molecular dynamics. By default the program uses constant number, volume and energy. However, the canonical ensemble can be chosen if constant temperature is prefered to constant energy. If NVT is selected then the NoseHoover thermostat parameter must also be given. It is important to choose a suitable value such that the temperature fluctuations are minimised. For constant pressure, variable cell shape MD, the NPT ensemble can be used (keyword "conp" must be present). In this case it is necessary to supply the thermostat parameter and the barostat parameter. Both again need tuning to get the best performance for each system. NPT ensemble is implemented as a modified NoseHoover form based on Melchionna et al., Mol. Phys. 78 (1993) 533. 
See also:  md, integrator, tau_barostat, tau_thermostat. 
Topic:  tau_barostat 
Type:  Option 
Format:  tau_barostat tau <s/ns/ps/fs> 
Units:  s, ns, ps or fs; default is ps 
Default:  1 ps 
Use:  Species the relaxation time for the barostat if the integrator is set to type "stochastic". 
See also:  integrator, md, tau_thermostat. 
Topic:  tau_thermostat 
Type:  Option 
Format:  tau_thermostat tau <s/ns/ps/fs> 
Units:  s, ns, ps or fs; default is ps 
Default:  1 ps 
Use:  Species the relaxation time for the thermostat if the integrator is set to type "stochastic". 
See also:  integrator, md, tau_barostat. 
Topic:  intconserved 
Type:  Option 
Format:  intconserved pr_cons 
Units:  eV 
Default:  0.0 
Use:  Specifies the integral of the conserved quantity so far for use in an MD run for correct restarting. 
See also:  md, integrator, conserved. 
Topic:  tether 
Type:  Option 
Format:  tether n1n2 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 24,7 will do that. 
See also:  md. 
Topic:  shellmass 
Type:  Option 
Format:  shellmass species_symbol ratio 
Default:  ratio = 0.0 
Use:  Specifies that shells will get assigned masses in shell model molecular dynamics. If shells have a mass their equations of motion
are integrated as for a core. "ratio" is the fraction of the total
mass of an ion which will be assigned to the shell. It has to be
selected so that the shell motions are significantly faster than
the motions of the cores. GULP calculates "wave numbers" for the
core/shell relative motion if this option is specified to assist
in the selection of a suitable ratio. Note that the finite mass
algorithm is not compatible with breathing shells  the iterations
option should be used instead in this case.
The shellmass ratio should be specified for each species, unlike
previous versions.
e.g.
shellmass Al 0.25 O 0.12

See also:  iterations, md. 
Topic:  mdarchive 
Type:  Option 
Format:  mdarchive file_name 
Use:  Specifies name of archive file for molecular dynamics run. This file is in MSI's archive file format and can be read by Insight II. If this option is given the current structure is written to the specified file with the frequency specified using 'write'. Note it is also necessary to specify the "output arc" option to trigger the writing of an arc file. 
See also:  md, write, output. 
Topic:  velocities 
Type:  Option 
Format:  velocities <angs/ps> atom_no velocity_x velocity_y velocity_z 
Units:  Angstroms / ps 
Default:  None 
Use:  Specifies the current Cartesian velocities in an MD simulation and can be used for restarting such a run. Can also be used to set the initial velocities. 
See also:  md, accelerations. 
Topic:  accelerations 
Type:  Option 
Format:  accelerations <no. of accelerations> atom_no (acceleration_x acceleration_y acceleration_z) x no. of accelerations 
Units:  Angstroms / ps in powers appropriate to order 
Default:  None 
Use:  Specifies the current Cartesian accelerations in an MD simulation and can be used for restarting such a run. Can also be used to set the initial values. Depending on the algorithm, different orders of acceleration are required. For example, Gear fifth order requires 4, and velocity Verlet requires 1. 
See also:  md, velocities. 
Topic:  absolute_coordinates 
Type:  Option 
Format:  absolute_coordinates atom_no x y z 
Units:  Angstroms 
Use:  Specifies the absolute Cartesian coordinates of the atoms. Used for restarting MD calculations and determining properties, such as diffusion coefficients, where the migration across cell boundaries must be correctly tracked. 
See also:  md. 
Topic:  cvec 
Type:  Option 
Format:  cvec no_of_vector x y z 
Units:  Angstroms 
Use:  For constant pressure MD, specifies the Cartesian cell vectors at the current time step of a MD simulation so that the cell dynamics can be restarted. 
See also:  md, caver, aver, current_time. 
Topic:  caver 
Type:  Option 
Format:  caver sum_a sum_b sum_c sum_alpha sum_beta sum_gamma sum_vol 
Units:  Angstroms for distances / degrees for angles 
Use:  The cumulative sum of all cell parameters and the volume is specified so that the averages can be correctly determined on restarting. 
See also:  md, aver, cfaver, current_time, absolute_coordinates. 
Topic:  aver 
Type:  Option 
Format:  aver sum_velocity_squared sum_energy sum_virial sum_temperature sum_cons sum_cst no_of_averaging_points 
Units:  Angstroms and ps as appropriate. 
Use:  Specifies various sum of values required for correct restarting of the averages during MD. 
See also:  md, caver, cfaver, current_time, absolute_coordinates. 
Topic:  cfaver 
Type:  Option 
Format:  cfaver sum_lambdaR sum_lambdaV 
Units:  eV/Angstrom 
Use:  Specifies the sum of the values for the constraint force during an MD run. Used to restart average values correctly. LambdaR is the distance constraint force in the velocity Verlet algorithm, while LambdaV is the velocity constraint force. 
See also:  aver, caver, md. 
Topic:  current_time 
Type:  Option 
Format:  current_time time <ps> 
Units:  ps 
Use:  Specifies the current total time during an MD simulation, so that restarting can be performed from the correct time step. 
See also:  md, aver, caver, absolute_coordinates. 
Topic:  iterations 
Type:  Option 
Format:  iterations n <gradient norm> <noextrapolate> <order_of_extrapolation> 
Default:  n = 10, gradient norm = 1.0D10, order of extrapolation = 8 
Use:  Specifies that shell model molecular dynamics shall be performed with massless shells. This is the default for molecular dynamics if shells are present. The shell positions are optimised in every time step for n iterations or until the specified gradient norm for the shells only is reached. Convergence of the shell gradients is crucial for the conservation of the momentum of the system. By default shell extrapolation using rational function interpolation is turned on, using a function of order 8. If "noextrapolate" is specified then this is turned off. Extrapolation usually greatly reduces the number of cycles for optimisation. 
See also:  shellmass. 
Topic:  conserved 
Type:  Keyword 
Use:  Causes the conserved quantity for the MD ensemble to be output where applicable. 
Topic:  hexagonal 
Type:  Keyword 
Use:  Causes a rhombohedral structure to be output in hexagonal form in the dumpfile. 
Topic:  potgrid 
Type:  Option 
Format:  potgrid <xmin xmax ymin ymax zmin zmax> nx ny nz 
Units:  fractional (3D) / fractional/Angstroms (2D) / Angstroms (cluster) 
Use:  Calculates the electrostatic potential at a grid of points. The limits of the grid are given by xmin,xmax,ymin,ymax,zmin and zmax in fractional units for a periodic system and in cartesian coordinates for a cluster. These values can be omitted for a periodic system, in which case they default to 0 for the minimum and 1 for the maximum (ie the whole unit cell). The integer values nx, ny, nz control how many points are calculated in each direction. The number of points will be one greater than the number input. For example, a value of nx=5 will generate 6 points at 0.0, 0.2, 0.4, 0.6, 0.8 and 1.0. 
See also:  pot, potential, potsites. 
Topic:  potsites 
Type:  Option 
Format:  potsites <cart> <au> x1 y1 z1 x2 y2 z2 etc..... 
Units:  fractional/Cartesian as appropriate to dimensionality 
Default:  none 
Use:  Allows the user to specify points in space at which the electrostatic potential should be calculated. Note that it is necessary to also specify the "pot" keyword to trigger the calculation of the potential. 
See also:  pot, potential, potgrid. 
Topic:  accuracy 
Type:  Option 
Format:  accuracy <exponent> < 
Units:  none 
Default:  8.0 < 4 20 > 
Use:  Controls the accuracy of the electrostatic summations. Note : the last two values only apply to 1D systems. The first value is the target number of converged significant figures in the electrostatic energy or the fractional uncertainty in the electrostatic energy, where the value is used as an exponent (i.e. 10**(exponent)). This determines the real and reciprocal space cutoffs of the Ewald sum (3D) and Parry sum (2D) for a given value of rspeed. For 1D systems a direct real space approach is used, as per CRYSTAL. Here the energy is converged to the same precision by searching for the number of neutral cells that must be included in each direction in the sum. The last parameter indicates the upper bound to be used while the second optional parameter is the order of the series used in the numerical integrals. Generally the default values should be sufficient. 
See also:  rspeed. 
Topic:  c6 
Type:  Keyword 
Use:  The dispersion energy, as represented by 1/r**6 terms as part of the Buckingham, Lennardjones and General potentials, is actually quite slow to converge in real space. By specifying this keyword the C6 terms are evaluated using an Ewaldlike 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 oneword 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 threedimensional then x, y and z are assumed to be in fractional units. If the system is a cluster then they are assumed to be in angstroms. nstep is the number of points to be sampled along the translation vector (this leads to nstep+1 calculations including the first and last points). The subset of atoms to which the translation is to be applied is defined by adding a "T" flag to the end of the coordinate lines of these atoms. 
See also:  nofirst_point. 
Topic:  nofirst_point 
Type:  Keyword 
Default:  do first point 
Use:  Requests that the translate option exclude the initial starting structure from the calculation and only does the translated calculations. 
See also:  translate. 
Topic:  gdcrit 
Type:  Option 
Default:  4.0 
Use:  Optimisation of defects involves a force balance method, rather than direct minimisation of the energy. The method is implemented in GULP such that initially the energy is minimised until the gradient norm is sufficiently small, at which point the step length is based on (H1).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 suboption of the observables section. 
See also:  zero_potential, potsites, pot, potgrid. 
Topic:  library 
Type:  Option 
Format:  library name_of_library <nodump> 
Use:  Allows the user to access libraries of existing interatomic potentials. If the word "nodump" is included then all the potentials selected from the library will be excluded from the dumpfile, otherwise they are included and the library call removed. NB If including a keyword line in the library file then this should preceed the options to guarantee correct processing 
See also:  libff, libdump, preserve_Q. 
Topic:  libff 
Type:  Keyword 
Use:  Indicates that fitting flags should be read from any library files if this is a fitting run. 
See also:  library, libdump. 
Topic:  libdump 
Type:  Keyword 
Use:  Indicates that library symbols should be dumped to a restart file. NB This option will create an a restart file that is incompatible with GULP at the moment. 
See also:  library, libff. 
Topic:  line_continuation 
Type:  Information 
Use:  To continue a line onto further lines the character "&" can be given at the end of the line.
e.g. the following input could be given in the two
following ways:
buck Si core O shel 1280.0 0.3 0.0 0.0 12.0 1 0 0 or buck Si core O shel & 1280.0 0.3 0.0 0.0 12.0 & 1 0 0 
Topic:  bsm 
Type:  option 
Format:  bsm <exponential> <single_exponential> <kcal/kjmol> if harmonic form:
atom_symbol/atomic_number <core/shel> K r0 <2 x flags> if exponential form: atom_symbol/atomic_number <core/shel> K rho r0 <3 x flags> if single_exponential form: atom_symbol/atomic_number <core/shel> K rho r0 <3 x flags>

Units:  K in eVAngs**2, r0 in Angstroms K in eV, rho in Angstroms**1 
Default:  = harmonic Type = harmonic 
Use:  Specifies the breathing shell force constant, K, and equilibrium radius, r0, for the spherical breathing
shell model.
E(bs) = 1/2 * K * (r  r0)**2 or the constants of the exponential restoring term: E(bs) = K * [exp(rho*(rr0)) + exp(rho*(rr0))] or the constants of the single_exponential restoring term: E(bs) = K * exp(rho*(rr0))

See also:  breathe, nobreathe, simultaneous. 
Topic:  save 
Type:  Keyword 
Use:  Causes the region 2 matrices, derived from the bulk second derivatives, to be saved to disk as fort.44 for use in restarts. This is important for large bulk materials where the second derivatives are expensive to recalculate. 
See also:  restore, defect. 
Topic:  restore 
Type:  Keyword 
Use:  Causes the region 2 matrices, derived from the bulk second derivatives, to be restored from disk (fort.44) for use in restarts. This is important for large bulk materials where the second derivatives are expensive to recalculate. The fort.44 file must have been generated in a previous run. 
See also:  save, defect. 
Topic:  deflist 
Type:  Option 
Format:  deflist nvacancy ninterstitial nvacancy x atom numbers, ninterstitial x atom numbers 
Use:  Used by the program to enable restarts when mode2a is greater than or equal to 3. Normally this should only need to be written by GULP, rather than the user. 
See also:  defect, reldef, centre, region, restore, save, size. 
Topic:  reldef 
Type:  Option 
Format:  reldef nreg1 x atom numbers 
Use:  Used by the program to enable restarts when performing defect calculations involving bond specifications. This command lists the perfect atom number that each defect atom started life as. A zero indicates an interstitial species. Normally this list should only need to be written by the program rather than the user. 
See also:  defect, deflist, centre, region, restore, save, size. 
Topic:  nod2sym 
Type:  Keyword 
Use:  Turns off the use of symmetry for second derivatives in bulk and defect calculations. Primarily of use for debugging purposes. If using variable charges this option is used implicitly. 
See also:  defect. 
Topic:  tscale 
Type:  Option 
Format:  tscale value <s/ns/ps/fs> 
Units:  s, ns, ps or fs; default is ps. 
Use:  Controls how long in simulation time the temperature scaling is to be applied for. By default this is set equal to the length of the equilibration phase of the run. 
See also:  md, equilibration, production, timestep, sample, write. nolist, temperature, delayforce, endforce, momentum_correct. 
Topic:  timestep 
Type:  Option 
Format:  timestep value <s/ns/ps/fs> 
Units:  s, ns, ps or fs; default is ps 
Use:  Specifies the timestep for integration in a molecular dynamics simulation. A value must be supplied for an MD run. 
See also:  md, equilibration, production, sample, write, nolist,. tscale, temperature, delayforce, endforce, momentum_correct. 
Topic:  equilibration 
Type:  Option 
Format:  equilibration value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  if integer, then value is by default a multiple of the timestep or if noninteger then by default is the time in picoseconds. 
Use:  Specifies the simulation time to be spent equilibrating the kinetic and potential energy distributions prior to the production phase of the molecular dynamics run. 
See also:  md, production, sample, write, temperature, timestep. tscale, nolist, delayforce, endforce, momentum_correct. 
Topic:  production 
Type:  Option 
Format:  production value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  if integer, then value is by default a multiple of the timestep or if noninteger then by default is the time in picoseconds. 
Use:  Specifies the simulation time to be spent collecting production data for subsequent analysis. 
See also:  md, equilibration, , sample, write, temperature, timestep. tscale, nolist, delayforce, endforce, momentum_correct. 
Topic:  sample 
Type:  Option 
Format:  sample value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  if integer, then value is by default a multiple of the timestep or if noninteger then by default is the time in picoseconds. 
Use:  Controls how often the properties of the molecular dynamics run are to be sampled and output to the standard output channel. Averaged properties are also based on these samples. 
See also:  md, timestep, equilibration, production, temperature,. tscale, write, nolist, delayforce, endforce. 
Topic:  momentum_correct 
Type:  Option 
Format:  momentum_correct natom_equilibration <natom_production> 
Default:  All moving atoms to be corrected during both phases 
Units:  None 
Use:  By default linear momentum is removed during both equilibration and production. This option allows the user to restrict the
correction to a subset of atoms that come first in the input
deck, either during equilibration or production, or both.
For example, if the system consists of 100 atoms and all atoms
should have their momenta corrected during equilibration, but
only the first 10 atoms need to be corrected during production
then the input would be:
momentum_correct 100 10

See also:  md, timestep, equilibration, production, temperature,. tscale, write, nolist, delayforce, endforce, sample. 
Topic:  write 
Type:  Option 
Format:  write value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  if integer, then value is by default a multiple of the timestep or if noninteger then by default is the time in picoseconds. 
Use:  Determines how often the program writes to the molecular dynamics dumpfile during the production phase of the run for subsequent analysis. 
See also:  md, timestep, equilibration, production, temperature,. tscale, sample, nolist, delayforce, endforce. 
Topic:  delayforce 
Type:  Option 
Format:  delayforce value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  default is time in picoseconds. 
Default:  0.0 
Use:  Specifies a delay time before any external force is applied to the simulation. Can be used to prevent the force being applied during equilibration. 
See also:  md, production, sample, write, temperature, timestep. tscale, nolist, equilibration, external_force,. td_external_force, endforce. 
Topic:  endforce 
Type:  Option 
Format:  endforce value <s/ns/ps/fs> 
Units:  s, ns, ps or fs  default is time in picoseconds. 
Default:  0.0 
Use:  Specifies a time after which any external force is removed from the simulation. 
See also:  md, production, sample, write, temperature, timestep. tscale, nolist, equilibration, external_force,. td_external_force, delayforce. 
Topic:  md 
Type:  Keyword 
Use:  Specifies that a molecular dynamics run is to be performed 
See also:  timestep, temperature, equilibration, production, sample,. tscale, write, cutp, integrator, nolist_md, minimum_image,. nomolecularinternalke, momentum_correct, mdmaxtemp. 
Topic:  mdmaxtemp 
Type:  Option 
Format:  mdmaxtemp scale_factor 
Default:  100.0 
Use:  This option allows MD runs where the temperature is exploding for one reason or another to be trapped and terminated. When the temperature exceeds the target temperature by a factor of greater than the number specified then the run will stop. If this occurs then common causes are that the timestep is too long, the structure was in a high energy state to start with and the potential can't be dissipated fast enough, the thermostat parameter is unsuitable, or that there are discontinuities or other flaws in the potential energy surface input. Another common cause is that the system size being used is too small leading to large fluctuations in the ensemble averages. 
See also:  md, temperature, mdmaxvolchange. 
Topic:  mdmaxvolume 
Type:  Option 
Format:  mdmaxvolume scale_factor 
Default:  100.0 
Use:  This option allows MD runs where the unit cell volume is exploding for one reason or another to be trapped and terminated. When the volume exceeds the initial volume by a factor of greater than the number specified then the run will stop. If this occurs then common causes are that the timestep is too long, the structure was in a high energy state to start with and the potential can't be dissipated fast enough, the barostat parameter is unsuitable, or that there are discontinuities or other flaws in the potential energy surface input. Another common cause is that the system size being used is too small leading to large fluctuations in the ensemble averages. 
See also:  md, temperature, mdmaxtemp. 
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 nonlist based method. 
See also:  three, four, md. 
Topic:  frequency 
Type:  Option 
Format:  frequency <n> no. value <kpoint_number> <weight> (x n, on separate lines) 
Units:  cm1 
Use:  Subsection of observables, used for specifying frequencies for fitting to. The first number is the position of the mode required in order of increasing frequency. The third number is optionally the k point number to fit at with reference to the k point list for the present configuration. e.g. frequency 2 1 0.0 6 902.0 2 
See also:  observables, elastic, phonon, piezoelectric, sdlc, hfdlc, weight. 
Topic:  epsilon/sigma 
Type:  Option 
Format:  epsilon <kcal/kjmol> <Atomic symbol/atomic number> epsilon sigma <2 x flags for fitting> 
Units:  epsilon in eV and sigma in Angstroms 
Use:  Specifies epsilon and sigma values for each species type to be used in combination rules to obtain LennardJones 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 LennardJones potential parameters where specified. 
See also:  epsilon, lennard. 
Topic:  electronegativity 
Type:  Option 
Format:  <Atomic symbol/atomic number> chi <mu> <2 x flags for fitting> 
Units:  Chi and mu in eV 
Use:  Allows the user to specify the parameters needed for the electronegativity equalisation method for determining charges. Note that if the flags are not specified they are assumed to be zero. 
See also:  eem, qelectronegativity, smelectronegativity. 
Topic:  qelectronegativity 
Type:  Option 
Format:  <Atomic symbol/atomic number> chi <mu> <radius> <3 x flags for fitting> 
Units:  Chi and mu in eV, radius in Ang 
Use:  Allows the user to specify the parameters needed for the QEq electronegativity equalisation method for determining charges. Note that if the flags are not specified they are assumed to be zero. 
See also:  eem, electronegativity, qeq, smelectronegativity. 
Topic:  smelectronegativity 
Type:  Option 
Format:  <Atomic symbol/atomic number> chi mu zeta Znuc <4 x flags> 
Units:  Chi and mu in eV, Znuc in a.u., zeta in Angstroms**1 
Use:  Allows the user to specify the parameters needed for the Streitz and Mintmire electronegativity equalisation method for determining charges. Note that if the flags are not specified they are assumed to be zero. 
See also:  sm, eem, electronegativity, qeq, qelectronegativity. 
Topic:  sm 
Type:  Keyword 
Use:  Turns on calculation of variable charges using the formulation of Streitz and Mintmire. Here the charge is partitioned into a fixed nuclear point charge and a variable charge distribution with the shape of a 1s orbital. To use this option parameters must be specified with the smelectronegativity option too. If the keyword is given as "smzz" then the Znuc_iZnuc_j energy term given by Streitz and Mintmire, but neglected as part of the twobody energy is included explicitly. 
See also:  smelectronegativity, eem, qeq. 
Topic:  bulk_noopt 
Type:  Keyword 
Use:  Stops Gulp from performing optimisations during the bulk run  this is of use when performing defect calculations when you only want the runtype to apply to the defect section. 
See also:  defect, centre, size, region_1, noanisotropic_2b. 
Topic:  qmmm 
Type:  Option 
Format:  qmmm <mechanical/electronic> 
Units:  None 
Default:  No QM/MM scheme 
Use:  Controls whether a QM/MM scheme is used to modify the energy in GULP, and if so which scheme. The two options are:
mechanical: This implies that the interactions within the MM regions and between the QM and MM regions are calculated, but not within the QM region. electronic: This implies the same as mechanical embedding, except that the Coulomb interactions between the QM and MM regions are also excluded since these are assumed to be accounted for by the QM portion of the calculation. NB: At present there are restrictions on which facilities will work in combination with this option. Only 0D calculations with up to first derivatives are generally enabled for all models. 
Topic:  move_2a_to_1 
Type:  Option 
Format:  move_2a_to_1 <radius> 
Units:  Angstroms 
Default:  none 
Use:  At the end of a defect calculation, region 2a ions within the specified radius will be moved into region 1 for the dumpfile at their relaxed positions. This enables a better set of starting positions to be input for a restart with a larger region 1 as the ions will be approximately optimised to start with. If no radius is specified then all region 2a ions will be moved. Should the number of ions exceed the maximum allowed for region 1 then the ions will be moved up to the final shell of ions that will fit. The radius value must not be less than the region 1 radius. 
See also:  defect, centre, size, region_1, vacancy, interstitial,. impurity, bulk_noopt. 
Topic:  noanisotropic_2b 
Type:  Keyword 
Use:  The region 2b energy is calculated for an anisotropic solid by default using ra*rb/r**6. This keyword forces the program to use the isotropic formula 1/r**4. The only real use for this keyword is when trying to compare with CASCADE results which use the more approximate isotropic form. 
See also:  mode2a, defect, centre, region_1, vacancy, impurity,. interstitial, bulk_noopt. 
Topic:  mode2a 
Type:  Option 
Default:  1 
Use:  The displacements in region 2a can be calculated by a number of different approximations to the force acting on the region 2a
ions. Five modes are available at the moment for this purpose:
1 => use electrostatic force of region 1 screened by dielectric
constant
2 => use electrostatic force of region 1 screened by dielectric
constant, but neglecting contribution to derivatives of
region 1
3 => use electrostatic force of defects screened by dielectric
constant
4 => use electrostatic force of defects screened by dielectric
constant, but neglecting contribution to derivatives of
region 1
5 => consider interaction of region 2a only with defects
By default the program uses method 4 for charged defects as this offers the best compromise between accuracy and computational effort. It is recommended that a comparison is made with mode2a=1 as a check. For optimisation the most efficient approach could be to optimise first with a higher mode and then restart in mode 1. 
See also:  defect, centre, region_1, move_2a_to_1, noanisotropic_2b,. vacancy, interstitial, impurity, noanisotropic, gdcrit,. bulk_noopt. 
Topic:  size 
Type:  Option 
Format:  size radius_region_1 <radius_region_2a> <old_radius_region_1> 
Units:  Angstroms 
Default:  none 
Use:  Specifies the region 1 and 2a radii for use in defect calculations. If no value is specified for region 2 then it is set equal to the region 1 radius. When restarting from a dumpfile containing an explicit region 1 specification, but with a larger region 1 radius, then the old region 1 radius from the previous run must also be given to ensure a correct restart. 
See also:  defect, centre, region_1, vacancy, interstitial, impurity,. bulk_noopt. 
Topic:  centre 
Type:  Option 
Format:  centre <atomic symbol> <atom number> <mol no.> <cart/frac> <x y z> 
Use:  Defines the location of the defect centre for a defect calculation. The location can be specified in one of 4 ways; (1) Atomic symbol  places the defect centre at the atom site as specified at the start of the defect calculation. e.g. centre Mg1 shel (2) Atom number  places the defect centre at the site of the atom given by the number in the asymmetric unit. e.g. centre 3 (3) Cartesian coordinates  explicit specification of centre e.g. centre cartesian 0.2 1.3 0.53 (4) Fractional coordinates  explicit specification of centre based on the fractional coordinates. If "cart" or "frac" is not specified, this is the default. e.g. centre 0.25 0.25 0.25 (5) Molecule number  places the defect centre at the centre of the molecule whose number has been given. 
See also:  defect, size, region_1, regi_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 noncharge neutral unit cells, or with the dipole correction energy. 
See also:  region_1, centre, size, regi_before, vacancy,. impurity, interstitial, frequency, noanisotropic, save. restore, gdcrit, 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, regi_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, unfix. 
Topic:  gradient 
Type:  Keyword 
Use:  Calculate gradients but do not optimise 
See also:  conp, conv, cellonly, isotropic, finite, unfix, and shell. 
Topic:  gradients 
Type:  Option 
Format:  gradients <units> atom_no. x y z <weight> 
Units:  eV <eV/Angs or au/Angs or au> 
Default:  all fitted gradients are zero 
Use:  Subsection of observables, used for specifying the x, y and z components of the derivatives on the atom number given for The atom number should refer to the order of the atoms in the asymmetric unit. Derivatives should be symmetry adapted if symmetry is being used (i.e. weighted by the number of symmetry related atoms of the type). Cartesian gradients may be supplied by specifying units. 
See also:  observables, elastic, sdlc, hfdlc, piezo, energy, and stress. 
Topic:  stress 
Type:  Option 
Format:  stress stress_no stress_value <weight> 
Units:  eV 
Default:  all fitted stresses are zero 
Use:  Subsection of observables, used for specifying the stress components for fitting to. Here the stress_no is as follows:
1 => xx 2 => yy 3 => zz 4 => yz 5 => xz 6 => xy Note that stresses are dependent on the cell orientation and so take care when specifying. 
See also:  observables, gradients. 
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 illconditioned. Also the NewtonRaphson 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 selfconsistent. This leads to all derivatives being incorrect as dE/dQ is no longer zero. If Coulomb subtracted potentials are to be used then charges must be calculated for the initial geometry and then frozen. Note: Phonon calculations are limited with the EEM keyword to the gamma point without the LO/TO splitting. Note: Only region 1 atoms are included in EEM and fixed charges will be taken for region 2. 
See also:  qeq, dcharge, sm, electronegativity, gasteiger, qbond. 
Topic:  qbond 
Type:  Keyword 
Use:  Indicates that charges should be calculated using bond increments. Here the charge on the site is the sum of the increments associated with each bond. These increments are specified using the qincrement option. 
See also:  qeq, eem, gasteiger, qincrement. 
Topic:  qincrement 
Type:  Option 
Format:  qincrement atom1 atom2 delta 
Default:  delta = 0.0 
Use:  If the keyword qbond is given then the charges on the atoms are determined by bond increments given by this option. An example
of the input is:
qincrement O core C core 0.24 NB: The order of the atoms is important in that the sign of delta changes if the order is reversed. Consequently if atom1 and atom2 are of the same type then delta must be zero. Hence, the value of delta is applied with the input sign to atom1 and the negative of this to atom2. 
See also:  qeq, eem, gasteiger, qbond. 
Topic:  gasteiger 
Type:  Keyword 
Use:  Indicates that Gasteiger charges should be calculated according to the method in Tetrahedron, 36, 32193288 (1980). The Gasteiger charges are geometry independent and only depend on the connectivity of the molecule. Hence it is important to ensure that the bonding is correct at the start of the calculation and the "fix" keyword is also recommend to avoid potential discontinuities. Parameters are available for H, C, N, O, S and the halogens. For C, N and O the electronegativities used depend on the hybridisation. In the absence of formal atom typing, GULP makes the approximation that the hybridisation state is the obvious one for the coordination number, i.e. for C, 4 bonds => sp3, 3 bonds => sp2, 2 bonds => sp, for N, 3 bonds => sp3, 2 bonds => sp2, 1 bond => sp, and for O, 2 bonds => sp3, 1 bond => sp2. 
See also:  eem, qeq, molq, fix, bond, gasttol, gastiter, qbond. 
Topic:  gasttol 
Type:  Option 
Format:  gasttol tolerance 
Units:  Electrons 
Default:  0.001 
Use:  Sets the tolerance on the change in the charges between iterations of the Gasteiger scheme. The value is set here for consistency with the original paper, which used 0.001 of an electron, but more converged values can be obtained by lowering the tolerance 
See also:  eem, gasteiger, gastiter, qeq. 
Topic:  gastiter 
Type:  Option 
Format:  gastiter maximum_number_iterations 
Units:  None 
Default:  20 
Use:  Sets the maximum number of iterations that are allowed during the Gasteiger charge scheme. 
See also:  eem, gasteiger, gasttol, qeq. 
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 twobody potentials or molecule options. However, in a coreshell model the potential due to the other component of an atom is excluded. It is now possible to also use "pot" for defect calculations in which case GULP returns the electrostatic potential at the sites of the asymmetric unit of region 1. This potential does not include the displacements in region 2a. Note : when using pot in combination with QEq the potential calculated is that resulting from q/r, not the integral expression used within a QEq determination of the charges. 
See also:  efg, potential, nodpsym, potsites, potgrid. 
Topic:  nodpsym 
Type:  Keyword 
Use:  When performing a calculation of the site potentials for region 1 in a defect calculation, the values are normally only output for the asymmetric unit. If this keyword is specified then symmetry is still used in the defect calculation, but the site potentials are output for all sites in region 1. 
See also:  pot. 
Topic:  conv 
Type:  Keyword 
Use:  Set flags for constant volume optimisation. If cellonly, conv or conp are not specified for a calculation that requires derivatives  individual flags are needed. 
See also:  conp, cellonly, breathe, nobreathe, noflags, shell, isotropic. 
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, isotropic. 
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, isotropic. 
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, isotropic. 
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, isotropic. 
Topic:  nobreathe 
Type:  Keyword 
Use:  Excludes radii from the optimisation variables. 
See also:  conp, conv, noflags, shell, breathe, cellonly, isotropic. 
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, isotropic. 
Topic:  isotropic 
Type:  Keyword 
Use:  Only allow isotropic cell expansion and contraction during optimisation. 
See also:  conp, conv, orthorhombic. 
Topic:  orthorhombic 
Type:  Keyword 
Use:  Only allow cell lengths to change, but not angles, during optimisation or MD. 
See also:  conp, conv, isotropic, cello. 
Topic:  free_energy 
Type:  Keyword 
Use:  Use Gibbs freeenergy as the quantity to be calculated/optimised instead of the internal energy. This uses the phonon density of states to calculate the vibrational partition function and thereby the free energy. Note: It is best not to use gamma point phonons in such calculations since the Born charge correction is not applied in a free energy minimisation. 
See also:  phonon, nozeropt, static_first, zsisa, scmaxsearch. 
Topic:  static_first 
Type:  Keyword 
Use:  Run a static optimisation first before the free energy energy minimisation. This should always be done unless restarting a job from a previously optimised structure. However, because this would negate the effects of a restart the default action is not to do this. 
See also:  phonon, nozeropt, free_energy, and zsisa. 
Topic:  nozeropt 
Type:  Keyword 
Use:  Exclude zero point energy term from phonon/free energy calculation  this has the advantage that the conventional energy minimised structure corresponds to the zero kelvin structure. 
See also:  phonon, free_energy. 
Topic:  noenergy 
Type:  Keyword 
Use:  Do not calculate energy. 
Topic:  nodensity_out 
Type:  Keyword 
Use:  Do not write phonon density of states curve to output channel. 
Topic:  broaden_dos 
Type:  Keyword and option 
Default:  0.2 
Use:  An approximation to the delta function is used in order to line Lorentzian broaden the phonon density of states peaks. If given
as a keyword then the default broadening is applied or if used
as an option the user may specify their own broadening factor.
e.g. broaden 0.3 The expression used for the broadening is: w(f) = b/[pi*(1 + (b*(f  f0))**2)] where w is the fractional weight at frequency f of a peak at frequency f0. b is the broadening factor and is the inverse of the halfwidth at halfmaximum parameter. Note, the smaller the factor, the greater the broadening. The range of the plot is automatically extended when broadening is turned on to allow the highest frequency peak to decay to 1/100th of its original magnitude. 
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:  unfix 
Type:  Keyword 
Use:  By default, if GULP sets the flags for a system automatically then one atom will be fixed to remove translational invariance, which would be fatal to a Hessian based optimiser. For first derivative methods, there is no such need and they may work better by not fixing any atoms. The unfix keyword tells GULP not to fix any of the atoms. 
See also:  opti, noflags, conp, conv. 
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. 
See also:  gdcrit, gtol, gmax. 
Topic:  gmax 
Type:  Option 
Format:  gmax <opt/fit> real value 
Units:  fractional 
Default:  0.001 for opt / 0.001 for fit 
Use:  Maximum allowed individual gradient for optimisation/fitting. Value may appear on same line as option or on the following line. If gmax > 1.0 => gmax=10**(gmax) If opt/fit is not supplied then value is applied to both. 
See also:  gdcrit, gtol, ftol. 
Topic:  gtol 
Type:  Option 
Format:  gtol <opt/fit> real value 
Units:  fractional 
Default:  0.0001 for opt / 0.0001 for fit 
Use:  Gradient tolerance for optimisation/fitting. Value may appear on same line as option or on the following line. If gtol > 1.0 => gtol=10**(gtol) If opt/fit is not supplied then value is applied to both. 
See also:  gdcrit, gmax, ftol. 
Topic:  bond 
Type:  Keyword 
Use:  Print out bond length analysis at beginning and end of run. NOTE : The way in which this keyword works has changed for version 1.4. Whereas in older versions all distances less than the sum of the covalent radii multiplied by a tolerance were considered to be bonded, now only the atoms which are bonded in the calculation are listed. This therefore allows for the influence of the "nobond" and "connect" options. 
See also:  distance, average, nobond, connect. 
Topic:  angle 
Type:  Keyword 
Use:  Print out all valid threebody angles found for the threebody potentials. 
Topic:  linmin 
Type:  Keyword 
Default:  no printing 
Use:  Print out details of line minimisations. 
Topic:  both 
Type:  Option 
Default:  both 
Use:  All subsequent potentials to be treated as both intra and intermolecular when molecule option is active. 
See also:  molecule, molq, molmec, inter, intra. 
Topic:  scale 
Type:  Option 
Format:  scale <real number> 
Units:  none 
Default:  1.0 
Use:  Scales subsequent cell vectors and cartesian coordinates by the scale factor. 
Topic:  vectors 
Type:  Option 
Format:  vectors <angs/au> x y z for vector 1 x y z for vector 2 x y z for vector 3 <6 x optimisation flags> 
Units:  Angstrom (default) or au 
Use:  Specifies the cartesian components of the lattice vectors. Either "vectors" or "cell" must be included. Strain optimsation flags appear on last line. 
Topic:  svectors 
Type:  Option 
Format:  svectors <angs/au> x y for vector 1 x y for vector 2 <2 x optimisation flags> 
Units:  Angstrom (default) or au 
Use:  Specifies the cartesian components of the surface vectors. Either "svectors" or "scell" must be included for a surface. Strain optimsation flags appear on last line. 
See also:  scell. 
Topic:  pvector 
Type:  Option 
Format:  pvector <angs/au> x for vector <1 x optimisation flags> 
Units:  Angstrom (default) or au 
Use:  Specifies the cartesian component of the polymer vector. Either "pvector" or "pcell" must be included for a polymer. Strain optimsation flags appear on last line. 
See also:  pcell. 
Topic:  cell 
Type:  Option 
Format:  cell <angs/au> a b c alpha beta gamma <6 x optimisation flags> 
Units:  Angstrom (default) or au for a, b, c and degrees for angles 
Use:  Crystallographic unit cell. Either "vectors" or "cell" must be given. For optimisations or fitting, flags must be set unless cellonly, conp or conv are specified. 
See also:  vectors. 
Topic:  scell 
Type:  Option 
Format:  scell <angs/au> a b alpha <3 x optimisation flags> 
Units:  Angstrom (default) or au for a, b and degrees for angle 
Use:  Surface unit cell. Either "svectors" or "scell" must be given for a surface. For optimisations or fitting, flags must be set unless cellonly, conp or conv are specified. 
See also:  svectors, sfrac, sregion2. 
Topic:  pcell 
Type:  Option 
Format:  pcell <angs/au> a <1 x optimisation flag> 
Units:  Angstrom (default) or au for a 
Use:  Polymer unit cell. Either "pvector" or "pcell" must be given for a polymer. For optimisations or fitting, flags must be set unless cellonly, conp or conv are specified. 
See also:  pvector. 
Topic:  cartesian 
Type:  Option 
Format:  cartesian <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> <angs/au> at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> <%/T> or at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> <%/T> or at.sym. <species type> x y z <charge> <occupancy> <radius> <3 x flags> <%/T> 
Units:  Angstrom (default) or au for coordinates and electrons for charge, radius in Angstroms 
Use:  Cartesian coordinates and charges for all species in the unit cell. Either the atomic number or the symbol may be supplied, followed
by the species type. If the species type is omitted then it is
assumed to be a core. Individual charges may be supplied for each
ion or the charges for each type of species given using the
species option. If the charges are given, then optionally site
occupancies may also be specified. Optimisation flags are only
needed if cellonly, conv, bulk, conp or shell are not specified.
If the "region" suboption is specified, then this tells the program
the region number for the following atoms. In a surface calculation
region 2 is held fixed. If the "rigid" suboption is also specified
after "region" then the region is created as a rigid body so that
all atoms are constrained with respect to each other. By specifying
a string after this containing x, y and/or z, the region may be
allowed to move in particular directions. For example, in an interface
calculation, a region could be specified that is allowed to only relax
in the z direction by using:
cart region 3 rigid z If a "T" is specified then the atom is marked for the translate option If a "%" is specified then the atom is part of a growth slice if it is in region 1 of a surface calculation. 
See also:  fractional, ditto, spacegroup. 
Topic:  fractional 
Type:  Option 
Format:  fractional at no. x y z <charge> <occupancy> <radius> <3 x optimisation flags> or at.sym. <species type> x y z <charge> <occupancy> <radius> <3 x flags> 
Units:  Fractional and electrons, except for radius in Angstroms 
Use:  Internal coordinates and charges for all species in the unit cell. Either the atomic number or the symbol may be supplied, followed by the species type. If the species type is omitted then it is assumed to be a core. Individual charges may be supplied for each ion or the charges for each type of species given using the species option. If the charges are given, then optionally site occupancies may also be specified. Similarly, if the charge and occupancy are given, then the radius of a breathing shell may also be present. Optimisation flags are only needed if cellonly, conv, bulk, conp or shell are not specified. 
See also:  cartesian, ditto, spacegroup, cell. 
Topic:  sregion2 
Type:  Option 
Format:  sregion2 atom_number 
Units:  none 
Use:  Specifies the first atom in the slab that is in region 2. Region 2 is the region that contains the fixed atoms that represent the bulk in a surface calculation. Atoms in region 2 will automatically be fixed during geometry optimisation and the selfenergy of the region will be excluded from the surface energy of the slab  i.e. the surface energy calculated will be for one side, that of region 1. 
See also:  sfrac, scell, sbulkenergy. 
Topic:  sbulkenergy 
Type:  Option 
Format:  sbulkenergy <bulk energy of surface region 1> 
Units:  eV 
Use:  Specifies the energy that the atoms of a surface region 1 would have had in the bulk material. This value is determined when building the surface slab and is required to calculate the surface energy. As an example, consider a surface region 1 of formula Mg24O24  here the value would be 24 times the value of the bulk MgO energy for the primitive cell as calculated by GULP. 
See also:  sregion2. 
Topic:  totalenergy 
Type:  Option 
Format:  totalenergy <total energy of bulk unit cell> 
Units:  eV 
Use:  This option is written out by GULP as information for the generation of a surface calculation input by GDIS based on a restart file. 
See also:  sbulkenergy. 
Topic:  dhkl 
Type:  Option 
Format:  dhkl <width of growth slice> <au> 
Units:  Angstrom 
Use:  This specifies the spacing of the hkl planes which is equivalent to the width of the growth slice for the calculation of the attachment energy. This should only be specified for an unrelaxed surface. For a general surface the growth slice can be marked by adding a "%" sign to the end of the coordinate line. 
See also:  sfractional, cartesian. 
Topic:  sfractional 
Type:  Option 
Format:  sfractional <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> at.sym. <species type> x y z <charge> <occupancy> <radius> <3 x flags> <T/%> 
Units:  Fractional for x and y, Angstroms for z and radius, and electrons 
Default:  For region 2, rigid is the default. 
Use:  Internal coordinates and charges for all species in the surface cell. Either the atomic number or the symbol may be supplied, followed
by the species type. If the species type is omitted then it is
assumed to be a core. Individual charges may be supplied for each
ion or the charges for each type of species given using the
species option. If the charges are given, then optionally site
occupancies may also be specified. Similarly, if the charge and
occupancy are given, then the radius of a breathing shell may
also be present. Optimisation flags are only needed if cellonly,
conv, bulk, conp or shell are not specified.
If the "region" suboption is specified, then this tells the program
the region number for the following atoms. In a surface calculation
region 2 is held fixed. If the "rigid" suboption is also specified
after "region" then the region is created as a rigid body so that
all atoms are constrained with respect to each other. By specifying
a string after this containing x, y and/or z, the region may be
allowed to move in particular directions. For example, in an interface
calculation, a region could be specified that is allowed to only relax
in the z direction by using:
sfrac region 3 rigid z If a "T" is specified then the atom is marked for the translate option If a "%" is specified then the atom is part of a growth slice if it is in region 1 of a surface calculation. 
See also:  scell, sregion2. 
Topic:  pfractional 
Type:  Option 
Format:  pfractional <region <n> <qm/mm> <rigid <xyz>>> <nonrigid> at.sym. <species type> x y z <charge> <occupancy> <radius> <3 x flags> 
Units:  Fractional for x Angstroms for y and z, and electrons, radius in Angstroms 
Use:  Internal coordinates and charges for all species in the polymer cell. Either the atomic number or the symbol may be supplied, followed by the species type. If the species type is omitted then it is assumed to be a core. Individual charges may be supplied for each ion or the charges for each type of species given using the species option. If the charges are given, then optionally site occupancies may also be specified. Similarly, if the charge and occupancy are given, then the radius of a breathing shell may also be present. Optimisation flags are only needed if cellonly, conv, bulk, conp or shell are not specified. 
See also:  pcell. 
Topic:  cutd 
Type:  Option 
Format:  cutd cutoff_distance <angs/au> 
Units:  Angstrom (default) or au 
Default:  2.0 Angstroms 
Use:  Controls search for bond lengths. 
See also:  bond. 
Topic:  cutp 
Type:  Option 
Format:  cutp cutoff_distance <polynomial/cosine/voter/exponential/mdf> <taper range> <angs/au> 
Units:  Angstrom (default) or au 
Default:  Use individual potential values / polynomial 
Use:  Maximum interatomic potential cutoff if less than individual value This can be optionally followed by a taper range. If this is set
to a nonzero 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
StillingerWeber potentials (as these go to zero at the cutoff any
way) and spline potentials (which can be constructed to go to zero
as well). Either a polynomial or cosine taper form can be used.
The form of the Voter taper is: E_smooth(r) = E(r)  E(rcut) + (rcut/m)*(1  (r/rcut)**m)*(dE(rcut)/dR) The form of the exponential taper is: E_smooth(r) = E(r)*f_cut(r) where f_cut(r) = exp(1/(rcutr)) for r < rcut and = 0 for r >= rcut Note that in the case of the Voter and exponential tapers there is no taper range since it applies over the whole range. The form of the MDF (MeiDavenportFernando) taper is: E_smooth(r) = E(r)*f_cut(r) where f_cut(r) = 1.0 for r < r_m and = 0 for r >= rcut. In between it takes the value f_cut(r) = ((1  x)**3)*(1+3x+6x**2), where x = (rr_m)/(rcutr_m). Here r_m is the start of the taper range.

Topic:  bocharge 
Type:  Option 
Format:  bocharge <staper> atom1 atom2 deltaQ Rmin Rmax 
Units:  au 
Default:  None for potential / use cosine taper 
Use:  Specifies the parameters for the taper function used in determining bond order charges as a function of environment. The charge on an
ion is determined as:
Atom 1: Q = sum [  deltaQ*H(r) ] Atom 2: Q = sum [ + deltaQ*H(r) ] Here the sum is over all atoms of the approriate type within the cutoff radius, Rmax. H(r) is taper function that acts between Rmin and Rmax. In the original paper of Jiang and Brown a cosine taper is used and this is the default. However, the suboption allows the sine taper of Watanabe et al (Jpn. J. Appl. Phys. 38, L367 (1999)) to be used which has better behaviour for the second derivatives at the cutoff.

See also:  botwobody, borepulsive, boattractive, boselfenergy, sw2jb, sw3jb. 
Topic:  boselfenergy 
Type:  Option 
Format:  boselfenergy atom1 Kq <rho> q0 
Units:  Kq in eV, rho in a.u., q0 in a.u. 
Default:  Rho = 1.0 
Use:  Specifies the self energy for bond order charges, as introduced by Jiang and Brown:
E = Kq*exp(rho/(q  q0)) if q > q0 for q0 > 0 or E = Kq*exp(rho/(q  q0)) if q > q0 for q0 < 0 else E = 0

See also:  botwobody, borepulsive, boattractive, bocharge, sw2jb, sw3jb. 
Topic:  botwobody 
Type:  Option 
Format:  botwobody <kcal/kjmol> atom1 atom2 A B za zb rtaper rmax <4*flags>
or botwobody combine atom1 atom2 chiR chiA <2*flags>

Units:  A and B in eV, za and zb in 1/Angstroms, rtaper and rmax in Angs 
Default:  none 
Use:  Specifies the parameters for the twobody form of a bondorder potential of the Tersoff form:
E = f(r)[A.exp(za.r).(BOr)  B.exp(zb.r).(BOa)] where f(r) is a taper function that smooths the decay from rtaper to rmax, BOr and BOa are the bond orders for the repulsive and attractive terms, respectively. These terms are set by separate options. If the combine suboption is specified then the parameters are generated using Tersoff's combination rules from the values for the corresponding element's selfself interaction. The chi values then scale the repulsive and attractive terms. 
See also:  borepulsive, boattractive, bocharge, boselfenergy. 
Topic:  borepulsive 
Type:  Option 
Format:  borepulsive atom1 alpha m n lambda <3*flags>
or borepulsive theta atom1 alpha m n lambda c d h <6*flags> NB The value of m cannot be fitted and therefore there is no flag 
Units:  lambda in 1/Angstroms All other quantities are unitless. 
Default:  none 
Use:  Sets the parameters for the bondorder in the repulsive term as given by
BOr = (1 + (alpha*zeta)**n)**(1/2n) For case without "theta" suboption; zeta = Sum(rik) [f(rik).exp(lambda**m.(rijrik)**m)] else; zeta = Sum(rik) [f(rik).g(theta).exp(lambda**m.(rijrik)**m)] f(rik) = cosine taper function g(theta) = 1 + (c/d)**2  c**2/[d**2 + (h  cos(theta))**2] Note that the cutoffs are derived from the values for the corresponding botwobody potential. 
See also:  botwobody, boattractive, bocharge, boselfenergy. 
Topic:  boattractive 
Type:  Option 
Format:  boattractive atom1 alpha m n lambda <3*flags>
or boattractive theta atom1 alpha m n lambda c d h <6*flags> NB The value of m cannot be fitted and therefore there is no flag 
Units:  lambda in 1/Angstroms All other quantities are unitless. 
Default:  none 
Use:  Sets the parameters for the bondorder in the attractive term as given by
BOa = (1 + (alpha*zeta)**n)**(1/2n) For case without "theta" suboption; zeta = Sum(rik) [f(rik).exp(lambda**m.(rijrik)**m)] else; zeta = Sum(rik) [f(rik).g(theta).exp(lambda**m.(rijrik)**m)] f(rik) = cosine taper function g(theta) = 1 + (c/d)**2  c**2/[d**2 + (h  cos(theta))**2] Note that the cutoffs are derived from the values for the corresponding botwobody potential. 
See also:  botwobody, borepulsive, bocharge, boselfenergy. 
Topic:  potential_interpolation 
Type:  Option 
Format:  potential_interpolation number_of_points 
Units:  None 
Default:  Do not use interpolation 
Use:  Requests that linear interpolation of potentials is used to accelerate the calculation where possible at the expense of numerical precision. The larger the number of points the greater will be the precision (values of 100,000 & larger are typical). Currently this technique is only used in MD. 
Topic:  buckingham 
Type:  Option 
Format:  buckingham <inter/intra> <bond/x12/x13/mol/o14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> atom1 atom2 A rho C <rmin> rmax <3*flags> 
Units:  A in eV, rho in Angs, C in eV*Angs**6 If kcal is given : A in kcal, rho in Angs, C in kcal*Angs**6 If kjmol is given: A in kJmol1, 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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential, cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

See also:  c6. 
Topic:  spline 
Type:  Option 
Format:  spline <cubic> <reverse> <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <type_of_bond> atom1 atom2 <shift> <rmin> rmax <1*flag> energy_1 distance_1 energy_2 distance_2 : : energy_n distance_n 
Units:  Energies in eV, distances in Angs 
Default:  rational function spline, shift = 0.0 
Use:  Spline potential  flag for fitting (0/1) of shift. atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
If the option "reverse" is specified then the spline information
will be read as distance then energy, ie the reverse order to
normal.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13
interaction.
When specified as bonded, potential cutoffs are omitted from input.

Topic:  buck4 
Type:  Option 
Format:  buck4 <inter/intra> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 A rho C <rmin> cut1 rminimum cut2 rmax <4*flags> 
Units:  A in eV, rho in Angs, C in eV*Angs**6, distances in Angstroms 
Default:  none 
Use:  Four range Buckingham potential  optimisation flags for fitting (0/1) atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
The form of the potential is:
from rmin to cut1 : E=Aexp(r/rho)
from cut1 to rminimum: E=a0+a1*r+a2*r**2+a3*r**3+a4*r**4+a5*r**5
from rminimum to cut2: E=b0+b1*r+b2*r**2+b3*r**3
from cut2 to rmax : E=C/r**6
The potentials are subjected to the constraint that the functions and
their first and second derivatives must be continuous at the boundary
points, and also that the function must have a stationary point at
rminimum (hopefully a minimum!).
intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential, cutoffs are omitted from input.

Topic:  tsuneyuki 
Type:  Option 
Format:  tsuneyuki <form2> <inter/intra/bond> <x12/x13/mol/o14> <type_of_bond> atom1 atom2 Q1 Q2 zeta <rmin> rmax <1*flag> 
Units:  Q1 & Q2 in a.u., zeta in Angstroms**1 
Default:  form1 
Use:  Specifies the shortrange Coulomb correction described by Tsuneyuki et al PRL, 61, 869 (1988). Note that the role of the charges is inverted relative
to the paper in order that charge neutrality is achieved in the longrange
limited. It is assumed that this was a typo. The correction to the Coulomb
term is given by:
U = [Q1.Q2  q1.q2]g(r)/r where q1 & q2 are the regular charges specified elsewhere, and g(r) is: Form1: g(r) = (1+z.r)exp(2z.r) Form2: g(r) = (1 + 11(z.r)/8 + 3(z.r)**2/4 + (z.r)**3/6)exp(2z.r) where z is used as a shorthand for zeta

Topic:  lennard 
Type:  Option 
Format:  lennard <epsilon> <zero> <esff> <combine/geometric> <m> <n> <inter/intra> <bond/x12/x13/mol/o14> <type_of_bond> <kcal/kjmol> <ener/grad> <all> <scale14> atom1 atom2 (A B/epsilon sigma) <rmin> rmax <2*flags> 
Units:  A in ev*Angs**m, B in ev*Angs**n, epsilon in eV, sigma in Angs 
Default:  m=12, n=6 
Use:  LennardJones 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/(mn)) c2 = (m/(mn)) r = sigma => E = zero c1 = (n/(mn))*(m/n)**(m/(mn)) c2 = (m/(mn))*(m/n)**(n/(mn)) If combine is specified as well as epsilon, then combination rules are used to obtain the epsilon and sigma parameters based on the values for individual species. The combination rules are as follows: epsilon = 2*sqrt(e1*e2)(s1**3.s2**3)/(s1**6+s2**6) sigma = ((s1**6+s2**6)/2)**1/6 where e1, e2, s1 and s2 are the atom related parameters. Alternatively, if geometric combination rules are specified then this becomes: epsilon = sqrt(e1*e2) sigma = (s1+s2)/2 If combine is specified for a standard lennardjones 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 12 interaction and x13 => exclude 12 and 13 interaction. If "all" is specified as a suboption, then LennardJones potentials will be automatically created and added for all combinations of A/B or epsilon/sigma, as appropriate, based on the values that have been specified up to that point. In this case, the line following should only have the rmin and rmax to be used for all the potentials. e.g. lennard 12 6 combine all 0.0 12.0 When specified as bonded potential, cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

See also:  epsilon, atomab, c6. 
Topic:  igauss 
Type:  Option 
Format:  igauss <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 A b r0 <rmin> rmax <3*flags> 
Units:  A in eV, b in Angs**2, r0, rmin and rmax in Angs 
Default:  none 
Use:  This option specifies the use of an inverted Gaussian potential between two atoms. The form of the energy is:
E =  A.exp(b(rr0)**2) intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input.

Topic:  covexp 
Type:  Option 
Format:  covexp <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> atom1 atom2 D a r0 <rmin> rmax <3*flags> 
Units:  D in eV, a in Angs**1, r0, rmin and rmax in Angs 
Default:  none 
Use:  Covalentexponential 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*(rr0)**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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

Topic:  morse 
Type:  Option 
Format:  morse <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> <etaper> <ener/grad> <type_of_bond> atom1 atom2 De a r0 <coul> <rmin> rmax <3*flags> 
Units:  De in eV, a in Angs1, r0 in Angs, coul in none 
Default:  none 
Use:  Morse potential  optimisation flags for fitting. coul = 1.0 => coulomb subtracted.
The format of the data assumes that rmin is the least important
entry. I.e., if one of the optional parameters, coul or rmin,
is missing it is assumed that coul is present and rmin
is set to zero.
atom1 and atom2 may be specified either by atomic number or symbol which in the latter case can be followed by a species type. If no species type is given then type is assumed to be core. E = De.((1exp(a(rr0)))**2  1.0)  coul.qi.qj/r If "etaper" is specified then the potential is scaled by: exp(1/(rmaxr)) to ensure that the potential (excluding the Coulomb subtraction) goes to zero at the cutoff. In this case, the energy/gradient options cannot be used. Note that the potential can also be written as: E = De.(exp(2a(rr0))  2exp(a(rr0)))  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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

Topic:  fermidirac 
Type:  Option 
Format:  fermidirac <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> atom1 atom2 a b r0 <rmin> rmax <3 x flags> 
Units:  a in eV, b in Angs1, r0 in Angs 
Default:  none 
Use:  FermiDirac potential  optimisation flags for fitting. atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = a/(1+exp(b(rr0))) 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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

Topic:  erferfc 
Type:  Option 
Format:  erferfc <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> atom1 atom2 A alpha beta <rmin> rmax <3 x flags> 
Units:  A in eV, alpha and beta in Angs 
Default:  none 
Use:  Specifies the parameters of an erferfc potential, which has the form: E_ij = A.erf(r/alpha).erfc(r/beta)/r

See also:  qerfc, reperfc, erfpot. 
Topic:  erfpot 
Type:  Option 
Format:  erfpot <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> atom1 atom2 A alpha <rmin> rmax <2 x flags> 
Units:  A in eV, alpha in Angs 
Default:  none 
Use:  Specifies the parameters of an erf potential, which has the form: E_ij = A.erf(r/alpha)/r

See also:  qerfc, reperfc, erfpot. 
Topic:  reperfc 
Type:  Option 
Format:  reperfc <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond> atom1 atom2 A beta <rmin> rmax <3*flags> 
Units:  A in eV and beta in Angs 
Default:  none 
Use:  Specifies the parameters of an reperfc potential, which has the form: E_ij = A.erfc(r/beta)/r

See also:  qerfc, erferfc, erfpot. 
Topic:  meidavenport 
Type:  Option 
Format:  meidavenport <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 phi0 delta gamma r0 <rmin> rmax <4*flags> 
Units:  phi0 in eV, r0 in Angs and delta & gamma are dimensionless. 
Default:  none 
Use:  Specifies the parameters for the twobody component of the MeiDavenport potential (PRB, 46, 21 (1992)):
E_ij =  phi0*(1 + delta*(r/r0  1))*exp(gamma*(r/r0  1))

See also:  eam_density, eam_functional. 
Topic:  ljbuffered 
Type:  Option 
Format:  ljbuffered <m> <n> 
Units:  A in eV*Angs**m, B in eV*Angs**n, r0 in Angs 
Default:  m = 12, n = 6, r0 = 0.0 
Use:  Buffered LennardJones potential, where r0 is added to the distance. atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A/(r + r0)**m  B/(r + r0)**n intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input.

Topic:  qtaper 
Type:  Option 
Format:  qtaper <intra/inter> <bond/x12/x13/mol/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.(1f(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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input.

Topic:  qerfc 
Type:  Option 
Format:  qerfc <intra/inter> <bond/x12/x13/mol/o14> <au/nm/pm> <ener/grad> <type_of_bond> atom1 atom2 rho rmax <1*flag> 
Units:  rho and rmax in Angstroms 
Default:  none 
Use:  Screened Coulomb interaction using the complementary error function. E = [qi.qj/r].erfc(r/rho) intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance. NOTE : The keyword "noelectrostatics" should be included when using this potential to turn off the normal Ewald sum, otherwise the Coulomb interaction will be double counted. 
See also:  noelectrostatics. 
Topic:  qoverr2 
Type:  Option 
Format:  qoverr2 <intra/inter> <bond/x12/x13/mol/o14> <au/nm/pm> <ener/grad> atom1 atom2 rmax <1*flag> 
Units:  rmax in Angstroms 
Default:  none 
Use:  Computes the charge interaction as a local one based on: E = [qi.qj/r**2] intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance. NOTE : The keyword "noelectrostatics" should be included when using this potential to turn off the normal Ewald sum, otherwise the Coulomb interaction will be double counted. NOTE : This expression is used for the Coulomb term in Accelrys's implementation of Dreiding 
See also:  noelectrostatics. 
Topic:  qwolf 
Type:  Option 
Format:  qwolf <eta> <rmax> 
Units:  eta in inverse Angstroms and rmax in Angstroms 
Default:  none 
Use:  Calculates the electrostatic energy using the approximation to the Ewald sum due to Wolf et al (J. Chem. Phys., 110, 8254, 1999):
Eij = [qi.qj/r].erfc(eta*r)  lim{r>rmax}([qi.qj/rmax].erfc(eta*rmax)) Ei =  (erfc(eta*rmax)/(2*rmax) + eta/sqrt(pi))*qi**2 Note: it is up to the user to set the eta and rmax values such that the Ewald limit is recovered. At present the Wolf sum cannot be used with a defect calculation. 
See also:  noelectrostatics. 
Topic:  delta 
Type:  Option 
Format:  delta <fit> <real value> 
Units:  fractional 
Default:  0.00001 for ordinary fitting / 0.0001 for relax fitting 
Use:  Differencing interval used in numerical procedures. One delta value is possible according to the suboption 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 HermannMaugain 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 nonstandard P 21/A setting of P 21/C the input should be:
space P 1 21/A 1

See also:  origin, valid_spacegroups, symmetry_operator. 
Topic:  nosymmetry 
Type:  Keyword 
Use:  Switches off symmetry after generating unit cell. For nonprimitive 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 unit matrix with BFGS method. 
See also:  simul, relax, genetic, fbfgs, delta. 
Topic:  fbfgs 
Type:  Keyword 
Use:  Perform fitting run using full BFGS method. This involves the calculation of the full numerical hessian instead of just the diagonal elements. 
See also:  fit. 
Topic:  genetic 
Type:  Keywrd 
Use:  Given contents of unit cell use a genetic algorithm to find possible atomic coordinates. (global optimiser) A local minimisation can then be performed on the best configurations 
See also:  predict, anneal, contents, global, and cost. 
Topic:  genetic 
Type:  Option 
Use:  Start of genetic algorithm options section, closed by "end" 
See also:  tournament, crossover, mutation, discrete,. configurations, best, maximum, minimum, dmaximum, dminimum. 
Topic:  tournament 
Type:  Option 
Format:  tournament initial <final> <stepsize> 
Default:  0.8 <0.8> <0.0> 
Use:  Part of ga options section. Specifies the tournament selection probability. The higher the value, the more likely it is that the better configuration will be selected. If <initial> value is less than <final> value then after 20 iterations tournament incremented by <stepsize>. If optimisation stuck in local min then if stepsize nonzero 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 nonzero 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 nonzero tournament is reset to <initial> OR (ii) grid fixed then mutation rate changed. 
See also:  genetic, anneal, option, and grid. 
Topic:  configurations 
Type:  Option 
Format:  configurations n <max configs> <stepsize> 
Default:  10 <10> <0 or 2> 
Use:  Part of ga options section. Specifies the number of configurations to be used in the genetic algorithm procedure. Number of configurations must be even. If maximum number of configurations greater than n then population will expand by stepsize (default 2) every iteration until <n=max> afterwhich <stepsize> new random configurations will replace current <stepsize> worst configurations. <stepsize> also specifies how many of the best configurations survive into the next iteration without changing! 
See also:  genetic, and predict. 
Topic:  unique 
Type:  Option 
Format:  unique d 
Default:  d=0.0d0 
Use:  Part of ga options section. Any 2 candidates to be optimised must have a cost function difference of at least d. 
Topic:  best 
Type:  Option 
Format:  best n <every m> <only> 
Default:  Best 2 candidates at the end of global search may be optimised. 
Use:  Part of ga options section. If used then the best 'n' candidates found (after every m iterations) may be optimised at the end. If 'only' specified then a maximum of n candidates may be optimised ie the best n from iterations m, 2m, 3m, ... 
See also:  genetic, and predict. 
Topic:  discrete 
Type:  Option 
Format:  discrete <no. to set>=N <variables to be set>xN <discretation number>xN 
Default:  6 
Use:  Part of genetic options section. When two is raised to the power of this number it gives the discretisation interval for a fitted variable. The higher the value, the greater the resolution of the fitting. 
See also:  genetic. 
Topic:  minimum 
Type:  Option 
Format:  minimum <no. to set>=N <variables to be set>xN <minimum value>xN 
Default:  0.0 
Use:  Part of genetic options section. Specifies the minimum value allowed in the fitting procedure. 
See also:  genetic. 
Topic:  maximum 
Type:  Option 
Format:  maximum <no. to set>=N <variables to be set>xN <maximum value>xN 
Default:  Twice initial value. 
Use:  Part of genetic options section. Specifies the maximum allowed value of a given parameter. 
See also:  genetic. 
Topic:  dminimum 
Type:  Option 
Format:  dminimum <x> <y> <z> 
Default:  0.0 
Use:  Part of genetic options section. Specifies the minimum value used as a default in genetic optimisation. According to the dimensionality the arguments supplied should be: 2D => z 1D => y & z 0D => x & y & z By specifying a minimum value, this allows GAs to be used for non3D systems. 
See also:  genetic. 
Topic:  dmaximum 
Type:  Option 
Format:  dmaximum <x> <y> <z> 
Default:  0.0 
Use:  Part of genetic options section. Specifies the maximum value used as a default in genetic optimisation. According to the dimensionality the arguments supplied should be: 2D => z 1D => y & z 0D => x & y & z By specifying a maximum value, this allows GAs to be used for non3D systems. 
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,. gradients, hfrefractive_index, srefractive_index, piezoelectric,. frequency, gradient, potential, entropy, bornq, monopoleq, cv,. stress, fbond, fangle, reaction. 
Topic:  time 
Type:  Option 
Format:  time time_limit <seconds/minutes/hours> 
Units:  seconds (default), minutes or hours 
Default:  Infinity! 
Use:  Specifies time limit for calculation. 
Topic:  variables 
Type:  Option 
Format:  keyword 
Default:  none 
Use:  Specifies fitting variables associated with different species  valid options are charge, split, and shift. Also allows constraints to be applied. 
See also:  constrain, charge, split, shift. 
Topic:  shift 
Type:  Option 
Format:  shift energy_shift <ev/au/kcal/kjmol1> 
Units:  eV (default), au, kcal or kJmol1 
Default:  0.0 eV 
Use:  Shifts energy by this amount  mainly for use in fitting ab initio energy surfaces. Shift is applied to all subsequent configurations until the value of shift is changed by another shift directive. Shift can also appear in the variables section as a command to cause the shift to be fitted. 
See also:  sshift. 
Topic:  sshift 
Type:  Option 
Format:  sshift scale_factor 
Units:  none 
Default:  1.0 
Use:  Scales the shift value for the present configuration. Allows energies of structures with different numbers of formula units to be fitted. 
See also:  shift. 
Topic:  threebody 
Type:  Option 
Format:  three <exponential/vessal/cosine> <k3> <k4> <nbeq/nbne nbond> <intra/inter> <bond/mol> <kcal/kjmol> atom1 atom2 atom3 k <k3> <k4> theta0 <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <24 flags> 
Units:  k in eVrad**2, theta0 in degrees, rmin & rmax in Angs, k3 in eVrad**3 k4 in eVrad**4 
Default:  none 
Use:  Threebody 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 * (thetatheta0)**2
Exponentially decaying form is also available: E(three) = 1/2 * k * (thetatheta0)**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*(theta0pi)**2) B = (theta0pi)**2  (thetapi)**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*(thetatheta0)**2 + 1/6*k3*(thetatheta0)**3 + 1/24*k4*(thetatheta0)**4 Formats: three k3 atom1 atom2 atom3 k k3 theta0 rmax12 rmax13 rmax23 <3xflags> three k4 atom1 atom2 atom3 k k4 theta0 rmax12 rmax13 rmax23 <3xflags> three k3 k4 atom1 atom2 atom3 k k3 k4 theta0 rmax12 rmax13 rmax23 <4xflags> Cosine of theta can also be used instead of theta, if the cosine option is used : E(three) = 1/2*k*(cos(theta)cos(theta0))**2 intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species where 12 and 13 are bonded. The type of bond suboption can be used to control which bonded atoms the potential applies to. For a threebody potential, the bond type for the two bonds connected to the pivot atom can be supplied and then checked before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition, a bond may specified as regular (default), cyclic or exocyclic. the order of the bond type options matches the order of the pivot atom  end atom pairs. For example, if a potential acts for the triad S  C  O, where the CS bond is a regular bond and the CO is an exocyclic double bond then the input would look like: three bond single regular double exocyclic C core S core O core ...... etc Conditions can also be placed on a potential to check the number of bonds associated with the pivot atom (e.g. if a potential is designed for a 90 degree angle it might be necessary to check that the number of bonds is four or six for square planar or octahedral). The conditions are placed using one or more instances of "nbeq" or "nbne" followed by an integer. Here "nbeq" imples no. of bonds must equal and "nbne" number of bonds must not equal. Hence, "nbeq 4" would require the pivot to have 4 bonds. When multiple terms are used, the logic of nbeq is concatinated with "or", whereas that of nbne is joined by "and". Therefore "nbne 4 nbne 6" would apply to an atom with 3 bonds, but not one with 4 or 6. NB It's important to specify the first bond as being of "regular" type so that the "exocyclic" attribute is correctly assigned to the second bond since the first term is assumed to apply to the first bond, whereas the second applies to the second bond.

See also:  axilrodteller, angle, stillingerweber, exponential, bcross, uff3,. ureybradley, murrellmottram, bacross, lin3, hydrogenbond, equatorial. 
Topic:  lin3 
Type:  Option 
Format:  lin3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K isign n <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <flag> 
Units:  K in eV, rmin and rmax in Angstroms 
Default:  none 
Use:  ESFF linear threebody form : E(three) = K * (1 + isign*cos(n*theta)) intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species were 12, 23 and 13 are bonded.

See also:  axilrodteller, angle, stillingerweber, exponential, bcross,. ureybradley, murrellmottram, bacross, three, hydrogenbond, equatorial,. uff3. 
Topic:  uff1 
Type:  Option 
Format:  uff1 <intra/inter> <bond> <kcal/kjmol> atom1 r theta x D zeta Zeff type tor Koop Thetaoop Chi <10 x flags> 
Units:  r & x in Ang, theta & thetaoop in degrees, D, Koop, chi and tor in eV, Zeff in a.u. 
Default:  none 
Use:  Specifies the species parameters for UFF force field generation by combination rules. 
See also:  umorse. 
Topic:  umorse 
Type:  Keyword 
Use:  By default the UFF generation rules use a harmonic potential for the bonded interaction. By specifying this keyword, the Morse potential is used instead of harmonic. 
See also:  uff1. 
Topic:  uff3 
Type:  Option 
Format:  uff3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K theta0 rmin(12) rmax(12) rmin(13) rmax(13) rmin(23) rmax(23) <flag> 
Units:  K in eV, theta0 in degrees, rmin and rmax in Angstroms 
Default:  none 
Use:  UFF nonlinear threebody form : E(three) = K * (C0 + C1*cos(theta) + C2*cos(2*theta)) Here the coefficients are related to theta0 by: C2 = 1/(2*sin(theta0))**2 C1 =  4*C2*cos(theta0) C0 = C2*(2*(cos(theta0))**2 + 1) intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species were 12, 23 and 13 are bonded.

See also:  axilrodteller, angle, stillingerweber, exponential, bcross, lin3,. ureybradley, murrellmottram, bacross, three, hydrogenbond, equatorial. 
Topic:  equatorial 
Type:  Option 
Format:  equatorial <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K n beta r0 <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <3*flag> 
Units:  K in eV, r0, rmin and rmax in Angstroms and beta in inverse Angstroms 
Default:  none 
Use:  ESFF equatorial threebody form : E(three) = (2K/n**2) * (1  cos(n*theta)) + 2K*exp(beta*(r13  r0)) Here r13 is the distance between the atoms 13 in the triad. intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species were 12, 23 and 13 are bonded.

See also:  axilrodteller, angle, stillingerweber, exponential, bcross. ureybradley, murrellmottram, bacross, three, hydrogenbond,. lin3, uff3. 
Topic:  axilrodteller 
Type:  Option 
Format:  axilrodteller <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <flag> 
Units:  k in eV*Angstroms**9, rmin & rmax in Angstroms 
Default:  none 
Use:  AxilrodTeller threebody 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 12, 23 and 13 are bonded.

See also:  three, angle, exponential, stillingerweber, bcross, ureybradley,. murrellmottram, bacross, hydrogenbond, equatorial, uff3, lin3. 
Topic:  murrellmottram 
Type:  Option 
Format:  murrellmottram <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K rho r012 r013 r023 <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <5*flags> c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 <11*flags> 
Units:  K in eV, r012,r013,r023,rmin,rmax in Angstroms 
Use:  Specifies the MurrellMottram threebody potential; E(three) = K.P(Q1,Q2,Q3).exp(rho.Q1) P(Q1,Q2,Q3) = c0 + c1.Q1 + c2.Q1**2 + c3(Q2**2 + Q3**2) + c4.Q1**3 + c5.Q1(Q2**2 + Q3**2) + c6(Q3**3  3.Q3.Q2**2) + c7.Q1**4 + c8.Q1**2.(Q2**2+Q3**2) + c9.(Q2**2+Q3**2)**2 + c10.Q1(Q3**3  3.Q3.Q2**2) R1 = (r12r012)/r012 R2 = (r13r013)/r013 R3 = (r23r023)/r023 Q1 = (R1+R2+R3)/sqrt(3) Q2 = (R2R3)/sqrt(2) Q3 = (2*R1R2R3)/sqrt(6) intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species were 12, 23 and 13 are bonded.

See also:  three, angle, axilrodteller, stillingerweber, bcross, ureybradley,. exponential, bacross, hydrogenbond, equatorial, uff3. 
Topic:  exponential 
Type:  Option 
Format:  exponential <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K rho1 rho2 rho3 <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(23)> rmax(23) <4*flags> 
Units:  K in eV, rho1/2/3 in Angstroms**1 
Use:  Exponentially decaying threebody 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 12, 23 and 13 are bonded.

See also:  three, angle, axilrodteller, stillingerweber, bcross, ureybradley,. murrellmottram, bacross, hydrogenbond, equatorial, uff3. 
Topic:  stillingerweber 
Type:  Information 
Info:  The 2 and 3 body potentials of StillingerWeber are available using the potential types sw2 and sw3, respectively. 
See also:  sw2, sw2jb, sw3, sw3jb. 
Topic:  sw2 
Type:  Option 
Format:  sw2 <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 A rho B rmin rmax <3*flags> 
Units:  A in eV, B in Angs**4, rho in Angs 
Use:  StillingerWeber's twobody potential with cutoff smoothing such that potential goes to zero at rmax:
E = A.exp(rho/(rrmax)).(B/r**4  1)

See also:  sw3, sw2jb, sw3jb. 
Topic:  sw2jb 
Type:  Option 
Format:  sw2jb <intra/inter> <bond/x12/x13/o14> <kcal/kjmol> <scale14> atom1 atom2 A rho B Q <rmin> rmax <4*flags> 
Units:  A in eV, B in Angs**4, rho in Angs, Q in a.u. 
Use:  Jiang and Brown's variant of StillingerWeber's twobody potential which includes charge dependent bond softening
E = A.exp(rho/(rrmax)).(B/r**4  1)*F(qi,qj) F(qi,qj) = exp(1/Q)exp(1/(qi + qj  Q)) if qi+qj < Q F(qi,qj) = 0 if qi+qj > Q See Chem. Eng. Sci., 49, 2991 (2000) for more details. 
See also:  sw3, sw2, sw3jb. 
Topic:  sw3 
Type:  Option 
Format:  sw3 <modified> <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4*flags> 
Units:  K in eV, theta in degrees, rho1 and rho2 in Angstroms 
Use:  StillingerWeber's threebody potential with cutoff smoothing E(three) = K * exp(rho1/(r12rmax12) + rho2/(r13rmax13))(cosct0)**2 where cos = cos(theta(jik)) and ct0 = cos(theta0) intra/inter can also be specified for molecular calculations, as can bond. Note that unlike most potentials, the specification of the cutoff distances is still required when using the "bond" suboption since the values act as parameters to the model.

See also:  three, angle, exponential, axilrodteller, bcross, sw2, sw2jb, ureybradley,. murrellmottram, bcoscross, bacross, hydrogenbond, equatorial, sw3jb, uff3,. lin3. 
Topic:  sw3jb 
Type:  Option 
Format:  sw3jb <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K theta0 rho1 rho2 Q <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <5*flags> 
Units:  K in eV, theta in degrees, rho1 and rho2 in Angstroms, Q in a.u. 
Use:  Jiang and Brown's variant of StillingerWeber's threebody potential with chargedependent softening
E(three) = K*F12*F13*exp(rho1/(r12rmax12) + rho2/(r13rmax13))(cosct0)**2 where cos = cos(theta(jik)) and ct0 = cos(theta0) F12(q1,q2) = exp(1/Q)exp(1/(q1 + q2  Q)) if q1+q2 < Q F12(q1,q2) = 0 if q1+q2 > Q F13(q1,q3) = exp(1/Q)exp(1/(q1 + q3  Q)) if q1+q3 < Q F13(q1,q3) = 0 if q1+q3 > Q See Chem. Eng. Sci., 49, 2991 (2000) for more details. intra/inter can also be specified for molecular calculations, as can bond. Note that unlike most potentials, the specification of the cutoff distances is still required when using the "bond" suboption since the values act as parameters to the model.

See also:  three, angle, exponential, axilrodteller, bcross, sw2, sw2jb, ureybradley,. murrellmottram, bcoscross, bacross, hydrogenbond, equatorial, sw3, lin3,. uff3. 
Topic:  bcoscross 
Type:  Option 
Format:  bcoscross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K b m n r1 r2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4*flags> 
Units:  K in eV/Angs**2, r1 and r2 in Angstroms, b, m and n are unitless. 
Use:  Bondbond cross term three body potential with cosine angle dependance: E(three) = K * (1 + b*cos(n.theta)**m) * (r12  r1) * (r13  r2) intra/inter can also be specified for molecular calculations, as can bond. If bond is given no cutoff is required as the potential will only act between species were 12 and 13 are bonded.

See also:  three, angle, exponential, axilrodteller, stillinger, ureybradley,. murrellmottram, bacross, bcross, hydrogenbond, equatorial, lin3, uff3. 
Topic:  bcross 
Type:  Option 
Format:  bcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K r1 r2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <3*flags> 
Units:  K in eV/Angs**2, r1 and r2 in Angstroms 
Use:  Bondbond 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 12 and 13 are bonded.

See also:  three, angle, exponential, axilrodteller, stillinger, ureybradley,. murrellmottram, bacross, hydrogenbond, equatorial, lin3, uff3. 
Topic:  bacross 
Type:  Option 
Format:  bacross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K1 K2 r1 r2 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <5*flags> 
Units:  K1 and K2 in eV/(Angs*rad), r1 and r2 in Angstroms, theta0 in degrees 
Use:  Bondangle cross term three body potential E(three) = [K1*(r12  r1) + K2*(r13  r2)].(thetatheta0) 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 12 and 13 are bonded.

See also:  three, angle, exponential, axilrodteller, stillinger, ureybradley,. murrellmottram, bcross, hydrogenbond, equatorial, lin3, uff3. 
Topic:  ureybradley 
Type:  Option 
Format:  ureybradley <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol> atom1 atom2 atom3 K r0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags> 
Units:  K in eV/Angs**2, r0 in Angstroms 
Use:  Harmonic distance potential between atoms which are 13 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 12 and 13 are bonded.

See also:  three, angle, exponential, axilrodteller, stillinger, bcross, lin3,. ureybradley, murrellmottram, bacross, hydrogenbond, equatorial,. uff3. 
Topic:  hydrogenbond 
Type:  Option 
Format:  hydrogenbond <intra/inter> <kcal/kjmol> <m> <n> <p> <taper> <dreiding> atom1 atom2 atom3 A B <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags> or if taper is specified: atom1 atom2 atom3 A B theta_min theta_max <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags> 
Units:  A in eV*Ang**m, B in eV*Ang**n 
Default:  = 12, n = 10, p = 4 m = 12, n = 10, p = 4 
Use:  Specifies a threebody hydrogen bond potential of form: If theta > 90 degrees : E(three) = (A/(r**m)  B/(r**n))*(cos(theta))**p If theta =< 90 degrees : E(three) = 0.0 where r is the distance between atoms 2 and 3, and theta is the angle between the 12 and 13 vectors. If the dreiding suboption is specified then the rule that the potential will only be applied when H is bonded to one of the following donor atoms N, O, F, S, Cl, Br, I is used. 
See also:  three, angle, exponential, axilrodteller, stillinger, bcross,. ureybradley, murrellmottram, bacross, equatorial, lin3, uff3. 
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. NB: The species command does not overwrite the charges of ions that are specified individually on the coordinate input line. 
See also:  library, preserve_Q. 
Topic:  preserve_Q 
Type:  Keyword 
Use:  If charges are given in a library or via the species command these can potentially overwrite charges input on the end of a coordinate line. By specifying this keyword GULP preserves the state of the charges from the coordinate input and prevents overwriting. Note that if fitting of charges is specified or a method that generates charges, such as eem or qeq, these options will still lead to the charges being modified. 
See also:  species, library. 
Topic:  polarisability 
Type:  Option 
Format:  polarisability atom_symbol <core/shell> dipolar_polarisability 
Units:  dipolar_polarisability in Angs**3 
Default:  Polarisability is equal to zero, except for shell contribution 
Use:  Allows the inclusion of point ion polarisability in a calculation. At the moment this is nonself consistent, i.e. induced moments on different centres do not interact. 
Topic:  dump 
Type:  Option 
Format:  dump <every <integer n> noover> <channel> <cart> <connectivity> <filename a20> 
Default:  no dumpfile, n=1 if every is given 
Use:  Generates dumpfile after fitting or optimisation. File is created on fortran channel 12. To change, specify either another channel number or a filename. If "every" is specified then a dumpfile will be written after every n cycles of fitting or optimisation. If "noover" is also specified then the dumpfile won't be overwritten every write, but labelled with a unique number. If "connectivity" is specified then the connectivity list will be written to the dump file. Note that this will only be done for the current configuration. NB: Although the filename can be anything you like it is proposed that the conventional extension be .grs (.res was being used but this conflicts with other software). 
Topic:  harmonic 
Type:  Option 
Format:  harmonic <k3> <k4> <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> atom1 atom2 k2 <k3> <k4> r0 <coul> <rmin> rmax <24*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*(rr0)**2 + 1/6 K3*(rr0)**3 + 1/24 K4*(rr0)**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 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential, cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

See also:  spring, squaredharmonic, forceconstant. 
Topic:  field 
Type:  Option 
Format:  field magnitude <direction> 
Units:  eV/(Ang.a.u.) 
Use:  Applies an electric field to a system in a nonperiodic direction. Consequently, this option can only be used for molecules, polymers and
surfaces. The specification of the direction can either be given by the
relevant axis (z, for a surface; y or z for a polymer; x, y or z for a
molecule) or in the case of a 0D system a general vector may be specified
as 3 numbers in Cartesian space. Examples of valid input lines are:
Surface: field 1.5 z Polymer: field 1.5 y Molecule: field 1.5 x OR field 1.5 0.2 0.3 0.4 If the direction is not specified then the default is to apply the field along the z axis. Because the absolute energy is undefined, the energy relative to the initial state is used during minimisations. Note also that only one field can be defined per configuration. NB: You must fix at least one atom in the direction of field application otherwise the energy will head asymptotically for minus infinity!!! The units of the electric field are eV/Ang per unit charge in atomic units. This means an ion of charge +1.0 will experience a force equal to the electric field input. 
Topic:  forceconstant 
Type:  Option 
Format:  forceconstant <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <type_of_bond> atom1 atom2 kL kT <rmin> rmax <2*flag> 
Units:  kL and kT in eV*Angs**2 
Use:  Force constant potential  includes the force constants between a pair of atoms, known as the longitudinal (kL) and transverse (kT) force
constants. This is useful for vibrational calculations, but note that
the energy and gradient are likely to be inconsistent.
NB: Don't use this potential in an optimisation since it will go
horribly wrong due to the above!
atom1 and atom2 may be specified either by atomic number or symbol which in the latter case can be followed by a species type. If no species type is given then type is assumed to be core. d2E/(da.db) = (kL  kT)*a.b/r2 + delta_a.b*kT intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential, cutoffs are omitted from input. The words energy or gradient may be given on the first line resulting in energy or gradient offsets being applied such that the specified quantity goes to zero at the cutoff distance.

See also:  harmonic. 
Topic:  squaredharmonic 
Type:  Option 
Format:  squaredharmonic <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <grad> <scale14> <type_of_bond> atom1 atom2 k2 r0 <coul> <rmin> rmax <2*flags> 
Units:  k2 in eV*Angs**4, r0 in Angs, coul in none 
Use:  GROMOS bonded potential  optimisation flags for fitting. coul = 1.0 => coulomb subtracted
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = 1/4 K2*(r**2  r0**2)**2  coul*qi*qj/r intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. When specified as bonded potential, cutoffs are omitted from input.

See also:  spring, harmonic. 
Topic:  cuts 
Type:  Option 
Format:  cuts cutoff_distance <angs/au> 
Units:  Angstrom (default) or au 
Default:  0.6 Angstroms 
Use:  Coreshell cutoff distance  should be set to be the same as the maximum coreshell 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. NB: DO NOT specify charges on the coordinate line for the atoms that you wish to be influenced by this option since they will be held fixed as they are NOT overwritten by the species option. 
Topic:  Cv 
Type:  Option within "observables" 
Format:  Cv value <weight> <j/kmol> 
Units:  eV/(Kmol) (default) or J/(Kmol) 
Default:  Heat capacity not to be fitted 
Use:  Specifies the experimental heat capacity (Cv) for fitting. Remember that it is important to set the temperature for the structure otherwise the heat capacity will be zero. Also you should ensure that sufficient K points are sampled to give an accurate value. Remember that the value should be per mole of primitive unit cells, not just per mole when Z does not equal 1. 
See also:  observables, entropy, elastic, sdlc, hfdlc, bulk, shear,. bornq, and weight. 
Topic:  entropy 
Type:  Option within "observables" 
Format:  entropy value <weight> <j/Kmol> 
Units:  eV/(Kmol) (default) or J/(Kmol) 
Default:  Entropy not to be fitted 
Use:  Specifies the experimental vibrational entropy for fitting. Remember that it is important to set the temperature for the structure otherwise the entropy will be zero. Also you should ensure that sufficient K points are sampled to give an accurate value. Remember that the value should be per mole of primitive unit cells, not just per mole when Z does not equal 1. 
See also:  observables, cv, elastic, sdlc, hfdlc, bulk, shear,. bornq, and weight. 
Topic:  bulk_modulus 
Type:  Option 
Format:  bulk_modulus <weight> 
Units:  GPa 
Default:  bulk modulus not to be fitted 
Use:  Subsection of observables, used for specifying the experimental bulk modulus for fitting. By default, the Reuss definition of the bulk modulus is used. However, the Voigt and Hill definitions can be used by specifying the appropriate keyword. 
See also:  observables, elastic, sdlc, hfdlc, shear_modulus, weight, bornq,. hill, voigt. 
Topic:  shear_modulus 
Type:  Option 
Format:  shear_modulus <weight> 
Units:  GPa 
Default:  shear modulus not to be fitted 
Use:  Subsection of observables, used for specifying the experimental shear modulus for fitting. By default, the Reuss definition of the bulk modulus is used. However, the Voigt and Hill definitions can be used by specifying the appropriate keyword. 
See also:  observables, elastic, sdlc, hfdlc, bulk_modulus, srefractive,. hfrefractive, weight, bornq, hill, voigt. 
Topic:  hill 
Type:  Keyword 
Default:  Reuss convention for bulk/shear modulus 
Use:  Specifies that the Hill convention is used for the bulk modulus. The Hill convention takes the average of the Reuss and Voigt values. 
See also:  bulk_modulus, shear_modulus, elastic, fit, observables,. voigt. 
Topic:  voigt 
Type:  Keyword 
Default:  Reuss convention for bulk/shear modulus 
Use:  Specifies that the Voigt convention is used for the bulk modulus. The Voigt convention takes the average of the elastic constants in the 13 x 13 block. 
See also:  bulk_modulus, shear_modulus, elastic, fit, observables,. hill. 
Topic:  elastic 
Type:  Option 
Format:  elastic <n> <gpa> i j elastic constant E(i,j) <weight> 
Units:  GPa 
Default:  no elastic constants to be fitted 
Use:  Subsection of observables, used for specifying experimental elastic constants for fitting. Only give unique elastic constants. Units are the same as THBREL and as output in GULP. 
See also:  piezoelectric, sdlc, hfdlc, srefractive, hfrefractive, weight,. bornq. 
Topic:  piezoelectric 
Type:  Option 
Format:  piezoelectric <n> <stress/strain> i <x/y/z> piezoelectric constant p(i,alpha) <weight> 
Units:  C/m**2 for piezoelectric strain constants 10**9 C/N for piezoelectric stress constants 
Default:  no piezoelectric constants to be fitted  constants are strains 
Use:  Subsection of observables, used for specifying values of piezoelectric stress and strain constants for fitting. Units are the same as output from the program and it is only necessary to give unique piezoelectric constants. 
See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, bornq. 
Topic:  hfdlc 
Type:  Option 
Format:  hfdlc <n> i j dielectric constand hfe(i,j) <weight> 
Units:  none 
Default:  no high frequency dielectric constants to be fitted 
Use:  Subsection of observables, used for specifying experimental high frequency dielectric constants for fitting. Only give unique high frequency dielectric constants. 
See also:  elastic, piezoelectric, sdlc, weight, srefractive, hfrefractive,. bornq. 
Topic:  sdlc 
Type:  Option 
Format:  sdlc <n> i j dielectric constant se(i,j) <weight> 
Units:  none 
Default:  no static dielectric constants to be fitted 
Use:  Subsection of observables, used for specifying experimental static dielectric constants for fitting. Only give unique static dielectric constants. 
See also:  elastic, piezoelectric, hfdlc, weight, srefractive, hfrefractive,. bornq. 
Topic:  bornq 
Type:  Option 
Format:  bornq n i <xx/yy/zz/xy/xz/yz> Zeff <weight> 
Units:  atomic units 
Default:  no Born effective charges to be fitted 
Use:  Subsection of observables, used for specifying values of Born effective charges for fitting. Note that i is the
atom number in the unit cell, not the asymmetric unit,
and the two letter code indicates the tensorial component
to be considered. Note: The Born effective charge tensor is
antisymmetric (i.e. Zxy =  Zyx )
Example : bornq 1 1 xx 1.95 Here n (after bornq) represents the number of lines of input to follow. Note: Born effective charges cannot currently be calculated with electronegativity equalisation. 
See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo. monopoleq. 
Topic:  monopoleq 
Type:  Option 
Format:  monopoleq <n> i Qi <weight> 
Units:  atomic units 
Default:  no monopole charges to be fitted 
Use:  Subsection of observables, used for specifying values of charges for fitting. Note that i is the
atom number in the unit cell, not the asymmetric unit.
Example : monopoleq 1 1 1.95

See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo. bornq. 
Topic:  fbond 
Type:  Option 
Format:  fbond <n> i j rij <weight> 
Units:  Angstroms 
Default:  no bond lengths to be fitted 
Use:  Subsection of observables, used for specifying values of bond lengths for fitting. Here i and j are the atom numbers
whose bond is to be fitted and rij is the bond length.
NB For periodic systems the nearest image is taken.
Example : fbond 1 1 2 0.96 NB This option is intended for use with relaxed fitting. 
See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo. bornq, monopoleq, fangle, relax, reaction. 
Topic:  fangle 
Type:  Option 
Format:  fangle <n> i j k theta <weight> 
Units:  Degrees 
Default:  no bond angles to be fitted 
Use:  Subsection of observables, used for specifying values of bond angles for fitting. Here i, j and k are the atom numbers
whose bond angle is to be fitted and theta is the angle. The
atom i is the pivot atom (i.e. the angle is jik).
NB For periodic systems the nearest image is taken.
Example : fangle 1 1 2 3 109.54 NB This option is intended for use with relaxed fitting. 
See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo. bornq, monopoleq, fbond, relax, reaction. 
Topic:  reaction 
Type:  Option 
Format:  reaction <n> ncfg energy <weight> (icfg fcfg) x ncfg 
Units:  eV 
Default:  no reaction energies to be fitted 
Use:  Subsection of observables, used for specifying reaction energies in terms of configuration energies.
In the input line, ncfg is the number of configurations to be used in the reaction (which must be less than or equal to the number specified in the input so far), and then for each ncfg case the configuration number and scale factor is given, followed Example : If configuration 1 is H2O, configuration 2 is CO and configuration 3 is the 2H2O...CO complex whose heat of formation is 0.21 eV and a weight of 10.0 is desired then the input for this would like: reaction 1 3 0.21 10.0 1 2.0 2 1.0 3 1.0 i.e. The coefficients are negative for the lefthand side and positive for the RHS. 
See also:  elastic, sdlc, hfdlc, weight, srefractive, hfrefractive, piezo. bornq, monopoleq, fbond, relax, reaction. 
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/kjmol1> <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 <harmonic> <intra/inter> <bond/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> norder atom1 atom2 (norder+1)*coeff <r0> rmin rmax <(norder+1)*flags> order of coefficients = lowest to highest 
Units:  eV and Angstroms 
Default:  none 
Use:  Polynomial potential, order = 15: E = c0 + c1*r + c2*r**2 + ... + cn*r**n If suboption harmonic is specified, then the polynomial is premultiplied by a harmonic term: E = (r  r0)**2 * (c0 + c1*r + c2*r**2 + ... + cn*r**n) for r < r0 E = 0 for r > r0 intra/inter can also be specified for molecular calculations, as can bond. If bond is given then potential will only act between bonded atoms. x12 => exclude 12 interaction and x13 => exclude 12 and 13 interaction. 
Topic:  
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 coreshell to be varied during fitting while maintaining the initial total charge. This directive must be part of the variables section. NB: DO NOT specify charges on the coordinate line for the atoms that you wish to be influenced by this option since they will be held fixed as they are NOT overwritten by the species option. 
Topic:  element 
Type:  Option 
Format:  word 
Default:  data as in file eledata 
Use:  Section for changes in element properties. 
See also:  symbol, mass, covalent, ionic, vdw. 
Topic:  symbol 
Type:  Option 
Format:  symbol at.no. <symbol(a2)> 
Default:  as per periodic table 
Use:  Allows atomic symbols to be changed. Command is part of element section. 
Topic:  mass 
Type:  Option 
Format:  mass at.no. <mass> 
Units:  atomic units 
Default:  as per periodic table 
Use:  Allows atomic masses to be changed. Note that species symbols can also be used for the mass to set different masses for different
species of the same element:
element mass O1 16.0 mass O2 17.0 end or the older form of using the atomic number can be used: element mass 8 16.0 end Command is part of element section. 
Topic:  covalent 
Type:  Option 
Format:  covalent at.no. <radius> 
Units:  Angstroms 
Default:  standard literature value 
Use:  Allows covalent radii to be changed. Used in bond and molecule calculations. Command is part of element section. 
Topic:  vdw 
Type:  Option 
Format:  vdw at.no. <radius> 
Units:  Angstroms 
Default:  standard literature value 
Use:  Allows VDW radii to be changed. Command is part of element section. 
Topic:  ionic 
Type:  Option 
Format:  ionic at.no. <radius> 
Units:  Angstroms 
Default:  value for most common oxidation state normally in octahedral environment 
Use:  Allows ionic radii to be changed. To be used in breathing shell model eventually. Command is part of element section. 
Topic:  general 
Type:  Option 
Format:  general <m> <n> <ener/grad> <intr/inte> <bon/x12/x13/mol/o14> <kcal/kjmol> <scale14> <type_of_bond> atom1 atom2 A rho C <rmin> rmax <3*flags> 
Units:  A in eV*Angs**m, rho in Angs, C in eV*Angs**n 
Default:  m=0 n=6 
Use:  General potential  optimisation flags for fitting (0/1). This potential is a combination of a Buckingham and LennardJones.
On the first line, general may be followed by m and n, which
are the powers of r (12 6 => LJ 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 12 interaction and x13 => exclude 12 and 13 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/mol/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 12 interaction and x13 => exclude 12 and 13 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 either an input connectivity or by automatically locating bonds based on covalent radii and removes the coulombic interactions within the molecule. See "molq" if you wish to retain the coulomb terms. This option allows intra and inter molecular potentials to be specified. 
See also:  molq, molmec, fix_molecule, rtol, nobond, inter, intra, both,. 14_scale, noautobond. 
Topic:  inter 
Type:  Option 
Default:  both 
Use:  All subsequent potentials to be treated as intermolecular when molecule option is active. 
See also:  molecule, molq, molmec, intra, both, and 14_scale. 
Topic:  intra 
Type:  Option 
Default:  both 
Use:  All subsequent potentials to be treated as intramolecular when molecule option is active. 
See also:  molecule, molq, molmec, inter, both, and 14_scale. 
Topic:  constrain 
Type:  Option 
Format:  For geometric or (non)linear fit: constrain <fit> <no. of constraints>
nvari nfix coefficient <offset> <power>
For geometric mean fit: constrain <fit> <no. of constraints> nvari1 nvari2 mean nfix <coefficient> 
Default:  no constraints, <coefficient>=1.0 
Use:  Allows geometrical variables within configuration to be constrained to be equal to preserve symmetry. By also specifying
"fit" this allows the constraint of fitted parameters instead.
option within variables section.
nvari = no. of variable(s) to allow to vary
nfix = no. of variable to be constrained
coefficient = multiplier that relates values
which is normally 1 or 1.
offset = additive shift between the coordinates
power = power to which value is raised (1 for a linear case)
Geometric constraints: Variable numbers are coded as strains = 16, internal variable n of atom i = 3*(i1)+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 3D systems, there is an ambiguity due to the presence of periodic replications. GULP will use the two nearest images for the constraints. Fitting constraints: Variable numbers refer to the number of the parameter as included in the variables table, which in general is the same as the order of specification in the input. If nvar1=nvar2 for geometric mean constraints then the square root of just the one parameter is taken. Note that the variable numbers for the constraint command in fitting may be changed in the restart file relative to those in the input. This is to take account of the reordering of potentials. To input multiple constraints the number can be added after the constraint command. Note: The ability to raise the variable to power is currently only available for fitting constraint, though it shouldn't be needed for geometric variables anyway.

See also:  outcon. 
Topic:  outcon 
Type:  Keyword 
Use:  By default any contraints generated by the program automatically are not dumped to the restart file unless the user has also added some constraints. This is to prevent errors when users use the restart file, but with nosym specified. Specifying outcon on the keyword line will cause the program to dump all constraints regardless. 
See also:  constrain. 
Topic:  output 
Type:  Option 
Format:  output <filetype> <filename> 
Default:  no output files 
Use:  Write files suitable for other programs. Available filetypes are marvin, thbrel, xtl, xr, cssr, arc
xyz, trajectory, history, fdf, drv, frc, cif, str, pressure
osc, phonon and cml :
marvin  generates a file suitable for input to Marvin for surface calculations. Index of surface plane needs to be added first, though this may be passed through GULP to the marvin input but using the "marvin" option. If the file extension ".mvn" is not given by the user it will be added by the program. e.g. output marvin alumina produces alumina.mvn If a file for Marvin2 is required, then use the suboption marvin2 instead. e.g. output marvin2 alumina thbrel  converts the final bulk structure into a file format suitable for the THBREL suite of programs. Not all features are readily transferable between the programs so no guarantee is made that the input file is perfect and for similar reasons both programs may not always yield the same results unless the user is careful to make sure the files are equivalent. If a phonon run has been requested then the output is modified for THBPHON instead of THBREL. xtl  this is only applicable to crystal structures with a single structure per file. Produces a .xtl file for input into the BIOSYM software, though use of the archive file is better unless symmetry is present. If the filename input is not already terminated with ".xtl" then this will be added by the program. e.g. output xtl alumina produces alumina.xtl xr  this will output a modified CSSR file suitable for input into the Oxford Materials graphical interface program Crysalis. The file will have the extension ".xr" added. At the moment this is only applicable to 3D systems. e.g. output xr alumina produces alumina.xr cssr  this will output a CSSR file suitable for input into the MSI graphical interface Cerius2. The file will have the extension ".cssr" added. At the moment this is only applicable to 3D systems. e.g. output cssr alumina produces alumina.cssr arc  alternatively known as a ".car" file. This option produces archive files suitable for input into the BIOSYM Insight software and will handle bulk, cluster and defect calculations, all with multiple structures. The username should input a root name, e.g. output arc alumina The program will then produce archive file names with either "_3D", "_defe", or "_0D" appended to distinguish the files resulting from a particular section of the run. If multiple structures are present then an underscore followed by the structure number will be added, all followed by ".arc". e.g. if the above input for alumina contained two bulk structures then the files produced would be "alumina_bulk_1.arc" and "alumina_bulk_2.arc". If the word "movie" is specified then all structures during an optimisation will be included in the arcfile, rather than just the final one, so that the optimisation may be viewed. e.g. output movie arc alumina Note : for MD runs the name of the archive file is set by "mdarchive" to avoid overwriting the optimisation archive file if present. Also in the case of MD the file is only written during the production phase. It is also possible to specify a frequency for the output: e.g. output movie 5 arc alumina This would output an archive file frame every 5 steps during the movie. The default is to output at every step. 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 nonperiodic systems. When called with a periodic case just the Cartesian coordinates will be output, without the unit cell. e.g. output xyz cluster produces cluster.xyz If the word "movie" is specified then all structures during an optimisation will be included in the xyz file, rather than just the final one, so that the optimisation may be viewed. e.g. output movie xyz cluster trajectory  this is a binary file which stores the coordinates and velocities from a molecular dynamics run, as well as some of the system properties. This file is used by the Cerius interface to generate a .trj file for analysis in Cerius. Note that this file is only written during the production phase by default. e.g. output trajectory alumina For this suboption the further option "ascii" may be specified in order to obtain an ASCII format trajectory file. Note that this is less efficient for disk space usage! e.g. output trajectory ascii alumina Furthermore, the suboption "equil" may be added to force writing during the equilibration phase of the simulation. The default extension for this file type is .trg history  this is a text file in the DLPOLY HISTORY file format containing the structure and velocities sampled from a MD run. This file can be used for postMD analysis using the same programs as for DLPOLY such as "After". fdf  this is a text file in the Flexible Data Format of Alberto Garcia and Jose M. Soler. This file can then form the basis of an input deck for the program SIESTA. drv  this is a text file containing the energy and appropriate derivatives calculated by GULP at the last function evaluation. This can be used for QM/MM schemes. frc  this is a text file containing the energy and appropriate force constants for cores only calculated by GULP during a phonon calculation. This can be used for QM/MM schemes, such as in the program QMPOT. A phonon calculation must be specified otherwise no file will be output. cif  this is only applicable to crystal structures with a single structure per file. Produces a .cif file for input into a variety of programs. If the filename input is not already terminated with ".cif" then this will be added by the program. Note that at present the files are output in P1 regardless of symmetry for simplicity. e.g. output cif alumina produces alumina.cif str  this is a file in the CRYSTAL98 format, suitable for reading by DLV. If the filename input is not already terminated with ".str" then this will be added. If multiple structures are specified then the filename will be modified so that a separate file can be written for each structure. phonon  this option leads to the density of states from a phonon calculation and any dispersion curve points being output to the files <filename>.dens and <filename>.disp, respectively, in a format suitable for input into a curve plotting program. frequency  this option produces a list of frequencies over all k points for use in an analysis program. A typical application might be in the calculation of the Gruneisen parameter by differencing of the frequencies with respect to the cell volume. The file can either be output in binary format (to maintain precision  the default): e.g. output freq binary <filename> or as ordinary text: e.g. output freq text <filename> pressure  this option outputs a file containing the pressure tensor during a molecular dynamics run, both instanteously and as an average. File is output as <filename>.pre using units of GPa. osc  this is a text file containing the oscillator strengths for the phonon modes so that the frequency dependent data can be handled in post processing. cml  this is a Chemical Markup Language output file which contains all the important information about the calculation in an XML format. This output is suitable for various database tools and for data transfer between CMLenabled applications.

See also:  marvin, dump. 
Topic:  rspeed 
Type:  Option 
Format:  rspeed rspeed_value 
Default:  1.0 
Use:  Relative speed for reciprocal and real space terms to be calculated. Formulae for determining optimum eta value assume rspeed=1.0. However, calculations can be speeded up by using larger values for small systems (e.g. 2.0) or small values for large systems (0.25) as reciprocal space calculation is generally faster. 
See also:  noexclude, qwolf, ewaldrealradius, accuracy. 
Topic:  ewaldrealradius 
Type:  Option 
Format:  ewaldrealradius value 
Default:  none 
Use:  Normally the Ewald sum real and reciprocal space radii are chosen automatically to minimise the number of terms, subject to the value of the rspeed parameter. However, when using the spatial algorithm it is advantageous to control the real space extent of the Ewald sum to ensure that the system can be decomposed into sufficent regions. The value specified fixes the real space cutoff and the reciprocal space cutoff is calculated in order to achieve the target accuracy given by the accuracy option. 
See also:  noexclude, qwolf, rspeed, accuracy. 
Topic:  compare 
Type:  Keyword 
Default:  no comparison 
Use:  Causes a table comparing the initial and final structures to printed out both for bulk and defects. 
Topic:  torsion 
Type:  Option / Keywrd 
Format:  torsion <intra/inter> <bond> <esff> <dreiding> <kcal/kjmol> <type_of_bond> atom1 atom2 atom3 atom4 k <+/>n <phi0> rmax(12) rmax(23)
rmax(34) rmax(41) <1 x flag>
or if esff option is specified atom1 atom2 atom3 atom4 k1 k2 <+/>n rmax(12) rmax(23) rmax(34) rmax(41) <2 x flags> E = k*(1+isign*cos(n*phiphi0)) ESFF : E = k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)

Units:  k/k1/k2 in eV, isign is +1 or 1 according to the sign of n, rmax in Angstroms, phi0 in degrees 
Default:  if phi0 is not given it is assumed to be zero 
Use:  Torsional potential about atoms 2 and 3. k is half the barrier and nphase is the periodicity. The optional flag is for fitting of k.
If rmax(41) is input as zero then rmax(41) is set to infinity.
Note that when rmax(41) 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 ij, jk and kl 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. If the suboption dreiding is specified then the force constant is divided by the number of torsional interactions for each central jk pair to ensure a constant torsional barrier for the jk bond. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  ryckaert, outofplane, torexp, tortaper, torangle, uff4. 
Topic:  tortaper 
Type:  Option 
Format:  tortaper <bond/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond> atom1 atom2 atom3 atom4 k <+/>nphase <phi0> rtaper rmax(12)
rmax(23) rmax(34) rmax(41) <1 x flags>
or if esff option is specified atom1 atom2 atom3 atom4 k1 k2 <+/>nphase rtaper rmax(12) rmax(23) rmax(34) rmax(41) <2 x flags> 
Units:  k/k1/k2 in eV, isign is +1 or 1 according to the sign of nphase, rtaper and rmax in Angstroms, phi0 in degrees 
Default:  if phi0 is not given it is assumed to be zero 
Use:  Specifies a torsional potential with tapering of the cutoffs over rtaper of the form: E = k*(1+isign*cos(nphase*phiphi0))*f(r12)*f(r23)*f(r34) ESFF : E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)] *f(r12)*f(r23)*f(r34) where f(r) is a cosine tapering function. If the suboption dreiding is specified then the force constant is divided by the number of torsional interactions for each central jk pair to ensure a constant torsional barrier for the jk bond. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, torharm, outofplane, torexp, torangle, uff4. 
Topic:  torexp 
Type:  Option 
Format:  torexp <bond/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond> atom1 atom2 atom3 atom4 k <+/>nphase <phi0> rho12 rho23 rho34 rmax(12)
rmax(23) rmax(34) rmax(41) <4 x flags>
or if esff option is specified atom1 atom2 atom3 atom4 k1 k2 <+/>nphase rho12 rho23 rho34 rmax(12) rmax(23) rmax(34) rmax(41) <5 x flags> 
Units:  k/k1/k2 in eV, isign is +1 or 1 according to the sign of nphase, rho12/23/34 and rmax in Angstroms, phi0 in degrees 
Default:  if phi0 is not given it is assumed to be zero 
Use:  Specifies an exponentially decaying torsional potential of the form: E = k*(1+isign*cos(nphase*phiphi0))*exp(r12/rho12)*exp(r23/rho23)*exp(r34/rho34) ESFF : E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)]* *exp(r12/rho12)*exp(r23/rho23)*exp(r34/rho34) If the suboption dreiding is specified then the force constant is divided by the number of torsional interactions for each central jk pair to ensure a constant torsional barrier for the jk bond. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, torharm, outofplane, torexp, uff4. 
Topic:  torharm 
Type:  Option 
Format:  torharm <intra/inter/bond> <kcal/kjmol> <dreiding> <type_of_bond> atom1 atom2 atom3 atom4 K <phi0> rmax(12) rmax(23) rmax(34) <2 x flags> 
Units:  K in eV/rad**2, phi0 in degrees 
Default:  none, phi0 = 0 if omitted 
Use:  Specifies a harmonic torsional potential. Note that this is not a sensible choice for a convenientional torsional potential, but is used by some
forcefields for an improper torsional angle. The form of the potential is:
E = 1/2 K(phi  phi0)**2 If the suboption dreiding is specified then the force constant is divided by the number of torsional interactions for each central jk pair to ensure a constant torsional barrier for the jk bond. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, torangle, torexp, outofplane, uff4. 
Topic:  uff4 
Type:  Option 
Format:  uff4 <intra/inter/bond> <kcal/kjmol> <dreiding> <type_of_bond> atom1 atom2 atom3 atom4 K n <phi0> rmax(12) rmax(23) rmax(34) rmax(41) <1 x flag> 
Units:  K in eV, phi0 in degrees 
Default:  none, phi0 = 0 if omitted 
Use:  Specifies a torsional potential of the UFF form: E = 1/2 K*(1  cos(n.phi0)*cos(n.phi)) n is an integer and there is only a flag for K The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, torangle, torexp, outofplane, torharm. 
Topic:  torangle 
Type:  Option 
Format:  torangle <intra/bond> <kcal/kjmol> <dreiding> <type_of_bond> atom1 atom2 atom3 atom4 K theta0 theta0' rmax(12) rmax(23) rmax(34) <3 x flags> 
Units:  K in eV/rad**2, theta0 & theta0' in degrees 
Default:  none 
Use:  Specifies a torsional  angle cross potential. The form of the potential is: E = K.cos(phi).(theta  theta0).(theta'  theta0') where theta is the angle between 123 & theta' is between 234 If the suboption dreiding is specified then the force constant is divided by the number of torsional interactions for each central jk pair to ensure a constant torsional barrier for the jk bond. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, torharm, torexp, outofplane, uff4. 
Topic:  ryckaert 
Type:  Option 
Format:  ryckaert (or torsion ryck) norder <type_of_bond> atom1 atom2 atom3 atom4 k0 rmax(12) rmax(23) rmax(34) rmax(14) <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.
The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the torsion will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, outofplane, torangle, torharm, torexp, uff4. 
Topic:  inversion 
Type:  Option 
Format:  inversion <squared> <intra/inter/bond/mol> <only3> <kcal/kjmol> atom1 atom2 atom3 atom4 k <k0> rmax(12) rmax(13) rmax(14) <1 x flag> 
Units:  k in eV, k0 in degrees 
Default:  none 
Use:  Out of plane energy  energy penalty for atom 1 lying out of the plane of atoms 2, 3 and 4. This form uses the
Dreiding planar expression:
E = k.(1  cos(phi)) where phi is the angle between the plane of the centre atom and two others with the bond from the centre atom to the third atom. Note that because phi depends on which of the 3 different angles is chosen, GULP computes the contribution for all 3 cases and takes the average. If the suboption "squared" is specified then the modified form given below is used: E = 1/2 (k/sin(k0)**2).(cos(phi)  cos(k0))**2 and k0 must be input. If the only3 suboption is specified then the potential applies where an atom has exactly 3 bonds present. 
See also:  torsion, ryckaert, torangle, torharm, torexp, xoutofplane, outofplane. 
Topic:  outofplane 
Type:  Option 
Format:  outofplane <inter/intra> <bond> <only3> <kcal/kjmol> atom1 atom2 atom3 atom4 k <k4> <rmin(12)> rmax(12) <rmin(13)> rmax(13) <rmin(14)> rmax(14) <12 x flag> 
Units:  k in eV*Angs**2, k4 in eV*Angs**4 
Default:  rmin values = 0, k4 = 0 
Use:  Out of plane energy  harmonic energy penalty for atom 1 lying out of the plane of atoms 2, 3 and 4. Used for ring systems
which should be planar:
E = k.d**2 + k4.d**4, where d=distance to the plane If the only3 suboption is specified then the potential applies where an atom has exactly 3 bonds present. 
See also:  torsion, ryckaert, torangle, torharm, torexp, xoutofplane, inversion, xangleangle. 
Topic:  xoutofplane 
Type:  Option 
Format:  xoutofplane <intra/inter/bond/mol> <kcal/kjmol> <type_of_bond> atom1 atom2 atom3 atom4 atom5 atom6 k rmax(12) rmax(13) rmax(14) rmax(25) rmax(26) <1 x flag> 
Units:  k in eV*Angs**2 
Default:  none 
Use:  Specifies an cross  out of plane potential of form: E = k.d1.d2 where d1 is the out of plane distance of atom 1 from the plane of atoms 2/3/4 and d2 is the out of plane distance of atom 2 from the plane of atoms 1/5/6. This functional form is used in the CVFF forcefield. This is a sixbody potential. The type of bond suboption can be used to control which bonded atoms the potential applies to. If specified, the central bond of the sixbody term will be checked for type before applying the potential. Valid type of bond options are: single, double, triple, quadruple, resonant, amide. In addition a bond may specified as regular (default), cyclic or exocyclic.

See also:  torsion, ryckaert, torangle, torharm, torexp, outofplane, uffoop. 
Topic:  xangleangle 
Type:  Option 
Format:  xangleangle <inter/intra> <bond> <kcal/kjmol> atom1 atom2 atom3 atom4 k(213/4) k(312/4) k(412/3) theta0(213) theta0(214) theta0(314) & rmax(12) rmax(13) rmax(14) <3 x flag> 
Units:  All k in eV*rad**2 and all theta0 in degrees 
Default:  none 
Use:  Angleangle cross potential for all angles about a central atom, atom 1: E = k(213/4)*(theta(213)  theta0(213))*(theta(214)  theta0(214)) + k(312/4)*(theta(312)  theta0(312))*(theta(314)  theta0(314)) + k(412/3)*(theta(412)  theta0(412))*(theta(413)  theta0(413))

See also:  torsion, ryckaert, torangle, torharm, torexp, xoutofplane, inversion, outofplane. uffoop. 
Topic:  uffoop 
Type:  Option 
Format:  uffoop <intra/inter/bond/mol> <only3> <kcal/kjmol> atom1 atom2 atom3 atom4 k C0 C1 C2 rmax(12) rmax(13) rmax(14) <4 x flags> 
Units:  k in eV, C0, C1, C2 are unitless 
Default:  none 
Use:  Out of plane energy  energy penalty for atom 1 lying out of the plane of atoms 2, 3 and 4. This form uses the
Universal Force Field expression:
E = k.(C0 + C1*cos(phi) + C2*cos(2*phi)) where phi is the angle between the plane of the centre atom and two others with the bond from the centre atom to the third atom. Note that because phi depends on which of the 3 different angles is chosen, GULP computes the contribution for all 3 cases and takes the average. If the only3 suboption is specified then the potential applies where an atom has exactly 3 bonds present. 
See also:  torsion, ryckaert, torangle, torharm, torexp, xoutofplane, inversion, outofplane. 
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 illconditioned. 
See also:  numdiag, dfp, positive, conjugate, lbfgs. 
Topic:  lbfgs 
Type:  Keyword 
Use:  Use limited memory BFGS for optimisation. This is useful where a system is too large to allow the storage of the full Hessian matrix and so a limited part of it is stored instead. The size of the memory used depends on the value of lbfgs_order which is set as an option. 
See also:  numdiag, dfp, positive, conjugate, unit, lbfgs_order. 
Topic:  lbfgs_order 
Type:  Option 
Format:  lbfgs_order <integer_value> 
Units:  None 
Default:  10 
Use:  Specifies the order of the limited memory BFGS algorithm. The larger the value the more memory will be used, but the more rapid the convergence will be. Designed for use with large systems where the full Hessian cannot be stored. 
See also:  numdiag, dfp, positive, conjugate, unit, lbfgs. 
Topic:  numdiag 
Type:  Keyword 
Use:  Use numerical estimates of the diagonal elements as a starting point for the hessian. Can be useful when exact hessian is illconditioned. 
See also:  unit, dfp, positive, conjugate, lbfgs. 
Topic:  dfp 
Type:  Keyword 
Use:  Use the DavidonFletcherPowell updating formula instead of BFGS. 
See also:  unit, numdiag, positive, conjugate, lbfgs. 
Topic:  positive 
Type:  Keyword 
Use:  Ensure that the hessian always behaves as positive definite during NewtonRaphson by ensuring the search vector has the same sign as as the gradient vector. 
See also:  unit, numdiag, dfp, conjugate, lbfgs. 
Topic:  conjugate 
Type:  Keyword 
Use:  Use conjugate gradients to optimise geometry, instead of second derivative based methods. 
See also:  dfp, numdiag, unit, positive, lbfgs. 
Topic:  conjugate 
Type:  Option 
Format:  conjugate n 
Default:  never 
Use:  Part of genetic section. After n iterations the odd top 5 configurations are minimised locally using a method of conjugate gradients. 
Topic:  hessian 
Type:  Keyword 
Use:  Causes details of the hessian matrix to be output. For calculations employing the RFO method then the eigenvalues, eigenvectors and the gradients transformed into the local modes are output for every cycle. For NewtonRaphson 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:  Coreshell spring potential  optimisation flags for fitting. Spring potl does not need cutoffs as the maximum is set by cuts and the minimum is zero. Only atom1 needs to be specified as this potential is specifically for core shell pairs. Atom1 can be given either by atomic number or symbol which in the latter case can be followed by a species type. If no species type is given then type is assumed to be core. 
See also:  coshspring. 
Topic:  coshspring 
Type:  Option 
Format:  coshspring <kcal/kjmol> atom1 k2 d <2 x flags> 
Units:  k2 in eV/Angs*2, d in Angs 
Default:  None 
Use:  Coreshell spring potential with cosh functional form. Coshspring potl does not need cutoffs as the maximum is set by cuts and the minimum is zero. Only atom1 needs to be specified as this potential is specifically for core shell pairs. Atom1 can be given either by atomic number or symbol which in the latter case can be followed by a species type. If no species type is given then type is assumed to be core. 
See also:  spring. 
Topic:  coulomb 
Type:  Option 
Format:  coulomb <intra/inter> <bond/x12/x13/o14> <scale14> atom1 atom2 <scale> <rmin> rmax <flag> 
Units:  rmin and rmax in Angs, scale in fractional 
Default:  scale = 1.0 
Use:  Coulomb subtraction potential only Coulomb potl does not need coulomb offset
when acting as a coreshell 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 12 interaction and x13 => exclude 12 and 13 interaction  this can also be achieved through the command molmec. o14 => only act between atoms which are 14, i.e. separated by 3 bonds When specified as bonded potential cutoffs are omitted from input.

See also:  molmec. 
Topic:  delf 
Type:  Option 
Format:  delf energy change 
Units:  eV 
Default:  none 
Use:  Maximum change per step of minimisation of the function before Hessian is recalculated. 
Topic:  marvin 
Type:  Option 
Use:  Allows a section of text to be inserted into a marvin input file by surrounding text by "marvin" before the first line and "end" after the last line. 
See also:  output. 
Topic:  nosderv 
Type:  Keyword 
Use:  Stops the use of symmetry in calculating the first derivatives, but not the energy during line searches. This causes the program to revert to behaving like Gulp0.4 and earlier versions. The user should never need to use this option as it will slow down the code and is only useful for algorithm checking purposes. 
Topic:  nobond 
Type:  Option 
Format:  nobond species1 species2 
Use:  Excludes bond formation between two species during molecule search. 
See also:  molecule, molq, molmec, bond, and connect. 
Topic:  connect 
Type:  Option 
Format:  connect atom1 atom2 <type_of_bond> <imageX> <imageY> <imageZ> 
Default:  If imageX, imageY, imageZ are not specified then take the nearest image. 
Use:  Forces a bond to be formed between atom1 and atom2 where atom1 and atom2 are the numbers of atoms in the full unit cell. Requires one
of the molecule keywords to be included to have any affect. The
parameters imageX, imageY and imageZ specify which translational
image of atom 2 should be used. Valid values are 1, 0, 1, where 0
means the image in the central cell, 1 means the image in the
negative direction and +1 in the positive one.
e.g. connect 1 2 1 0 1 Optionally, the type of bond can be specified and this information can be used in applying the correct force field terms where applicable. Valid bond types are: single, double, triple, quadruple, resonant, amide, cyclic and exocyclic. For example, an exocyclic double bond can be specified as: connect 1 2 double exocyclic 1 0 1 If not specified, the bonds are assumed to be single bonds. NB: For the connect information to be used one of the molecule keywords must be specified. 
See also:  molecule, molq, molmec, nobond, bond, noautobond. 
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 either an input connectivity or by automatically locating bonds based on covalent radii, but retains the coulombic interactions within the molecule. See "molecule" if you wish to remove the coulomb terms. This option allows intra and inter molecular potentials to be specified. Works for isolated molecules and 1, 2 and 3D periodic molecules provided repeat directions lie parallel to crystallographic axes, where appropriate. 
See also:  molecule, molmec, rtol, fix_molecule, nobond, inter, intra, both. 14_scale, noautobond. 
Topic:  molmec 
Type:  Keyword 
Default:  no molecules 
Use:  Program locates molecules based on either an input connectivity or by automatically locating bonds based on covalent radii and subtracts coulomb terms between bonded atoms and between atoms bonded to a common third atom. This option is needed when using molecular mechanics potentials, such as in the CVFF forcefield. Works for isolated molecules and 1,2 and 3D periodic molecules provided repeat directions lie parallel to crystallographic axes, where appropriate. 
See also:  molq, molecule, rtol, fix_molecule, nobond, inter, intra, both. 14_scale, noautobond. 
Topic:  noautobond 
Type:  Keyword 
Default:  Automatically locate bonds in molecules based on covalent radii 
Use:  Specifies that GULP should not try to automatically locate bonds based on the sum of covalent radii. Bonds are then completely controlled by the "connectivity" option. 
See also:  molecule, molq, rtol, fix_molecule, nobond, inter, intra, both,. 14_scale, molmec. 
Topic:  14_scale 
Type:  Information 
Info:  Many organic forcefields require the scaling of 14 two body interactions. Typically a factor of a 1/2 is used. This can be achieved in GULP. Nearly all twobody 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 14 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. Note: For materials with charges it is important to consider the effect of the LO/TO splitting. 
See also:  kpoints, dispersion, shrink, eigenvectors, lower_symmetry,. project_dos, output, nozeropt, gamma_direction_of_approach, omega,. dynamical_matrix, meanke. 
Topic:  dynamical_matrix 
Type:  Keyword 
Use:  Causes GULP to output the dynamical matrix from a phonon calculation. 
See also:  phonon. 
Topic:  eigenvectors 
Type:  Keyword 
Use:  Generate eigenvectors as well as eigenvalues during a phonon calculation. This option is automatically implied when projected phonon densities of states are required. The maximum number of atoms is reduced by 7/10 when generating eigenvectors. Both real and imaginary components of the eigenvectors are output, but remember that when two or more frequencies are degenerate there are an infinite number of possible vectors that can be created by taking linear combinations. All eigenvectors output are orthonormal. 
See also:  phonon, lower_symmetry, project_dos, and intensity. 
Topic:  lower_symmetry 
Type:  Keyword 
Use:  Use imaginary phonon modes to lower the symmetry of a structure. This is particularly useful when an optimised structure has imaginary frequencies and help is needed as to how to distort the geometry to obtain the true minimum. This keyword requires a phonon run to be performed and the keyword "eigenvectors" is implicit. 
See also:  phonon, eigenvectors, slower. 
Topic:  meanke 
Type:  Keyword 
Use:  Requests that GULP prints out a decomposition of the mean kinetic energy of vibration projected onto each lattice site. Note that this keyword requires that a phonon calculation be specified and that the temperature is nonzero. Furthermore, this will only currently work for a single temperature rather than a temperature range. 
See also:  phonon, eigenvector. 
Topic:  slower 
Type:  Option 
Format:  slower <value> 
Units:  None 
Default:  0.001 
Use:  This is the scale factor by which the eigenvectors will be multiplied when attempting to lower the symmetry along an imaginary mode direction. 
See also:  lower_symmetry. 
Topic:  intensity 
Info:  Infrared phonon intensities are output when the eigenvectors 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.
Examples: To project on to atoms 4, 7 and 10: project_dos 1 4 7 10 To project on to all species C1 and O3: project_dos 1 C1 O3

See also:  phonon, eigenvectors, output. 
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, kfull. 
Topic:  nokpoints 
Type:  Keyword 
Use:  Prevents output of list of k points for each configuration. 
Topic:  dispersion 
Type:  Option 
Format:  dispersion <no. of lines, default=1> <no. of k points per line> x1 y1 z1 to x2 y2 z2 <to x3 y3 z3 .....> 
Units:  x, y and z are fractions of reciprocal lattice vectors 
Default:  none 
Use:  Specifies the start and end points of lines through k space along which the phonon dispersion will be calcluated.
Examples: dispersion 2 20 0.0 0.0 0.0 to 0.5 0.5 0.5 to 0.5 0.0 0.0 0.5 0.0 0.0 to 0.5 0.5 0.0 This would produce two plots, the first containing two parts and the second only one. Both plots would contain a total of 20 k points.

See also:  phonon, shrink, kpoints, box, kfull. 
Topic:  kfull 
Type:  Keyword 
Use:  When the unit cell is centred, the K points specified are taken as being for the primitive cell by default. When this keyword is specified, the K points given by the kpoints and dispersion options are taken to be for the full centred cell instead. Note the calculation is still performed using the primitive cell, but at the points in reciprocal space that relate to the full cell. 
See also:  kpoints, dispersion. 
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 cm1 
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> <step0> 
Units:  Kelvin (or Centigrade if C added, or Fahrenheit if F added) 
Default:  0 K, no steps (for phonons) 100 K for simulated annealing 
Use:  Specifies temperature of a structure for use in the calculation of phonon properties, such as the entropy, free energy and heat capacity.
Also specifies the temperature for molecular dynamics and Monte Carlo
runs, including annealling.
Temperature can optionally be followed by an increment, a number of steps, (and a first step for MD). Phonons If a range is given, then the phonon properties will be calculated at each temperature value over the range. Note that if present during a free energy calculation this will result in the last temperature being used for the run. For CPU time reasons a range should not be used during a free energy minimisation. Molecular dynamics / Monte Carlo Here the option is used to set the temperature of the run or the schedule of temperatures for an anneal. For example, if the initial temperature is to be 298 K for the first 300 steps and then is to increase to 398 K over a 1000 steps, the input would look like: temperature 298 0.1 1000 300

See also:  phonon, free, predict, anneal, ftol, factor, and ttol. 
Topic:  pressure 
Type:  Option 
Format:  value_of_pressure <GPa/kPa/Pa/atm/Nm2/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:  storevectors 
Type:  Keyword 
Use:  Use algorithms, where possible, that involve storing a table of interatomic vectors that lie within the cutoff distance. Currently this applies only to molecular dynamics. The idea is that by reducing the frequency with which the vectors are searched for, the calculation will be considerably speeded up in return for a small loss of precision. The frequency of updating, controlled by the "resetvectors" option, should be tested for the particular system of study. 
See also:  resetvectors, extracutoff. 
Topic:  resetvectors 
Type:  Option 
Format:  resetvectors no_of_steps 
Units:  None 
Default:  1 
Use:  Specifies the frequency with which the interatomic vector table is updated if using the storevectors keyword. 
See also:  storevectors, extracutoff. 
Topic:  extracutoff 
Type:  Option 
Format:  extracutoff value 
Units:  Angstroms 
Default:  0.0 
Use:  When using the storevectors algorithm, this option specifies the extra amount to be added to the global cutoff when deciding which vectors to store. It allows for atoms to move across the boundary between updates. 
See also:  storevectors, resetvectors. 
Topic:  operators 
Type:  Keyword 
Use:  Causes the program to print out the rotation matrix and shifts for all bulk symmetry operators. Primarily a debugging keyword. 
Topic:  symmetry_cell 
Type:  Option 
Format:  symmetry_cell <cell type> 
Default:  Triclinic 
Use:  When specifying the symmetry manually, this allows the user to set the cell type. Allowed values are triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, rhombohedral and cubic. 
See also:  symmetry_operator. 
Topic:  symmetry_operator 
Type:  Option 
Format:  symmetry_operator r(1,1) r(1,2) r(1,3) t(1) r(2,1) r(2,2) r(2,3) t(2) r(3,1) r(3,2) r(3,3) t(3) 
Units:  None / Fractional 
Use:  Specifies the symmetry operators for a 3D system manually. The matrix r specifies the rotational matrix and the vector t specifies the translational component of the rototranslational operator. Note that the identity operator is always present and should not be given again. If specified, this option causes any spacegroup specified to be ignored. 
See also:  spacegroup, origin, symmetry_cell. 
Topic:  predict 
Type:  Keyword 
Use:  General Algorithm for Structure Prediction Pregulp 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:  Option 
Format:  seed q 
Default:  1.0 
Use:  Initial pointer used in random number generation whereever random numbers are used. 
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 success 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. 
Number  Label  Number  Label  Number  Label 

1  P 1  2  P 1  3  P 2 
4  P 21  5  C 2  6  P M 
7  P C  8  C M  9  C C 
10  P 2/M  11  P 21/M  12  C 2/M 
13  P 2/C  14  P 21/C  15  C 2/C 
16  P 2 2 2  17  P 2 2 21  18  P 21 21 2 
19  P 21 21 21  20  C 2 2 21  21  C 2 2 2 
22  F 2 2 2  23  I 2 2 2  24  I 21 21 21 
25  P M M 2  26  P M C 21  27  P C C 2 
28  P M A 2  29  P C A 21  30  P N C 2 
31  P M N 21  32  P B A 2  33  P N A 21 
34  P N N 2  35  C M M 2  36  C M C 21 
37  C C C 2  38  A M M 2  39  A B M 2 
40  A M A 2  41  A B A 2  42  F M M 2 
43  F D D 2  44  I M M 2  45  I B A 2 
46  I M A 2  47  P M M M  48  P N N N 
49  P C C M  50  P B A N  51  P M M A 
52  P N N A  53  P M N A  54  P C C A 
55  P B A M  56  P C C N  57  P B C M 
58  P N N M  59  P M M N  60  P B C N 
61  P B C A  62  P N M A  63  C M C M 
64  C M C A  65  C M M M  66  C C C M 
67  C M M A  68  C C C A  69  F M M M 
70  F D D D  71  I M M M  72  I B A M 
73  I B C A  74  I M M A  75  P 4 
76  P 41  77  P 42  78  P 43 
79  I 4  80  I 41  81  P 4 
82  I 4  83  P 4/M  84  P 42/M 
85  P 4/N  86  P 42/N  87  I 4/M 
88  I 41/A  89  P 4 2 2  90  P 4 21 2 
91  P 41 2 2  92  P 41 21 2  93  P 42 2 2 
94  P 42 21 2  95  P 43 2 2  96  P 43 21 2 
97  I 4 2 2  98  I 41 2 2  99  P 4 M M 
100  P 4 B M  101  P 42 C M  102  P 42 N M 
103  P 4 C C  104  P 4 N C  105  P 42 M C 
106  P 42 B C  107  I 4 M M  108  I 4 C M 
109  I 41 M D  110  I 41 C D  111  P 4 2 M 
112  P 4 2 C  113  P 4 21 M  114  P 4 21 C 
115  P 4 M 2  116  P 4 C 2  117  P 4 B 2 
118  P 4 N 2  119  I 4 M 2  120  I 4 C 2 
121  I 4 2 M  122  I 4 2 D  123  P 4/M M M 
124  P 4/M C C  125  P 4/N B M  126  P 4/N N C 
127  P 4/M B M  128  P 4/M N C  129  P 4/N M M 
130  P 4/N C C  131  P 42/M M C  132  P 42/M C M 
133  P 42/N B C  134  P 42/N N M  135  P 42/M B C 
136  P 42/M N M  137  P 42/N M C  138  P 42/N C M 
139  I 4/M M M  140  I 4/M C M  141  I 41/A M D 
142  I 41/A C D  143  P 3  144  P 31 
145  P 32  146  R 3  147  P 3 
148  R 3  149  P 3 1 2  150  P 3 2 1 
151  P 31 1 2  152  P 31 2 1  153  P 32 1 2 
154  P 32 2 1  155  R 3 2  156  P 3 M 1 
157  P 3 1 M  158  P 3 C 1  159  P 3 1 C 
160  R 3 M  161  R 3 C  162  P 3 1 M 
163  P 3 1 C  164  P 3 M 1  165  P 3 C 1 
166  R 3 M  167  R 3 C  168  P 6 
169  P 61  170  P 65  171  P 62 
172  P 64  173  P 63  174  P 6 
175  P 6/M  176  P 63/M  177  P 6 2 2 
178  P 61 2 2  179  P 65 2 2  180  P 62 2 2 
181  P 64 2 2  182  P 63 2 2  183  P 6 M M 
184  P 6 C C  185  P 63 C M  186  P 63 M C 
187  P 6 M 2  188  P 6 C 2  189  P 6 2 M 
190  P 6 2 C  191  P 6/M M M  192  P 6/M C C 
193  P 63/M C M  194  P 63/M M C  195  P 2 3 
196  F 2 3  197  I 2 3  198  P 21 3 
199  I 21 3  200  P M 3 (P M 3)  201  P N 3 (P N 3) 
202  F M 3 (F M 3)  203  F D 3 (F D 3)  204  I M 3 (I M 3) 
205  P A 3 (P A 3)  206  I A 3 (I A 3)  207  P 4 3 2 
208  P 42 3 2  209  F 4 3 2  210  F 41 3 2 
211  I 4 3 2  212  P 43 3 2  213  P 41 3 2 
214  I 41 3 2  215  P 4 3 M  216  F 4 3 M 
217  I 4 3 M  218  P 4 3 N  219  F 4 3 C 
220  I 4 3 D  221  P M 3 M  222  P N 3 N 
223  P M 3 N  224  P N 3 M  225  F M 3 M 
226  F M 3 C  227  F D 3 M  228  F D 3 C 
229  I M 3 M  230  I A 3 D 
Nonstandard space groups:
C 1 / C 1
Alternative settings of the above space groups should also be valid