GULP help file


Keywords in alphabetical order

PDFcut  PDFkeep  abs  alamode  allbonds  allow_gt_1  angle  anneal  atomic_stress  average  bond  breathe  broaden_dos  bulk_noopt  c6  ceigen  cellonly  com_nomass  compare  conjugate  conp  conserved  conv  coreinfo  cosmic  cosmo  cost  dcharge  debug  decimal_only  defect  delta_dipole  derv2  derv3  dfp  dipole  distance  dynamical_matrix  eckart  eem  eembond  efg  eharmonic  eigenvectors  eregion  fastfd  fbfgs  fit  fix_molecule  force_minimisation  frame   free_energy  frequencies  fsprop  full  gasteiger  genetic  ghostcell  global  gradient  groupvelocity  grueneisen  hessian  hexagonal  hideshells  hill  include_imaginary  intensity  isotropic  kcal  kfull  kjmol  lbfgs  libdump   libff  linmin  lower_symmetry  madelung  makeEigenArrays  marvinSE  md  meanke  minimum_image  molecule  molmec  molq  montecarlo  msd  neb  newda  no4duplicates  noaddshells  noanisotropic_2b  noautobond  nobreathe  nod2sym  nod3  nodensity_out  nodneb  nodpsym  nodsymmetry  noelectrostatics  noenergy  noexclude  nofirst_point  noflags  nofrequency  nokpoints  noksymmetry  nolist_md  nomcediff  nomodcoord  nomolecularinternalke  nononanal  nopartial  noqeem  noquicksearch  noreal  norecip  norepulsive_cutoff  norotate  norxQ  nosasinitevery  nosderv  noshellzero  nosymmetry  nowidth  nowrap  nozeropt  num3  numdiag  numerical  ocell  oldintensity  oldunits  oldvarorder  operators  optimise  optlower  orthorhombic  outcon  pacha  pdf  phonon  polarisation  positive  pot  predict  pregionforce  preserve_Q  property  prt_eam  prt_four  prt_six  prt_three  prt_two  pureQ  qbond  qeq  qextrapolate  qiterative  qok  qsas  raman  regi2a  regi_before  relax  rephase  restore  rfo  rigid  save  shell  shopt  simplex  simultaneous  single  site_energy  sm  sopt  spatial  spme  static_first  steepest  storevectors  strain  stress_out  synchronous  thermalconductivity  transition_state  umorse  unfix  unit  veck  voigt  xray  zero_potential  zsisa 

Options in alphabetical order

3coulomb  absdipolemoment  absolute_coordinates  accelerations  accuracy  ala_cutoff  ala_disp  ala_mode  ala_processors  ala_shrink  anisotropic_pressure  ashift  atomab  aver  axilrod-teller  bacoscross  bacross  bagcross  balcross  baskes  bbar  bcoscross  bcross  becke_johnson_c6  best  blocksize  boattractive  bocharge  bocnswitch  bocntolerance  bocoordination  bondtype  boonebody  borepulsive  bornq  boselfenergy  both  botwobody  box  brenner  bsm  bspline  buck4  buckingham  buffered_lj  bulk_modulus  cartesian  catomic_stress  caver  cell  centre  cfaver  cfm_fermi  cfm_gaussian  cfm_harmonic  cfm_power  charge  chemshell_mode  cmm  configurations  connect  constrain  contents  coordno  cosh-spring  cosmoframe  cosmoshape  coulomb_subtract  covalent  covexp  crossover  cstrain  current_time  cutd  cutmany  cutp  cuts  cv  cvec  cwolf  damped_dispersion  default_weight  deflist  delay_field  delay_force  delf  delta  dhkl  dielectric_constant  discrete  dispersion  ditto  dmaximum  dminimum  dump  eam_alloy  eam_density  eam_functional  eam_potential_shift  edip_accuracy  edip_coordination  edip_threebody  edip_twobody  edip_zmax  einstein  elastic  electronegativity  element  end_field  end_force  energy  ensemble  entropy  epsilon/sigma  equatorial  equilibration  erferfc  erfpot  erongi  ewaldrealradius  exp2  exponential_three_body  exppowers  external_force  external_potential  extracutoff  factor  fangle  fbond  fc_supercell  fcartesian  fcell   fenergy  fermi-dirac  ffractional  field  finite  fix_atom  forceconstant  fractional  frequency  frqtol  ftol  fvectors  g3coulomb  gamma_angular_steps  gamma_direction_of_approach  gastdamping  gastiter  gastparam  gasttol  gcmcexistingmolecules  gcmcmolecule  gcmcspecies  gcoulomb  gdcrit  general  genetic  gexp  ghost_supercell  gmax  gradients  grid  grimme_c6  gtol  harmonic  hfdlc  hfrefractive_index  high-fq dielectric  hydrogen-bond  igauss  ignore  impurity  include  index_k  initial_coordinates  intconserved  integrator  inter  interstitial  intra  inversion  ionic  iterations  j2  j3  keyword  kim_model  kpoints  lbfgs_order  lennard  library  lin3  line  ljbuffered  lorentzian_tolerance  lowest_mode  manybody  marvin  mass  maths  matrix_format  maxcyc  maximise  maximum  mcchemicalpotential  mccreate  mcdestroy  mclowest  mcmaxdisplacement  mcmaxrotation  mcmaxstrain  mcmeans  mcmove  mcoutfreq  mcrotate  mcsample  mcspecies  mcstep  mcstrain  mcswap  mctrial  mcvolume  mdarchive  mdmaxtemp  mdmaxvolume  meam_density  meam_functional  meam_rhotype  meam_screening  mei-davenport  mincell  minimum  mm3angle  mm3buck  mm3stretch  mode  mode2a  molatom  molrigid  momentum_correct  monopoleq  morse  move_2a_to_1  murrell-mottram  mutation  name  nebiterations  nebrandom  nebreplica  nebspring  nebtangent  nebtolerance  nmr  nobond  observables  odirection  omega  omega_af  omega_damping  origin  outofplane  output  p_flexible  p_isotropic  parallel  pcell  pdf  pfinite  pfractional  piezoelectric  plane_lj  plumed_input  plumed_log  pointsperatom  poisson_ratio  polarisability  polynomial  potential  potential_interpolation  potgrid  potsites  ppp3body  pressure  primitive_vectors  print  production  project_dos  pvector  qelectronegativity  qeqiter  qeqradius  qeqtol  qerfc  qgrid  qincrement  qiterations  qmmm  qonsas  qoverr2   qreaxff  qsolver  qtaper  qwolf  radial_force  random  rangeforsmooth  rbins  rcartesian  rcell  rcspatial  rdirection  reaction  reaxff0_bond  reaxff0_lonepair  reaxff0_over  reaxff0_penalty  reaxff0_torsion  reaxff0_valence  reaxff0_vdw  reaxff1_angle  reaxff1_include_under  reaxff1_lonepair  reaxff1_morse  reaxff1_over  reaxff1_radii  reaxff1_under  reaxff1_valence  reaxff2_bo  reaxff2_bond  reaxff2_morse  reaxff2_over  reaxff2_pen  reaxff3_angle  reaxff3_conjugation  reaxff3_hbond  reaxff3_pen  reaxff4_torsion  reaxff_chi  reaxff_gamma  reaxff_mu  reaxff_q0  reaxff_qshell  reaxff_r12  reaxffsmooth  reaxfftol  region_1  reldef  reperfc  resetvectors  rfo_eig  rfo_grad  rfractional  rmax  rspeed  rtol  ryckaert  rydberg  sample  sasexclude  sasparticles  sbulkenergy  scale  scan_cell  scell  scmaxsearch  screened_coulomb  sdlc  seed  segmentsperatom  sfinite  sfractional  shear_modulus  shellmass  shift  shrink  siginc  size  slater  slower  smelectronegativity  solventepsilon  solventradius  solventrmax  spacegroup  species  spin  spline  split  spring  sqomega  squaredharmonic  srefractive_index  sregion2  srglue  sshift  start  static dielectric   stepmx  stop  strain_derivative  stress  supercell  svectors  sw2  sw2gen  sw2jb  sw3  sw3jb  switch_minimiser  switch_stepmx  symbol  symmetry_cell  symmetry_number  symmetry_operator  synciterations  syncsteps  synctolerance  tau_barostat  tau_thermostat  td_external_force  td_field  temperature  terse  tether  three-body  threshold  time  timestep  title  torangle  torcosangle  torexp  torharm  torsion  tortaper  totalenergy  tournament  tpxo  translate  trap  tscale  tsuneyuki  ttol  twist  uff1  uff3  uff4  uff_bondorder  uffoop  unfreeze  unique  units  update  urey-bradley  vacancy  variables  vbo_twobody  vdw  vectors  velocities  volume  weight  wmax  wmin  write  xangleangle  xcosangleangle  xoutofplane  xtol  youngs_modulus  zbl 

Information in alphabetical order

14_scale  Ctrl_C  line_continuation  scale14  stillinger-weber  trajectory_format  valid_spacegroups 

PDFcut

Type Keyword
Use As "PDF", but 'cut off' (ignore) all phonon contributions greater than
a given "wmax" ("pdf "block input option) or less than a given "wmin"
("pdf" block input option).
See also PDFkeep pdf nowidth nofreq rmax rbins wmin wmax units xray

PDFkeep

Type Keyword
Use As "PDFcut", but 'keep' all phonon contributions greater than a given
"wmax" (pdf block input option) or less than a given "wmin" (pdf block
input option) by setting w=wmax or w = wmin respectively.
See also PDFcut pdf nowidth nofreq rmax rbins wmin wmax units xray

abs

Type Keyword
Use During fitting, take the absolute value of fitting parameters where
appropriate to prevent them from going negative.
See also fit

alamode

Type Keyword
Use Compute the thermal conductivity using Alamode. For this to work
Alamode must be installed on your computer and the environment
variable ALAMODE_DIR set to point to the root directory of Alamode.
In this mode GULP will call the program alm to obtain the finite
difference patterns required for the system, compute the forces
for these displacements, and fit the force constants using alm.
The cost of this process depends on the force constant cutoffs
and the precision is determined by the displacement magnitude.
See also thermalconductivity ala_disp ala_cutoff ala_shrink ala_processors
ala_mode

allbonds

Type Keyword
Use When using eembond GULP tries to find the minimal set of bonds
need for EEM that avoid rings that cause the inversion of the EEM
matrix to become singular. Specifying this keyword forces the code
to work with all bonds. However, this means iterative solution has
to be used and prevents the use of analytic second derivatives.
See also eembond

allow_gt_1

Type Keyword
Default Do not allow partial occupancies on a site to exceed 1.
Use Tells GULP to allow the sum of partial occupancies on a
given site to be allowed to exceed one without treating
the particles as separate entities that have accidentally
been superimposed.
NB: This option should be used with caution as it physically
not usually sensible to have a site occupancy greater than
one. The main use is to allow different atom types to be
constrained to move together to allow the construction of
more complex potential forms.

angle

Type Keyword
Use Print out all valid three-body angles found for the three-body
potentials.

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 performed on the best configuration.
See also predict cost global temperature

atomic_stress

Type Keyword
Use Causes the atomic stresses to be output at the final geometry.
These are the atomic contributions to the strain derivatives.
For 3D systems the stresses in GPa are output, while for all
cases the strain derivative per atom is output in eV.
NB: This feature requires that symmetry is turned off during
the calculation.
See also stress_out catomic_stress

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

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 bondtype

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 ocell

broaden_dos

Type Keyword and option
Format broaden_dos <scale/gaussian> b
Default b = 0.2
Units cm-1 (default) or fractional (scale)
Use An approximation to the delta function is used in order to line
Lorentzian broaden the phonon density of states peaks. If given
as a keyword then the default broadening is applied or if used
as an option the user may specify their own broadening factor.
e.g. broaden 0.3
The expression used for the broadening is:
w(f) = b/[pi*(1 + (b*(f - f0))**2)]
where w is the fractional weight at frequency f of a peak at
frequency f0. b is the broadening factor and is the inverse
of the half-width at half-maximum parameter.
Note, the smaller the factor, the greater the broadening.
The range of the plot is automatically extended when broadening is
turned on to allow the highest frequency peak to decay to 1/100th of
its original magnitude.
In the case of thermal conductivity calculations, there is the
option to have a fixed broadening (default) or to scale the
average frequency difference (if scale is specified).
If "gaussian" is specified then Gaussian broadening will be used:
w(f) = b/sqrt(pi) * exp(-(b*(f-f0))**2)
See also phonon project output lorentzian_tolerance thermalconductivity
box

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

c6

Type Keyword
Use The dispersion energy, as represented by 1/r**6 terms
as part of the Buckingham, Lennard-jones and General
potentials, is actually quite slow to converge in
real space. By specifying this keyword the C6 terms
are evaluated using an Ewald-like approach, thus
achieving much greater accuracy in the energy for
only a small amount of extra computational expense.
When this option is used the rmax value for the
potential only influences the short range repulsion
component. As the truncation distance for these terms
is also controlled by the program, the best thing is
to just specify a large cutoff and let the program
decide.

ceigen

Type Keyword
Default Do not output eigenvalues and eigenvectors of elastic constants
Use If present then the eigenvalues and eigenvectors of the elastic
constant tensor will be output. These can provide information
regarding the elastic stability of the system.
See also piezoelectric sdlc hfdlc srefractive hfrefractive weight
bornq young poisson elastic

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 ocell
strain cstrain

com_nomass

Type Keyword
Default Use centre of mass for rigid molecules
Use If specified then remove the mass weighting when determining the centre of a
a rigid molecule.
See also molq molmec fix_molecule rtol nobond inter intra both
14_scale noautobond bondtype molatom rigid molecule molrigid

compare

Type Keyword
Default no comparison
Use Causes a table comparing the initial and final structures to be printed
out both for bulk and defects.

conjugate

Type Keyword
Use Use conjugate gradients to optimise geometry, instead of second
derivative based methods.
See also dfp numdiag unit positive lbfgs steepest
and
Type Option
Format conjugate n
Default never
Use Part of genetic section. After n iterations the odd top 5
configurations are minimised locally using a method of conjugate
gradients.

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 ocell

conserved

Type Keyword
Use Causes the conserved quantity for the MD ensemble to be output where
applicable.

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

coreinfo

Type Keyword
Use Outputs atomic information on all atoms (cores, not shells, if using shell model)
used in phonon calculations. Details given for each core in the primitive cell.
Lists species mass, neutron scattering length (bbar), incoherent and coherent
neutron scattering area, and atomic position in both Cartesian and Fractional
coordinates. This option is purely for information, and does not change the
behaviour of GULP. Where partial occupancies used, output is for the mean-
field atom on each site.
See also Keywords: makeEigenArrays

cosmic

Type Keyword
Use Invokes a modified form of the COSMO algorithm that
imposes the constraint of an Integral Charge (normally
zero) on the system. This is important for periodic
systems where charge neutral is a requirement for a
converged lattice sum.
If a surface is non-charge neutral then the net surface
charge is balanced by the net charge on the solvent
accessible surface. This requires the "qok" keyword
to be specified.
See also pointsperatom segmentsperatom solventepsilon
solventradius solventrmax vdw nosasinitevery
cosmoframe cosmoshape rangeforsmooth qsas
sasparticles qiterative cwolf pureQ cosmo
matrix_format

cosmo

Type Keyword
Use Causes a solvation energy calculation to be performed
using the COSMO model. For details of the method see:
A. Klamt and G. Schueuermann, JCS Perkin Trans 2, 799 (1993)
Here the system is immersed in an effective continuum
solvent with a user-specified dielectric constant and
solvent molecule radius. A solvent-accessible surface
is then constructed around the molecule/surface where
charges are induced that interact with the underlying
material.
See also pointsperatom segmentsperatom solventepsilon
solventradius solventrmax vdw nosasinitevery
cosmoframe cosmoshape rangeforsmooth qsas
sasparticles qiterative cwolf pureQ cosmic
matrix_format

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 anneal
and
Type Genetic Option
Format cost <kb value_kb> <kc value_kc> <kq value_kq> <ks value_ks>
Default kb=1.0 kc=1.0 kq=1.0 ks=0.0
Use Specify a weighting factor for the various components of the cost
function, where kb represent the bond valence contribution, kc
the coordination contribution, kq the Coulombic repulsion between
like charged ions and ks a sort of bond valence term between like
charged ions.

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 noqeem

debug

Type Keyword
Use Could do anything! For programmers' use only.

decimal_only

Type Keyword
Default Use fractions in output where appropriate.
Use Specifying this keyword suppresses the use of fractions in
output from GULP.

defect

Type Keyword
Use When used as a keyword this causes a defect calculation to be
performed at the end of any bulk calculations. This option
cannot currently be used in conjuction with the background
neutralising charge for non-charge neutral unit cells, or
with the dipole correction energy.
See also region_1 centre size regi_before vacancy
impurity interstitial frequency noanisotropic save
restore gdcrit bulk_noopt

delta_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.
When delta_dipole is specified the dipole D is defined
relative to the dipole for the initial configuration
being zero. This is useful where an electric field is
applied to an equilibrium system, generating a net dipole.
Note that defect calculations cannot be performed when
this term is present.
NB: delta_dipole and dipole are mutually exclusive - if
both are specified then delta_dipole will be applied
See also field dipole initial_dipole

derv2

Type Keyword
Use Debugging keyword that causes GULP to output the internal-internal
second derivative matrix when second derivatives are generated.
See also derv3

derv3

Type Keyword
Use Debugging keyword that causes GULP to output the internal-strain
second derivative matrix when second derivatives are generated.
See also derv2

dfp

Type Keyword
Use Use the Davidon-Fletcher-Powell updating formula instead of BFGS.
See also unit numdiag positive conjugate lbfgs steepest

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 / (2.epsilon_r + 1).V
where D is the dipole per unit cell and V is the volume.
epsilon_r is dielectric constant of the medium, which is
usually 1.
By default the Ewald sum assumes that there is no dipole
moment across the crystal, while this term is applicable
to cases where there is a permenant dipole. Note
that the dipole is ambiguous in many cases because it
depends on the termination of the crystal at the surface
and hence this correction should be used with care!
Note that defect calculations cannot be performed when
this term is present.
NB: delta_dipole and dipole are mutually exclusive - if
both are specified then delta_dipole will be applied
See also field delta_dipole dielectric_constant

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".

dynamical_matrix

Type Keyword
Use Causes GULP to output the dynamical matrix from a phonon calculation.
See also phonon

eckart

Type Keyword
Use For molecules it causes an Eckart transformation to be performed
on dynamical matrix. This removes the rotational and translational
contamination of the vibration modes. Currently only applies to
0-D systems.
See also phonon raman inten msd

eem

Type Keyword
Use Calculate charges by Mortiers EEM.
oldeem invokes the original set of parameters.
Only available for H, C, N, O, F, Si, Al and P.
If specified with optimise then the charges will be recalculated at
every point of the optimisation.
NB Electronegativity equalisation schemes should NOT
be used in combination with Coulomb subtraction of
any form otherwise the calculation of the charges and
the energy will not be self-consistent. This leads to
all derivatives being incorrect as dE/dQ is no longer
zero. If Coulomb subtracted potentials are to be used
then charges must be calculated for the initial geometry
and then frozen.
Note: Phonon calculations are limited with the EEM keyword
to the gamma point without the LO/TO splitting.
Note: Only region 1 atoms are included in EEM and fixed
charges will be taken for region 2.
See also qeq dcharge sm electronegativity gasteiger qbond pacha noqeem
eembond

eembond

Type Keyword
Use Calculate charges by split bond charge electronegativity
This is closely related to EEM and can use many of the same
variants such as QEq, SM, and pacha. The major difference is
that charge is only transfered between atoms that are bonded
and so the charge on an atom is the sum of its bond charges.
This means that the total charge within a molecule is conserved
and long-distance unphysical charge transfer is prevented.
However, there are some restrictions:
1) This approach can only be applied to charge neutral systems
at present since a net charge cannot be automatically
redistributed.
2) The energy surface is discontinuous if a bond breaks or forms.
3) The iterative QEq special case for hydrogen is not available
in this form at present, though increasingly this is not used.
See also qeq dcharge sm electronegativity gasteiger qbond pacha noqeem
eem allbonds

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

eharmonic

Type Keyword
Use Calculate the implicit harmonic relaxation energy, but do not optimise.
This uses the Hessian and forces to compute the energy of optimisation
if the system was perfectly harmonic, but without iteratively refining
the coordinates. It allows a single point calculation to provide an
estimate of the energy that would result from optimisation.
See also conp conv cellonly isotropic finite unfix shell single
optimise md montecarlo gradient ocell

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.
Both real and imaginary components of the eigenvectors are
output, but remember that when two or more frequencies are
degenerate there are an infinite number of possible vectors
that can be created by taking linear combinations.
All eigenvectors output are orthonormal.
See also phonon lower symmetry project_dos eckart intensity msd

eregion

Type Keyword
Default Don't print region energies
Use Causes GULP to output the energy broken down into regions.
NB Not all potential types currently support this feature and
for many body potentials it may not be meaningful where they
span multiple regions. Use with care!

fastfd

Type Keyword
Use Switch the algorithm for bond order potential calculations (including
EDIP, Brenner and ReaxFF) to a faster finite difference approach.
See also

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

fit

Type Keyword
Use Perform fitting run using unit matrix with BFGS method.
See also simul relax genetic fbfgs delta simplex abs

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 molatom

force_minimisation

Type Keyword
Use Causes an optimisation run to use the gradient norm as the quantity for minimisation
rather than the energy. Useful for situation where the absolute energy is not well
defined, such as systems under uniaxial stress.
See also anisotropic_pressure

frame

Type Keyword
Default Use coordinates as input
Use Causes the coordinates of a 0-D system (molecule) to be rotated to the
standard frame of reference based on the non-mass weighted moment of
inertia tensor of the cores.
NB: Use of this keyword is not compatible with the use of flags and
constraints at present. It is recommend that a single point calculation
is used to change the frame first and then any flag/constraints specified
using the restart file.
See also cartesian

free_energy

Type Keyword
Use Use Gibbs free-energy as the quantity to be calculated/optimised
instead of the internal energy. This uses the phonon density of
states to calculate the vibrational partition function and thereby
the free energy. Note: It is best not to use gamma point phonons
in such calculations since the Born charge correction is not applied
in a free energy minimisation. Hence the default k point (if none
specified) is (1/4,1/4,1/4). However, the use of the "shrink" option
is recommended to converge the free energy.
NB: Not currently available for rigid molecules
See also phonon nozeropt static_first zsisa scmaxsearch lowest_mode shrink

frequencies

Type Keyword
Use Causes GULP to compute the frequencies for a defect calculation
in the Mott-Littleton scheme.
NB: This is approximate since it assumes that regions 1 and 2
are uncoupled with respect to their vibrations.
See also phonon

fsprop

Type Keyword
Default properties calculated with infinitesimal strains
Use Specifies that properties should be computed using derivatives
computed for finite strain.
By default all derivatives are evaluated based on the assumption
of infinitesimal strain relative to the current structure. If the
strain keyword is specified then the strains are taken relative
to the initial cell parameters as a reference point. This causes
the strain derivatives to be changed as they are at finite strain.
If the keyword property is given with the keyword strain then the
use of finite strain derivatives is turned off during property
evaluation to yield the standard property values. If this keyword
is specified then properties are computed using derivatives at
finite strain which will alter the values.
See also strain property numerical

full

Type Keyword
Use Causes the nosymmetry keyword to produce the full, instead of the
primitive, unit cell.
See also nosymmetry

gasteiger

Type Keyword
Use Indicates that Gasteiger charges should be calculated according
to the method in Tetrahedron, 36, 3219-3288 (1980). The Gasteiger
charges are geometry independent and only depend on the connectivity
of the molecule. Hence it is important to ensure that the bonding
is correct at the start of the calculation and the "fix" keyword
is also recommended to avoid potential discontinuities. Parameters
are available for H, C, N, O, S and the halogens. For C, N and O
the electronegativities used depend on the hybridisation. In the
absence of formal atom typing, GULP makes the approximation that
the hybridisation state is the obvious one for the coordination
number, i.e. for C, 4 bonds => sp3, 3 bonds => sp2, 2 bonds => sp,
for N, 3 bonds => sp3, 2 bonds => sp2, 1 bond => sp, and for O,
2 bonds => sp3, 1 bond => sp2.
See also eem qeq molq fix bond gasttol gastiter qbond pacha gastparam
gastdamping noqeem eembond molatom

genetic

Type Keyword
Use Given contents of unit cell use a genetic algorithm to find
possible atomic coordinates. (global optimiser)
A local minimisation can then be performed on the best configurations
See also predict anneal contents global cost

ghostcell

Type Keyword
Use When using the fc_supercell approach to compute phonons based on
finite differencing of first derivatives there can be problems
for some models where images of the same atom interact with each
other. The main case where this occurs is for bond order potentials,
including brenner, EDIP, ReaxFF. Note that for brenner analytic
second derivatives are available and so there is no need to use
finite differences, whereas for EDIP and ReaxFF this is not the case.
The solution to this problem is to compute the force constants for a
supercell (specified using this option) and then the ghostcell keyword
tells the code to compute the phonons as though they were for the
original smaller cell from which the supercell was constructed.
NB: At present this keyword can only be used in serial.
See also phonon fc_supercell ghost_supercell

global

Type Keyword
Use After finding possible crystal coordinates (because keyword
predict specified) dump out restart files before performing local
minimisation of the best structures.
See also predict genetic anneal

gradient

Type Keyword
Use Calculate gradients but do not optimise, provided the single
keyword is not specified.
See also conp conv cellonly isotropic finite unfix shell single
optimise md montecarlo eharmonic fix_atom ocell

groupvelocity

Type Keyword
Use Calculate the group velocities of the phonons at each k point
See also thermalconductivity broaden_dos temperature lorentzian_tolerance

grueneisen

Type Keyword
Use Calculate the Grueneisen parameters for the phonons
See also phonon groupvelocity thermal_conductivity shrink kpoint

hessian

Type Keyword
Use Causes details of the Hessian matrix to be output. For calculations
employing the RFO method then the eigenvalues, eigenvectors and the
gradients transformed into the local modes are output for every cycle.
For Newton-Raphson calculations, the inverse Hessian is output after
each exact recalculation, but not after updating.
See also optimise matrix_format

hexagonal

Type Keyword
Use Causes a rhombohedral structure to be output in
hexagonal form in the dumpfile.

hideshells

Type Keyword
Default Show shell coordinates and other details in the output.
Use Causes the output of details of the shells to be suppressed in the output.
See also noaddshells

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 young poisson

include_imaginary

Type Keyword
Default Imaginary frequencies excluded from DOS / dispersion
Use Specifies that imaginary frequencies should be included
in the output of density of states or dispersion plots.
See also phonon nodensity

intensity

Type Keyword
Info Infra-red phonon intensities are output when the eigenvectors
have been calculated using "eigen". This keyword also triggers
the printing of intensity. Intensities are in nominal
units of charge**2. Raman intensities are also now output.
However, it should be noted that they are approximate and only
valid for systems with a single type of bond in (such as a
silicate).
NB: From version 4.0.5 onwards the IR intensities are computed
using the Born effective charge tensor, where available,
rather than the sum of core and shell charges. For simple rigid
ion models there is no difference, but for more complex models
there may be some change.
NNB: Intensities should usually be calculated at the gamma point
and to ensure the proper symmetry it is recommended to specify
nononanal as a keyword to turn off the non-analytic correction.
See also oldintensity eigen nononanal eckart msd

isotropic

Type Keyword
Use Only allow isotropic cell expansion and contraction during
optimisation. For molecular dynamics this keyword requires the
use of the default integrator (stochastic).
See also conp conv orthorhombic ocell

kcal

Type Keyword
Default eV
Use Output the energy components in kcal rather than eV.
Useful for comparing energies against other programs
See also kjmol

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

kjmol

Type Keyword
Default eV
Use Output the energy components in kJ/mol rather than eV.
Useful for comparing energies against other programs
See also kcal

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

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

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

linmin

Type Keyword
Default no printing
Use Print out details of line minimisations.

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 calculation of eigenvectors
is required, though from version 5.1 onwards these will not be
output unless eigenvectors is explicitly specified as a keyword.
NB: If applying to molecules then it is recommended that the
eckart keyword is also used to ensure that rotations are not
included in the frequencies calculated.
See also phonon eigenvectors slower optlower switch frqtol

madelung

Type Keyword
Use If the cell is cubic, then a Madelung correction can be
applied to the electrostatics of a charged system to
put the energy to zero. This assumes a single point ion
excess charge (e.g. one charged ion in a box). The
energy correction is given by:
E = 1/2 alpha*Q**2/(epsilon_0*L)
where alpha is the Madelung constant (2.8373 for a simple
cubic case), Q is the excess charge and L the side of the
cubic box.
See also qok

makeEigenArrays

Type Keyword
Use Stores phonon information (frequencies and eigenvectors) in internal arrays for
further calculations. This information is generated by phonon and eigen
keywords (automatically called if makeEigenArrays is set). This keyword
should not need to be explicitly set unless testing. It is not currently
compatible with parallel runs.
See also pdf nowidth nofreq

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)

md

Type Keyword
Use Specifies that a molecular dynamics run is to be performed
NB: Not currently available for rigid molecules
See also timestep temperature equilibration production sample
tscale write cutp integrator nolist_md minimum_image
nomolecularinternalke momentum_correct mdmaxtemp tether

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 non-zero. Furthermore, this will only
currently work for a single temperature rather than a temperature
range.
See also phonon eigenvector msd

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.
NB: The minimum image approach is incompatible with the spatial
algorithm and so if both are specified the spatial algorithm will
be used.
See also md spatial

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 bondtype molatom rigid com_nomass molrigid

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 3-D periodic molecules provided
repeat directions lie parallel to crystallographic axes, where
appropriate.
See also molq molecule rtol fix_molecule nobond inter intra both
14_scale noautobond bondtype molatom rigid

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 3-D periodic molecules provided repeat directions
lie parallel to crystallographic axes, where appropriate.
See also molecule molmec rtol fix_molecule nobond inter intra both
14_scale noautobond bondtype molatom rigid

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 mcswap nomcediff

msd

Type Keyword
Info Compute the mean-squared displacements for atoms based on the
phonon calculation. The three Cartesian components are output
based on the sum over all k points (where applicable).
See also phonon intensity eigenvector meanke

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 synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional rcell fcell fvectors

newda

Type Keyword
Use if specified this selects the new defect algorithm
in which all ions in region 2 that interact with
region 1 are stored. The advantage of this approach
is that there is no need to add and then subtract
contributions from the non-defective region 1 to the
short range energy. This leads to increased numerical
stability, but tends to be slower than the old
algorithm except where numerical problems slow down
the rate of convergence. The other downside is that
the storage needed for region 2a will be larger.
When using the Embedded Atom Model this algorithm
must be used and will therefore automatically be
selected.
See also defect

no4duplicates

Type Keyword
Use If specified, then duplication of torsions by potentials with wildcards is
removed. This means the wildcard potential will only act where there is no
other potential with fewer wildcard elements for the end terms. As an example,
if the torsions H-C1-C2-H and X-C1-C2-X were specified then the second torsion
would be excluded for the case where the end atoms were both H, but would act
for H-C1-C2-C3. Currently only applies to standard torsions and not impropers.
See also torsion

noaddshells

Type Keyword
Default Add shells where they are missing in the input.
Use If specified then no shells will be added.
See also hideshells

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

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 bondtype molatom

nobreathe

Type Keyword
Use Excludes radii from the optimisation variables.
See also conp conv noflags shell breathe cellonly isotropic ocell

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 nod3 nosderv

nod3

Type Keyword
Use Turns off the calculation of third derivatives for ShengBTE
output. Allows just the second derivatives to be obtained.
See also output num3

nodensity_out

Type Keyword
Use Do not write phonon density of states curve to output channel.

nodneb

Type Keyword
Use Turns off the doubly nudged elastic band method and uses the singly
nudged formalism.
See also nebspring nebtolerance neb synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional rcell fcell fvectors

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

nodsymmetry

Type Keyword
Use Switches off the use of symmetry in defect calculations.
See also defect

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

noenergy

Type Keyword
Use Do not calculate energy.

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

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

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 ocell

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

nokpoints

Type Keyword
Use Prevents output of list of k points for each configuration.

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

nolist_md

Type Keyword
Use By default list based methods are used for three and four
body terms in molecular dynamics to avoid problems with
discontinuities in the energy as atoms move over cutoffs.
It also increases the speed of the three and four body
terms dramatically. Specifying "nolist" will cause the
program to use the standard non-list based method.
See also three-body four md

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

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.

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

nononanal

Type Keyword
Use If present, then the non-analytic correction to the phonons at
the gamma point is excluded. This was always true for versions
of GULP prior to 1.4 and so this keyword allows backwards
compatability while leading to an incorrect LO/TO splitting.
From version 4.2.0 the default has been changed and this correction
is no longer included for a configuration unless the
gamma_direction_of_approach is explicitly input or a dispersion
curve is requested.
Note: The Born effective charges are not presently available
with electronegativity equalisation and therefore this keyword
will automatically be set.
See also phonon gamma_direction_of_approach gamma_angular_steps intensity

nopartial

Type Keyword
Use Used in conjuction with PDF keywords, suppresses output of partial pair
distributions.
See also PDFcut PDFkeep nowidth

noqeem

Type Keyword
Use Causes the electrostatic contribution to be excluded from the EEM
calculation. Invoke this will make the charge calculation geometry
independent.
See also eem qeq dcharge sm electronegativity gasteiger qbond pacha
eembond

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!

noreal

Type Keyword
Use Do not calculate real space contributions to the energy and
derivatives.
See also norecip

norecip

Type Keyword
Use Do not calculate reciprocal space contributions to the energy and
derivatives.
See also noreal

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

norotate

Type Keyword
Default Allow rigid molecules to rotate
Use If specified then rotation of rigid molecules is not included in an
optimisation.
See also rigid

norxQ

Type Keyword
Use If specified then this turns off the calculation of charges within ReaxFF
See also reaxff_chi reaxff_mu reaxff_gamma qiterative

nosasinitevery

Type Keyword
Use Causes the SAS calculation not to be reinitialised at
every step of the calculation. It is generally recommended
to reinitialise to ensure that calculation results are
independent of the starting point. It also avoids potential
energy surface discontinuities due to the history of segment
creation.
See also cosmo

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.
See also nod2sym

noshellzero

Type Keyword
Default Shell coordinates can be zero in simultaneous fit
Use This keyword causes GULP to displace shell coordinates away from zero
during a simultaneous fit (by 0.01). This used to be the default but
was turned off to make the fitting of energy surfaces with shells
easier.
See also relax fit breathe noflags simultaneous

nosymmetry

Type Keyword
Use Switches off symmetry after generating unit cell.
For non-primitive systems the final unit cell is primitive.
See also spacegroup origin valid_spacegroups symmetry_operator

nowidth

Type Keyword
Use Used in conjunction with PDF keywords, prevents output of individual
pairwise contributions to the PDF peak widths in a .wid file
See also PDFcut PDFkeep nowidth nofreq

nowrap

Type Keyword
Use Stops coordinates from being wrapped back into the unit cell
This is a pseudonym for the nomodcoord keyword.
See also nomodcoord

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 lowest_mode

num3

Type Keyword
Use Forces the use of numerical third derivatives for force constant evaluation
even when analytic third derivatives are available. This is only needed
for debugging purposes. At present this keyword only applies to the calculation
of force constants for output to ShengBTE.
See also numerical output shopt threshold nod3

numdiag

Type Keyword
Use Use numerical estimates of the diagonal elements as a starting point
for the Hessian. Can be useful when exact Hessian is ill-conditioned.
See also unit dfp positive conjugate lbfgs steepest

numerical

Type Keyword
Use Forces the use of numerical second derivatives for property evaluation
even when analytic second derivatives are available. This is only needed
for debugging purposes.
NB: If using numerical in combination with fc_supercell it is important
to make sure that the interaction range for a given force term is less
than the size of the unit cell being used. If this is not the case then
there will be some error in the phasing of the second derivatives. In
other words, the gamma point results will be correct, but the dispersion
away from gamma may contain errors. This problem is most likely to happen
for small cells when using bondorder or manybody potentials since
interactions become coupled over longer ranges.
NB: Numerical derivatives can be in error in cases where the finite
differences go across cutoff boundaries!
See also property sfinite pfinite fc_supercell num3

ocell

Type Keyword
Use Use cell parameters instead of strains for optimisation of the cell
By default GULP uses strain derivatives for unit cell optimisation.
However, if you wish to fix cell parameters with flags then this will
be easier with this keyword since the flags will refer directly to
the cell parameters rather than strains.
See also conv cellonly breathe nobreathe noflags shell isotropic scan_cell
strain

oldintensity

Type Keyword
Use Specifies that the old IR intensities, as per pre-GULP-4.0.5,
be computed instead of the new values based on the Born effective
charge tensor.
See also intensity eigen msd

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.

oldvarorder

Type Keyword
Use In order to make parallelisation of the second derivatives easier
the order of variables in optimisation has been changed such that
internal coordinates appear before cell variables. Specifying this
keyword returns the order to that used in earlier versions of GULP
for backward compatibility. Note that the order shouldn't change
the answers and so this keyword is primarily for debugging and code
verification.
See also optimise

operators

Type Keyword
Use Causes the program to print out the rotation matrix and shifts for
all bulk symmetry operators. Primarily a debugging keyword.

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 transition_state rfo unfix single md montecarlo
eharmonic fix_atom oldvarorder hessian ocell

optlower

Type Keyword
Use Causes an optimisation to be performed after the lower_symmetry
task has been performed as part of the same run. Note that it is
normally worthwhile using the switch option to get the minimiser
to change to rfo after lower_symmetry has been performed.
See also phonon eigenvectors slower lower_symmetry switch

orthorhombic

Type Keyword
Use Only allow cell lengths to change, but not angles, during
optimisation or MD.
See also conp conv isotropic cellonly ocell

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

pacha

Type Keyword
Use Turns on calculation of variable charges using the formulation
of Marc Henry known as Pacha. See ChemPhysChem, 3, 561-569
(2002) for more details. At present the parameters for this
method in GULP are limited to elements below number 102 in the periodic
table.
See also sm eem qeq gasteiger noqeem external_potential
eembond

pdf

Type Keyword
Use Calculate the Pair Distribution Function up to a given maximum radius (rmax)
by summing peak widths calculated for each atomic pair. Makes use of the
theory of Chung and Thorpe for calculating PDFs from phonon information
Phonon information will be generated according to a full Monkhorst-Pack grid,
with a specified density (using the shrink option). It is essential that all
k-points are evaluated within a single gamma-centred Brillouin Zone; this
is automatically enforced through the use of the "shift" keyword.
See also PDFcut PDFkeep nowidth nofreq optimise rmax rbins shrink bbar siginc xray

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 box
project_dos output nozeropt gamma_direction_of_approach omega
dynamical_matrix meanke frequencies eckart box fc_supercell
msd ghostcell alamode ala_disp ala_cutoff groupvelocity
grueneisen threshold

polarisation

Type Keyword
Use If specified then the polarisation state of the system is output
in C/m**2 for bulk unit cells. NB: It is important to note that the
absolute polarisation is ill-defined and has no particular
significance. Only changes in polarisation as a function of
deformation are useful for defining quantities such as the
piezoelectric constants.
NB: Currently only includes atom and shell charges, but not induced
dipoles.

positive

Type Keyword
Use Ensure that the Hessian always behaves as positive definite during
Newton-Raphson by ensuring the search vector has the same sign as
as the gradient vector.
See also unit numdiag dfp conjugate lbfgs steepest

pot

Type Keyword
Use Print out electrostatic site potentials and their first derivatives.
If cell multipole method is specified then this technique will be
also used in the calculation of the potential for clusters. Note
that the potential calculated is not corrected for Coulomb subtract
options in the two-body potentials or molecule options. However, in
a core-shell model the potential due to the other component of an
atom is excluded.
It is now possible to also use "pot" for defect
calculations in which case GULP returns the electrostatic
potential at the sites of the asymmetric unit of region 1.
This potential does not include the displacements in
region 2a.
Note : when using pot in combination with QEq the potential calculated
is that resulting from q/r, not the integral expression used within a
QEq determination of the charges.
See also efg potential nodpsym potsites potgrid

predict

Type Keyword
Use General Algorithm for Structure Prediction Pre-gulp routine.
Given contents of unit cell atomic coordinates are found using a
global optimiser (simulated annealing or genetic algorithm).
See also genetic anneal contents global cost
and
Type Option
Use Start of global optimiser options section, closed by "end"
See also minimum maximum discrete configurations conjugate
tournament crossover mutation seed grid

pregionforce

Type Keyword
Use If present, this causes the force on each region to be output.
See also sfractional

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

property

Type Keyword
Default properties not calculated
Use Causes properties to be calculated and output.
For 3-D systems this includes the elastic constants, dielectric
constants, piezoelectric constants, sound wave velocities, bulk
and shear moduli, and Youngs modulus.
For 0-D systems this leads to the calculation of the moment of
inertia tensor and, if the temperature is greater than zero,
the calculation of the rotational and translational partition
functions, plus the free energy. Because the rotational partition
function depends on the symmetry number, this can be input by the
user, otherwise it will default to 1.
NB: If the Einstein option is used then the properties for
molecules will be incorrect as translation and rotational will
be hindered
See also numerical temperature pressure symmetry_number raman fsprop
ceigen

prt_eam

Type Keyword
Use Output the density and energy associated with atoms during an EAM calculation.
For a MEAM calculation, the density printed is the total when summed over the
component orders.
See also eam_functional eam_density prt_two prt_four prt_three prt_six

prt_four

Type Keyword
Use Output the fourbody energy contributions. The atoms are output in
the order of the torsion, 1-2-3-4, or with the middle atom as number 1
for the out of plane terms.
See also prt_eam prt_two prt_three prt_six

prt_six

Type Keyword
Use Output the sixbody energy contributions.
See also prt_eam prt_four prt_three prt_two

prt_three

Type Keyword
Use Output the threebody energy contributions. Atom 1 is the pivot atom
when output.
See also prt_eam prt_two prt_four prt_six

prt_two

Type Keyword
Use Output the real space twobody energy contributions.
See also prt_eam prt_four prt_three prt_six

pureQ

Type Keyword
Use By default, a Wolf sum is used to evaluate the Coulomb
potential in periodic systems when applied to the SAS
- SAS interaction matrix (A) in COSMO/COSMIC. For
consistency, this is retained in 0-D where it is not
necessary. This keyword causes a pure 1/r Coulomb
potential to be used instead.
See also cosmo cosmic cwolf

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 noqeem eembond

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 self-consistent. This leads to
all derivatives being incorrect as dE/dQ is no longer
zero. If Coulomb subtracted potentials are to be used
then charges must be calculated for the initial geometry
and then frozen.
Note: it is important to investigate the effect of
qeqradius on the degree of convergence and CPU time.
Note: Phonon calculations are limited with the QEq keyword
to the gamma point without the LO/TO splitting.
Note: Only region 1 atoms are included in QEq and fixed
charges will be taken for region 2.
See also eem qeqtol qeqiter qeqradius dcharge sm qelectronegativity
gasteiger pacha noqeem external_potential

qextrapolate

Type Keyword
Use Try to extrapolate the charges forward during MD with the reaxFF algorithm. Only works
when qiterative is also specified.
See also reaxff_chi reaxff_mu reaxff_gamma reaxff_qshell qiterative

qiterative

Type Keyword
Use Invokes the use of an iterative method to solve for charges in a
variable charge scheme, rather than matrix inversion. This applies
both COSMO/COSMIC calculations, where the charge is induced on the
solvent accessible surface, and to variable charge schemes including
ReaxFF, EEM, and QEq. This algorithm is usually superior for large
systems, especially in the case of ReaxFF where it offers linear-scaling
due to sparsity. For parallel calculations this option must be used
for variable charge algorithms since parallel matrix inversion is not
yet implemented.
NB: To obtain precise second derivatives by finite differences then
it is best NOT to use this keyword since it will generate more numerical
noise.
See also cosmo cosmic reaxff_mu reaxff_chi reaxff_gamma qsolver qiterations

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.
See also madelung

qsas

Type Keyword
Use Causes the charges on the segments of the solvent
accessible surface to be output, as well as the total
charge and dipole(s).
See also cosmo cosmic qonsas

raman

Type Keyword
Default Raman susceptibilities not calculated
Use Causes Raman susceptibilities to be calculated and output.
The quantities output are the derivatives of:
(1/(4*pi))(epsilon_infinity - delta_ab)
Here epsilon_infinity is the high frequency dielectric
constant tensor and delta_ab is the delta function that is
one for xx, yy, zz and otherwise 0. This quantity is the
same as q.(D**-1).q, where q is the vector shell charges,
and D is the matrix of shell-shell second derivatives.
Note that this will only have an effect if a shell model is
used since it involves the high frequency polarisability.
It also requires that a property calculation is performed
since it uses the high frequency dielectric constant tensor.
NB: The calculation of this quantity requires analytical
third derivatives and so is only available for certain
potential models (pairwise, three- and four-body terms).
See also property rdirection eckart

regi2a

Type keyword
Use print out region 2a in the output
See also region_1 regi_before defect

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

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

rephase

Type Keyword
Use Changes the eigenvector phases so the component with the largest magnitude is
all real for all eigenvectors, and renormalizes to unity. This makes visualisation
of eigenvectors simpler. Called as a dependent keyword by other keywords, for
example PDF.
See also PDF

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

rfo

Type Keyword
Use Invoke the Rational Function Optimisation (RFO) method for searching
for stationary points. By default the optimiser searches for the
minimum and may prove advantageous over the standard optimiser if the
Hessian is ill-conditioned. Also the Newton-Raphson method will yield
transition states if started too close to one, whereas the RFO method
will find the minimum.
Transition_state is a special case of rfo, in which the optimiser is
to converge to a first order transition state.
For transition state calculations, the updating scheme is DFP by
default instead of BFGS as the former is not biased towards positive
definiteness of the Hessian.
See also optimise transition_state rfo_eig rfo_grad

rigid

Type Keyword
Default Molecules are fully flexible
Use Specifies that molecules should be treated as rigid bodies.
Flags for rigid molecules are specified using the atoms of the
molecule. The 3 flags for the first atom in the molecule control
the centre of mass; the 3 flags for the second atom control the flags
for the quaternions.
NB: Not all features in GULP are currently compatible with rigid
molecules, such as molecular dynamics and free energy minimisation.
See also molq molecule rtol fix_molecule nobond inter intra both
14_scale noautobond bondtype molatom molmec norotate
molrigid

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

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 ocell

shopt

Type Keyword
Use If numerical third derivatives are being used to determine the force constants
for output to ShengBTE then this uses an algorithm in which only the cores are
finite differenced and the shells are optimised at every point. This is typically
less numerically precise than the default method where the shells are handled by
matrix multiplication.
See also numerical output num3

simplex

Type Keyword
Use Use the simplex algorithm for fitting instead of unit matrix with BFGS method.
See also fit simul relax genetic fbfgs delta

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 noshellzero

single

Type Keyword
Use Calculate energy only - default calculation.
See also optimise gradient md montecarlo

site_energy

Type Keyword
Default site energies not printed
Use Tells GULP to write out the site energies if possible.
Currently this is implemented in routines that compute
the forces and so you should use "gradients", "opti"
or "md" in the run type to ensure there is some output.
See also gradients optimise md

sm

Type Keyword
Use Turns on calculation of variable charges using the formulation
of Streitz and Mintmire. Here the charge is partitioned into a
fixed nuclear point charge and a variable charge distribution
with the shape of a 1s orbital. To use this option parameters
must be specified with the smelectronegativity option too.
If the keyword is given as "smzz" then the Znuc_i-Znuc_j energy
term given by Streitz and Mintmire, but neglected as part of the
two-body energy is included explicitly.
See also smelectronegativity eem qeq pacha gasteiger noqeem external_potential
eembond qeqradius

sopt

Type Keyword
Use Specifies that the details of shell optimisations during MD be output
See also shellmass iterations md

spatial

Type Keyword
Use Requests that a spatial decomposition algorithm is used wherever
possible to try to achieve linear scaling with system size.
NB: The minimum image approach is incompatible with the spatial
algorithm and so if both are specified the spatial algorithm will
be used.
NNB: The spatial algorithm is designed for large systems that typically
have low symmetry and so this keyword will have no effect if a space
group is present.
See also rcspatial minimum_image

spme

Type Keyword
Use Use the smoothed particle mesh Ewald sum where possible instead of the
standard Ewald sum. Note that this option only currently has first
derivatives and does not support the calculation of site energies or
use of multiple regions. The main use for molecular dynamics or optimisation
of large systems. Note that the values of rspeed and qgrid should be tuned
to give the best performance for the desired precision.
NB: This keyword is currently incompatible with variable charge models,
calculation of site energies, atomic stresses and rigid molecules.
See also accuracy rspeed qgrid bspline

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 zsisa lowest_mode

steepest

Type Keyword
Use Use steepest descents weighted by the average diagonal Hessian
element instead of the diagonal elements multiplying the gradients.
See also unit numdiag positive conjugate lbfgs dfp

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

strain

Type Keyword
Use Instead of using the actual unit cell as input/output, a reference
cell is used along with a specified set of strains to record the
change in the cell.
See also scan_cell ocell vectors cell cstrain

stress_out

Type Keyword
Use Causes the stresses to be output at the final geometry. This is
the same as the strain derivatives divided by the volume and
converted to GPa, plus correction for any external pressure.
NB: When using the strain keyword and cstrain option, then
the stress is defined with respect to the reference cell and
accordingly the volume of this cell is used.
See also atomic_stress strain cstrain

synchronous

Type Keyword
Use Invokes a synchronous transit run to try to find the transition state
between two structures. This is similar to an NEB run where you specify
the initial and final configurations, but the process uses two images
that are moved towards each other until they converge on the transition
state (i.e. like a 2 image climbing image NEB).
See also neb nebreplica synciterations synctolerance
fcartesian ffractional fcell fvectors

thermalconductivity

Type Keyword
Use Calculate the thermal conductivity of a solid at a given
temperature. This method uses a gamma point phonon calculation
for a supercell to estimate the thermal conductivity using the
method of Allen and Feldman, Phys. Rev. B, 48, 12581 (1993).
The output includes the mode diffusivities, Di (in cm^2/s),
and the overall thermal conductivity (in W/(m.K)). Note that
in this approximation the precise value obtained depends on
the degree of broadening of the density of states, controlled
by the broaden_dos option, the drop tolerance for the Lorentzian
broadening function, the temperature used, and finally the size
of the supercell (until converged with increasing size). Also
note that the non-analytic correction to the phonons at gamma
is turned off for a thermal conductivity calculation.
In order to correctly allow for the acoustic mode contribution
to thermal conductivity then a lower bound frequency should be
specified for the Allen-Feldman contribution and an analytic
integration used, as described under the omega_af option.
NB: Here the heat capacity for the modes is computed using the
full quantised expression from lattice dynamics, rather than
approximating the value from equipartition, as used in some
other work.
If the thermal conductivity is required more accurately and for
ordered solids then GULP can write out the files required for
use with the program ShengBTE that implements the Boltzmann
Transport Equations. To obtain the thermal conductivity via this
route the steps are:
1) Run a GULP calculation to optimise the structure and compute
the gamma point phonons with the option "output shengbte"
specified. Note that the third order force constants will be
computed analytically if possible, or numerically if they are
not available. To force the use of numerical third derivatives
the keyword "num3" can be specified. It is important to note
that the range of third order force constants output depends
on the size of the supercell specified using the "super" option.
2) Modify the file CONTROL to ensure that the correct temperature
k point sampling (ngrid) and broadening are specified for your
system.
3) Use the files CONTROL, FORCE_CONSTANTS_2ND and FORCE_CONSTANTS_3RD
as the inputs for ShengBTE.
4) Assuming the run is successful then the final overall thermal
conductivity will be given in the file BTE.kappa_scalar as the
last line (converged value from final iteration).
Alternatively GULP can use Alamode (if installed) to compute the
thermal conductivity and phonon lifetimes. To do this it is important
to set the environment variable ALAMODE_DIR to point to the root
directory of Alamode.
NB: This option should be used with caution with rigid molecules
since intramolecular vibrations are excluded.
See also broaden_dos temperature lorentzian_tolerance omega_af
groupvelocity output num3 supercell ghost_supercell
alamode ala_disp ala_cutoff

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 optimise rfo

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

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 optimise noflags conp conv fix_atom

unit

Type Keyword
Use Use unit diagonal matrix as starting point for Hessian.
Can be useful when exact Hessian is ill-conditioned.
See also numdiag dfp positive conjugate lbfgs

veck

Type Keyword
Use Specifies that an alternative reciprocal space algorithm is used in
which the inner loop is over k vectors and the outer (parallelised)
loop is over atoms. This may scale better on some platforms, but is
usually slower overall.
See also rspeed accuracy index_k ewaldrealradius dielectric_constant

voigt

Type Keyword
Default Reuss convention for bulk/shear modulus
Use Specifies that the Voigt convention is used for the bulk
modulus. The Voigt convention takes the average of the
elastic constants in the 1-3 x 1-3 block.
See also bulk_modulus shear_modulus elastic fit observables
hill young poisson

xray

Type Keyword
Use For PDF calculations, if this keyword is specified then the scattering
lengths will be set using the atomic number of the element rather than
using the neutron value in order to simulate X-ray data.
See also pdf bbar element siginc

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

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 lowest_mode shrink

3coulomb

Type Option
Format 3coulomb <intra/inter> <bond> <nbeq/nbne nbond>
atom1 atom2 atom3 scale <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23
Units scale in fractional, distances in Angstroms
Use Coulomb subtraction between atoms that are connected by a three-body term:
E(three) = - scale.q2.q3/r23
where q2 and q3 are the charges of the atoms 2 and 3.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger bcross lin3
urey-bradley murrell-mottram bacross hydrogen-bond equatorial
uff3 bagcross j3 ppp3body

absdipolemoment

Type Option
Format absdipolemoment
value <weight>
Units Debye
Default no dipole moment to be fitted
Use Subsection of observables, used for specifying an experimental
absolute dipole moment for fitting. Here the square root of the
dipole moment components along each axis are used so that the
quantity is rotationally invariant.
See also observables

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 initial_coordinates

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

accuracy

Type Option
Format accuracy <exponent> <<Euler-Maclaurin_order> <maximum-cell> <acc-1D>>
Units none
Default 12.0 < 4 200 8.0>
Use Controls the accuracy of the electrostatic summations. Note : the last two
values only apply to 1-D systems. The first value is the target number of
converged significant figures in the electrostatic energy or the fractional
uncertainty in the electrostatic energy, where the value is used as an
exponent (i.e. 10**-(exponent)). This determines the real and reciprocal
space cut-offs of the Ewald sum (3-D) and Parry sum (2-D) for a given value
of rspeed.
For 1-D systems a direct real space approach is used, as per CRYSTAL. Here
the energy is converged to the precision specified by acc-1D by searching
for the number of neutral cells that must be included in each direction in
the sum. The maximum-cell indicates the upper bound to be used while the
second optional parameter is the order of the series used in the numerical integrals.
Generally the default values should be sufficient.
See also rspeed veck index_k spme dielectric_constant ewaldrealradius

ala_cutoff

Type Option
Format ala_cutoff cutoff_harm cutoff_cubic <none> <au>
Units Angstrom, unless au is specified in which case it will be atomic units
Default 8.0 Angstroms for both harmonic and cubic force constants.
Use Specifies the force constant cutoff (distance beyond which force
constants are assumed to be zero) for the thermal conductivity
calculation with Alamode. Note that the cost increases rapidly
with the size of the cutoff since larger supercells are needed and
more terms must be computed. Separate values can be specified for
harmonic (cutoff_harm) and cubic (cutoff_cubic) terms, or a single
value for both. If "none" is specified then no cutoff is applied
(i.e. the cutoff is determined by the size of the cell input).
See also alamode ala_disp thermal_conductivity ala_shrink ala_processors ala_mode

ala_disp

Type Option
Format ala_disp disp_harm disp_cubic <au>
Units Angstrom, unless au is specified in which case it will be atomic units
Default 0.005 / 0.01 for harmonic and cubic force constants, respectively.
Use Specifies the displacements for finite difference calculation of the
harmonic (disp_harm) and cubic (disp_cubic) force constants when
using Alamode.
See also alamode ala_cutoff thermal_conductivity ala_shrink ala_processors ala_mode

ala_mode

Type Option
Format ala_mode <all/pattern/displace/fit_harmonic/fit_cubic/bte>
Default all
Use Specifies the operations to be performed when interacting with Alamode.
A full calculation involves the following sequence of steps:
- Set up of the input for Alamode to generate the displacement patterns
- Perform the displacements to generate the force constants and set up
the input to fit this
- Fit the harmonic force constants
- Fit the cubic force constants
- Compute the thermal conductivity via the Boltzmann Transport Equations
GULP can perform all of these in a single call (all) or the individual
steps (pattern/displace/fit_harmonic/fit_cubic/bte in the above order)
via sequential calls.
If running in parallel then the use of sequential calls may be preferred
since both GULP and Alamode can be run in parallel. If using MPICH then
the combined option (all) should also run in parallel as recursive use
of MPI is not blocked.
See also alamode ala_disp thermal_conductivity ala_shrink ala_processors ala_cutoff

ala_processors

Type Option
Format ala_processors ncore
Units None
Default Same number of cores as GULP is running on.
Use Specifies the number of processors that will be used by Alamode.
Since the thermal conductivity calculation can be more expensive
than the force constant evaluation, this allows more processors
to be used for the Alamode part of the calculation.
See also alamode thermalconductivity ala_disp ala_cutoff ala_shrink ala_mode

ala_shrink

Type Option
Format ala_shrink ix <iy> <iz>
Units ix, iy and iz are dimensionless integers
Default 1 1 1
Use Specifies the shrinking factors in reciprocal space. The higher the
shrinking factor the more extensively k space is sampled. One value
may be given, in which case the shrinking factor is used isotropically
or three anisotropic values can be given. These shrinking factors will
be used for calls to Alamode.
See also alamode thermalconductivity ala_disp ala_cutoff ala_processors ala_mode

anisotropic_pressure

Type Option
Format anisotropic_pressure P_xx P_yy P_zz P_yz P_xz P_xy (for 3-D)
anisotropic_pressure P_xx P_yy P_xy (for 2-D)
anisotropic_pressure P_xx (for 1-D)
Units GPa
Default No anisotropic pressure
Use This option allows the user to apply a general constant stress, such
as a uniaxial stress. Because the energy is not defined for anisotropic
pressure, except via a set of integrals between states, then the use
of force minimisation, rather than energy minimisation is required for
optimisation.
If both pressure and anisotropic pressure are specified then
the two are added together. For anisotropic pressure, this must be
specified after the structure otherwise the information may not be
correctly processed since this depends on the dimensionality.
Note that stresses are dependent on the cell orientation and so take
care when specifying.
See also pressure force_minimisation

ashift

Type Option
Format ashift <ev/au/kcal/kjmol-1>
atomic_symbol value <1xflag>
Units eV (default), au, kcal or kJmol-1
Default 0.0
Use Specifies a species specific energy shift (i.e. a one-body potential).
Usually this term is not needed since it is just a constant. However,
it may prove useful during fitting of ab initio energy surfaces.
e.g.
ashift
O2 0.34
The above would apply an energy shift to each O2 atom in a structure
of 0.34 eV.
See also shift sshift

atomab

Type Option
Format atomab
<Atomic_symbol/atomic_number> A B <2 x flags for fitting>
Units eV*Angs**m and eV*Angs**n
Use Specifies A and B values for each species type to be used in
combination rules to obtain Lennard-Jones potential parameters
where specified.
See also epsilon lennard

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

axilrod-teller

Type Option
Format axilrod-teller <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) <rmin(2-3)>
rmax(2-3) <flag>
Units k in eV*Angstroms**9, rmin & rmax in Angstroms
Default none
Use Axilrod-Teller three-body potential:
E(three) = k (1+3*cos(theta1)*cos(theta2)*cos(theta3))
-------------------------------------------
(r12*r13*r23)**3
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2, 2-3 and 1-3 are bonded.
See also three-body angle exponential stillinger-weber bcross urey-bradley
murrell-mottram bacross hydrogen-bond equatorial uff3 lin3 3coulomb
bagcross j3 ppp3body

bacoscross

Type Option
Format bacoscross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K1 K2 r1 r2 theta0 <rmin12> rmax12 <rmin13> rmax13
<rmin23> rmax23 <5*flags>
Units K1 and K2 in eV/Angs, r1 and r2 in Angstroms, theta0 in degrees
Use Bond-angle cosine cross term three body potential
E(three) = [K1*(r12 - r1) + K2*(r13 - r2)].(cos(theta)-cos(theta0))
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bcross hydrogen-bond equatorial lin3 uff3 bacross
3coulomb bagcross j3 ppp3body

bacross

Type Option
Format bacross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol/degree>
atom1 atom2 atom3 K1 K2 r1 r2 theta0 <rmin12> rmax12 <rmin13> rmax13
<rmin23> rmax23 <5*flags>
Units K1 and K2 in eV/(Angs*rad), r1 and r2 in Angstroms, theta0 in degrees
Use Bond-angle cross term three body potential
E(three) = [K1*(r12 - r1) + K2*(r13 - r2)].(theta-theta0)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bcross hydrogen-bond equatorial lin3 uff3
bacoscross 3coulomb bagcross j3 ppp3body

bagcross

Type Option
Format bagcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K r1 r2 theta0 m n p <rmin12> rmax12 <rmin13> rmax13
<rmin23> rmax23 <4*flags>
Units K in eV/((Angs**(m+n))*(rad**p)), r1 and r2 in Angstroms, theta0 in degrees
Use Bond-angle general cross term three body potential:
E(three) = K*[(r12 - r1)**m]*[(r13 - r2)**n].(theta-theta0)**p
This potential is designed to represent general anharmonic coupling
terms for a force field up to three-body terms.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bcross hydrogen-bond equatorial lin3 uff3
bacoscross 3coulomb bacross balcross j3 ppp3body

balcross

Type Option
Format balcross <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K r1 r2 isign n m p <rmin12> rmax12 <rmin13> rmax13
<rmin23> rmax23 <3*flags>
Units K in eV/(Angs**(m+p))), r1 and r2 in Angstroms
Use Bond-angle linear cross term three body potential:
E(three) = K*[(r12 - r1)**m]*[(r13 - r2)**p].(1 + isign*cos(n*theta))
This potential is designed to represent anharmonic coupling
terms for a force field up to three-body terms for linear angles.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bcross hydrogen-bond equatorial lin3 uff3
bacoscross 3coulomb bacross bagcross j3 ppp3body

baskes

Type Option
Format baskes <a4> <n>
atom1 atom2 Ec A alpha r0 Z1 wF d <rmin> rmax <5xflags>
Z2S_1 s_1 Z2S_2 s_2
if the potential is specified as "baskes a4" then the format is:
atom1 atom2 Ec A alpha r0 Z1 wF d gamma lambda <rmin> rmax <7xflags>
Z2S_1 s_1 Z2S_2 s_2
Z2S and s are only input if n > 0
Units Ec in eV; gamma and r0 in Angstroms; A, Z1, Z2S, s, alpha, d, wF and lambda are unitless
Default None, n=0
Use This option specifies the two-body potential between atoms need for the MEAM
method. The form is constructed based on the difference between the Rose
equation of state and the form of the embedding function for a reference
structure (such as fcc, bcc, hcp, etc).
The form of the potential is:
E = - (2/Z1)*Ec*{(1+a+d*a**3)*exp(-a) + A*(rho_ref(r)/rho0)*ln((rho_ref(r)/rho0))}
unless "a4" is specified in which case there is an extra term:
E = - (2/Z1)*Ec*{(1+a+d*a**3+gamma*a**4*exp(-lambda*a**2)/r)*exp(-a) +
A*(rho_ref(r)/rho0)*ln((rho_ref(r)/rho0))}
where:
Z1 = the number of nearest neighbours in the reference structure (NB no fitting flag)
Ec = cohesive energy of the reference structure
r0 = equilibrium distance in the reference structure
rho0 = density for equilibrium reference structure (comes from meam_functional)
rho_ref(r) = density for reference structure when distance is r.
a = (alpha/r0)*(r-r0)
d = unitless factor that modifies shape of equation - usually 0.0
wF = unitless factor that weights the i vs j contributions - for pure phases this is
1.0, but for alloys will be 0 < wF < 1. For phase of composition AB3 with atoms
input in the order A then B, then wF will be 0.25 (the weight for component A).
If B is input first then it would be 0.75.
gamma = distance factor that modifies shape of equation
lambda = exponent that modifies the shape of the equation
The value of rho_ref(r) is given by the following expression:
rho_ref(r) = sqrt[ sum(l=0->3) s_l*t_l*rho_l(r)**2 ]
where rho_l = exp(-(b_l/r0)*(r-r0))
here t_l is the coefficient of the l'th order density square in MEAM and s_l is a
geometric factor for the reference structure in question that depends on the l'th
order. Note that s_0 is equal to Zd**2 in the notation of Baskes and co-workers.
NB: In earlier versions of GULP the b and t coefficients were specified explicitly
for this potential. However, they are now obtained directly from the MEAM density
in order to avoid duplication. Similarly the rho0 used to be specified, but this is
now obtained from the MEAM functional.
If n = 0 (default) then the 1NN form of MEAM is used.
If n > 0, then the 2NN form of MEAM is selected instead. Here the pair potential
is generated according to:
phi(R) = psi(R) + sum(i=1,n) (-Z2S/Z1)**i.psi(s**i.R)
where:
Z2S = the number of second neighbours in the reference structure x screening function, S
s = is the scale factor for the second neighbour distance relative to the first one
phi = effective pair potential
psi = (2/Z1)*(Ec(R)-F(rho(R))
See also meam_functional meam_density

bbar

Type Option
Format bbar at.no. <bbar>
Units Angstrom
Use Used within element option input block, overwrites the default neutron
scattering length for a specified element. (at. no. or symbol may be used)
NB: If the keyword xray is specified then the atomic number will be used
instead of the neutron scattering length
See also coreinfo element siginc xray

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 Bond-bond cross term three body potential with cosine angle dependance:
E(three) = K * (1 + b*cos(n.theta)**m) * (r12 - r1) * (r13 - r2)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bacross bcross hydrogen-bond equatorial lin3 uff3
3coulomb bagcross j3 ppp3body

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 Bond-bond cross term three body potential:
E(three) = K * (r12 - r1) * (r13 - r2)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger urey-bradley
murrell-mottram bacross hydrogen-bond equatorial lin3 uff3 3coulomb
bagcross j3 ppp3body

becke_johnson_c6

Type Option
Format becke_johnson_c6 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 C6 r0 <rmin> rmax <2*flags>
Units C6 in eV*Angs**6, r0 in Angs
Default None
Use Specifies potential parameters for the Becke-Johnson form of damped C6 term.
The energy is of the form:
E = - C6/(r**6 + r0**6)
See also damped_dispersion grimme_c6

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 predict

blocksize

Type Option
Format blocksize <atoms/sas> nblocksize
Default atoms = 1, sas = 12
Units none
Use This parameter is an integer that decides how the second
derivatives are divided over the processes when running
in parallel. The number is used to control the efficiency
of the parallel work in Scalapack / Blacs, but also in
GULP itself. The real number used for atoms is actually
3*nblocksize in order to divide the coordinates of the atoms
so that the x, y, z components of an atom are all on the same
node. If nblocksize is too large then load balance will
be an issue, while if it is too small then Scalapack will
lose efficiency.
Specifying atoms or sas allows control over the individual
blocksizes for matrices relating to atoms, or the solvent
accessible surface, respectively.
NB: The blocksize must be a factor of the number of atoms,
and the number of shells, if appropriate, in each configuration.
Therefore 1 is a safe value that will always work, but other
values may be possible depending on the system.
See also matrix_format maths

boattractive

Type Option
Format boattractive <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda <2*flags>
or
boattractive theta <zrl> <gik> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c d h <5*flags>
or
boattractive kumagai <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c1 c2 c3 c4 c5 h <8*flags>
or
boattractive mmp <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c0 c1 c2 c3 c4 <7*flags>
NB The value of m cannot be fitted and therefore there is no flag
Units lambda in 1/Angstroms
All other quantities are unitless.
Default If atom2 is not given then it will be set to be a wildcard, X, so
that the potential applies to all pairs involving atom1
m = 3, omega_ik = 1
Use Sets the parameters that define the value of zeta in the bond order
expression specified via boonebody for the attractive term. Zeta for
atom i is evaluated from the sum over all atoms, k, bonded to i, but
excluding k=j when applying the bond order to the i-j bond specified
via botwobody.
For case without "theta" sub-option;
zeta = Sum(rik) [f(rik).omega_ik.exp(lambda**m.(rij-rik)**m)]
else;
zeta = Sum(rik) [f(rik).g(theta).omega_ik.exp(lambda**m.(rij-rik)**m)]
f(rik) = cosine taper function
g(theta) = 1 + (c/d)**2 - c**2/[d**2 + (h - cos(theta))**2]
Note that the cut-offs are derived from the values for the corresponding
botwobody potential. By default the angular parameters in g(theta) are
taken based on the i-j interaction. In some models these parameters are
set based on the i-k interaction instead. In this case the "gik" sub-option
should specified after "theta".
If the "zrl" sub-option is specified then the alternative form
of Billeter et al (Phys. Rev. B, 73, 155329 (2006)) is used in which
the exponential part of zeta becomes:
exp((lambda_ij*rij - lambda_ik*rik)**m)
Because lambda is now specific to each pair of atoms, it is recommended
that the zrl form is specified for all bond-order potentials or none,
rather than mixing forms.
If the "kumagai" sub-option is specified then the theta term becomes:
g(theta) = c1 + g_o(theta)*g_a(theta)
g_o(theta) = c2*(h - cos(theta))**2/(c3 + (h - cos(theta))**2)
g_a(theta) = 1 + c4*exp(-c5*(h-cos(theta))**2)
If the "mmp" sub-option is specified then the theta term becomes:
g(theta) = (sum(n=0->4) c_n*cos(n*theta))**2
This is the form of the angular potential required for the MMP potential
as given in Monteverde et al, J. Phys. Condens. Matter, 25, 425801 (2013)
NB: Because of the introduction of pair-wise specific terms, input files
from earlier versions will needed to be changed for mixed element systems.
NB: For mixed systems, the order of the atoms is important since the i-k
parameters are not necessarily the same as k-i. If "symmetric" is specified
as a sub-option then i-k and k-i will be set to be the same and only one
direction need be specified.
See also botwobody borepulsive bocharge boselfenergy bocoordination

bocharge

Type Option
Format bocharge <staper>
atom1 atom2 deltaQ Rmin Rmax
Units au
Default None for potential / use cosine taper
Use Specifies the parameters for the taper function used in determining
bond order charges as a function of environment. The charge on an
ion is determined as:
Atom 1: Q = sum [ - deltaQ*H(r) ]
Atom 2: Q = sum [ + deltaQ*H(r) ]
Here the sum is over all atoms of the approriate type within the
cutoff radius, Rmax. H(r) is taper function that acts between Rmin
and Rmax. In the original paper of Jiang and Brown a cosine taper
is used and this is the default. However, the sub-option allows the
sine taper of Watanabe et al (Jpn. J. Appl. Phys. 38, L367 (1999))
to be used which has better behaviour for the second derivatives at
the cutoff.
See also botwobody borepulsive boattractive boselfenergy sw2jb sw3jb
bocoordination

bocnswitch

Type Option
Format bocnswitch zb zt
Units None
Default zb = 0.20039, zt = 0.49751
Use Specifies the 2 universal values that are used in the coordination
switching function in the Tersoff ZRL model. See paper below for
more information, and this is the source of the default values:
Billeter et al, Phys. Rev. B, 73, 155329 (2006).
NB: zt+zb must be less than 1 and zt-zb must be greater than 0
NNB: The original switching function in the above paper leads to
a highly discontinuous energy and so a modified form is implemented
here in 2 ways (the int(z) term is left out and sin is replaced by cos)
See also botwobody borepulsive boattractive bocharge sw2jb sw3jb
boselfenergy bocoordination bocntolerance

bocntolerance

Type Option
Format bocntolerance tol
Units None
Default tol = 0.000001
Use Specifies the tolerance on the coordination number from an
integer to trigger calculating derivatives.
See also botwobody borepulsive boattractive bocharge sw2jb sw3jb
boselfenergy bocoordination bocnswitch

bocoordination

Type Option
Format bocoordination
atom1 c1 c2 z0 E0 <4*flags>
Units c1, c2 and E0 in eV
Default c1, c2 = 0, E0 = 0, z0 = 0
Use Specifies the Tersoff augmentation term based on coordination number, as
well as the self energy. These were proposed in the Tersoff ZRL form of
Billeter et al, Phys. Rev. B, 73, 155329 (2006).
E = c1*delta_z + c2*(delta_z**2) + E0
See also botwobody borepulsive boattractive bocharge sw2jb sw3jb
boselfenergy bocnswitch bocntolerance

bondtype

Type Option
Format bondtype species1 species2 type_of_bond <regular/cyclic/exocyclic>
Default type_of_bond = single
Use Sets the default type of bond between two species.
Valid bond types are: single, double, triple, quadruple, resonant,
amide, custom, half, quarter, and third. For example, a default
double bond between two carbons of type C2 can be specified as:
bondtype C2 C2 double
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also molecule molq molmec bond connect noautobond nobond molatom

boonebody

Type Option
Format boonebody
atom1 alphaA alphaB nA nB <4*flags>
Units alphaA, alphaB, nA and nB are unitless
Default none
Use Specifies the parameters for the Tersoff bond order potential
that depend on the atom whose bond order sum is being computed.
The coefficients that scale the repulsive and attractive terms are
given by:
BOr = (1 + (alphaA*zeta)**nA)**(-1/2nA)
BOa = (1 + (alphaB*zeta)**nB)**(-1/2nB)
Here zeta is given by the sum over neighbours, k, of i (excluding j)
and the parameters are set via borepulsive and boattractive (see these
options for the relevant equations).
See also borepulsive boattractive bocharge boselfenergy bocoordination botwobody

borepulsive

Type Option
Format borepulsive <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda <2*flags>
or
borepulsive theta <zrl> <gik> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c d h <5*flags>
or
borepulsive kumagai <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c1 c2 c3 c4 c5 h <8*flags>
or
borepulsive mmp <zrl> <symmetric>
atom1 <atom2> <m> <omega_ik> lambda c0 c1 c2 c3 c4 <7*flags>
NB The value of m cannot be fitted and therefore there is no flag
Units lambda in 1/Angstroms
All other quantities are unitless.
Default If atom2 is not given then it will be set to be a wildcard, X, so
that the potential applies to all pairs involving atom1
m = 3, omega_ik = 1
Use Sets the parameters that define the value of zeta in the bond order
expression specified via boonebody for the repulsive term. Zeta for
atom i is evaluated from the sum over all atoms, k, bonded to i, but
excluding k=j when applying the bond order to the i-j bond specified
via botwobody.
For case without "theta" sub-option;
zeta = Sum(rik) [f(rik).omega_ik.exp(lambda**m.(rij-rik)**m)]
else;
zeta = Sum(rik) [f(rik).g(theta).omega_ik.exp(lambda**m.(rij-rik)**m)]
f(rik) = cosine taper function
g(theta) = 1 + (c/d)**2 - c**2/[d**2 + (h - cos(theta))**2]
Note that the cut-offs are derived from the values for the corresponding
botwobody potential. By default the angular parameters in g(theta) are
taken based on the i-j interaction. In some models these parameters are
set based on the i-k interaction instead. In this case the "gik" sub-option
should specified after "theta".
If the "zrl" sub-option is specified then the alternative form
of Billeter et al (Phys. Rev. B, 73, 155329 (2006)) is used in which
the exponential part of zeta becomes:
exp((lambda_ij*rij - lambda_ik*rik)**m)
Because lambda is now specific to each pair of atoms, it is recommended
that the zrl form is specified for all bond-order potentials or none,
rather than mixing forms.
If the "kumagai" sub-option is specified then the theta term becomes:
g(theta) = c1 + g_o(theta)*g_a(theta)
g_o(theta) = c2*(h - cos(theta))**2/(c3 + (h - cos(theta))**2)
g_a(theta) = 1 + c4*exp(-c5*(h-cos(theta))**2)
If the "mmp" sub-option is specified then the theta term becomes:
g(theta) = (sum(n=0->4) c_n*cos(n*theta))**2
This is the form of the angular potential required for the MMP potential
as given in Monteverde et al, J. Phys. Condens. Matter, 25, 425801 (2013)
NB: Because of the introduction of pair-wise specific terms, input files
from earlier versions will needed to be changed for mixed element systems.
NB: For mixed systems, the order of the atoms is important since the i-k
parameters are not necessarily the same as k-i. If "symmetric" is specified
as a sub-option then i-k and k-i will be set to be the same and only one
direction need be specified.
See also botwobody boattractive bocharge boselfenergy bocoordination

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 qreaxff young poisson

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
bocoordination

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 molatom

botwobody

Type Option
Format botwobody <kcal/kjmol> <cosine/mdf/murty>
atom1 atom2 A B za zb rtaper rmax <5*flags>
or
botwobody combine <cosine/mdf/murty>
atom1 atom2 chiR chiA <2*flags>
Units A and B in eV, za and zb in 1/Angstroms, rtaper and rmax in Angs
oa and ob are unitless
Default none, taper = mdf
Use Specifies the parameters for the twobody form of a bond-order
potential of the Tersoff form:
E = f(r)[A.exp(-za.r).(BOr) - B.exp(-zb.r).(BOa)]
where f(r) is a taper function that smooths the decay from rtaper
to rmax, BOr and BOa are the bond orders for the repulsive and
attractive terms, respectively. These terms are set by separate
options. If the combine sub-option is specified then the parameters
are generated using Tersoff's combination rules from the values for
the corresponding element's self-self interaction. The chi values
then scale the repulsive and attractive terms.
The sub-options cosine, mdf and murty are used to select the form of
taper that is used. Early versions of GULP used the cosine taper, but
this leads to numerical instabilities in the second derivatives for some
cases. For backwards compatibility it may be necessary to use cosine
to reproduce results. The murty taper form was used by Kumagai et al
in their form of the Tersoff potential along with the corresponding
modified angular term.
See also borepulsive boattractive bocharge boselfenergy bocoordination boonebody

box

Type Option
Format box <dispersion/density> <size/number> value
Units size in cm-1
Default number for dispersion = 25
number for density = 64
Use Allows the user to change the box size or number of boxes used for
outputting the phonon density of states or/and phonon dispersion
curves.
For example, to change the resolution of the phonon density of
states to 10 cm^-1:
box density size 10
See also phonon dispersion shrink broaden_dos

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. Parameters
are also available for F, but should not be used if oxygen is present.
The option REBO is a synonym for this option.
If the model number is given as 1 (i.e. "brenner 1") then the original
Brenner model will be used. This option has parameters for C, H and Si
using the extended parameter set given in Dyson and Smith, Surf. Sci.,
355, 140 (1996)
See also spatial

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
Defaults Type = harmonic
Use Specifies the breathing shell force constant, K, and
equilibrium radius, r0, for the spherical breathing
shell model.
E(bs) = 1/2 * K * (r - r0)**2
or the constants of the exponential restoring term:
E(bs) = K * [exp(rho*(r-r0)) + exp(-rho*(r-r0))]
or the constants of the single_exponential restoring term:
E(bs) = K * exp(rho*(r-r0))
See also breathe nobreathe simultaneous

bspline

Type Option
Format bspline norder
Units none
Default norder = 8
Use Specifies the B-spline interpolation order in SPME.
See also rspeed veck accuracy ewaldrealradius spme qgrid

buck4

Type Option
Format buck4 <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A rho C <rmin> cut1 rminimum cut2 rmax <4*flags>
Units A in eV, rho in Angs, C in eV*Angs**6, distances in Angstroms
Default none
Use Four range Buckingham potential - optimisation flags for fitting (0/1)
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
The form of the potential is:
from rmin to cut1 : E=Aexp(-r/rho)
from cut1 to rminimum: E=a0+a1*r+a2*r**2+a3*r**3+a4*r**4+a5*r**5
from rminimum to cut2: E=b0+b1*r+b2*r**2+b3*r**3
from cut2 to rmax : E=-C/r**6
The potentials are subjected to the constraint that the functions and
their first and second derivatives must be continuous at the boundary
points, and also that the function must have a stationary point at
rminimum (hopefully a minimum!).
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.

buckingham

Type Option
Format buckingham <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 A rho C <rmin> rmax <3*flags>
Units A in eV, rho in Angs, C in eV*Angs**6
If kcal is given : A in kcal, rho in Angs, C in kcal*Angs**6
If kjmol is given: A in kJmol-1, rho in Angs, C in kJmol*Angs**6
Default none
Use Buckingham potential - optimisation flags for fitting (0/1).
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A.exp(-r/rho) - C/r**6
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also c6 mm3buck slater

buffered_lj

Type Option
Format buffered_lj <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 epsilon r0 delta gamma <rmin> rmax <4*flags>
Units epsilon in eV, r0, rmin and rmax in Angs
Default none
Use This option specifies the use of a buffer 14-7 Lennard-Jones potential.
The form is that used by AMOEBA for interactions:
E = epsilon*[((1+delta)/(rho+delta))**7]*[(1+gamma)/(rho**7+gamma)-2]
where rho = r/r0
See also epsilon atomab c6 lennard

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 young poisson

cartesian

Type Option
Format cartesian <region <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 Specifies the Cartesian coordinates and charges for all species.
Either the atomic number or the symbol may be supplied, followed
by the species type. If the species type is omitted then it is
assumed to be a core. Individual charges may be supplied for each
ion or the charges for each type of species given using the
species option. If the charges are given, then optionally site
occupancies may also be specified. Optimisation flags are only
needed if cellonly, conv, bulk, conp or shell are not specified.
If the "region" sub-option is specified, then this tells the program
to treat the atoms as a group where the collective coordinates can be
specified to be fixed or not in a given direction. By default, the
regions are treated as being for a surface calculation where region 1
is free to relax while region 2 is held fixed. Regions are numbered
according to the order in which they appear in the input.
If the "rigid" sub-option is also specified after "region" then the region
is created as a rigid body so that all atoms are constrained with respect
to each other. By specifying a string after this containing x, y and/or z,
the region may be allowed to move in particular directions. For example,
in an interface calculation, a region could be specified that is allowed
to only relax in the z direction by using:
cart region 3 rigid z
NB: The "region" sub-option must come before any of the other related
sub-options.
If a "T" is specified then the atom is marked for the translate option
If a "%" is specified then the atom is part of a growth slice if it
is in region 1 of a surface calculation.
See also fractional ditto spacegroup frame

catomic_stress

Type Option
Format catomic_stress
1 xx yy zz yz xz xy
2 xx yy zz yz xz xy
etc
Units eV
Default None
Use Gives the current average of the atomic stresses needed from MD
Used for MD restart or information.
See also atomic_stress

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

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.
NB: For non-periodic systems there is no need to specify a cell
See also vectors scan_cell primitive_vectors pcell scell

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.
e.g. centre mol 2
See also defect size region_1 regi_before
impurity vacancy impurity interstitial frequency bulk_noopt

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

cfm_fermi

Type Option
Format cfm_fermi <kcal/kjmol>
atom1 atom2 k zeta r0 R w rmax <5*flags>
Units k in eV, r0, w and R in Ang, zeta in Ang**-1
Default none
Use Specifies a Fermi-Dirac like inter potential for the central force model
as described by Bresme (J. Chem. Phys. 115, 7564 (2001)).
E = [k/(1+exp(zeta*(r - r0)))]*t(r)
where
t(r) = 0.5*(1 + tanh((r-R)/w))
See also cfm_harmonic cfm_power cfm_gaussian

cfm_gaussian

Type Option
Format cfm_gaussian <kcal/kjmol>
atom1 atom2 k zeta r0 R w rmax <5*flags>
Units k in eV, r0, w and R in Ang, zeta in Ang**-2
Default none
Use Specifies a Gaussian inter potential for the central force model
E = [k*exp(-zeta*(r - r0)**2)]*t(r)
where
t(r) = 0.5*(1 + tanh((r-R)/w))
NB: If w < 0 then t(r) = 1
See also cfm_harmonic cfm_power cfm_fermi

cfm_harmonic

Type Option
Format cfm_harmonic <kcal/kjmol>
atom1 atom2 k r0 R w rmax <4*flags>
Units k in eV/Ang**2, r0, w and R in Ang
Default none
Use Specifies a harmonic intra potential for the central force model
as described by Bresme (J. Chem. Phys. 115, 7564 (2001)).
E = [0.5*k*(r - r0)**2]*[1 - t(r)]
where
t(r) = 0.5*(1 + tanh((r-R)/w))
NB: If w < 0 then t(r) = 1
See also cfm_power cfm_gaussian cfm_fermi

cfm_power

Type Option
Format cfm_power <kcal/kjmol>
atom1 atom2 A power R w rmax <4*flags>
Units k in eV*Ang**power, w and R in Ang, power is unitless
Default none
Use Specifies a power-law inter potential for the central force model
as described by Bresme (J. Chem. Phys. 115, 7564 (2001)).
E = [A/r**power]*t(r)
where
t(r) = 0.5*(1 + tanh((r-R)/w))
NB: If w < 0 then t(r) = 1
See also cfm_harmonic cfm_gaussian cfm_fermi

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.
See also fit observables monopoleq

chemshell_mode

Type Option
Format chemshell_mode <init/calc>
Default No chemshell output
Use Sets the ChemShell output mode to be init or calc.
NB: Only is used if GULP has been compiled to work with
recent versions of ChemShell.
See also

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.

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
is greater than n then population will expand by stepsize (default
2) every iteration until <n=max> after which <stepsize> new random
configurations will replace current <stepsize> worst configurations.
<stepsize> also specifies how many of the best configurations
survive into the next iteration without changing!
See also genetic predict

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 usually -1, 0, 1,
where 0 means the image in the central cell, -1 means the image in
the negative direction and +1 in the positive one.
e.g.
connect 1 2 1 0 -1
Optionally, the type of bond can be specified and this information
can be used in applying the correct force field terms where applicable.
Valid bond types are: single, double, triple, quadruple, resonant,
amide, custom, half, quarter, third, cyclic, and exocyclic. For example,
an exocyclic double bond can be specified as:
connect 1 2 double exocyclic 1 0 -1
If not specified, the bonds are assumed to be single bonds. Note that
the bond order used in UFF for each type_of_bond can be set using the
option uff_bondorder.
NB: For the connect information to be used one of the molecule
keywords must be specified.
See also molecule molq molmec nobond bond noautobond uff_bondorder bondtype
molatom

constrain

Type Option
Format For geometric or (non-)linear fit:
constrain <fit> <no._of_constraints>
nvari nvart nfixi nfixt 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 = index of variable to allow to vary
nvart = type of variable to allow to vary
nfixi = index of variable to be constrained
nfixt = type 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:
Variables are now specified using an index and a type. The type can
be a coordinate (x,y,z), a radius (r), a cell parameter (c), a cell
strain (s), a rigid molecule centre of mass (xcom,ycom,zcom), or a
rigid molecule quaternion (xqtn,yqtn,zqtn). If the type is a coordinate
or radius then the index is the number of atom in the asymmetric unit,
whereas for strains the index is the strain number. For cell parameters,
1 => a, 2 => b, 3 => c, 4 => alpha, 5 = beta, 6 = gamma (NB cell
parameters can only be constrained if the keyword has been specified
that forces optimisation in terms of cell parameters rather than strains).
For rigid molecules, the index is the molecule number. Note that rigid
molecule constraints can only be applied between 2 centre of mass coordinates
or 2 quaternion coordinates since mixing of types is not usually
sensible.
As an example, to constrain the z coordinate of atom 6 to be half that
of the x coordinate of atom 3 this would be input as:
3 x 6 z 0.5 0.0
To constrain the radii of the same atoms to be different by 0.2 Ang:
3 r 6 r 1.0 0.2
Additive use of geometric constraints is allowed so that an
atom may be fixed at the centroid of two other atoms. When
this is the case for 3-D systems, there is an ambiguity
due to the presence of periodic replications. GULP will
use the two nearest images for the constraints.
Fitting constraints:
Variable numbers refer to the number of the parameter as included
in the variables table, which in general is the same as the order
of specification in the input. If nvar1=nvar2 for geometric mean
constraints then the square root of just one parameter is taken.
Note that the variable numbers for the constraint command in
fitting may be changed in the restart file relative to those in
the input. This is to take account of the reordering of potentials.
To input multiple constraints the number can be
added after the constraint command.
Note: The ability to raise the variable to power is currently only
available for fitting constraint, though it shouldn't be needed
for geometric variables anyway.
See also outcon

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 observed coodination numbers are used as default.
Can only be used when keyword predict included or when a single
calculation required and all coordinates are known/supplied.

coordno

Type Option
Format coordno <n>
i rcut cn <weight>
Units Angstroms for rcut
Default no coordination numbers to be fitted
Use Subsection of observables, used for specifying values of
coordination numbers for fitting. Here i is the atom number
whose coordination number is to be fitted, rcut is the cutoff
distance for including neighbours in the coordination shell,
and cn is the target value of the coordination number.
Example:
coordno 1
3 2.4 6 1000.0
NB This option is intended for use with relax fitting.
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq qreaxff fbond fangle relax reaction

cosh-spring

Type Option
Format cosh-spring <kcal/kjmol>
atom1 k2 d <2 x flags>
Eqn E = k2*d**2*(cosh(r/d) - 1)
Units k2 in eV/Angs*2, d in Angs
Default None
Use Core-shell spring potential with cosh functional form.
Cosh-spring potential does not need cutoffs as the maximum is set by cuts
and the minimum is zero.
Only atom1 needs to be specified as this potential is specifically
for core shell pairs. Atom1 can be given either by atomic number
or symbol which in the latter case can be followed by a species
type. If no species type is given then type is assumed to be core.
See also spring

cosmoframe

Type Option
Format cosmoframe
M(1,1) M(2,1) M(3,1)
M(1,2) M(2,2) M(3,2)
M(1,3) M(2,3) M(3,3)
Units none
Default Current local frame
Use Specifies the local frame for the system as used in a
previous run so that a job can be restarted consistently.
See also cosmo

cosmoshape

Type Option
Format cosmoshape <octahedron/dodecahedron>
Units none
Default octahedron
Use Specifies the basic polyhedron used to construct the SAS
used in COSMO. The original approach used a dodecahedron
but an octahedron is more symmetric.
See also cosmoframe pointsperatom segmentsperatom

coulomb_subtract

Type Option
Format coulomb_subtract <intra/inter> <bond/x12/x13/x14/o14/g14> <scale14>
atom1 atom2 <scale> <rmin> rmax <flag>
Units rmin and rmax in Angs, scale in fractional
Default scale = 1.0
Use Coulomb subtraction potential only
Coulomb potential does not need Coulomb offset
when acting as a core-shell spring, see cuts
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = - scale*qi.qj/rij
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction - this can also be achieved through the command molmec.
o14 => only act between atoms which are 1-4, i.e. separated by
3 bonds
When specified as bonded potential cutoffs are omitted from input.
See also molmec 3coulomb

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.
See also element

covexp

Type Option
Format covexp <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 D a r0 <rmin> rmax <3*flags>
Units D in eV, a in Angs**-1, r0, rmin and rmax in Angs
Default none
Use Covalent-exponential potential form (see Phys. Rev. B, 60, 7234 (1999))
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = -D*exp(-a*(r-r0)**2/(2r))
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.

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 is incremented by <stepsize>. If the optimisation
is stuck in a local minimum then if stepsize non-zero tournament is reset
to <initial>.
See also genetic anneal tpxo

cstrain

Type Option
Format cstrain strain_1 <strain_2> ... <strain_6>
Units None
Default 0.0
Use Specifies the initial strains to be applied to the unit cell.
The number of expected input values depends on the dimensionality of
the system:
3-D => 6 strains (1=xx,2=yy,3=zz,4=yz,5=xz,6=xy)
2-D => 3 strains (1=xx,2=yy,3=xy)
1-D => 1 strain (1=xx)
NB: These values are only used if strain is specified as a keyword.
See also strain cell vectors ocell scan_cell

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

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

cutmany

Type Option
Format cutp cutoff_scale_factor
Units Fractional
Default 0.5
Use Manybody calculations with EAM and MEAM can be accelerated when
second derivatives are being used in optimisation by reducing the
cutoff for cross-terms that only contribute to Hessian matrix but
not the energy or first derivatives. This scale factor can be used
to choose the balance between being exact (1.0) and fast (0.0).
Usually a good local approximation to the Hessian is sufficient
and so fractions much less than 1 can still converge quickly while
speed ups of an order of magnitude can be obtained.
See also cutp cuts manybody

cutp

Type Option
Format cutp cutoff_distance <polynomial/cosine/voter/exponential/mdf/p7> <taper_range> <angs/au>
Units Angstrom (default) or au
Default Use individual potential values / polynomial
Use Maximum interatomic potential cutoff if less than individual value
This can be optionally followed by a taper range. If this is set
to a non-zero value then all short range potentials are tapered
smoothly to zero over this range such that the energy, first and
second derivatives remain continuous. This facility is particularly
useful for MD where discontinuities can lead to drift in the energy/
temperature. Note that tapering does not apply to Coulomb subtracts,
Stillinger-Weber potentials (as these go to zero at the cut-off any
way) and spline potentials (which can be constructed to go to zero
as well). The types of taper that can be used are:
polynominal => 5th order polynomial
p7 => 7th order polynomial over whole range (as per ReaxFF)
cosine => cosine function
exponential => exponential function - see below
voter => form suggested by Voter - see below
mdf => form suggested by Mei-Davenport-Fernando - see below
The form of the Voter taper is:
E_smooth(r) = E(r) - E(rcut) + (rcut/m)*(1 - (r/rcut)**m)*(dE(rcut)/dR)
The form of the exponential taper is:
E_smooth(r) = E(r)*f_cut(r)
where f_cut(r) = exp(-1/(rcut-r)) for r < rcut and = 0 for r >= rcut
Note that in the case of the Voter, exponential and p7 tapers there is
no taper range since it applies over the whole range.
The form of the MDF (Mei-Davenport-Fernando) taper is:
E_smooth(r) = E(r)*f_cut(r)
where f_cut(r) = 1.0 for r < r_m and = 0 for r >= rcut.
In between it takes the value f_cut(r) = ((1 - x)**3)*(1+3x+6x**2), where
x = (r-r_m)/(rcut-r_m). Here r_m is the start of the taper range.
See also cutmany cuts

cuts

Type Option
Format cuts cutoff_distance <angs/au>
Units Angstrom (default) or au
Default 0.8 Angstroms
Use Core-shell cutoff distance - should be set to be the same as the
maximum core-shell harmonic distance. If spring potential is used
then cutoff is set equal to cuts to avoid errors.
See also cutp cutmany

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
young poisson bornq weight

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

cwolf

Type Option
Format cwolf <eta> <rmax>
Units eta in inverse Angstroms and rmax in Angstroms
Default none
Use The particle - particle Coulomb interaction matrix for
the COSMO/COSMIC method is determined using the Wolf
sum in real space. This option controls the eta value
and cutoff for this summation. Small eta and large
cutoff leads to convergence towards the Ewald / Parry
result for periodic systems.
See also cosmo cosmic pureQ

damped_dispersion

Type Option
Format damped <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 C6 C8 C10 <b6> <b8> <b10> <rmin> rmax <6*flags>
Units C6 in eV*Angs**6, C8 in eV*Angs**8, C10 in eV*Angs**10
b6, b8 and b10 in Angs**-1
Default C8=0, C10=0, b6=0, b8=0, b10=0
Use Specifies potential parameters for damped dispersion potential
form of Tang and Toennies (J. Chem. Phys. 80, 3726 (1984)).
If the coefficients b6 and b8 are zero then the potential is
undamped. The functional form is:
E = -(C6/r**6)*f6(r) -(C8/r**8)*f8(r) -(C10/r**10)*f10(r)
where f2n(r) is given by:
f2n(r) = 1 - { sum(k=0->2n) [(b*r)**k]/k!} * exp(-b*r)
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
Note that this potential cannot yet be used with the c6 keyword.
See also grimme_c6 becke_johnson_c6

default_weight

Type Option
Format default_weight <type> weight
where type is one of angle, bond, cell_length, cell_angle, coord, radius,
dipole, elastic, energy, dielectric, frac, freq, grad, modulus, stress, qtn
Units None
Use Changes the default weights for the structure or properties.
The following are the types of weights that can be changed and
their default values:
angle angle observable 1.0
bond bond length observable 1.0
cell_length cell parameter weight in relax fit 1000.0
cell_angle cell parameter weight in relax fit 1000.0
coord Cartesian coordinate weight (0-2-D) 1000.0
dipole dipole moment 10.0
elastic elastic constant tensor component 0.01
energy energy (absolute or reaction) 1.0
frac fractional coordinate in relax fit (3-D) 10000.0
freq vibrational frequency or phonon mode 1.0
grad gradient in a conventional fit 1.0
modulus bulk or Young's modulus 1.0
qtn gradient on a quaternion 1.0
radius atom radius 1000.0
stress stress value in conventional fit 1.0
See also weight

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

delay_field

Type Option
Format delay_field value <s/ns/ps/fs>
Units s, ns, ps or fs - default is time in picoseconds.
Default 0.0
Use Specifies a delay time before any time-dependent field is
applied to the simulation. Can be used to prevent the
field being applied during equilibration.
See also md production sample write temperature timestep
tscale nolist equilibration external_force
td_external_force end_force td_field field end_field

delay_force

Type Option
Format delay_force value <s/ns/ps/fs>
Units s, ns, ps or fs - default is time in picoseconds.
Default 0.0
Use Specifies a delay time before any external force is
applied to the simulation. Can be used to prevent the
force being applied during equilibration.
See also md production sample write temperature timestep
tscale nolist equilibration external_force
td_external_force end_force

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.

delta

Type Option
Format delta <fit> <real value>
Units fractional
Default 0.00001 for ordinary fitting / 0.0001 for relax fitting
Use Differencing interval used in numerical procedures.
One delta value is possible according to the sub-option word
supplied. This value corresponds to the differencing interval
for gradients during fitting (fit). Previously values were
also possible in connection with free energy minimisation.
However, these are no long needed with analytical derivatives.

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.
NB: The attachment energy cannot currently be computed if using KIM models.
See also sfractional cartesian

dielectric_constant

Type Option
Format dielectric_constant value
Default 1.0
Units None
Use Specifies the dielectric constant for Coulomb interactions between charged
particles.
NB: This should usually just be equal to 1 unless using a coarse-grained model.
NNB: This option is NOT compatible with Mott-Littleton calculations (defect).
See also ewaldrealradius qwolf accuracy rspeed screened_coulomb dipole

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

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 calculated.
Examples:
dispersion 2 20
0.0 0.0 0.0 to 0.5 0.5 0.5 to 0.5 0.0 0.0
0.5 0.0 0.0 to 0.5 0.5 0.0
This would produce two plots, the first containing two parts
and the second only one. Both plots would contain a total of
20 k points.
If this is a 2-D system then there are only x and y components:
dispersion 2 20
0.0 0.0 to 0.5 0.5 to 0.5 0.0
0.5 0.0 to 0.5 0.5
Similarly for a 1-D system then there is only the x components:
dispersion 1 20
0.0 to 0.5
See also phonon shrink kpoints box kfull

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.

dmaximum

Type Option
Format dmaximum <x> <y> <z>
Default 0.0
Use Part of genetic options section. Specifies the maximum value
used as a default in genetic optimisation. According to the
dimensionality the arguments supplied should be:
2-D => z
1-D => y & z
0-D => x & y & z
By specifying a maximum value, this allows GAs to be used for
non-3D systems.
See also genetic

dminimum

Type Option
Format dminimum <x> <y> <z>
Default 0.0
Use Part of genetic options section. Specifies the minimum value
used as a default in genetic optimisation. According to the
dimensionality the arguments supplied should be:
2-D => z
1-D => y & z
0-D => x & y & z
By specifying a minimum value, this allows GAs to be used for
non-3D systems.
See also genetic

dump

Type Option
Format dump <every <n> noover> <old> <channel> <cart> <connectivity> <generated> <filename a20>
Default no dumpfile, n=1 if every is given
Use Generates dumpfile after fitting or optimisation.
File is created on fortran channel 12. To change, specify either
another channel number or a filename. If "every" is specified
then a dumpfile will be written after every n cycles of fitting
or optimisation. If "noover" is also specified then the dumpfile won't be
overwritten every write, but labelled with a unique number.
If "connectivity" is specified then the connectivity list will be
written to the dump file. Note that this will only be done for the
current configuration.
If "generated" is specified then this will force the dumping of explicit
potentials generated by automated rules (e.g. using uff1).
If "old" is used then the line length for restarts is restricted to 80
characters for backward compatibility.
NB: Although the filename can be anything you like it is proposed that
the conventional extension be .grs (.res was being used but this
conflicts with other software).
NNB: During Monte Carlo and Molecular Dynamics calculations the use of
a small value for the frequency of dumping may significantly lower the
speed of the calculation.

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 unscaled function of the density.
See also manybody eam_functional eam_density scmaxsearch

eam_density

Type option
Format eam_density <power n/fpower/exponential n/gaussian n/cubic/quadratic/quartic/voter/glue/evoter/mei-davenport/baskes/vbo/spline>
atom1 <atom2> C (power law) <1 x flag >
atom1 <atom2> C rn (fractional power law) <2 x flag >
atom1 <atom2> A B r0 (exponential) <3 x flags>
atom1 <atom2> A B r0 (gaussian) <3 x flags>
atom1 <atom2> A r0 (quadratic) <2 x flags>
atom1 <atom2> A r0 (cubic) <2 x flags>
atom1 <atom2> A r0 (quartic) <2 x flags>
atom1 <atom2> A beta (voter) <2 x flags>
atom1 <atom2> A beta (evoter) <2 x flags>
atom1 <atom2> c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags>
atom1 <atom2> r1 r2 rm (glue)
b1_3 b1_2 b1_1 b1_0
b2_3 b2_2 b2_1 b2_0
b3_3 b3_2 b3_1 b3_0
atom1 <atom2> A beta r0 (baskes) <3 x flags>
atom1 <atom2> c sigma gamma r0 delta (vbo) <5 x flags>
atom1 <atom2> A B C D rmin r0 (spline) <4 x flags>
atom1 <atom2> A B r0 (morse2) <3 x flags>
Units Distances are in Angstrom
Use Specifies the density due to a given atom1 at another
atomic centre (atom2) in the Embedded Atom Model (EAM).
This density is only calculated for pairs of atoms
where the "manybody" potential has been specified
so that the user can control which atoms are part
of the EAM.
Where no atom2 is specified then the density is applied to
all atoms allowed by the manybody potential, regardless of
species type.
The density can take one of several functional forms:
Power Law:
rho(i) = C*rij**(-n)
e.g. eam_density power 6
Ni core 729.7
Fractional power Law:
rho(i) = C*rij**(-rn)
e.g. eam_density fpower
Ni core 729.7 6.1
Exponential:
rho(i) = A*(rij**n)*exp(-B(rij-r0))
e.g. eam_density exponential 0
Ni core 500.0 4.0 3.52
Gaussian:
rho(i) = A*(rij**n)*exp(-B(rij-r0)**2)
e.g. eam_density gaussian 2
Ni core 400.0 3.0 3.52
Quadratic:
rho(i) = A*(rij-r0)**2 if r < r0, else = 0
Cubic:
rho(i) = A*(rij-r0)**3 if r < r0, else = 0
Quartic:
rho(i) = A*(rij-r0)**4 if r < r0, else = 0
Voter:
rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))
eVoter:
rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))*exp(-1/(rmax - r))
Mei-Davenport:
rho(i) = sum(l=0->5) (c_l/12)*(r/r0)**l
In the above, rmax is the cutoff for the potential from the manybody
option that controls the range of the density.
Glue:
if r < r1
rho(i) = b1_3*(r-r1)**3 + b1_2*(r-r1)**2 + b1_1*(r-r1) + b1_0
if r1 =< r < r2
rho(i) = b2_3*(r-r2)**3 + b2_2*(r-r2)**2 + b2_1*(r-r2) + b2_0
if r2 =< r < rm
rho(i) = b3_3*(r-rm)**3 + b3_2*(r-rm)**2 + b3_1*(r-rm) + b3_0
Note that the cut-offs are set by the manybody potential except
for the glue model where the maximum cutoff, rm, is a parameter
of the model.
Baskes:
rho(i) = A*exp(-beta((rij/r0)-1))
VBO:
rho(i) = c*sigma*N*exp(-gamma/(1 - sqrt(r/delta)))
where N is a normalisation constant given by:
N = exp(gamma/(1 - sqrt(r0/delta)))
Spline: This is effectively one piece of a cubic spline.
rho(i) = A*(rij-r0)**3 + B*(rij-r0)**2 + C*(rij-r0) + D if rmin < r < r0, else = 0
Morse2: (squared morse)
rho(i) = (A*((1 - exp(-B*(rij-r0)))**2 - 1))**2
e.g. eam_density morse2
Ni core 2.3 1.35 2.22
See also manybody eam_functional scmaxsearch eam_alloy prt_eam meam_density

eam_functional

Type option
Format eam_functional <square_root> <power n> <banerjea_smith n> <johnson/glue/foiles/mei-davenport/baskes/vbo/igarashi/spline/numeric>
if square_root or power :
atom1 A_1 <flag>
atom2 A_2 <flag> etc...
if banerjea_smith :
atom1 F0_1 F1_1 rho0_1 <3*flags>
atom2 F0_2 F1_2 rho0_2 <3*flags> etc...
if johnson :
atom1 F0_1 F1_1 rho0_1 alpha beta gamma <6*flags>
atom2 F0_2 F1_2 rho0_2 alpha beta gamma <6*flags> etc...
if glue :
atom1 rho1 rho2
c1_4 c1_3 c1_2 c1_1 c1_0
c2_4 c2_3 c2_2 c2_1 c2_0
c3_3 c3_2 c3_1 c3_0
atom2 rho1 rho2
c1_4 c1_3 c1_2 c1_1 c1_0
c2_4 c2_3 c2_2 c2_1 c2_0
c3_3 c3_2 c3_1 c3_0
if foiles :
atom1 F0_1 F1_1 F2_1 F3_1 <4*flags>
atom2 F0_2 F1_2 F2_2 F3_2 <4*flags> etc...
if mei-davenport :
atom1 Ec_1 alpha_1 beta_1 gamma_1 delta_1 phi0_1 s_1_1 s_2_1 s_3_1 <9*flags>
atom2 Ec_2 alpha_2 beta_2 gamma_2 delta_2 phi0_1 s_1_2 s_2_2 s_3_2 <9*flags> etc...
if baskes :
atom1 Ec_1 A_1 rho0_1 <2*flags>
atom2 Ec_2 A_2 rho0_2 <2*flags> etc...
if vbo :
atom1 A_1 rn_1 <2*flags>
atom2 A_2 rn_2 <2*flags> etc...
if igarashi :
atom1 A_1 B_1 <2*flags>
atom2 A_2 B_2 <2*flags> etc...
if spline :
atom1 A_1 B_1 C_1 D_1 rho0_1 rho_max_1 <4 x flags>
atom2 A_2 B_2 C_2 D_2 rho0_2 rho_max_2 <4 x flags>
if numeric :
atom1 filename
Units A, B, C, D, AE0, F0, Ec, phi0 and F1 in eV, rho0/rho_max//alpha/beta/gamma/rn are dimensionless
Default square_root, A = 1.0
Use specifies how the total energy contribution of an atom
in the Embedded Atom Model depends on the density at that
site. The current possibilities are:
Square_root:
E = - sum(i) A(i)*(rho(i))**1/2
this is the most common functional, as used in the Sutton-Chen potential
Power:
E = - sum(i) A(i)*(rho(i))**1/n
this is just a generalisation of the above case
VBO:
E = - sum(i) A(i)*(rho(i))**rn
this is a further generalisation of the power case
Banerjea_smith:
E = - sum(i) F0 [1-ln(r)/n]*r**1/n + F1*r
where r = rho(i)/rho0(i)
this is the functional of Banerjea and Smith (Phys. Rev. B,
37, 6632 (1988)) - note that in this case that are atom
dependent parameters also to be specified (F0, F1, rho0)
where rho0 is the electron density at equilibrium.
Johnson:
E = - sum(i) F0 [1-ln(x)]*x + F1*y
where x = (rho(i)/rho0(i))**(alpha/beta)
and y = (rho(i)/rho0(i))**(gamma/beta)
this functional is similar to that of Banerjea & Smith and is due
to Johnson (PRB, 39, 12554 (1989)).
Glue:
if rho < rho1
E = c1_4*(rho-rho1)**4 + c1_3*(rho-rho1)**3 + c1_2*(rho-rho1)**2 +
c1_1*(rho-rho1) + c1_0
if rho1 =< rho < rho2
E = c2_4*(rho-rho2)**4 + c2_3*(rho-rho2)**3 + c2_2*(rho-rho2)**2 +
c2_1*(rho-rho2) + c2_0
if rho2 =< rho
E = c3_3*(rho-rho2)**3 + c3_2*(rho-rho2)**2 + c3_1*(rho-rho2) + c3_0
this is the functional from Ercolessi et al, Phil. Mag. A, 58, 213 (1988).
NB: At present there are no fitting parameters since there are constraints
on the coefficients to ensure a smooth and continuous function.
Foiles:
E = sum(i) F0*rho(i)**2 + F1*rho(i) + F2*(rho(i)**(5/3)/(F3 + rho(i)))
Mei-Davenport:
E = sum(i) - Ec*[1-(alpha/beta)*ln(rho(i))]*rho(i)**(alpha/beta) +
sum(m=1->3) 0.5*phi0*s_m*exp(-(sqrt(m)-1)*gamma)*
[1+(sqrt(m)-1)*delta-sqrt(m)*delta*ln(rho(i))/beta]*
rho(i)**(sqrt(m)*gamma/beta)
Baskes:
E = - sum(i) AE0*x*ln(x)
where x = (rho(i)/rho0(i))
this functional is similar to that of Banerjea & Smith and Johnson, but
is simplified to enable the parameters from the MEAM paper of Baskes to
be input directly. AE0 is the combination of E0 and A from the above paper.
Igarashi:
E = - sum(i) A(i)*(rho(i)*(1 + B(i)*rho(i))**1/2
this functional form was proposed in Igarashi et al, Phil. Mag. B, 63,
603 (1991).
Spline:
if rho_max > rho > rho0:
E = - sum(i) [A(i)*(rho(i)-rho0)**3 + B(i)*(rho(i)-rho0)**2 + C(i)*(rho(i)-rho0) + D(i)]
else
E = 0
Numeric:
If this sub-option is specified then the EAM functional is read from a numeric tabulation
in an external file. This file is in the "funcfl" format from ParaDyn / DYNAMO 86.
See also eam_density manybody scmaxsearch eam_alloy prt_eam

eam_potential_shift

Type Option
Format eam_potential_shift <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <ener/grad> <kjmol/kcal/au> <scale14>
atom1 atom2 g beta <rmin> rmax <2*flags>
Units beta is in inverse Angstroms, g is nominally unit less as it is multiplied
by a conversion constant to place it in eV
Default None
Use Specifies a two-body shift of the EAM potential energy component based on
the functional form of the Voter-Chen density. Needed to work with the
embedding potential in the format used by Paradyn.
The form of the potential is
E = 2.0*g*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also manybody eam_functional eam_density

edip_accuracy

Type Option
Format edip_accuracy accuracy1 accuracy2
Units None
Default accuracy1 = 0.000001, accuracy2 = 0.0000000001
Use Controls the truncation of the exponential terms in the interaction energies of
EDIP. The parameter accuracy1 controls where the taper starts, while accuracy2
controls where the taper ends. Therefore accuracy1 must be greater than accuracy2.
Although no taper is formally required, this option can reduce the cost of EDIP
with negligible effect on the accuracy.
See also edip_coordination edip_twobody edip_threebody edip_zmax fastfd

edip_coordination

Type Option
Format edip_coordination
species <core/shell> alpha flow fhigh <1 x flag>
or
edip_coordination pi
species <core/shell> alpha flow fhigh Zdih Zrep c0 plow phigh <4 x flags>
Units flow, fhigh, plow, phigh, c0 in Angstroms
Default None
Use Specifies the parameters for the EDIP model coordination number. In the simplest
form the coordination number is just a spherical term that is given by:
Z = sum f(r_ij)
where f(r_ij) = 1 if r < flow, 0 if r > fhigh, and inbetween it is given by
exp(alpha/(1-r_ij**-3)).
If "pi" is specified as a sub-option then contributions for pi bonding are added.
See also edip_twobody edip_threebody edip_zmax edip_accuracy fastfd

edip_threebody

Type Option
Format edip_threebody
species1 <core/shel> species2 <core/shel> species3 <core/shell> &
lambda0 lambda' Z0 gamma gamma' q <6 x flags>
or
edip_threebody modified
species1 <core/shel> species2 <core/shel> species3 <core/shell> &
lambda0 lambda' Z0 gamma gamma' q kq <7 x flags>
or
edip_threebody original
species1 <core/shel> species2 <core/shel> species3 <core/shell> &
lambda mu eta gamma gamma' q <6 x flags>
Default None
Use Specifies the parameters for the EDIP model threebody contribution.
Here the default form is that of Nigel Marks, whereas the original
form follows the paper of Justo et al, PRB, 58, 2539 (1998).
NB: Here the convention of N.A. Marks, J. Phys. Cond. Matter, 14,
2901-2927 (2002) is followed, where lambda0 = lambda0*gammap**2/q
relative to the form in the earlier PRB, 63, 035401 (2000) paper.
Note that the implementation here (optionally) includes a small modification
that is not described in the papers in that there is an extra
parameter, kq that can be included. When Zi < 2 then the form of h changes to be
kq*(1 + cos(theta)) and so the extra value of kq is input.
See also edip_twobody edip_coordination edip_zmax edip_accuracy fastfd

edip_twobody

Type Option
Format edip_twobody
species1 <core/shel> species2 <core/shel> epsilon B p beta sigma a a' <7 x flags>
Default None
Use Specifies the parameters for the EDIP model twobody contribution.
The functional form of the term is:
U2(r,Z) = epsilon*[(B/r)**p - exp(-beta*Z**2)].exp(sigma/(r - a -a'*Z))
NB In earlier versions the power p was not explicit given as it defaulted to the
value used by Marks for carbon of 4 (Phys. Rev. B, 63, 035401 (2000)). Now the
code has been generalised so that a value can be input.
See also edip_coordination edip_threebody edip_zmax edip_accuracy fastfd

edip_zmax

Type Option
Format edip_zmax Zmax
Units None
Default 6.0
Use In the EDIP method, the interactions are truncated according to the following term;
exp(sigma/(r - a - a'*Z))
where a and a' are parameters. Here the cut-off is dependent on the coordination
number, Z. While GULP iteratively tries to ensure that all atoms are found in the
neighbour list based on the current cut-off, the Z value is approximated by the
uncorrected value (i.e. no torsional corrections). In cases where discontinuities
are found (should be rare) then the value of Zmax should be increased manually.
See also edip_coordination edip_twobody edip_threebody edip_accuracy fastfd

einstein

Type Option
Format einstein <cart>
atomnumber x0 y0 z0 k
Units x0/y0/z0 in fractional for periodic directions and Cartesian for
non-periodic, unless "cart" specified, in which case all are
Cartesian in 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.
E = (1/2)*k*[(x-x0)**2 + (y-y0)**2 + (z-z0)**2]
Note: This option must be used with a fixed unit cell.
See also plane_lj

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 young poisson ceigen

electronegativity

Type Option
Format electronegativity
<Atomic_symbol/atomic_number> chi <mu> <Q0> <E0> <2 x flags for fitting>
or
electronegativity <qrange/qmin/qmax>
<Atomic_symbol/atomic_number> chi <mu> <Q0> <E0> <qmin> <qmax> <2 x flags for fitting>
Units Chi, mu, and E0 in eV, Q0, qmin, qmax in a.u.
Default Q0 = 0.0, E0 = 0.0
Use Allows the user to specify the parameters needed for the
electronegativity equalisation method for determining
charges. Note that if the flags are not specified they
are assumed to be zero.
Q0 is the charge about which the electronegativity equations
are quadratic. In most methods this is zero, but need not be.
For example, the EQeq method assigns values of Q0 not equal
to zero.
E0 is an additive constant for the energy of an atom. This is
only really needed when using multiple q ranges to ensure
energy matching.
The sub-options qrange, qmin, and qmax control whether the
values apply for a given value of charge. By default the values
apply to all values of charge (q). If qmin is specified then
they are only applied to charges larger than qmin, while if qmax
is given the they are applied when q is less than qmax. When
qrange is specified then the values apply for qmin =< q < qmax.
NB: If no parameters are input then the default values will be
used for all charge values. However, if parameters are input
then this will override the default values and the user must
set parameters for all relevant ranges of charge.
See also eem qelectronegativity smelectronegativity noqeem external_potential
eembond

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 nmr spin

end_field

Type Option
Format end_field value <s/ns/ps/fs>
Units s, ns, ps or fs - default is time in picoseconds.
Default 0.0
Use Specifies an end time for any time-dependent field
applied to the simulation. Can be used to stop the
field being applied.
See also md production sample write temperature timestep
tscale nolist equilibration external_force
td_external_force end_force td_field field delay_field

end_force

Type Option
Format end_force value <s/ns/ps/fs>
Units s, ns, ps or fs - default is time in picoseconds.
Default 0.0
Use Specifies a time after which any external force is
removed from the simulation.
See also md production sample write temperature timestep
tscale nolist equilibration external_force
td_external_force delay_force

energy

Type Option
Format energy_of_configuration <ev/kcal/au/kjmol-1> <weight>
Default energy in eV, weight = 1.0
Use Subsection of observables, assigns energy to successive
configurations for fitting.
See also fenergy

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 Nose-Hoover
thermostat parameter must also be given. It is important
to choose a suitable value such that the temperature
fluctuations are minimised. For constant pressure,
variable cell shape MD, the NPT ensemble can be used
(keyword "conp" must be present). In this case it is
necessary to supply the thermostat parameter and the
barostat parameter. Both again need tuning to get the
best performance for each system. NPT ensemble is
implemented as a modified Nose-Hoover form based on
Melchionna et al., Mol. Phys. 78 (1993) 533.
See also md integrator tau_barostat tau_thermostat

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
young poisson bornq weight

epsilon/sigma

Type Option
Format epsilon <kcal/kjmol> <mm3> <bond/x12/x13/x14/mol/o14/g14>
<Atomic_symbol/atomic_number> epsilon sigma <2 x flags for fitting>
Units epsilon in eV and sigma in Angstroms
Use Specifies epsilon and sigma values for each species type to be
used in combination rules to obtain Lennard-Jones potential
parameters where specified.
If the sub-option "mm3" is specified then the epsilon and sigma values
are applied to mm3buck potentials rather than Lennard-Jones.
If one of the bonding related sub-options is specified then the epsilon
and sigma values are only applied to potentials with a matching bonding
specification. An example of where this is needed is CHARMM, which has
different values for 1-4 interactions as opposed to general VDW terms.
See also lennard atomab mm3buck

equatorial

Type Option
Format equatorial <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K n beta r0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3)
<rmin(2-3)> rmax(2-3) <3*flag>
Units K in eV, r0, rmin and rmax in Angstroms and beta in inverse Angstroms
Default none
Use ESFF equatorial three-body form :
E(three) = (2K/n**2) * (1 - cos(n*theta)) + 2K*exp(-beta*(r13 - r0))
Here r13 is the distance between the atoms 1-3 in the triad.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2, 2-3 and 1-3 are bonded.
See also axilrod-teller angle stillinger-weber exponential bcross
urey-bradley murrell-mottram bacross three hydrogen-bond
lin3 uff3 3coulomb bagcross ppp3body

equilibration

Type Option
Format equilibration value <s/ns/ps/fs>
Units s, ns, ps or fs - if integer, then value is by default
a multiple of the timestep or if non-integer then by
default is the time in picoseconds.
Use Specifies the simulation time to be spent equilibrating
the kinetic and potential energy distributions prior to
the production phase of the molecular dynamics run.
See also md production sample write temperature timestep
tscale nolist delay_force end_force momentum_correct

erferfc

Type Option
Format erferfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond>
atom1 atom2 A alpha beta <rmin> rmax <3 x flags>
Units A in eV, alpha and beta in Angs
Default none
Use Specifies the parameters of an erferfc potential, which has the form:
E_ij = A.erf(r/alpha).erfc(r/beta)/r
See also qerfc reperfc erfpot

erfpot

Type Option
Format erfpot <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond>
atom1 atom2 A alpha <rmin> rmax <2 x flags>
Units A in eV, alpha in Angs
Default none
Use Specifies the parameters of an erf potential, which has the form:
E_ij = A.erf(r/alpha)/r
See also qerfc reperfc erfpot

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 keyword include

ewaldrealradius

Type Option
Format ewaldrealradius value
Default none
Use Normally the Ewald sum real and reciprocal space radii are chosen
automatically to minimise the number of terms, subject to the value
of the rspeed parameter. However, when using the spatial algorithm
it is advantageous to control the real space extent of the Ewald
sum to ensure that the system can be decomposed into sufficent regions.
The value specified fixes the real space cut-off and the reciprocal
space cut-off is calculated in order to achieve the target accuracy
given by the accuracy option.
See also noexclude qwolf rspeed accuracy veck index_k dielectric_constant

exp2

Type Option
Format exp2 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K rho2 r12_0 rho3 r13_0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3)
<rmin(2-3)> rmax(2-3) <5*flags>
Units K in eV, rho2/3 in Angstroms**-1, r12_0/r13_0/rmin/rmax in Angstroms
Use Exponentially decaying three-body potential with 2 exponentials only:
E(three) = K*exp(-rho2*(r12-r12_0)).exp(-rho3*(r13-r13_0))
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2, 2-3 and 1-3 are bonded.
See also three-body angle axilrod-teller stillinger-weber bcross urey-bradley
murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb
exponential bagcross j3

exponential_three_body

Type Option
Format exponential <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K rho1 rho2 rho3 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3)
<rmin(2-3)> rmax(2-3) <4*flags>
Units K in eV, rho1/2/3 in Angstroms**-1
Use Exponentially decaying three-body potential:
E(three) = K * exp(-rho1*r12).exp(-rho2*r13).exp(-rho3*r23)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2, 2-3 and 1-3 are bonded.
See also three-body angle axilrod-teller stillinger-weber bcross urey-bradley
murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb
exp2 bagcross j3 ppp3body

exppowers

Type Option
Format exppowers <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 A B0 B1 B2 B3 <rmin> rmax <4*flags>
Units A in eV, B0 in appropriate power of Angstroms
Default none
Use Exp-powers potential - this potential has multiple powers of r in the
exponential form.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A.exp(B0 + B1*r + B2*r**2 + B3*r**3)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also buckingham

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:
external_force
1 0.2 0.0 0.0
3 -0.2 0.0 0.0
See also td_external_force

external_potential

Type Option
Format external_potential
atomnumber V
Units V in eV/a.u.
Default 0.0 for all atoms and components
Use Specifies a constant external potential for the atoms specified.
Note that the atom number refers to the asymmetric unit and
that the user must ensure that the potential doesn't violate the
symmetry of the system. NB: Because the potential doesn't depend
on the geometry this option is not recommend for runs that involve
optimisation or use energy derivatives. The main use is intended
to be for QM/MM coupling with charge equilibration schemes.
Example:
potential
1 0.4
3 -0.1
See also eem qeq sm

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

factor

Type Option
Format factor theta
Default theta=0.9
Use Temperature reduction factor. A larger factor implies a faster
decay of simulated temperature.

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 j-i-k).
NB For periodic systems the nearest image is taken.
Example:
fangle 1
1 2 3 109.54
NB This option is intended for use with relax fitting.
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq qreaxff fbond relax reaction

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 relax fitting.
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq qreaxff fangle relax reaction

fc_supercell

Type Option
Format fc_supercell na nb nc
Default na = nb = nc = 0
Use Build force constants separately for cells beyond the standard
unit cell. The number of cells either side of the central one
is given by na, nb and nc in the respective directions. This will
lead to a total of (2*na + 1)*(2*nb + 1)*(2*nc + 1) cells.
The default algorithm for phonon calculations in gulp is to compute
analytic force constants for each k point without storing force
constants between k points. This option triggers GULP to use an
alternative approach in which the unphased force constants are
calculated for images of the central cell and stored separately.
These are then later used to generate phonons as a function of k
vector. This algorithm is potentially less expensive in CPU time
than the default, but has the potential to use a lot more memory.
This algorithm is particularly useful for force fields where
analytical second derivatives are not yet available.
NB: For some neighbour list based forces (usually bondorder, EDIP,
ReaxFF) the finite difference calculation of force constants can
contain errors where images of an atom have a non-zero interaction
with each other. In such cases, the solution is run with a supercell
specified and the ghostcell keyword that tells the code to compute
the force constants for the supercell, but to construct the phonons
as though they were for the original smaller cell.
See also kpoints dispersion shrink eigenvectors lower_symmetry
project_dos output nozeropt gamma_direction_of_approach omega
dynamical_matrix meanke frequencies eckart box phonon
numerical msd ghostcell ghost_supercell threshold

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 synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
rfractional ffractional rcell fcell neb fvectors

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 synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional rcell neb fvectors

fenergy

Type Option
Format free_energy_of_configuration <ev/kcal/au/kjmol-1> <weight>
Default free_energy in eV, weight = 1.0
Use Subsection of observables, assigns free energy to successive
configurations for fitting.
See also energy

fermi-dirac

Type Option
Format fermi-dirac <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond>
atom1 atom2 a b r0 <rmin> rmax <3 x flags>
Units a in eV, b in Angs-1, r0 in Angs
Default none
Use Fermi-Dirac potential - optimisation flags for fitting.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = a/(1+exp(b(r-r0)))
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.

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 synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional rcell fcell neb fvectors

field

Type Option
Format field magnitude <direction>
Units eV/(Ang.a.u.)
Use Applies an electric field to a system, usually in a non-periodic direction.
Consequently, this option should really only be used for molecules, polymers and
surfaces. The specification of the direction can either be given by the
relevant axis (z, for a surface; y or z for a polymer; x, y or z for a
molecule) or in the case of a 0-D system a general vector may be specified
as 3 numbers in Cartesian space. Examples of valid input lines are:
Surface:
field 1.5 z
Polymer:
field 1.5 y
Molecule:
field 1.5 x
OR
field 1.5 0.2 0.3 0.4
If the direction is not specified then the default is to apply the
field along the z axis.
The possibility of applying an electric field within 3-D boundary
conditions is also allowed for, in which case the field direction
can also be set using a cell vector (a, b or c), as well as by a
fractional or Cartesian vector:
field 1.5 b
field 1.5 0.2 0.3 0.4
field 1.5 cart 0.2 0.3 0.4
NB Be very careful if you do use 3-D boundary conditions as there
are many things that can go wrong and the physical interpretation
is complex since the Ewald sum will counter any induced dipole.
Unless you really know what you are doing, it is very strongly
suggested that you only apply an electric field in a non-periodic
direction. You should definite use the "nomod" keyword when working
with 3-D systems and an electric field.
NB: Symmetry will be automatically turned off if this option is used
for solids as the field will break the symmetry of the space group.
Because the absolute energy is undefined, the energy relative to the
initial state is used during minimisations. Note also that only one
field can be defined per configuration.
NB: You must fix at least one atom in the direction of field application
otherwise the energy will head asymptotically for minus infinity!!!
The units of the electric field are eV/Ang per unit charge in atomic units.
This means an ion of charge +1.0 will experience a force equal to the electric
field input.
NB: The use of an electric field is presently incompatible with the ReaxFF model
and analytic second derivatives for other variable charge models.
See also td_field dipole delta_dipole initial_coordinates

finite

Type Option
Format finite <first/second/all> <value>
Default Finite differences not to be used, but 0.0001 / all if finite is given
Units none (fractional)
Use Requests that the first derivatives with respect to the energy (or
free energy if keyword "free" is present) are calculated numerically
by central finite differences. If a value is specified after the
option then this specifies the fractional change to be used as the
step size. Note that if the value is too large then the gradients
will be inaccurate. However, if the value is too small then numerical
noise can lead to inaccuracies as well.
This option is largely only of use for checking analytical derivatives
during debugging and is intended for use with single point calculations.
See also gradients pfinite sfinite

fix_atom

Type Option
Format fix_atom <first/last/centre/none> <atom_no>
Units none
Default first (serial), last (parallel), centre (2-D)
Use When optimising a structure using second derivatives it is necessary
to fix one atom in order to stop translational invariance and prevent
the Hessian matrix from being singular. This option allows the user
to specify which atom is fixed in several ways:
1) Fix the first atom in a structure:
fix_atom first
or
fix_atom 1
This has generally been the default for GULP for most cases.
2) Fix the last atom in a structure:
fix_atom last
This is now the default for parallel second derivatives since it
allows for more efficient generation of the Hessian matrix by allowing
the same block cyclic distribution between the second derivatives and
variables for an otherwise unconstrained system. Note here that last
will fix the last core if shells are present, since fixing a shell
would not make sense in the context of electronic polarisation.
3) Fix the most central atom:
fix_atom centre
Fix the most central atom. For a molecule this would be in the middle,
while for a slab this is an atom furtherest from the surface.
4) Fix a general atom number:
fix_atom 5
Here the atom number is given in the primitive cell
5) Don't fix any atom:
fix_atom none
This does what it says. However, this means that second derivatives should
not be used since the Hessian cannot be inverted.
See also optimise gradient unfix unfreeze

forceconstant

Type Option
Format forceconstant <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <type_of_bond>
atom1 atom2 kL kT <rmin> rmax <2*flag>
Units kL and kT in eV*Angs**-2
Use Force constant potential - includes the force constants between a pair
of atoms, known as the longitudinal (kL) and transverse (kT) force
constants. This is useful for vibrational calculations, but note that
the energy and gradient are likely to be inconsistent.
NB: Don't use this potential in an optimisation since it will go
horribly wrong due to the above!
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
d2E/(da.db) = (kL - kT)*a.b/r^2 + delta_a.b*kT
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also harmonic

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

frequency

Type Option
Format frequency <n>
no. value <kpoint_number> <weight> (x n, on separate lines)
Units cm-1
Use Subsection of observables, used for specifying frequencies for
fitting to. The first number is the position of the mode required
in order of increasing frequency. The third number is optionally
the k point number to fit at with reference to the k point list
for the present configuration.
e.g.
frequency 2
1 0.0
6 902.0 2
See also observables elastic phonon piezoelectric sdlc hfdlc weight mode
frqtol

frqtol

Type Option
Format frqtol value
Units cm-1
Default 0.5 cm-1
Use When checking if there are imaginary modes through the use of the "lower"
keyword, the magnitude of the frequency is checked to see if it is smaller
than this tolerance.
See also observables elastic phonon piezoelectric sdlc hfdlc weight mode
frequency

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 xtol

fvectors

Type Option
Format fvectors <au>
x y z for vector 1 for 3D
x y z for vector 2 for 3D
x y z for vector 3 for 3D
or
x y z for vector 1 for 2D
x y z for vector 2 for 2D
or
x y z for vector 1 for 1D
Units Angstroms
Default None
Use Specifies the final unit cell for the nudged elastic band method
using the cell vectors. The number of vectors must match the
dimensionality of the system.
See also nebspring nebtolerance nodneb synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional rcell neb fcell

g3coulomb

Type Option
Format g3coulomb <intra/inter> <bond> <nbeq/nbne nbond>
atom1 atom2 atom3 A gamma <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 &
<2 x flags>
Units A in a.u., gamma in Ang**3, distances in Angstroms
Default rmin12 = rmin13 = rmin23 = 0.0
Use Coulomb subtraction between atoms that are connected by a three-body term:
E(three) = - A/(rij**3 + gamma)**(1/3)
This potential is useful when subtracting the Coulomb term used in
ReaxFF between fixed charges in order to mix a molecular mechanics
force field with this form of reactive model.
Here the term gamma represents 1/(gammai*gammaj)**3 where the gammai
and gammaj are terms from the ReaxFF force field. The A term is the
product of the two charges, A = q1*q2, in atomic units. The whole
term is then converted internally from units of e2/Ang to eV.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
See also gcoulomb 3coulomb

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

gamma_direction_of_approach

Type Option
Format gamma_direction_of_approach Kx Ky Kz
Units fractional
Default 1.0 1.0 1.0
Use Specifies the direction of approach to the gamma point for the
calculation of the nonanalytic correction to the dynamical
matrix due to the LO/TO splitting resulting from the electric
field in the crystal. This option allows the frequencies to be
calculated for a particular crystal orientation. Only used if
gamma_angular_steps is set to zero. Note that the value is also
ignored if a point is part of a dispersion curve, where the
direction of the curve is taken.
NB: Specification of this direction triggers the calculation of
the non-analytic correction for a single k point.
See also phonon nononanal gamma_angular_steps

gastdamping

Type Option
Format gastdamping <original/fixed/accelerate> damping_factor
Units None
Default damping_factor = 0.5, original
Use Controls the damping procedure during iterative solution
of the Gasteiger scheme. Here the damping factor is the
fraction of the old and new electronativities that are
used to propagate the charges. A small value of the damping
factor implies slow, but stable, convergence whereas a
large value can lead to fast convergence or oscillation.
In the original Gasteiger method the damping factor is
set to 1/2 and raised to the power of the iteration number.
This means that the calculation becomes more damped as it
progresses to guarantee convergence. The option to use
either a fixed damping or accelerated damping is provided.
However, this will yield different results from the original
Gasteiger method.
See also eem gasteiger gastiter qeq gastparam gasttol noqeem
eembond

gastiter

Type Option
Format gastiter maximum_number_iterations
Units None
Default 50
Use Sets the maximum number of iterations that are allowed
during the Gasteiger charge scheme.
See also eem gasteiger gasttol qeq gastparam gastdamping noqeem
eembond

gastparam

Type Option
Format gastparam species A B C <Q0> <4*flags>
Units A is in eV, B in eV/e, C in eV/e^2, Q0 in atomic units
Default As per original paper, Tetrahedron, 36, 3219-3288 (1980), Q0=0
Use Sets a species specific set of parameters for use in a
Gasteiger charge calculation. For example to set the values
for carbon type 4 with A = 7.98, B = 9.18 and C = 1.88, the
input would be:
gastparam C4 7.98 9.18 1.88
Q0 is the initial charge for the species, which is usually
zero. Note that the Gasteiger algorithm is designed to guarantee
convergence, but to a state that depends on the initial
charges and so Q0 is used to initialise each charge solution
rather than the values from the previous iteration.
See also eem gasteiger gasttol qeq gastiter gastdamping noqeem
eembond

gasttol

Type Option
Format gasttol tolerance
Units Electrons
Default 0.000001
Use Sets the tolerance on the change in the charges between
iterations of the Gasteiger scheme. The value is set here
for consistency with the original paper, which used 0.001
of an electron, but more converged values can be obtained
by lowering the tolerance
See also eem gasteiger gastiter qeq gastparam gastdamping noqeem
eembond

gcmcexistingmolecules

Type Option
Format gcmcexistingmolecules mol1 mol2 mol3 ...etc....
natmol1 atom1_1 atom1_2 atom1_3.... atom1_natmol1
natmol2 atom2_1 atom2_2 atom2_3.... atom2_natmol2
natmol3 atom3_1 atom3_2 atom3_3.... atom3_natmol3
etc...
Default No existing GCMC molecules in existing structure
Units None
Use Allows molecules in the current structure that are related to GCMC
molecules to be identified. The purpose of this option is to facilitate
restarts of GCMC runs. For example, if a system contains 3 molecules
where molecule numbers 2 and 3 were inserted by GCMC, while molecule 1
is a fixed framework into which the molecules are inserted then the
input would be:
gcmcexistingmolecules 2 3
2 5 6
2 7 8
Note that lines 2 and 3 identify that there are 2 atoms in molecule
2 numbered 5 & 6, while molecule 3 also has 2 atoms that are numbers
7 & 8 in the input for this structure.
Where there are many molecules a range can also be specified as follows:
gcmcexistingmolecules 4 to 8
See also mccreate mcdestroy montecarlo gcmcspecies gcmcmolecules

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.
Example gcmcmolecule
N core 0.0 0.0 -0.6
N core 0.0 0.0 0.6
See also mccreate mcdestroy montecarlo gcmcspecies gcmcexistingmolecules

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.
Example gcmcspecies 2
H core
O core
See also mccreate mcdestroy montecarlo gcmcmolecule

gcoulomb

Type Option
Format gcoulomb <intra/inter> <bond/x12/x13/x14/o14/g14> <scale14>
atom1 atom2 A gamma <rmin> rmax <flag>
Units A in a.u., gamma in Ang**3, distances in Angstroms
Default rmin = 0.0
Use Coulomb subtraction potential of ReaxFF form with gamma. This
potential is useful when mixing fixed charges in a ReaxFF calculation
with a molecular mechanics force field between the fixed charges
since it allows the ReaxFF charge term to be removed.
E = - A/(rij**3 + gamma)**(1/3)
Here the term gamma represents 1/(gammai*gammaj)**3 where the gammai
and gammaj are terms from the ReaxFF force field. The A term is the
product of the two charges, A = q1*q2, in atomic units. The whole
term is then converted internally from units of e2/Ang to eV.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction - this can also be achieved through the command molmec.
o14 => only act between atoms which are 1-4, i.e. separated by
3 bonds
When specified as bonded potential cutoffs are omitted from input.
See also molmec g3coulomb

gdcrit

Type Option
Default 4.0
Use Optimisation of defects involves a force balance
method, rather than direct minimisation of the
energy. The method is implemented in GULP such that
initially the energy is minimised until the gradient
norm is sufficiently small, at which point the step
length is based on -(H-1).g and no line search is
used (where H = second derivative matrix and g =
gradient vector). The criterion for switching
between these minimisation methods is given by
gdcrit/nvar, where nvar is the number of variables.
See also defect

general

Type Option
Format general <m> <n> <ener/grad> <intr/inte> <bon/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A rho C <rmin> rmax <3*flags>
Units A in eV*Angs**m, rho in Angs, C in eV*Angs**n
Default m=0 n=6
Use General potential - optimisation flags for fitting (0/1).
This potential is a combination of a Buckingham and Lennard-Jones.
On the first line, general may be followed by m and n, which
are the powers of r (12 6 => L-J potential). Rho=0.0 results in the
exponential term being removed. The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance. atom1 and atom2 may be specified either by atomic number or
symbol, which in the latter case can be followed by a species type.
If no species type is given then type is assumed to be core.
E = A.exp(-r/rho)/r**m - C/r**n <-E(rmax) <+Grad correction term>>
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
See also c6 zbl

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

gexp

Type Option
Default Use tournament probability.
Use Part of ga options section. If specified then probability of
success for a given configuration is weighted exponentially
with respect to how good the configuration is compared with the
other configurations within the present population.
See also tournament

ghost_supercell

Type Option
Format ghost_supercell <xyz/zyx> (ncells in x) (ncells in y) (ncells in z)
Default 1 1 1 (i.e. no underlying supercell), xyz
Use Tells GULP that the structure was generated by the supercell option
and so there is an underlying smaller unit cell. This is used for
calculations where force constants between different cell images
are needed. Main use is currently in generating files for ShengBTE,
or for finite difference calculation of phonons with neighbour list
based potentials.
The sub-options xyz or zyx indicate the order in which the supercell
was generated. Currently this information is not used by GULP but
provides information.
See also supercell ghostcell fc_supercell

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 xtol

gradients

Type Option
Format gradients <sum_shells> <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.
If the sub-option "sum_shells" is specified then the gradients
fitted are taken to be the sum of those for the core and shell
for the ion for this configuration. Currently this applies only
to the coordinates of the shells and not the radius.
See also observables elastic sdlc hfdlc piezo energy stress

grid

Type Option
Format grid min <max> <iter>
Default 64 by 64 by 64 fixed grid (i.e. min=max=6).
Use Part of ga options section. Allows the grid size to change after
iter (default=20) iterations from (2^min)^3 to (2^min+1)^3 to a
maximum number of grid points of (2^max)^3.
Note that when optimisation stuck within a local minimum and this
option word is used then grid size will begin changing again.
See also discrete

grimme_c6

Type Option
Format grimme_c6 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 C6 d r0 <rmin> rmax <3*flags>
Units C6 in eV*Angs**6, r0 in Angs, d is unitless
Default s_6 = 1, d = 20
Use Specifies potential parameters for the Grimme form of damped C6 term
(J. Comput. Chem., 27, 1787 (2006)). The energy is of the form:
E = - C6*fdmp(r)/r**6
where the damping function, fdmp is given by:
fdmp(r) = 1/[1 + exp(-d(r/r0 - 1))]
NB: Here the s6 parameter of Grimme is subsumed into the C6 terms.
See also damped_dispersion becke_johnson_c6

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 xtol

harmonic

Type Option
Format harmonic <k3> <k4> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 k2 <k3> <k4> r0 <coul> <rmin> rmax <2-4*flags>
Units k2 in eV*Angs**-2, r0 in Angs, coul in none, k3 in eV*Angs**-3
k4 in eV*Angs**-4
Defaults k3 = k4 = 0.0, coul = 0.0
Use Harmonic potential - optimisation flags for fitting.
coul = 1.0 => Coulomb subtracted
coul = 0.0 => not Coulomb subtracted
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = 1/2 K2*(r-r0)**2 + 1/6 K3*(r-r0)**3 + 1/24 K4*(r-r0)**4
-coul*qi*qj/r
k3 and k4 terms can be included as follows:
harm k3
atom1 atom2 k2 k3 r0 <coul> <rmin> rmax <3*flags>
harm k4
atom1 atom2 k2 k4 r0 <coul> <rmin> rmax <3*flags>
harm k3 k4
atom1 atom2 k2 k3 k4 r0 <coul> <rmin> rmax <4*flags>
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also spring squaredharmonic forceconstant mm3stretch e2pot

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 young poisson shear voigt bulk omega

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

high-fq dielectric

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

hydrogen-bond

Type Option
Format hydrogen-bond <intra/inter> <kcal/kjmol> <m> <n> <p> <taper> <dreiding>
atom1 atom2 atom3 A B <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags>
or if taper is specified:
atom1 atom2 atom3 A B <theta_min theta_max> <rmin12> rmax12 <rmin13> rmax13
<rmin23> rmax23 <2*flags>
Units A in eV*Ang**m, B in eV*Ang**n
Defaults m = 12, n = 10, p = 4
Use Specifies a three-body hydrogen bond potential of form:
If theta > 90 degrees :
E(three) = (A/(r**m) - B/(r**n))*(cos(theta))**p
If theta =< 90 degrees :
E(three) = 0.0
where r is the distance between atoms 2 and 3, and theta is the angle
between the 1-2 and 1-3 vectors.
If the dreiding sub-option is specified then the rule that the
potential will only be applied when H is bonded to one of the following
donor atoms N, O, F, S, Cl, Br, I is used.
Note that theta_min and theta_max are only input if the "taper" sub-option
is specified.
See also three-body angle exponential axilrod-teller stillinger bcross
urey-bradley murrell-mottram bacross equatorial lin3 uff3 3coulomb
bagcross j3 ppp3body

igauss

Type Option
Format igauss <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A b r0 <rmin> rmax <3*flags>
Units A in eV, b in Angs**-2, r0, rmin and rmax in Angs
Default none
Use This option specifies the use of an inverted Gaussian potential
between two atoms. The form of the energy is:
E = - A.exp(-b(r-r0)**2)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.

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 keyword include

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

include

Type Option
Format include filename
Use Includes a separate file into the GULP input. This allows common input
for a series of runs to be placed in one file and then read into multiple
inputs.
See also keyword ignore erongi

index_k

Type Option
Format index_k <integer_value>
Units none
Default 60
Use This specifies the limit on the looping indices for reciprocal lattice
vectors. If an error message appears that says that there are too many
reciprocal lattice vectors then it means that this value has been
exceeded. While the value can be increased, this may indicate that the
unit cell of your system is becoming too small and thereby causing the
volume of reciprocal space to become too large.
See also rspeed veck accuracy ewaldrealradius

initial_coordinates

Type Option
Format initial_coordinates
x1 y1 z1
x2 y2 z2
.....
xN yN zN
Units Angstroms
Use Specifies the initial Cartesian coordinates of the atoms. Used for
restarting calculations that specify an electric field or the
delta_dipole form of dipole energy.
See also md absolute_coordinates

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

integrator

Type Option
Format integrator <gear/velocity verlet/leapfrog verlet/stochastic> <iter>
Default stochastic (note this is a change from earlier versions)
Use Specifies the integration algorithm to be used in molecular
dynamics as being the Gear 5th order or either of the
velocity or leapfrog methods of Verlet. Currently the Gear
algorithm is only available in the NVE ensemble.
Details of the stochastic integrator can be found in G. Bussi
et al, J. Chem. Phys., 130, 074101 (2009).
See also md tau_barostat tau_thermostat p_isotropic p_flexible

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 14_scale molatom

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

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 molatom

inversion

Type Option
Format inversion <squared> <intra/inter/bond/mol> <only3> <kcal/kjmol>
atom1 atom2 atom3 atom4 k <k0> rmax(1-2) rmax(1-3) rmax(1-4) <1 x flag>
Units k in eV, k0 in degrees
Default none
Use Out of plane energy - energy penalty for atom 1 lying
out of the plane of atoms 2, 3 and 4. This form uses the
Dreiding planar expression:
E = k.(1 - cos(phi))
where phi is the angle between the plane of the centre atom and two
others with the bond from the centre atom to the third atom.
Note that because phi depends on which of the 3 different angles is
chosen, GULP computes the contribution for all 3 cases and takes the
average.
If the sub-option "squared" is specified then the modified form given
below is used:
E = 1/2 (k/sin(k0)**2).(cos(phi) - cos(k0))**2
and k0 must be input.
If the only3 sub-option is specified then the potential applies where
an atom has exactly 3 bonds present.
See also torsion ryckaert torangle torharm torexp xoutofplane outofplane

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.
See also element

iterations

Type Option
Format iterations n <gradient_norm> <noextrapolate> <order_of_extrapolation>
Default n = 100, gradient_norm = 1.0D-8, order of extrapolation = 8
Use Specifies that shell model molecular dynamics shall be performed with
massless shells. This is the default for molecular dynamics if shells
are present. The shell positions are optimised in every time step for
n iterations or until the specified gradient norm for the shells only
is reached. Convergence of the shell gradients is crucial for the
conservation of the momentum of the system.
By default shell extrapolation using rational function interpolation
is turned on, using a function of order 8. If "noextrapolate" is
specified then this is turned off. Extrapolation usually greatly
reduces the number of cycles for optimisation.
See also shellmass sopt md

j2

Type Option
Format j2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 J2 <rmin> rmax <1*flag>
Units J2 in eV
Defaults rmin = 0.0
Use Adds an energy term to the two-body energy if an interaction is found.
Value of energy doesn't depend on distance between the atoms, as long as the
interaction is valid (i.e. less than the cutoff or according to the bonding criteria)
However, it is does depend on the "spin" assigned to each species involved:
E = - J2*spin_1*spin_2
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
See also harmonic spring squaredharmonic forceconstant mm3stretch spin j2

j3

Type Option
Format j3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 J3 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23
Units J3 in eV, distances in Angstroms
Use Adds an energy to the three-body contribution if a valid 3-body term
is found. The value does not depend on the distances or angle, just
the "spin" of the atoms involved:
E(three) = - J3*spin_1*spin_2*spin_3
This is used for addition of an Ising Hamiltonian to the energy.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger bcross lin3
urey-bradley murrell-mottram bacross hydrogen-bond equatorial
uff3 bagcross 3coulomb spin j2 ppp3body

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
See also include ignore erongi

kim_model

Type Option
Format kim_model <number_of_models>
name_of_model1
name_of_model2
:
name_of_modelN
NB: To allow for the use of long model names this is given
on the line after the option.
Units none
Default No KIM model is to be used, number_of_models = 1
Use This option allows the user to select models from
the OpenKIM project for use with GULP. Note that the
code must have been compiled with the -k option for mkgulp.
See OpenKIM documentation for more details.
If using multiple models then the number must be specified
and then each model name will be read from a separate line.
By default a single model name is expected.
NB: From version 5.2 of GULP onwards only OpenKIM version
2.0 is supported.
NB: At present KIM will only support a single type of each
element and so species types are ignored when being passed
to KIM.
NB: If using KIM models then it is not currently possible
to compute the attachment energy and so this will not be
output.

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 msd

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

lennard

Type Option
Format lennard <epsilon> <zero> <esff> <combine/geometric/product> <m> <n> <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <type_of_bond>
<kcal/kjmol> <ener/grad> <all> <scale14>
atom1 atom2 (A B/epsilon sigma) <rmin> rmax <2*flags>
If combination rules are specified then the format is:
atom1 atom2 <rmin> rmax
If combination rules and "all" are specified then the format is:
<rmin> rmax
Units A in ev*Angs**m, B in ev*Angs**n, epsilon in eV, sigma in Angs
Default m=12, n=6
Use Lennard-Jones potential - optimisation flags for fitting.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A/r**m - B/r**n
The exponents are by default 12 and 6, but these can be changed
by specifying values after the option word lennard. By specifying
epsilon after lennard this means that the input is in terms of
epsilon and sigma instead of A and B.
E = epsilon*(c1*(sigma/r)**m - c2*(sigma/r)**n)
Specifying "zero" allows the user to chose between sigma defined
as the potential energy minimum distance (default) or the distance
at which the potential energy goes to zero.
r = sigma => E = epsilon
c1 = (n/(m-n))
c2 = (m/(m-n))
r = sigma => E = zero
c1 = (n/(m-n))*(m/n)**(m/(m-n))
c2 = (m/(m-n))*(m/n)**(n/(m-n))
If combine is specified as well as epsilon, then combination rules
are used to obtain the epsilon and sigma parameters based on the
values for individual species. The combination rules are as follows:
epsilon = 2*sqrt(e1*e2)(s1**3.s2**3)/(s1**6+s2**6)
sigma = ((s1**6+s2**6)/2)**1/6
where e1, e2, s1 and s2 are the atom related parameters.
Alternatively, if geometric combination rules are specified then
this becomes:
epsilon = sqrt(e1*e2)
sigma = (s1+s2)/2
As a further alternative, if product combination rules are specified
then this becomes:
epsilon = sqrt(e1*e2)
sigma = sqrt(s1*s2)
If combine is specified for a standard lennard-jones potential
then the species values given in the "atomab" command are used
to obtain potential parameters using the following rules:
Aij = sqrt(Ai.Aj)
Bij = sqrt(Bi.Bj)
If esff is specified then this implies that the ESFF combination
rules will be used to calculate the potential parameters. This
automatically implies "combine" and that the functional form is
9/6. The parameters are then obtained from epsilon and sigma as
follows:
Aij = Ai.Bj + Aj.Bi
Bij = 3 * Bi.Bj
where Ai = sqrt(epsilon)*sigma**6
Bi = sqrt(epsilon)*sigma**3
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
If "all" is specified as a sub-option, then Lennard-Jones potentials
will be automatically created and added for all combinations of A/B
or epsilon/sigma, as appropriate. NB: This will be done based on the
values that have been specified up to that point and so be sure to get
the order right! In this case, the line following should only have the
rmin and rmax to be used for all the potentials.
e.g.
lennard 12 6 combine all
0.0 12.0
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also epsilon atomab c6 buffered_lj

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 precede the options to guarantee correct processing
See also libff libdump preserve_Q

lin3

Type Option
Format lin3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K isign n <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3)
<rmin(2-3)> rmax(2-3) <flag>
Units K in eV, rmin and rmax in Angstroms
Default none
Use ESFF linear three-body form :
E(three) = K * (1 + isign*cos(n*theta))
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2, 2-3 and 1-3 are bonded.
See also axilrod-teller angle stillinger-weber exponential bcross
urey-bradley murrell-mottram bacross three hydrogen-bond equatorial
uff3 3coulomb bagcross ppp3body

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.

ljbuffered

Type Option
Format ljbuffered <m> <n><intra/inter> <bond/x12/x13/x14/o14/g14/mol> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A B r0 <rmin> rmax <3*flags>
Units A in eV*Angs**m, B in eV*Angs**n, r0 in Angs
Default m = 12, n = 6, r0 = 0.0
Use Buffered Lennard-Jones potential, where r0 is added to the distance.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A/(r + r0)**m - B/(r + r0)**n
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.

lorentzian_tolerance

Type Option
Default 0.01
Use This option controls the drop tolerance for the Lorentzian
broadening that is used during a thermal conductivity
calculation. If the Lorentzian is below the input threshold
then it is set to zero.
e.g. lorent 0.001
See also phonon thermalconductivity broaden_dos

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
See also free zsisa

manybody

Type option
Format manybody
atom1 atom2 <taper_range> <rmin> rmax
Defaults rmin = 0, taper_range = 0
Use Specifies that a manybody potential should act between this
pair of atoms. This implies that the density of each atom
at the other will be calculated. The energy is subsequently
calculated as a function of the total density at each site.
This option is used as part of the Embedded Atom Model for
metals and is based on the ideas of Finnis-Sinclair and
subsequently other workers, such as Sutton-Chen.
The densities at each site are determined by the "eam_density"
option and the functional dependance on the total density
by "eam_functional".
Note that although for simplicity the manybody potential
appears as part of the two-body potentials, it is infact
many body at short-range, but tends to an effective pair
potential at long range. Also note that this potential type
is NOT compatible with <intra/inter/molmec> directives.
The density can be smoothly tapered to zero over a distance
which is input using the taper_range. Here the taper applies
from (rmax - taper_range) to rmax. In most MEAM potentials
the typical range used is 0.1 Angstroms.
The form of the taper used for the density is chosen to be
consistent with the MEAM literature:
fcut(x) = 1, for x >= 1
= 0, for x =< 0
= [1 - (1-x)**4]**2, for 0 < x < 1
where x = (rmax - r)/taperrange
See also eam_density eam_functional scmaxsearch noquicksearch

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

mass

Type Option
Format mass symbol <mass>
Units atomic units
Default as per periodic table
Use Allows atomic masses to be changed. Note that species symbols can
also be used for the mass to set different masses for different
species of the same element:
element
mass O1 16.0
mass O2 17.0
end
or the older form of using the atomic number can be used:
element
mass 8 16.0
end
Command is part of element section.
See also element

maths

Type Option
Format maths <eispack/lapack> <nodivide>
Default lapack with divide and conquer
Use Selects whether to use the Eispack or Lapack maths libraries
for finding the eigenvectors/eigenvalues of the dynamical
matrix. When compiled from source the Eispack library appears
to be significantly faster than straight Lapack, but if an
optimised maths library is linked instead of lapack.o/blas.o
then this may not be the case. However, the divide and conquer
form of Lapack is faster than Eispack and so this is now the
default. There is the chance of some loss of precision, and so
the other options are there for validation purposes.
See also phonon matrix_format blocksize

matrix_format

Type Option
Format matrix_format <hessian/cosmo> <triangular/twodimensional>
Default triangular in serial; twodimensional in parallel
Use The Hessian matrix and the COSMO A matrix are symmetric matrices and
therefore can be stored and used in either triangular or two-dimensional
form. For serial runs either format can be used with the more compact
triangular form being the default. In parallel then the two-dimensional
form must be used for compatibility with the parallel maths libraries used.
This option is mainly for debugging and checking purposes.
See also hessian cosmo

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.
See also stepmx optimise

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 optimise rfo transition_state

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

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.
Example mcchemicalpotential -1.00
See also mccreate mcdestroy mctrial montecarlo gcmcspecies mcvolume

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.
Example mccreate 0.25
See also mcdestroy mcmove mcrotate mctrial montecarlo mcswap
mcspecies

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.
Example mcdestroy 0.25
See also mccreate mcmove mcrotate mcstrain mctrial montecarlo mcswap
mcspecies

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.
Example mclowest -1140.6883129
See also mcstep mctrial montecarlo mcmeans

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.
Examples mcmaxdisplacement 0.1
mcmaxdisplacement 0.05 target 0.5 20
See also mcmove montecarlo

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.
Examples mcmaxrotation 90
mcmaxrotation 180 target 0.5 20
See also mcrotate montecarlo

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.
Examples mcmaxstrain 0.01
mcmaxstrain 0.15 target 0.5 30
See also mcstrain montecarlo

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.
Example mcmeans -3.45155 4.059
See also mcstep mctrial montecarlo mclowest

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.
Example mcmove 0.25
See also mccreate mcdestroy mcrotate mctrial montecarlo mcstrain mcswap
mcspecies

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.
Example mcoutfreq 1
See also mcsample montecarlo

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 sub-options atom, line and centre control the point about
which the molecule will be rotated, and in the case of line the
axis direction. For the default mode, centre, the molecule is
rotated about the centre of the molecule based on the average
coordinate. For atom, a random atom from within the molecule
is chosen and then the rotation attempted about this. For line,
two atoms are chosen at random and the rotation attempted about
this axis. If more than one word is specified then all types of
rotation specified will be tried according to a random choice.
Example mcrotate 0.25
See also mccreate mcdestroy mcmove mctrial mcmaxrotation montecarlo
mcstrain mcswap mcspecies

mcsample

Type Option
Format mcsample <frequency> <filename> <lowest>
Default 10 / gulp.gmc
Units None
Use Specifies the frequency for outputting configuration data to
a binary file for post-run analysis. The value is specified
as the number of accepted operations between writes. The
filename can be anything with up to 60 characters. The
extension ".gmc" is recommend as a convention.
The format of the file is as follows. Each configuration is
written as follows:
write(31)numat
write(31)energy
write(31)(atomicno(i),i=1,numat)
write(31)(atomictype(i),i=1,numat)
write(31)(xcoordinate(i),i=1,numat)
write(31)(ycoordinate(i),i=1,numat)
write(31)(zcoordinate(i),i=1,numat)
where the variables are as follows :
integer(i4) numat = total number of atoms
integer(i4) atomicno = atomic number of atom (1-maxele)
integer(i4) atomictype = atomic type of atom (0-9999)
real(dp) energy = total energy of system (eV)
real(dp) xcoordinate = Cartesian coord in X direction (Angs)
real(dp) ycoordinate = Cartesian coord in Y direction (Angs)
real(dp) zcoordinate = Cartesian coord in Z direction (Angs)
and the datatypes are given by :
integer, parameter :: i4 = selected_int_kind(9)
integer, parameter :: dp = kind(1.0d0)
Example mcsample 5 montesamples.gmc
See also montecarlo mcoutfreq

mcspecies

Type Option
Format mcspecies probability species1 species2
Default 0.0
Units None
Use Specifies the relative probability of species being transformed during
a Monte Carlo simulation. Note all probabilities are renormalised
at run time. A value of zero means that no transformation will be attempted.
This move will attempt to switch species1 to species2 or vice versa.
If species are defined with opposite spins then this move allows for spin
inversion in an Ising model.
Example mcspecies 0.25 Mg Ca
See also mccreate mcdestroy mcrotate mctrial montecarlo mcmove
mcmaxstrain mcstrain mcswap

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 consistent with the mean properties given and the second
one must obviously be smaller than the first.
Example mcstep 50 24
See also mcmeans mctrial montecarlo mclowest

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.
Example mcstrain 0.25
See also mccreate mcdestroy mcrotate mctrial montecarlo mcmove
mcmaxstrain mcswap mcspecies

mcswap

Type Option
Format mcswap <any/only> probability <npair> <species list>
Default 0.0 / any / 1 pair
Units None
Use Specifies the relative probability of ions being swapped during
a Monte Carlo simulation. Note all probabilities are renormalised
at run time. A value of zero means that no swapping will be attempted.
The suboptions control what species can be switched. If any is specified
then all atoms can be swapped. However, if only is specified a list of
species that can be swapped must be given. Note: Only swaps between
different species will be considered since otherwise the energy is
invariant. Furthermore, swaps involving atoms in molecules are not
allowed. Swapping involving species with shells should also be avoided
for now since the core/shell pair may get split.
npair specifies the number of pairs of atoms to be swapped as part of
a single attempted move. By default only 1 pair will be swapped.
Multiple mcswap options are allowed so that different groups of atoms
can be swapped in the same structure.
Example mcswap 0.25
mcswap only 0.25 2 Mg Ca
See also mccreate mcdestroy mcrotate mctrial montecarlo mcmove
mcmaxstrain mcstrain mcspecies

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 mcswap
mcspecies

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

mdarchive

Type Option
Format mdarchive <unique> file_name
Use Specifies name of archive file for molecular dynamics run. This file
is in MSI's archive file format and can be read by Insight II.
If this option is given the current structure is written to the
specified file with the frequency specified using 'write'. Note
it is also necessary to specify the "output arc" option to trigger
the writing of an arc file.
If the "unique" sub-option is specified then the atom symbols will
be appended with the atom number (within what is allowed by the
archive file format) to create different labels for analysis.
See also md write output

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

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

meam_density

Type option
Format meam_density order <power n/fpower/exponential n/gaussian n/cubic/quadratic/quartic/voter/glue/evoter/mei-davenport/baskes/vbo>
atom1 <atom2> C (power law) <1 x flag >
atom1 <atom2> C rn (fractional power law) <2 x flag >
atom1 <atom2> A B r0 (exponential) <3 x flags>
atom1 <atom2> A B r0 (gaussian) <3 x flags>
atom1 <atom2> A r0 (quadratic) <2 x flags>
atom1 <atom2> A r0 (cubic) <2 x flags>
atom1 <atom2> A r0 (quartic) <2 x flags>
atom1 <atom2> A beta (voter) <2 x flags>
atom1 <atom2> A beta (evoter) <2 x flags>
atom1 <atom2> c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags>
atom1 <atom2> A beta r0 (baskes) <3 x flags>
atom1 <atom2> c sigma gamma r0 delta (vbo) <5 x flags>
atom1 <atom2> A B C D rmin r0 (spline) <4 x flags>
if order > 0 then there will be addition lines of the following form for each higher order
C (power law) <1 x flag >
A B r0 (exponential) <3 x flags>
A B r0 (gaussian) <3 x flags>
A r0 (quadratic) <2 x flags>
A r0 (cubic) <2 x flags>
A r0 (quartic) <2 x flags>
A beta (voter) <2 x flags>
A beta (evoter) <2 x flags>
c0 c1 c2 c3 c4 c5 r0 (mei-davenport) <7 x flags>
A beta r0 (baskes) <3 x flags>
c sigma gamma r0 delta (vbo) <5 x flags>
NB: The maximum value of order is currently 3
Units Distances in Angstrom
Defaults order = 3
Use specifies the density due a given atom1 at another
atomic centre (atom2) in the Modified Embedded Atom Model (MEAM).
This density is only calculated for pairs of atoms
where the "manybody" potential has been specified
so that the user can control which atoms are part
of the EAM.
Where no atom2 is specified then the density is applied to
all atoms allowed by the manybody potential, regardless of
species type.
In the MEAM formalism the density is a sum of contributions over
a number of orders:
rho_tot(i)**2 = sum(order = 0->3) t_order*rho_order(i)**2
where t is a coefficient for each order.
The radial component of the density can take one of several functional forms:
Power Law:
rho(i) = C*rij**(-n)
e.g. meam_density 3 power 6
Ni core 729.7
429.2
219.5
106.2
Fractional power Law:
rho(i) = C*rij**(-rn)
e.g. meam_density 3 fpower
Ni core 729.7 6.1
429.2
219.5
106.2
Exponential:
rho(i) = A*(rij**n)*exp(-B(rij-r0))
e.g. meam_density 0 exponential 0
Ni core 500.0 4.0 3.52
Gaussian:
rho(i) = A*(rij**n)*exp(-B(rij-r0)**2)
e.g. meam_density 1 gaussian 2
Ni core 400.0 3.0 3.52
200.0 1.5 1.46
Quadratic:
rho(i) = A*(rij-r0)**2 if r < r0, else = 0
Cubic:
rho(i) = A*(rij-r0)**3 if r < r0, else = 0
Quartic:
rho(i) = A*(rij-r0)**4 if r < r0, else = 0
Voter:
rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))
eVoter:
rho(i) = A*r**6*(exp(-beta*r) + 2**9*exp(-2*beta*r))*exp(-1/(rmax - r))
Mei-Davenport:
rho(i) = sum(l=0->5) (c_l/12)*(r/r0)**l
Baskes:
rho(i) = A*exp(-beta((rij/r0)-1))
e.g. meam_density 1 baskes
N core 1.0 4.0 1.10
1.0 4.0 1.10
NB: This form is a re-working of the exponential form for convenience for MEAM.
In the above, rmax is the cutoff for the potential from the manybody
option that controls the range of the density.
VBO:
rho(i) = c*sigma*N*exp(-gamma/(1 - sqrt(r/delta)))
where N is a normalisation constant given by:
N = exp(gamma/(1 - sqrt(r0/delta)))
Note that the cut-offs are set by the manybody potential.
Spline: This is effectively one piece of a cubic spline.
rho(i) = A*(rij-r0)**3 + B*(rij-r0)**2 + C*(rij-r0) + D if rmin < r < r0, else = 0
See also manybody meam_functional scmaxsearch eam_alloy prt_eam eam_density baskes meam_screening
meam_rhotype

meam_functional

Type option
Format meam_functional order <square_root/power n/banerjea_smith n/johnson/glue/foiles/mei-davenport/baskes/vbo/spline>
if square_root or power :
atom1 A_1 <1*flag>
t_0 ... t_order <order+1*flags>
atom2 A_2 <1*flag> etc...
t_0 ... t_order <order+1*flags>
if banerjea_smith :
atom1 F0_1 F1_1 rho0_1 <3*flags>
t_0 ... t_order <order+1*flags>
atom2 F0_2 F1_2 rho0_2 <3*flags> etc...
t_0 ... t_order <order+1*flags>
if johnson :
atom1 F0_1 F1_1 rho0_1 alpha beta gamma <6*flags>
t_0 ... t_order <order+1*flags>
atom2 F0_2 F1_2 rho0_2 alpha beta gamma <6*flags> etc...
t_0 ... t_order <order+1*flags>
if glue :
atom1 rho1 rho2
c1_4 c1_3 c1_2 c1_1 c1_0
c2_4 c2_3 c2_2 c2_1 c2_0
c3_3 c3_2 c3_1 c3_0
t_0 ... t_order <order+1*flags>
atom2 rho1 rho2
c1_4 c1_3 c1_2 c1_1 c1_0
c2_4 c2_3 c2_2 c2_1 c2_0
c3_3 c3_2 c3_1 c3_0
t_0 ... t_order <order+1*flags>
if foiles :
atom1 F0_1 F1_1 F2_1 F3_1 <4*flags>
t_0 ... t_order <order+1*flags>
atom2 F0_2 F1_2 F2_2 F3_2 <4*flags> etc...
t_0 ... t_order <order+1*flags>
if mei-davenport :
atom1 Ec_1 alpha_1 beta_1 gamma_1 delta_1 phi0_1 s_1_1 s_2_1 s_3_1 <9*flags>
t_0 ... t_order <order+1*flags>
atom2 Ec_2 alpha_2 beta_2 gamma_2 delta_2 phi0_1 s_1_2 s_2_2 s_3_2 <9*flags> etc...
t_0 ... t_order <order+1*flags>
if baskes :
atom1 Ec_1 A_1 rho0_1 <3*flags>
t_0 ... t_order <order+1*flags>
atom2 Ec_2 A_2 rho0_2 <3*flags> etc...
t_0 ... t_order <order+1*flags>
if vbo :
atom1 A_1 rn_1 <2*flags>
t_0 ... t_order <order+1*flags>
atom2 A_2 rn_2 <2*flags> etc...
t_0 ... t_order <order+1*flags>
if igarashi :
atom1 A_1 B_1 <2*flags>
t_0 ... t_order <order+1*flags>
atom2 A_2 B_2 <2*flags> etc...
t_0 ... t_order <order+1*flags>
if spline :
atom1 A_1 B_1 C_1 D_1 rho0_1 rho_max_1 <4 x flags>
t_0 ... t_order <order+1*flags>
atom2 A_2 B_2 C_2 D_2 rho0_2 rho_max_2 <4 x flags>
t_0 ... t_order <order+1*flags>
Units A, B, C, D, AE0, F0, Ec, phi0 and F1 in eV, rho0/rho_max/alpha/beta/gamma/t0... are dimensionless
Default square_root, A = 1.0, order = 3
Use Specifies how the total energy contribution of an atom in the
Modified Embedded Atom Model depends on the density components at that
site. The current possibilities are:
Square_root:
E = - sum(i) A(i)*(rho(i))**1/2
this is the most common functional, as used in the Sutton-Chen
potential
Power:
E = - sum(i) A(i)*(rho(i))**1/n
this is just a generalisation of the above case
VBO:
E = - sum(i) A(i)*(rho(i))**rn
this is a further generalisation of the power case
Banerjea_smith:
E = - sum(i) F0 [1-ln(r)/n]*r**1/n + F1*r
where r = rho(i)/rho0(i)
this is the functional of Banerjea and Smith (Phys. Rev. B,
37, 6632 (1988)) - note that in this case that are atom
dependent parameters also to be specified (F0, F1, rho0)
where rho0 is the electron density at equilibrium.
Johnson:
E = - sum(i) F0 [1-ln(x)]*x + F1*y
where x = (rho(i)/rho0(i))**(alpha/beta)
and y = (rho(i)/rho0(i))**(gamma/beta)
this functional is similar to that of Banerjea & Smith and is due
to Johnson (PRB, 39, 12554 (1989)).
Glue:
if rho < rho1
E = c1_4*(rho-rho1)**4 + c1_3*(rho-rho1)**3 + c1_2*(rho-rho1)**2 +
c1_1*(rho-rho1) + c1_0
if rho1 =< rho < rho2
E = c2_4*(rho-rho2)**4 + c2_3*(rho-rho2)**3 + c2_2*(rho-rho2)**2 +
c2_1*(rho-rho2) + c2_0
if rho2 =< rho
E = c3_3*(rho-rho2)**3 + c3_2*(rho-rho2)**2 + c3_1*(rho-rho2) + c3_0
this is the functional from Ercolessi et al, Phil. Mag. A, 58, 213 (1988).
NB: At present there are no fitting parameters since there are constraints
on the coefficients to ensure a smooth and continuous function.
Foiles:
E = sum(i) F0*rho(i)**2 + F1*rho(i) + F2*(rho(i)**(5/3)/(F3 + rho(i)))
Mei-Davenport:
E = sum(i) - Ec*[1-(alpha/beta)*ln(rho(i))]*rho(i)**(alpha/beta) +
sum(m=1->3) 0.5*phi0*s_m*exp(-(sqrt(m)-1)*gamma)*
[1+(sqrt(m)-1)*delta-sqrt(m)*delta*ln(rho(i))/beta]*
rho(i)**(sqrt(m)*gamma/beta)
Baskes:
E = sum(i) A*Ec*x*ln(x)
where x = (rho(i)/rho0(i))
this functional is similar to that of Banerjea & Smith and Johnson, but
is simplified to enable the parameters from the MEAM paper of Baskes to
be input directly.
The value of order species the maximum order of the MEAM functional. Usually
MEAM involves components from order 0 to 3 and values outside this range are
not currently permitted.
For all functionals, the values of t_0, t_1, ... t_order are the coefficients
for the density contribution of each order.
Igarashi:
E = - sum(i) A(i)*(rho(i)*(1 + B(i)*rho(i))**1/2
this functional form was proposed in Igarashi et al, Phil. Mag. B, 63,
603 (1991).
Spline:
if rho_max > rho > rho0:
E = - sum(i) [A(i)*(rho(i)-rho0)**3 + B(i)*(rho(i)-rho0)**2 + C(i)*(rho(i)-rho0) + D(i)]
else
E = 0
See also meam_density manybody scmaxsearch eam_alloy prt_eam baskes meam_screening
meam_rhotype

meam_rhotype

Type Option
Format meam_rhotype <t21/t24> <sum/exponential/exphalf>
Units none
Default t24, exponential
Use There are several different formulations of MEAM that have evolved according
to both the number of angular momentum terms and the way that they are
combined. They can largely be broken down into the first, nearest-neighbour
form (1NN), and the revised second nearest neighhbour form (2NN).
In the original formulation there were 21 components of the density
while later forms adopt 24 (3 extra terms for the order = 3 case). Which form
is used can be selected using the sub-options:
t21 = 1NN 21 term expression
t24 = 2NN 24 term expression
There are also two different ways that the total density, rho, can be assembled
from the component density orders, rho_i. In the original version, 1NN, a simple
sum of the densities squared, square rooted, was used and this can be selected
by the sub-option, "sum":
rho = sqrt[ sum (i=0->order) (t_i*rho_i**2) ]
In later versions of the methodology (2NN) then a different form was proposed to
avoid issues with the density becoming negative;
rho = rho_0*G(gamma)
where;
G(gamma) = 2/(1 + exp(-gamma))
and;
gamma = [ sum (i=1->order) (t_i*(rho_i/rho_0)**2) ]
This second form, "exponential", is the default choice unless "sum" is given.
There is also an alternative form of exponential that some papers have used
that can be selected by "exphalf":
G(gamma) = exp(gamma/2)
See also meam_density manybody scmaxsearch eam_alloy prt_eam baskes meam_screening
meam_functional

meam_screening

Type Option
Format meam_screening
atom1 <atom2 atom3> Cmin Cmax
Units none
Default No screening (i.e. simple radial cut-offs applied), atom2 = atom3 = atom1
Use Controls the truncation of the MEAM density by applying a screening function to
the pairwise density between two atoms. For a pair of atoms, i-j, the screening
function is given by:
S_ij = Product(k=1,N,k.ne.i,k.ne.j) S_ikj
where S_ikj is given by the construct described in M.I. Baskes, Mater. Chem. Phys.,
50, 152-158 (1997):
S_ikj = f_e(x)
f_e(x) = 1 ; x >= 1
= [1 - (1-x)**4]**2 ; 1 > x > 0
= 0 ; x =< 1
x = (C - Cmin)/(Cmax - Cmin)
C = [2(X_ik + X_jk) - (X_ik - X_jk)**2 - 1]/[1 - (X_ik - X_jk)**2]
where X_ik = (r_ik/r_ij)**2 and X_jk = (r_jk/r_ij)**2
If only a single atom type is input then this is taken to be the
self term. However, when atom2 and atom3 are given then the term
becomes specific to a trio of atoms with the first atom being the
one that is doing the screening. Note that the order of atoms 2
and 3 does not make any difference.
NB: Analytic second derivatives are currently not available when
screening is turned on.
NB: Prior to version 4.3 there was only a single screening factor
for all atoms where as it is now species specific.
See also meam_density meam_functional meam_rhotype

mei-davenport

Type Option
Format mei-davenport <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 phi0 delta gamma r0 <rmin> rmax <4*flags>
Units phi0 in eV, r0 in Angs and delta & gamma are dimensionless.
Default none
Use Specifies the parameters for the two-body component of the Mei-Davenport
potential (PRB, 46, 21 (1992)):
E_ij = - phi0*(1 + delta*(r/r0 - 1))*exp(-gamma*(r/r0 - 1))
See also eam_density eam_functional

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

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

mm3angle

Type Option
Format mm3angle <nbeq/nbne nbond> <intra/inter> <bond/mol> <kcal/kjmol/degree>
atom1 atom2 atom3 k2 theta0 A B C D E <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) &
<rmin(2-3)> rmax(2-3) <7 flags>
Units k2 in eVrad**-2, B in rad**-1, C in rad**-2, D in rad**-3, E in rad**-4
A is unitless, theta0 in degrees, rmin & rmax in Angs
Default A = 0.021914, B = 0.014, C = 5.6, D = 7.0, E = 9.0
Use Three-body angle bending potential about atom1 in MM3 form. k2 is the force
constant and theta0 the equilibrium angle. The other constants control the
higher order angular terms. Optional flags are for fitting. Atom 1 is
the middle atom of the triad about which the force acts.
E(three) = (A*k2*(theta-theta0)^2)*[1-B*(theta-theta0) + C*10^-5*(theta-theta0)^2
- D*10^-7*(theta-theta0)^3 + E*10^-10*(theta-theta0)^4]
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
The order of the bond type options matches the order of the pivot atom
- end atom pairs. For example, if a potential acts for the triad
S - C - O, where the C-S bond is a regular bond and the C-O is an
exocyclic double bond then the input would look like:
mm3angle bond single regular double exocyclic
C core S core O core ...... etc
Conditions can also be placed on a potential to check the number of bonds
associated with the pivot atom (e.g. if a potential is designed for a 90
degree angle it might be necessary to check that the number of bonds is
four or six for square planar or octahedral). The conditions are placed
using one or more instances of "nbeq" or "nbne" followed by an integer.
Here "nbeq" imples no. of bonds must equal and "nbne" number of bonds must
not equal. Hence, "nbeq 4" would require the pivot to have 4 bonds. When
multiple terms are used, the logic of nbeq is concatenated with "or", whereas
that of nbne is joined by "and". Therefore "nbne 4 nbne 6" would apply to
an atom with 3 bonds, but not one with 4 or 6.
NB It's important to specify the first bond as being of "regular" type so
that the "exocyclic" attribute is correctly assigned to the second bond
since the first term is assumed to apply to the first bond, whereas the
second applies to the second bond.
See also axilrod-teller angle stillinger-weber exponential bcross uff3
urey-bradley murrell-mottram bacross lin3 hydrogen-bond equatorial
3coulomb exp2 bagcross three j3 ppp3body

mm3buck

Type Option
Format mm3buck <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond> <all>
atom1 atom2 A B C epsilon rv <rmin> rmax <5*flags>
or
mm3buck combine <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 A B C <rmin> rmax <3*flags>
or
mm3buck combine all <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
A B C <rmin> rmax <3*flags>
Units A, B and C are unitless, epsilon in eV, rv in Angs
If kcal is given : epsilon in kcal, rv in Angs
If kjmol is given: epsilon in kJmol-1, rv in Angs
Default none
Use MM3 form of Buckingham potential
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = epsilon*[A.exp(-B*r/rv) - C*(rv/r)**6]
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
If "combine" is given as a sub-option then combination rules are used
to compute the epsilon/sigma values based on the atomic values:
epsilon = sqrt(e1*e2)
sigma = (s1+s2)/2
If "all" is specified as a sub-option, then mm3buck potentials
will be automatically created and added for all combinations of
epsilon/sigma. NB: This will be done based on the values that
have been specified up to that point and so be sure to get the
order right! In this case, the line following should only have
the rmin and rmax to be used for all the potentials.
See also c6 buckingham epsilon slater

mm3stretch

Type Option
Format mm3stretch <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 k2 r0 <A B C> <coul> <rmin> rmax <5*flags>
Units k2 in eV*Angs**-2, r0 in Angs, A and coul are unitless, B and C in Angs**-1
Defaults coul = 0.0, A = 71.94, B = 2.55, C = 7/12
Use MM3 bond stretching potential
coul = 1.0 => Coulomb subtracted
coul = 0.0 => not Coulomb subtracted
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A*(K2*(r-r0)**2)*[1 - B*(r-r0)*(1 - C*B*(r-r0))]
For MM3 the values of A, B and C are constants equal to the default values.
NB: The second B in the equation (to give B^2 in the quartic term) is missing
in the original MM3 paper, but is added in the later literature.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also spring squaredharmonic forceconstant harm

mode

Type Option
Format mode
value <kpoint_number> <weight>
e1x e1y e1z
e2x e2y e2z
: : :
eNx eNy eNz
Units cm-1
Use Subsection of observables, used for specifying vibrational modes for
fitting to. This option differs from frequency in that instead of
supplying the mode number the eigenvectors for the modes are given.
GULP will then project all modes on to the eigenvectors and fit the
mode frequency with maximal overlap. This is mainly useful for fitting
ab initio vibrational data. Here e1x denotes the x vibrational eigenvector
component for atom 1, etc, up to the Nth atom. In the output of fitting
the overlap with the mode is given in the comparison of initial and final
values.
The second number after the frequency is optionally the k point number
to fit at with reference to the k point list for the present
configuration. Only currently implemented for real eigenvectors at
present and so only the gamma point should be used.
NB: The number of atoms whose eigenvectors are input corresponds to the
number of fully occupied core sites (as only these have vibrations).
Care must be taken when using shells or sites with multiple partial
occupancies.
NB: It is NOT recommended to use this option with relaxed fitting.
This is because optimisation will cause the frame of reference for the
system to change and so the projection may not be valid.
NB: It is important that the order of the atoms in the eigenvector list
matches that the GULP uses after the input is read in. Note that GULP
can sometimes change the order of the input atoms, though since usually
this only involves placing cores at the start and shells at the end
then this wouldn't alter the ordering of core eigenvector atoms.
See also observables elastic phonon piezoelectric sdlc hfdlc weight frequency

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

molatom

Type Option
Format molatom atom1 atom2 ...
Default Search over all atoms for molecules.
Use Specifies the atoms that are within a given molecule. This speeds up the
search for bonds and images by restricting the search to a given set of
atoms. The atom numbers refer to the order that the atoms are input to
the program.
e.g.
molatom 13 16 18 20 22
If molatom is used then this implies that the user must specify all
molecules manually. NB: A molecule must have 2 or more atoms otherwise
the molatom option will be ignored since individual atoms need not be
in a molecule.
See also molecule molq molmec nobond bond noautobond uff_bondorder bondtype
connect rigid molrigid

molrigid

Type Option
Format molrigid Natom Ncore
atom1 atom2 ... atomN
Q1 Q2 Q3
COM-x COM-y COM-z
atom1_x0 atom1_y0 atom1_z0
atom2_x0 atom2_y0 atom2_z0
: : :
atomNcore_x0 atomNcore_y0 atomNcore_z0
Units Quarternions are unitless, Cartesian coordinates of atoms in Angstroms.
Centre of mass is in fractional/Cartesian appropriate to the periodicity
of the system.
Default Search over all atoms for molecules.
Use Specifies the atoms that are within a given rigid molecule, similar to
the molatom option. Here the rigid molecule quaternions and centre of
mass are also given, as well as the coordinates of the atoms in the
reference frame. Normally this is written out by GULP and used for
restarting. NB: Natom is the number of atoms in the molecule, while
Ncore is the number of cores. All cores must appear in the atom list
before any shells.
If molrigid is used then this implies that the user must specify all
molecules manually. NB: A molecule must have 2 or more atoms otherwise
the molrigid option will be ignored since individual atoms need not be
in a molecule.
NB: When symmetry is being used then the quaternions take the value
of the equivalent molecule in the asymmetric unit and so the values
output here will not be the correct values for symmetry-related images
See also molecule molq molmec nobond bond noautobond uff_bondorder bondtype
connect rigid molatom

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 delay_force end_force sample

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 qreaxff

morse

Type Option
Format morse <intra/inter> <bond/x12/x13/x14/o14/g14> <kcal/kjmol> <zero> <scale14> <etaper> <ener/grad> <type_of_bond>
atom1 atom2 De a r0 <coul> <rmin> rmax <3*flags>
Units De in eV, a in Angs-1, r0 in Angs, coul in none
Default coul = 0.0
Use Morse potential - optimisation flags for fitting.
coul = 1.0 => Coulomb subtracted.
coul = 0.0 => not Coulomb subtracted.
The format of the data assumes that rmin is the least important
entry. I.e., if one of the optional parameters, coul or rmin,
is missing it is assumed that coul is present and rmin
is set to zero.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = De.((1-exp(-a(r-r0)))**2 - 1.0) - coul.qi.qj/r
If "etaper" is specified then the potential is scaled by:
exp(-1/(rmax-r))
to ensure that the potential (excluding the Coulomb subtraction)
goes to zero at the cutoff. In this case, the energy/gradient
options cannot be used.
Note that the potential can also be written as:
E = De.(exp(-2a(r-r0)) - 2exp(-a(r-r0))) - coul.qi.qj/r
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
The words energy or gradient may be given on the first line resulting
in energy or gradient offsets being applied such that the specified
quantity goes to zero at the cutoff distance.
If the "zero" sub-option is specified then the energy of the potential
is calculated relative to zero at the minimum rather than at dissociation.

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. The radius value must not be less than the region 1
radius and not greater than the region 2a value.
See also defect centre size region_1 vacancy interstitial
impurity bulk_noopt

murrell-mottram

Type Option
Format murrell-mottram <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K rho r012 r013 r023 <rmin(1-2)> rmax(1-2) <rmin(1-3)>
rmax(1-3) <rmin(2-3)> rmax(2-3) <5*flags>
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 <11*flags>
Units K in eV, r012,r013,r023,rmin,rmax in Angstroms
Use Specifies the Murrell-Mottram three-body potential;
E(three) = K.P(Q1,Q2,Q3).exp(-rho.Q1)
P(Q1,Q2,Q3) = c0 + c1.Q1 + c2.Q1**2 + c3(Q2**2 + Q3**2) + c4.Q1**3 +
c5.Q1(Q2**2 + Q3**2) + c6(Q3**3 - 3.Q3.Q2**2) +
c7.Q1**4 + c8.Q1**2.(Q2**2+Q3**2) + c9.(Q2**2+Q3**2)**2
+ c10.Q1(Q3**3 - 3.Q3.Q2**2)
R1 = (r12-r012)/r012 R2 = (r13-r013)/r013 R3 = (r23-r023)/r023
Q1 = (R1+R2+R3)/sqrt(3) Q2 = (R2-R3)/sqrt(2) Q3 = (2*R1-R2-R3)/sqrt(6)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2, 2-3 and 1-3 are bonded.
See also three-body angle axilrod-teller stillinger-weber bcross urey-bradley
exponential bacross hydrogen-bond equatorial uff3 3coulomb
bagcross j3 ppp3body

mutation

Type Option
Format mutation initial <final> <stepsize>
Default 1/(sum of discretisation values) <initial> <0.0>
Use Part of ga options section. Specifies the mutation probability
The higher the value, the more likely it is that mutations will
occur. If <initial> value is less than <final> value then after
20 iterations tournament is incremented by <stepsize>. If the optimisation
is stuck in a local minimum then either (i) if stepsize non-zero tournament
is reset to <initial> OR (ii) grid fixed then mutation rate changed.
See also genetic anneal grid

name

Type Option
Default none
Use Allows you to associate a one-word name with a particular
structure which is then displayed in the input banner for
that structure. Helps in indentification when working
with multiple structures in the same input file.
This option must precede the geometry specification for
a structure to avoid ambiguity in cases of multiple
structures.
Example:
name alumina

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 fvectors

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 non-zero value then a random
displacement is applied to the initial coordinates of each
replica. The input value is used to scale a random number
between 0 and 1.
See also nebspring nebtolerance nodneb
nebreplica nebtangent neb nebiterations rcartesian
fcartesian rfractional ffractional rcell fcell fvectors

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
greater than 2 and controls how accurately the reaction path is
discretised.
See also neb nebspring nebtolerance nodneb synchronous
nebtangent nebrandom nebiterations rcartesian fcartesian
rfractional ffractional rcell fcell fvectors

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 fvectors

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 fvectors

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 synchronous
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional rcell fcell fvectors

nmr

Type Option
Format nmr symbol chemical_shift_reference mean_shift fq
Units ppm for chemical_shift_reference and mean_shift, unitless for fq
Default None
Use Allows species specific parameters to be set for use in the
calculation of NMR chemical shifts within the Pacha method.
element
nmr C2 185.4 155.95 1.0
end
Command is part of element section.
See also element

nobond

Type Option
Format nobond species1 species2
Use Excludes bond formation between two species during molecule search.
See also molecule molq molmec bond connect noautobond bondtype molatom

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 qreaxff fbond fangle reaction young poisson coordno
sqomega volume fenergy

odirection

Type Option
Format odirection <frac> x_in y_in z_in x_out y_out z_out
Units dimensionless
Default no directions
Use If the frequency dependent properties are required for a
particular in/out direction combination then this option
specifies the 2 directions.
NOTE : This option only applies to a gamma point calculation
By default the directions are assumed to be in Cartesian space
unless the "frac" sub-option is given in which case they will
be taken relative to the crystal axes.
See also phonon omega omega_damping

omega

Type Option
Format omega frequency frequency_step no_of_steps
Units cm-1
Default frequency = frequency_step = 0.0 no_of_steps = 0
Use Specifies that frequency dependent properties be calculated
over a given range. "frequency" represents the initial frequency
while "frequency_step" is the interval between calculations.
Example:
omega 500.0 100.0 5
the above would calculate properties at a frequencies of 500,
600, 700, 800, 900 and 1000 cm-1. A no_of_steps = 0 implies a
calculation at a single frequency.
In the output of the frequency dependent dielectric constant
the first line contains the real part of the dielectric
function and the second one the complex part.
NOTE : This option only applies to a gamma point calculation
See also phonon odirection omega_damping

omega_af

Type Option
Format omega_af <rads> frequency <B> <v_s> <v_p>
Units cm-1 for frequency, s/km**2 for B, m/s for v_s and v_p
If "rads" is specified as a sub-option then B is in 10^14 rads**2/s
and frequency is in 10^12 rads/s.
Default 0.0
Use Specifies the minimum frequency to be used in a thermal conductivity
calculation in the Allen-Feldman contribution. If this option is
included then the contribution from propagating modes will be added
based on integrating the result for the Debye model from 0 to omega_af.
This relies on finding an approximation to the phonon lifetime as a
function of frequency based on the expression:
tau = B*omega**-2
from which the propagating contribution to the thermal conductivity
can be estimated by;
kappa_pr = 4*pi*k_B*(c**3)*B*omega_af*(2/v_s + 1/v_p)/3
where k_B is Boltzmann's constant, c is the speed of light, omega_af
is the frequency boundary between the propagating and Allen-Feldman
contributions and v_s/v_p are the velocities of the propagating
s- and p-waves, respectively.
This expression for B/omega_af in rads is:
kappa_pr = [k_B*B*omega_af/(2*pi**2)]*(2/v_s + 1/v_p)/3
If no value of v_s/v_p is input then these are approximated by the s- and
p-wave velocities calculated in the properties according to the Reuss
definition. If no value of B is input, then this is computed based
on a simple approximation. Here the maximum peak in the Allen-Feldman
mode diffusivity below omega_af is found and then this is used to
determine the value of B via a one point fit using;
D_pr(omega) = (1/3)*v_s**2*B*omega**-2
where D_pr(omega) is the mode diffusivity at the frequency of the
maximum, omega, below the cutoff. If there are no modes below the
value of omega_af specified then the propagating contribution can
only be computed if B is input manually. A more accurate value of
B could be found by fitting the low frequency Allen-Feldman region
outside of GULP and then using this as input.
See also thermalconductivity broaden_dos temperature lorentzian_tolerance

omega_damping

Type Option
Format omega_damping damping_factor
Units cm-1
Default 5.0 cm-1
Use Applies a damping factor to the frequency dependent optical
properties. This broads the peaks and prevents a singularity.
Note that the value is constrained to be greater than 1 x 10^-6
to ensure numerical stability.
See also omega odirection phonon

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.

outofplane

Type Option
Format outofplane <inter/intra> <bond> <only3> <kcal/kjmol>
atom1 atom2 atom3 atom4 k <k4> <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) <rmin(1-4)> rmax(1-4) <1-2 x flag>
Units k in eV*Angs**-2, k4 in eV*Angs**-4
Default rmin values = 0, k4 = 0
Use Out of plane energy - harmonic energy penalty for atom 1 lying
out of the plane of atoms 2, 3 and 4. Used for ring systems
which should be planar:
E = k.d**2 + k4.d**4, where d=distance to the plane
If the only3 sub-option is specified then the potential applies where an atom has exactly
3 bonds present.
See also torsion ryckaert torangle torharm torexp xoutofplane inversion xangleangle

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, pdf, qbo, cosmo, lammps, lammps_pots, dcd, eig
cml, inertia, kpt, castep_phonon, shengBTE, dipole, xsf :
marvin - generates a file suitable for input to Marvin for
surface calculations. Index of surface plane needs to be
added first, though this may be passed through GULP to the
marvin input but using the "marvin" option. If the file
extension ".mvn" is not given by the user it will be added
by the program.
e.g. output marvin alumina produces alumina.mvn
If a file for Marvin2 is required, then use the sub-option
marvin2 instead.
e.g. output marvin2 alumina
thbrel - converts the final bulk structure into a file format
suitable for the THBREL suite of programs. Not all features
are readily transferable between the programs so no guarantee
is made that the input file is perfect and for similar reasons
both programs may not always yield the same results unless the
user is careful to make sure the files are equivalent. If a
phonon run has been requested then the output is modified for
THBPHON instead of THBREL.
xtl - this is only applicable to crystal structures with a
single structure per file. Produces a .xtl file for input
into the BIOSYM software, though use of the archive file is
better unless symmetry is present. If the filename input is
not already terminated with ".xtl" then this will be added
by the program.
e.g. output xtl alumina produces alumina.xtl
xr - this will output a modified CSSR file suitable for
input into the Oxford Materials graphical interface
program Crysalis. The file will have the extension ".xr"
added. At the moment this is only applicable to 3D
systems.
e.g. output xr alumina produces alumina.xr
cssr - this will output a CSSR file suitable for input
into the MSI graphical interface Cerius2. The file will
have the extension ".cssr" added. At the moment this
is only applicable to 3D systems.
e.g. output cssr alumina produces alumina.cssr
arc - alternatively known as a ".car" file. This option produces
archive files suitable for input into the BIOSYM Insight software
and will handle bulk, cluster and defect calculations, all with
multiple structures. The username should input a root name,
e.g. output arc alumina
The program will then produce archive file names with either
"_3D", "_defe", or "_0D" appended to distinguish the files
resulting from a particular section of the run. If multiple
structures are present then an underscore followed by the
structure number will be added, all followed by ".arc".
e.g. if the above input for alumina contained two bulk structures
then the files produced would be "alumina_bulk_1.arc" and
"alumina_bulk_2.arc".
If the word "movie" is specified then all structures during an
optimisation will be included in the arcfile, rather than just
the final one, so that the optimisation may be viewed.
e.g. output movie arc alumina
Note : for MD runs the name of the archive file is set by
"mdarchive" to avoid overwriting the optimisation archive
file if present. Also in the case of MD the file is only
written during the production phase.
It is also possible to specify a frequency for the output:
e.g. output movie 5 arc alumina
This would output an archive file frame every 5 steps during the
movie. The default is to output at every step.
NB: The residue field has now been changed to contain the molecule
number, rather than the atom number or a dummy string.
xyz - this will output an xyz file suitable for
input into programs such as Molden and with slight
modification Unichem. The file will have the extension ".xyz"
At the moment this is only applicable to non-periodic
systems. When called with a periodic case just the Cartesian
coordinates will be output, without the unit cell.
e.g. output xyz cluster produces cluster.xyz
If the word "movie" is specified then all structures during an
optimisation will be included in the xyz file, rather than just
the final one, so that the optimisation may be viewed.
e.g. output movie xyz cluster
trajectory - this is a binary file which stores the coordinates
and velocities from a molecular dynamics run, as well as some
of the system properties. This file is used by the Cerius interface
to generate a .trj file for analysis in Cerius. Note that this
file is only written during the production phase by default.
e.g. output trajectory alumina
For this sub-option the further option "ascii" may be specified
in order to obtain an ASCII format trajectory file. Note that
this is less efficient for disk space usage!
e.g. output trajectory ascii alumina
Furthermore, the sub-option "equil" may be added to force writing
during the equilibration phase of the simulation.
The default extension for this file type is .trg
history - this is a text file in the DLPOLY HISTORY file format
containing the structure and velocities sampled from a MD run.
This file can be used for post-MD analysis using the same
programs as for DLPOLY such as "After".
fdf - this is a text file in the Flexible Data Format of Alberto
Garcia and Jose M. Soler. This file can then form the basis of
an input deck for the program SIESTA.
drv - this is a text file containing the energy and appropriate
derivatives calculated by GULP at the last function evaluation.
This can be used for QM/MM schemes. Note that if freezing is
being used then second derivatives may not be output since not
all derivatives may be calculated. To turn off freezing then
specify the keyword "noexclude".
frc - this is a text file containing the energy and appropriate
force constants for cores only calculated by GULP during a phonon
calculation. This can be used for QM/MM schemes, such as in the
program QMPOT. A phonon calculation must be specified otherwise
no file will be output. NB: Force constant matrices can also be
output in a format suitable for ShengBTE and Phonopy using the
output shengbte option.
cif - this is only applicable to crystal structures with a
single structure per file. Produces a .cif file for input
into a variety of programs. If the filename input is
not already terminated with ".cif" then this will be added
by the program. Note that at present the files are output
in P1 regardless of symmetry for simplicity.
e.g. output cif alumina produces alumina.cif
Strictly speak a cif file is only valid for 3-D systems, but
files can be output from GULP for 0-D, 1-D and 2-D with the
addition of a dummy cell parameter. This value can be set
from the option:
e.g. output cif 12.0 surface
will create a 3-D cif file with a dummy lattice parameter of
12 Angstroms for directions that are non-periodic. The default
dummy lattice parameter is 0 which implies that a cif file
shouldn't be written for the wrong periodicity.
str - this is a file in the CRYSTAL98 format, suitable for
reading by DLV. If the filename input is not already
terminated with ".str" then this will be added. If multiple
structures are specified then the filename will be modified
so that a separate file can be written for each structure.
phonon - this option leads to the density of states from a
phonon calculation and any dispersion curve points being
output to the files <filename>.dens and <filename>.disp,
respectively, in a format suitable for input into a curve
plotting program. If the sub-option "ir" is specified then
the density of states will be weighted by the IR intensities
e.g. output phonon ir alumina
frequency - this option produces a list of frequencies over all
k points for use in an analysis program. A typical application
might be in the calculation of the Gruneisen parameter by
differencing of the frequencies with respect to the cell volume.
The file can either be output in binary format (to maintain
precision - the default):
e.g. output freq binary <filename> <ndecimal>
or as ordinary text:
e.g. output freq text <filename> <ndecimal>
Here the optional value of ndecimal specifies how many decimal
places you get (up to a maximum of 12 since going further than
this would be non-sensical in double precision!).
pressure - this option outputs a file containing the pressure
tensor during a molecular dynamics run, both instanteously and
as an average. File is output as <filename>.pre using units of
GPa.
osc - this is a text file containing the oscillator strengths
for the phonon modes so that the frequency dependent data can
be handled in post processing. In this file the frequencies
are in wavenumbers, while the oscillator strengths are in cm^-2
pdf - this option sets the name for the .wid and .pdf files
created by the pdf keyword. The .wid file can be suppressed by
the nowidth keyword.
cosmo - this outputs a COSMO file in the Accelrys format for
visualisation of information relating to solvation an the
solvent accessible surface
lammps - this outputs a LAMMPS input files for a system based on
the information available to GULP. This includes a .lmp file
containing the structure and bonding information. If followed by
"var" then variable names will be used in the output.
lammps_pots - this outputs a LAMMPS file containing a tabulation
of any twobody potentials. There are 3 addition pieces of information
that can be provided which are the start of the range, r0, the end
of the range, rend, and the number of points, np.
e.g. output lammps_pots 0.1 9.0 1000 myfile
This would create a table from 0.1 to 9.0 Angstroms with 1000 points
and write it to a file called myfile.
cml - this is a Chemical Markup Language output file which
contains all the important information about the calculation
in an XML format. This output is suitable for various database
tools and for data transfer between CML-enabled applications.
eig - this outputs the eigenvectors for each K point as a file.
qbo - this file contains the charges and bond orders, as appropriate,
for a potential model.
e.g. output qbo myfile
The above command would produce a file myfile.qbo containing the
charges and bond orders for the final configuration. If the
values for all structures are required then the sub-option "append"
can be used:
e.g. output qbo append myfile
dcd - this file contains the coordinates from an MD trajectory and
can be used by programs such as VMD for analysis and visualisation.
inertia - output information on the moment of inertia tensor for
molecules at the final structure for each configuration
castep_phonon - this file contains the phonon information from multiple
K points in the same format as used for the program CASTEP. The default
extension for this is ".csp":
e.g. output castep_phon myfile.csp
kpt - this file list the k points within the asymmetric unit of the
Brillouin zone along with the symmetry unique images of the k point.
shengBTE - this causes the files needed to perform a ShengBTE run to be
output. This usually comprises the files CONTROL, FORCE_CONSTANTS_2ND,
FORCE_CONSTANTS_3RD that contain the system information and control
parameters, the second order force constants, and the third order force
constants, respectively. Note that the FORCE_CONSTANTS_2ND file is also
suitable for use with Phonopy.
NB: Since the calculation of the third order force constants is
potentially expensive expect this option to substantially increase
the computational cost of a run!!! The use of the keyword nod3 allows
the ShengBTE output to be restricted to second derivatives only.
NB: The option "threshold" controls the minimum size for force constants
to be output as non-zero
dipole - this causes GULP to output a text file that contains the
dipole of the system for each time step of a molecular dynamics run.
If the delta_dipole keyword is specifed then the dipole is computed
relative to the initial value. The units of the dipoles for this file
are Debye and the format has the current time in ps follow by the
three Cartesian components in the order x, y and z.
xsf - output a file in XCrySDen format. When performing MD it is possible
to output either a single XSF file or a sequence of files for single
frames with a number appended to differentiate them. The format is:
output xsf <seq/sym> myfile
where seq (sequential) is optional but if specified will result in multiple
files being output during molecular dynamics. Here myfile is the root name
for the file. For example;
output xsf seq myfile
would produce myfile000001.xsf, myfile000002.xsf, etc. If "sym" is specified
then atomic symbols are used instead of atomic numbers in the files. This
is relevant if using Aenet which expects symbols, whereas XCrySDen specifies
atomic numbers for the format.
cfg - output a file in the CFG format for reading by Ovito and AtomEye.
Optional quantities can be triggered by specifying a string with the
relevant letters after "-":
e => energy
f => root mean square force
x => forces in x
y => forces in y
z => forces in z
q => charges
d => change in charges
To trigger the output of all of these options the input would be:
output cfg -efxyzqd myfile
where "myfile" is the name of the cfg file.
See also marvin dump ghost_supercell num3 numerical shopt threshold nod3

p_flexible

Type Option
Format p_flexible
p_flx(1,1) p_flx(2,1) p_flx(3,1)
p_flx(1,2) p_flx(2,2) p_flx(3,2)
p_flx(1,3) p_flx(2,3) p_flx(3,3)
Use Used only for restarting a molecular dynamics simulation with the
stochastic integrator. Not intended for user input.
See also integrator

p_isotropic

Type Option
Format p_isotropic <value>
Use Used only for restarting a molecular dynamics simulation with the
stochastic integrator. Not intended for user input.
See also integrator

parallel

Type Option
Format parallel <avoid_communication>
Units none
Default Use communication.
Use This option controls various settings that relate to the
parallel algorithms used, where choices exist.
avoid_communication - if specified then communication is
minimised by recalculating on each node for some parts of
the code.
See also maths matrix_format blocksize

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 twist

pdf

Type Option
Format pdf <all>
<further options>
end
Use Opens pdf input block. This is used for the input of options used by pdf
calculations. Specifically, it should be used for the pdf options
rmax, rbins, wmax, wmin, units.
The block is opened with the word pdf and all further options read are
treated as pdf-related until the word end.
When working with multiple configurations, one pdf input block is needed
per configuration, unless the option all is given, when the options act on all
configurations. This allows PDF output to be comparable between configurations.
See also PDFcut PDFkeep nowidth nofreq rmax rbins wmax wmin units bbar siginc xray

pfinite

Type Option
Format pfinite delta
Default 0.00001
Units Angstroms
Use Sets the finite difference intervals to be used for the numerical
evaluation of phonons by central finite differencing of the
analytic first derivatives.
See also numerical sfinite

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

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
young poisson shear voigt bulk

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 Lennard-Jones potential between atom1 and a plane.
Because the method is only applicable to 2-D systems the plane
is assumed to be parallel to xy. The absolute position in z
is given by zcoord. For example to include an integrated L-J
12-6 potential (which would give m=10 and n=4) that acts on carbon
positioned at -0.75 Ang the input would look like:
plane_lj 10 4
C core -0.75 1000.0 14.0 0.0 12.0
See also lennard einstein

plumed_input

Type Option
Format plumed_input <plumed_file_name>
Units none
Default plumed_file_name = plumed.dat
Use By specifying this option GULP tried to use the plumed
plug-in with the input for this coming from an external
file.
See also md plumed_log

plumed_log

Type Option
Format plumed_log <plumed_log_name>
Units none
Default plumed_log_name = plumed.log
Use Specifies the name for the log file from Plumed
See also md plumed_input

pointsperatom

Type Option
Format pointsperatom <no. of points per atom>
Default 1082 (for dodecahedron) / (974 for octahedron)
Units None
Use Specifies the number of points per atom for the basic
sphere used to construct the solvent-accessible surface
in a COSMO calculation. The value must conform to the
following formula :
Dodecahedron
pointsperatom = 10*(3**k)*(4**l)+2
Octahedron
pointsperatom = 4*(3**k)*(4**l)+2
where k and l are integers. The larger the value of
this parameter, the more precise and expensive the
calculation will be.
See also cosmo segmentsperatom solventepsilon solventradius
solventrmax vdw cosmoshape rangeforsmooth

poisson_ratio

Type Option
Format poisson_ratio <n>
<xy/xz/yz> poissons_ratio <weight>
Units Dimensionless
Default no Poissons ratios to be fitted
Use Subsection of observables, used for specifying values of
Poisson's ratios for fitting.
Example To fit a Poisson's ratio of 0.23 for the x-z component
with a weight of 0.01:
poisson 1
xz 0.23 0.01
NB: The Poisson ratios are computed assuming that the
material is linear elastic orthotropic.
See also elastic sdlc hfdlc weight srefractive hfrefractive bornq
piezoelectric young shear voigt bulk

polarisability

Type Option
Format polarisability <damp> <bdamp> <langevin>
atom_symbol <core/shell> dipolar_polarisability <dipole_max>
Units dipolar_polarisability in Angs**3, bdamp in inverse Angstroms
dipole_max in a.u.*Angstroms (i.e. charge in atomic units and
distance in Angstroms)
Default Polarisability is equal to zero, except for shell contribution
bdamp = 0.0
Use Allows the inclusion of point ion polarisability in a calculation.
At the moment this is non-self consistent, i.e. induced moments on
different centres do not interact.
If "damp" is specified as a sub-option then short-range damping is
applied to the charge-dipole interaction using the Tang-Toennies
form as proposed by Madden and Wilson. The range of the damping is
controlled by the factor bdamp.
If "langevin" is specified as a sub-option then the induced dipole
is computed using a Langevin function that causes the dipole moment
to saturate at a maximum value, dipole_max. If this sub-option is
present then dipole_max must be specified and greater than zero.
See also spin

polynomial

Type Option
Format polynomial <harmonic> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
norder
atom1 atom2 (norder+1)*coeff <r0> <rmin> rmax <(norder+1)*flags>
order of coefficients = lowest to highest
Units eV and Angstroms
Default r0 = 0
Use Polynomial potential, order = 1-8:
E = c0 + c1*(r-r0) + c2*(r-r0)**2 + ... + cn*(r-r0)**n
If sub-option harmonic is specified, then the polynomial is premultiplied
by a harmonic term:
E = (r - r0)**2 * (c0 + c1*r + c2*r**2 + ... + cn*r**n) for r < r0
E = 0 for r > r0
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)

potential

Type Option
Format potential <reverse> <au>
x y z V <weight>
If "reverse" is specified then order is:
V x y z <weight>
Units V is in eV per electron charge in a.u., x, y and z are
the fractional coordinates of the site for a 3D system
or the cartesian coordinates for an isolated molecule.
Use Specifies the electrostatic potential at a given point
in space for use in fitting of electrostatic potential
surfaces as a means of deriving charges. This option is
a sub-option of the observables section.
See also zero_potential potsites pot potgrid

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.

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.
NB: If symmetry is turned off using the "nosym" option then the
fractional range will apply to the new cell that is generated.
See also pot potential potsites

potsites

Type Option
Format potsites <cart> <au>
x1 y1 z1
x2 y2 z2
etc.....
Units fractional/Cartesian as appropriate to dimensionality
Default none
Use Allows the user to specify points in space at which the electrostatic
potential should be calculated. Note that it is necessary to also
specify the "pot" keyword to trigger the calculation of the potential.
NB: If the potential sites are specified using fractional coordinates
for a centred cell (e.g. hexagonal) then they will be transformed to
the primitive setting automatically for consistency. In other words
the fractional coordinates are taken to be in the same frame of reference
as for the atomic coordinates input.
NB: If symmetry is turned off using the "nosym" option then the
fractional coordinates will be transformed as per the atomic fractional
coordinates.
See also pot potential potgrid

ppp3body

Type Option
Format ppp3body <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K rmin12 rmin13 rho <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3)
<rmin(2-3)> rmax(2-3) <4*flags>
Units K in eV, rho in Angstrom**-1, rmin12 and rmin13 in Angstrom
Use Threebody potential from the PPP coarse-graining approach
E(three) = K*exp(-rho*r13)*P(r12)*P(r13)
here P(r12) is a fifth order polynominal that switches between 1 at r12 < rmin12
and 0 for r12 > rmax(1-2) and P(r13) is the same thing for r13. Note that rmin12
is not the same as rmin(1-2) which should usual be zero for this potential.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2, 2-3 and 1-3 are bonded.
See also three-body angle axilrod-teller stillinger-weber bcross urey-bradley
murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb
exp2 bagcross j3 exponential

pressure

Type Option
Format pressure value_of_pressure <GPa/kPa/MPa/Pa/atm/Nm-2/kbar>
Units Gigapascals, kilopascals, megapascals, pascals, atmospheres, kbar (Default = GPa)
Default 0 GPa
Use Specifies pressure to be applied to structure. Causes energy to be
replaced by enthalpy in calculations.

primitive_vectors

Type Option
Format primitive_vectors npcore <angs/au>
x y z for vector 1
x y z for vector 2
x y z for vector 3
Units Angstrom (default) or au
Use Specifies the cartesian components of the primitive lattice vectors
as well as the number of cores in the primitive cell (npcore).
This option is for the benefit of thermal conductivity calculations
where the primitive cell is used to reduced the cost. The cell vectors
must still be specified using cell or vectors. Usually this option will
be written by GULP for restarting purposes, rather than added by the user.
See also cell vectors

print

Type Option
Format n = integer no.
Use Prints out current parameters during fitting whenever cycle number is
exactly divisable by n.
See also dump

production

Type Option
Format production value <s/ns/ps/fs>
Units s, ns, ps or fs - if integer, then value is by default
a multiple of the timestep or if non-integer then by
default is the time in picoseconds.
Use Specifies the simulation time to be spent collecting
production data for subsequent analysis.
See also md equilibration sample write temperature timestep
tscale nolist delay_force end_force momentum_correct

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 Projects the phonon density of states onto given sets of atoms.
Note that this requires the explicit calculation of the eigenvectors
for each k point. Atoms for projection must be cores and not
shells as the shells have no component in the DOS. Projections
will also be output to the .dens file if requested.
Examples:
To project on to atoms 4, 7 and 10:
project_dos 1
4 7 10
To project on to all species C1 and O3:
project_dos 1
C1 O3
NB: If an atom is part of a rigid molecule then the modes associated
with this molecule will be assigned as an equal fraction to each atom
in the molecule.
See also phonon eigenvectors output

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.
NB: For non-periodic systems there is no need to specify a vector
See also pcell scell svectors cell vectors

qelectronegativity

Type Option
Format qelectronegativity
<Atomic_symbol/atomic_number> chi <mu> <radius> <Q0> <E0> <3 x flags for fitting>
or
qelectronegativity <qrange/qmin/qmax>
<Atomic_symbol/atomic_number> chi <mu> <radius> <Q0> <E0> <qmin> <qmax> <3 x flags for fitting>
Units Chi, mu, and E0 in eV, radius in Ang, Q0, qmin, qmax in a.u.
Default Q0 = 0.0, E0 = 0.0
Use Allows the user to specify the parameters needed for the
QEq electronegativity equalisation method for determining
charges. Note that if the flags are not specified they
are assumed to be zero.
Q0 is the charge about which the electronegativity equations
are quadratic. In most methods this is zero, but need not be.
For example, the EQeq method assigns values of Q0 not equal
to zero.
E0 is an additive constant for the energy of an atom. This is
only really needed when using multiple q ranges to ensure
energy matching.
The sub-options qrange, qmin, and qmax control whether the
values apply for a given value of charge. By default the values
apply to all values of charge (q). If qmin is specified then
they are only applied to charges larger than qmin, while if qmax
is given the they are applied when q is less than qmax. When
qrange is specified then the values apply for qmin =< q < qmax.
NB: If no parameters are input then the default values will be
used for all charge values. However, if parameters are input
then this will override the default values and the user must
set parameters for all relevant ranges of charge.
See also eem electronegativity qeq smelectronegativity noqeem external_potential
eembond

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 noqeem

qeqradius

Type Option
Format qeqradius radius <taper_range>
Units Angstroms
Default 15.0 Ang with taper over 3 Ang
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.
NB: This radius also applies to the SM charge scheme
See also eem qeq qeqiter qeqtol dcharge noqeem sm

qeqtol

Type Option
Format qeqtol tolerance
Units Electrons
Default 0.0000001
Use Sets the tolerance on the change in the charges between
iterations of the QEq electronegativity equalisation
scheme. This only applies to systems which contain
hydrogen.
See also eem qeq qeqiter qeqradius dcharge noqeem

qerfc

Type Option
Format qerfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <au/nm/pm> <ener/grad> <type_of_bond>
atom1 atom2 rho rmax <1*flag>
Units rho and rmax in Angstroms
Default none
Use Screened Coulomb interaction using the complementary error function.
E = [qi.qj/r].erfc(r/rho)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
NOTE : The keyword "noelectrostatics" should be included when using
this potential to turn off the normal Ewald sum, otherwise the
Coulomb interaction will be double counted.
See also noelectrostatics

qgrid

Type Option
Format qgrid nqx nqy nqz
Units none
Default nqx = nqy = nqz = 24
Use Specifies the grid dimensions for use in SPME. It is important that the
user checks that the energy is converged with respect to this grid. The
size will depend on the system and weighting between real/reciprocal
space chosen. The grid dimension must be large than or equal to the B spline
order (default = 8)
See also rspeed veck accuracy ewaldrealradius spme bspline

qincrement

Type Option
Format qincrement
atom1 atom2 delta <1*flag>
Default delta = 0.0
Use If the keyword qbond is given then the charges on the atoms are
determined by bond increments given by this option. An example
of the input is:
qincrement
O2 core C core -0.24
O3 core C core 0.15
NB: The order of the atoms is important in that the sign of delta
changes if the order is reversed. Consequently if atom1 and atom2
are of the same type then delta must be zero. Hence, the value of
delta is applied with the input sign to atom1 and the negative of
this to atom2.
See also qeq eem gasteiger qbond noqeem eembond

qiterations

Type Option
Format qiterations n <convergence_tolerance>
Default n = 200, convergence_tolerance = 0.00000001
Use Allows the user to change the default number of iterations and
convergence tolerance for iterative charge solves triggered by
the qiteration keyword
See also qiterative

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 0-D calculations with
up to first derivatives are generally enabled for all models.

qonsas

Type Option
Format qonsas total_charge
Units Atomic units (i.e. electrons)
Default 0.0
Use Specifies the total charge on the SAS for the COSMIC method.
Note that for charged systems the SAS will be constructed so
that the charge is neutralised. This option adds to the
default charge on the SAS due to any net charge of the atoms.
See also cosmo cosmic qsas

qoverr2

Type Option
Format qoverr2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <au/nm/pm> <ener/grad>
atom1 atom2 rmax <1*flag>
Units rmax in Angstroms
Default none
Use Computes the charge interaction as a local one based on:
E = [qi.qj/r**2]
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
NOTE : The keyword "noelectrostatics" should be included when using
this potential to turn off the normal Ewald sum, otherwise the
Coulomb interaction will be double counted.
NOTE : This expression is used for the Coulomb term in Accelrys's
implementation of Dreiding.
See also noelectrostatics

qreaxff

Type Option
Format qreaxff <n>
i Qi <weight>
Units atomic units
Default no ReaxFF charges to be fitted
Use Subsection of observables, used for specifying values of
ReaxFF charges for fitting. Note that i is the
atom number in the unit cell, not the asymmetric unit.
Example:
qreaxff 1
1 1.95
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq

qsolver

Type Option
Format qsolver <itpack/lapack/bcg>
Units none
Default itpack (serial) / bcg (parallel)
Use Selects the algorithm for iterative charge solution in COSMO.
Note that itpack can only be used in serial.
See also qiterative parallel matrix_format

qtaper

Type Option
Format qtaper <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 C rmax <1*flag>
Units C in eV, rmax in Angs
Default none
Use Tapers the Coulomb interaction to a constant value, C, at short
distances. Currently implemented crudely as an interatomic
potential to stop Coulomb collapse. However, this won't avoid
numerical errors if atoms are started too close in the first
place. The potential uses a taper from rmax to 0.0 to match the
Coulomb potential using the charges of the species to the constant
value at the nucleus. This potential mimics the fact that at
short range the Coulomb term becomes damped by being an integral
rather than just a 1/r potential.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = [qi.qj/r].f(r) + C.(1-f(r)), where f(r) = polynomial taper
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential cutoffs are omitted from input.

qwolf

Type Option
Format qwolf <original/fennell> <eta> <rmax>
Units eta in inverse Angstroms and rmax in Angstroms
Default none
Use Calculates the electrostatic energy using the approximation to the Ewald
sum due to Wolf et al (J. Chem. Phys., 110, 8254, 1999):
Eij = [qi.qj/r].erfc(eta*r) - lim{r->rmax}([qi.qj/rmax].erfc(eta*rmax))
Ei = - (erfc(eta*rmax)/(2*rmax) + eta/sqrt(pi))*qi**2
Note: it is up to the user to set the eta and rmax values such that the
Ewald limit is recovered. At present the Wolf sum cannot be used with a
defect calculation.
NB: The original Wolf sum has energy and forces that are inconsistent
with each other (i.e. the forces are not the negative first derivative of the
energy). Hence GULP uses forces that are based on the Wolf energy by default.
If you want to force the use of the original Wolf sum then you can use the
"original" sub-option, but don't expect optimisations to converge properly.
You have been warned!
The "fennell" sub-option specifies that the alternative form of the Wolf
sum due to Fennell and Gezelter (J. Chem. Phys., 124, 234104 (2006)) be
used. The advantage of their method is that the potential and force are
consistent while neither is discontinuous at the cut-off radius. The only
downside is that the potential is different from the Ewald result. However,
potential differences (and therefore energetics) should be well-described.
The energy expression for this form is:
Eij = qi*qj*[erfc(eta*r)/r - erfc(eta*rmax)/rmax + (r - rmax)*
(erfc(eta*rmax)/rmax**2 +
(2*eta/sqrt(pi))*exp(-(eta*rmax)**2)/rmax)]
See also noelectrostatics

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.

random

Type Option
Format random ncall1 ncall2 ncall3 <G>
Units None
Default ncall1 = ncall2 = ncall3 = 0
Use This option is used for consistent restarting of runs that utilise
random numbers by keeping track of how many calls were made during
the previous run so that the position in the sequence of numbers
can be recreated on restart. There are three types of random number
generated in GULP at present and so the three numbers are to track the
number of calls for each generator.
The optional letter G at the end indicates that the Gaussian number
generator was called last; this is important in obtaining the proper
sequence going forward in some cases.
NB: This option is not intended for user setting and is included to
explain why this line is present in the restart file.
See also md

rangeforsmooth

Type Option
Format rangeforsmooth <range>
Units Angstroms
Default 0.0
Use Smooths the inclusion of points on the solvent-accessible
surface to make the energy surface more continuous.
See also cosmo pointsperatom segmentsperatom

rbins

Type Option
Format rbins <n>
Default 100
Use Used within the pdf input block for PDF calculations.
Sets the number of bins to be used for PDF correlation function output
See also PDFkeep PDFcut

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 fvectors

rcell

Type Option
Format rcell replica_number
a b c alpha beta gamma (for 3-D)
a b alpha (for 2-D)
a (for 1-D)
Units Angstroms for a/b/c & degrees for alpha/beta/gamma
Default None
Use Specifies the unit cell of a replica for the nudged elastic band
method. This option is primarily useful for restarting. If the
unit cells of the replicas are not given then the values are
initialised based on a linear interpolation between the initial
and final states. The number of cell parameters must match the
dimensionality of the initial system.
See also nebspring nebtolerance nodneb
nebreplica nebtangent nebrandom nebiterations rcartesian
fcartesian rfractional ffractional fcell neb fvectors

rcspatial

Type Option
Format rcspatial rcspatial_value <rcspatial_BO_value>
rcspatial anisotropic rcspatial_x rcspatial_y rcspatial_z <rcspatial_BO_x rcspatial_BO_y rcspatial_BO_z>
Units Angstroms
Default Set equal to the largest potential cutoff in real space.
Use Can be used to set the domain size in the spatial decomposition to make
it smaller than the potential cutoff. In this case looping over multiple
cells is needed.
If the anisotropic suboption is used then a different domain size is applied along each axis.
See also spatial

rdirection

Type Option
Format rdirection <frac> x_in y_in z_in x_out y_out z_out
Units dimensionless
Default x_in = y_in = z_in = x_out = y_out = z_out = 1
Use If the Raman susceptibilites are calculated then this
option specifies in the directions of the incident and
outgoing photons.
NOTE : This option only applies to a gamma point calculation
By default the directions are assumed to be in Cartesian space
unless the "frac" sub-option is given in which case they will
be taken relative to the crystal axes. In all cases, the
directions will be normalised, such that the absolute
magnitude does not influence the result.
See also phonon raman

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
by the target energy and optionally a weight.
Example:
If configuration 1 is H2O, configuration 2 is CO and configuration
3 is the 2H2O...CO complex whose heat of formation is -0.21 eV and
a weight of 10.0 is desired then the input for this would be like:
reaction 1
3 -0.21 10.0 1 -2.0 2 -1.0 3 1.0
i.e. The coefficients are negative for the left-hand side and positive
for the RHS.
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq qreaxff fbond relax reaction

reaxff0_bond

Type Option
Format reaxff0_bond p_boc1 p_boc2 <2 x flags>

reaxff0_lonepair

Type Option
Format reaxff0_lonepair p_lp1 <1 x flag>

reaxff0_over

Type Option
Format reaxff0_over p_ovun3 p_ovun4 p_ovun6 p_ovun7 p_ovun8 <5 x flags>

reaxff0_penalty

Type Option
Format reaxff0_penalty p_pen2 p_pen3 p_pen4 <3 x flags>

reaxff0_torsion

Type Option
Format reaxff0_torsion p_tor2 p_tor3 p_tor4 p_cot2 <4 x flags>

reaxff0_valence

Type Option
Format reaxff0_valence p_val7 p_val8 p_val9 p_val10 <4 x flags>

reaxff0_vdw

Type Option
Format reaxff0_vdw p_vdw1 <1 x flag>

reaxff1_angle

Type Option
Format reaxff1_angle
species <core/shell> p_val3 p_val5 <2 x flags>
Default None
Use Specifies the parameters for the species-wise angle parameters.
p_val3 is used in the calculation of the ReaxFF function f7 (eqn 13b).
p_val5 is used in the calculation of the ReaxFF function f8 (eqn 13c).
See also reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_morse
reaxff1_morse

reaxff1_include_under

Type Option
Format reaxff1_include_under
species <0/1>
Default 1 (yes) for 1st row elements and 0 (no) for everything else
Use In the ReaxFF formalism the under coordination formalism due to pi bonding
is modified for elements with a mass greater than 21 amu. This option
allows the user to select which form of the under coordination correction
is applied for each element. Here a value of 1 => first row formula and 0
implies the 2nd row form. No other values are allowed.
See also reaxff1_under

reaxff1_lonepair

Type Option
Format reaxff1_lonepair
species <core/shell> n_lp_opt p_lp2 <2 x flags>
Default None
Use Specifies the parameters for the species-wise lone pair energy parameters.
n_lp_opt is the optimal number of lone pairs used to construct delta_lp (eqn 9).
p_lp2 is the parameter that scales the lone pair energy for each atom (eqn 10).
See also reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_angle
reaxff1_morse

reaxff1_morse

Type Option
Format reaxff1_morse <au/kcal/kjmol>
species <core/shell> alpha Dij rvdw gamma_w <4 x flags>
Default None
Use Specifies the parameters for the species-wise morse parameters for the
VDW energy (eqns 21a and 21b). In the final morse potential,
Dij = sqrt(Dij(i)*Dij(j)), alpha_ij = sqrt(alpha(i)*alpha(j)),
r_vdw = 2*sqrt(rvdw(i)*rvdw(j))
See also reaxff1_radii reaxff1_valence reaxff1_over reaxff1_under reaxff1_angle
reaxff2_bo reaxff2_bond

reaxff1_over

Type Option
Format reaxff1_over
species <core/shell> p_boc3 p_boc4 p_boc5 p_ovun2 <4 x flags>
Default None
Use Specifies the parameters for the species wise overcoordination parameters.
Parameters p_boc3, p_boc4, p_boc5 are used to compute the functions f4 & f5
that correct the bond order (eqns 4e & 4f). The final parameter, p_ovun2, is
part of the overcoordination energy (eqn 11a).
See also reaxff1_radii reaxff1_valence reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse

reaxff1_radii

Type Option
Format reaxff1_radii
species <core/shell> r_sigma r_pi r_pipi <3 x flags>
Default None
Use Specifies the radii for a species that are to be used in the ReaxFF bond order
calculation. Here the uncorrected bond order is given by:
BO' = exp(p_bo1*(r/r_sigma)**p_bo2) + exp(p_bo3*(r/r_pi)**p_bo4) +
exp(p_bo5*(r/r_pipi)**p_bo6)
The remaining parameters, p_bo1 - p_bo6, are input via the reaxff2_bo option.
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff2_bo

reaxff1_under

Type Option
Format reaxff1_under
species <core/shell> p_ovun5 <1 x flag>
Default None
Use Specifies the parameter for the species-wise undercoordination parameters.
p_ovun5 scales the undercoordination energy (eqn 12).
See also reaxff1_radii reaxff1_valence reaxff1_over reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_include_under

reaxff1_valence

Type Option
Format reaxff1_valence
species <core/shell> Val_normal Val_boc Val_lp Val_angle <4 x flags>
Default None
Use Specifies the valence states for a species that are to be used in the ReaxFF
calculation of delta values. The value of delta' (eqn 3a) is given by:
delta'(i) = - Val_normal(i) + sum(j=1->neigh(i)) BO_ij'
There is a second valence used for delta'_boc (eqn 3b):
delta'_boc(i) = - Val_boc(i) + sum(j=1->neigh(i)) BO_ij'
There is a third valence used for delta_e (eqn 7) as part of the lone pair
energy:
delta_e(i) = - Val_lp(i) + sum(j=1->neigh(i)) BO_ij
There is a fourth valence used for delta_angle (eqn 13e):
delta_angle(i) = - Val_angle(i) + sum(j=1->neigh(i)) BO_ij
See also reaxff1_radii reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse

reaxff2_bo

Type Option
Format reaxff2_bo <over> <bo13>
species1 <core/shell> species2 <core/shell> p_bo1 p_bo2 p_bo3 p_bo4 p_bo5 p_bo6 <6xflags>
Default None
Use Specifies the pairwise parameters between species that are to be used in the
ReaxFF bond order calculation. Here the uncorrected bond order is given by:
BO' = exp(p_bo1*(r/r_sigma)**p_bo2) + exp(p_bo3*(r/r_pi)**p_bo4) +
exp(p_bo5*(r/r_pipi)**p_bo6)
The remaining parameters, r_sigma, r_pi, r_pipi, are input via the reaxff1_radii option.
The two sub-option words control if the bond order is corrected:
reaxff2_bo over => correct for overcoordination using f1
reaxff2_bo bo13 => correct for 1-3 terms using f4 and f5
reaxff2_bo over bo13 => correct for overcoordination using f1 and 1-3 terms using f4 and f5
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bond reaxff2_over reaxff2_morse reaxff2_pen

reaxff2_bond

Type Option
Format reaxff2_bond
species1 <core/shell> species2 <core/shell> De_sigma De_pi De_pipi p_be1 p_be2 <5xflags>
Default None
Use Specifies the pairwise parameters between species that are to be used in the
ReaxFF bond order energy. Here the bond order energy is given by:
E_bond = - De_sigma*BO_sigma*exp(p_be1*(1-(BO_sigma)**p_be2)) - De_pi*BO_pi
- De_pipi*BO_pipi
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_over reaxff2_morse reaxff2_pen

reaxff2_morse

Type Option
Format reaxff2_morse
species1 <core/shell> species2 <core/shell> De alpha r0 r_sigma r_pi r_pipi <6 x flags>
Default None
Use Specifies pairwise Morse potential parameters for ReaxFF
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff2_pen

reaxff2_over

Type Option
Format reaxff2_over
species1 <core/shell> species2 <core/shell> p_ovun1 <1 x flag>
Default None
Use Specifies the pairwise parameters between species that are to be used in the
ReaxFF overcoordination energy. Here the overcoordination energy is given by:
E_over_i = (sum(j=>neigh(i)) p_ovun1(ij).De_sigma.BO_ij).delta_lpcorr(i)
-------------------------------------------------------------
(delta_lpcorr(i) + Val_i) * (1 + exp(p_ovun2*delta_lpcorr(i))
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_morse reaxff2_pen

reaxff2_pen

Type Option
Format reaxff2_pen
species1 <core/shell> species2 <core/shell> p_pen1 p_pen2 p_pen3 <3 x flags>
Default None
Use Specifies pairwise penalty energy parameters for ReaxFF. The penalty energy is
given by:
Epen = sum [ p_pen1 * (BO_ij - delta_i - p_pen2*delta**4 - p_pen3)**2]
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff2_morse

reaxff3_angle

Type Option
Format reaxff3_angle <au/kcal/kjmol>
species1 <core/shell> species2 <core/shell> species3 <core/shell> &
theta_00 p_val1 p_val2 p_val4 p_val7 <p_val6> <6 x flags>
Default None
Use Specifies the parameters that determine the angular valence energy that depend
on a triad of species in the ReaxFF force field. Here species1 is the pivot
atom of the three-body like term. Here the valence energy is given by:
E_val = f7(BO_12)*f7(BO_13)*f8(delta(1))*p_val1*(1-exp(-p_val2*(theta_0 - theta)**2))
The function f7 is given by:
f7(BO) = 1 - exp(-p_val3*BO**p_val4)
If not explicitly given, the value of p_val6 is taken from the global value.
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_pen
reaxff3_conjugation

reaxff3_conjugation

Type Option
Format reaxff3_conjugation <au/kcal/kjmol>
species1 <core/shell> species2 <core/shell> species3 <core/shell> &
p_coa1 p_coa2 p_coa3 p_coa4 <4 x flags>
Default None
Use Specifies the parameters that determine the three-body conjugation energy that depend
on a triad of species in the ReaxFF force field. Here species1 is the pivot
atom of the three-body like term. Here the valence energy is given by:
E_val = p_coa1*(1/(1+exp(p_coa2*delta_1_val)))*
exp(-p_coa3*(-BO_12 + sum(n=1->neighbours of 2) BO_2n))*
exp(-p_coa3*(-BO_13 + sum(n=1->neighbours of 3) BO_3n))*
exp(-p_coa4*(BO_12 - 1.5)**2)*exp(-p_coa4*(BO_13 - 1.5)**2)
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle
reaxff3_hbond reaxff3_angle reaxff4_torsion

reaxff3_hbond

Type Option
Format reaxff3_hbond <au/kcal/kjmol>
species1 <core/shell> species2 <core/shell> species3 <core/shell> r0_hb p_hb1 &
p_hb2 p_hb3 <4 x flags>
Default None
Use Specifies the parameter that determines the hydrogen bonding energy that depends
on a triad of species in the ReaxFF force field (eqn 18). Here species1 is the pivot
atom of the three-body like term and is usually hydrogen.
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle
reaxff3_pen reaxff4_torsion

reaxff3_pen

Type Option
Format reaxff3_pen <au/kcal/kjmol>
species1 <core/shell> species2 <core/shell> species3 <core/shell> p_pen1 <1 x flag>
Default None
Use Specifies the parameter that determines the angular penalty energy that depends
on a triad of species in the ReaxFF force field (eqn 14a). Here species1 is the pivot
atom of the three-body like term.
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle
reaxff3_hbond reaxff3_conjugation reaxff4_torsion

reaxff4_torsion

Type Option
Format reaxff4_torsion <au/kcal/kjmol>
spec1 <core/shell> spec2 <core/shell> spec3 <core/shell> spec4 <core/shell> &
V1 V2 V3 p_tor1 p_cot1 <5 x flags>
Default None
Use Specifies the parameters that determine the torsional energy that depends
on a quartet of species in the ReaxFF force field (eqn 16a). Here the species
are connected 1-2-3-4 to yield the relevant torsional angle.
V1, V2, V3 are the barrier heights for different powers of the cosine of phi.
p_tor1 is a scaling factor for an exponent in the V2 contribution.
p_cot1 is a scaling factor for the conjugation energy (eqn 17a).
See also reaxff1_valence reaxff1_over reaxff1_under reaxff1_lonepair reaxff1_angle
reaxff1_morse reaxff1_radii reaxff2_bo reaxff2_bond reaxff2_over reaxff3_angle
reaxff3_pen reaxff4_torsion

reaxff_chi

Type Option
Format reaxff_chi
species <core/shell> chi <1 x flag>
Default None
Use Specifies the electronegativity for the species in the ReaxFF charge equilibration
scheme.
See also reaxff_mu reaxff_gamma qiterative reaxff_qshell norxQ reaxff_q0

reaxff_gamma

Type Option
Format reaxff_gamma
species <core/shell> gamma <1 x flag>
Default None
Use Specifies the shielding parameter gamma for the species in the ReaxFF charge equilibration
scheme.
See also reaxff_chi reaxff_mu qiterative reaxff_qshell norxQ reaxff_q0

reaxff_mu

Type Option
Format reaxff_mu
species <core/shell> mu <1 x flag>
Default None
Use Specifies the hardness for the species in the ReaxFF charge equilibration
scheme.
See also reaxff_chi reaxff_gamma qiterative reaxff_qshell norxQ reaxff_q0

reaxff_q0

Type Option
Format reaxff_q0
species <core/shell> q0
Default 0.0
Use Specifies the equilibrium isolated species charge in the ReaxFF charge equilibration
scheme.
See also reaxff_chi reaxff_gamma qiterative reaxff_qshell norxQ reaxff_mu

reaxff_qshell

Type Option
Format reaxff_qshell
species <core/shell> dMu Qs beta <3 x flags>
Default dMu = 0.0, Qs & beta no default
Use Specifies the optional shell structure modifier for the ReaxFF charges.
This term adds an extra energy term to the electronegativity equalisation
scheme that suppresses charges above a value Qs. This can often occur due
to shell structure that breaks the validity of the harmonic charge expansion.
The energy penalty takes the form of a fourth-order polynomial:
E_shell(q) = dMu*(q - Qs)**4 for q > Qs ; 0 for q < Qs
See also reaxff_chi reaxff_mu qiterative reaxff_gamma

reaxff_r12

Type Option
Format reaxff_r12
species <core/shell> r12 <1 x flag>
Default None
Use Test modification option at present.
See also reaxff_chi reaxff_mu qiterative reaxff_qshell reaxff_r12

reaxffsmooth

Type Option
Format reaxffsmooth k <lone/over/both>
Units k is unitless
Default No smoothing; k = 80.0; if specified then both
Use This option controls whether a smoothing factor is used for the lone pair terms
in ReaxFF. The original formalism has a discontinuity due to rounding to the integer
below a value. If specified, this option changes this to a smooth approximation to
the Heaviside function such that the discontinuity is removed, at the expense of
deviating from the original model. The smoothing uses the expression;
f(x) = 1/(1+exp(-k*(x-x0)))
where x0 is the nearest integer value and x is the actual value. As k tends to infinity
the function tends toward the original discontinuous form. However, if k is too small
then the smoothing function will not decay to 0/1 before (x-x0) reaches a half causing
problems. Therefore care is necessary if changing the default value of k.
There are two main energy terms that are influenced by this change - the over coordination
and lone pair energies. The sub-options "lone", "over" or "both" control which of the
energies the smoothing is applied to.
See also reaxffcutoff reaxfftol

reaxfftol

Type Option
Format reaxfftol bomin <anglemin> <angleprod> <hbondmin> <hbonddist> <torsionprod>
Use This command sets a number of tolerances that control the behaviour of ReaxFF.
bomin - the general threshold for bond orders in pairwise terms
anglemin - the threshold for bond orders in valence, penalty and 3-body conjugation
angleprod - a threshold for the product of bond orders (1-2 x 2-3, where 2 = pivot)
Hard coded in original program to 0.001, but this leads to discontinuities
hbondmin - threshold for A-H bond order in a hydrogen bond. Hard coded to 0.01 in
original code.
hbonddist - threshold for A...B distance in A-H...B hydrogen bond. Hard coded to
7.5 Ang in original code.
torsionprod- a threshold for the product of bond orders (1-2 x 2-3 x 3-4) for torsion
interactions.
See also reaxffcutoff reaxffsmooth

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

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

reperfc

Type Option
Format reperfc <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <ener/grad> <type_of_bond>
atom1 atom2 A beta <rmin> rmax <3*flags>
Units A in eV and beta in Angs
Default none
Use Specifies the parameters of an reperfc potential, which has the form:
E_ij = A.erfc(r/beta)/r
See also qerfc erferfc erfpot

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

rfo_eig

Type Option
Format rfo_eig value
Units eV/Ang**2
Default -0.001 eV/Ang**2
Use Tolerance on eigenvalues of the Hessian matrix to be labelled as
negative during RFO optimisation.
NB: The value can be input as positive since it is enforced that
it will be less than or equal to zero.
See also rfo rfo_grad

rfo_grad

Type Option
Format rfo_grad value
Units eV/Ang
Default 1.0 x 10**-8 eV/Ang
Use Tolerance on the projected gradient onto the Hessian mode for
the mode to be included in the active space for optimisation.
NB: If a value greater than 1 is input then it is assumed to
be the exponent (e.g. 2 -> 10**-2)
See also rfo rfo_eig

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 fvectors

rmax

Type Option
Format rmax <n>
Units Angstroms
Default 5.0
Use Used within the pdf input block for PDF calculations.
Sets the maximum radius for atomic pairs to be generated.
See also PDFkeep PDFcut

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 veck index_k dielectric_constant

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.

ryckaert

Type Option
Format ryckaert (or torsion ryck) norder <type_of_bond>
atom1 atom2 atom3 atom4 k0 rmax(1-2) rmax(2-3) rmax(3-4) rmax(1-4) <flags*norder+1>
norder*coefficients
Units k0 in eV, rmax in Angstroms, coefficients in eV
Default none
Use Torsional potential about atoms 2 and 3. Polynomial expansion in
cos(phi) up to fifth order maximum.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion outofplane torangle torharm torexp uff4 no4duplicates

rydberg

Type Option
Format rydberg <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 A B r0 <rmin> rmax <3*flags>
Units A in eV, r0 in Angs
Use Rydberg potential also found in the following article
Rose/Smith/Guinea/Ferrante potential (Phys. Rev. B,
29, 2963 (1984)) - used in modelling metals.
E = -A.[1+B*((r/r0)-1)].exp(-B*((r/r0)-1))

sample

Type Option
Format sample value <s/ns/ps/fs>
Units s, ns, ps or fs - if integer, then value is by default
a multiple of the timestep or if non-integer then by
default is the time in picoseconds.
Use Controls how often the properties of the molecular
dynamics run are to be sampled and output to the
standard output channel. Averaged properties are also
based on these samples.
See also md timestep equilibration production temperature
tscale write nolist delay_force end_force

sasexclude

Type Option
Format sasexclude natom_min <natom_max>
Default Include all particles as specified by sasparticles option
Use Allows the user to specifically exclude a range of atoms
from being involved in determining the solvent accessible
surface.
e.g.
sasexclude 10
would exclude atom 10 from contributing to the SAS, while
sasexclude 10 20
would exclude atoms from 10 to 20 from the SAS. Note that
the atom numbers are those in the full cell rather than
the asymmetric unit.
See also sasparticles

sasparticles

Type Option
Format sasparticles <cores_only/both_cores_and_shells>
Default cores_only
Use In all calculations the cores define the position of the
solvent accessible surface. This option controls whether
the potential is determined by the sum of the core and
shell charges at the core position (cores_only) or by
the explicit potential due to both the core and shell
(both)
See also cosmo sasexclude

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

scale

Type Option
Format scale <real_number>
Units none
Default 1.0
Use Scales subsequent cell vectors and cartesian coordinates by the
scale factor.

scan_cell

Type Option
Format scan_cell d_a d_b d_c d_alpha d_beta d_gamma nstep (for 3-D)
scan_cell d_a d_b d_alpha nstep (for 2-D)
scan_cell d_a nstep (for 1-D)
scan_cell strain e1 e2 e3 e4 e5 e6 nstep (for 3-D)
scan_cell strain e1 e2 e3 nstep (for 2-D)
scan_cell strain e1 nstep (for 1-D)
Units Angstrom for d_a, d_b, d_c and degrees for d_alpha, d_beta, d_gamma
Use Allows a scan over cell parameters to be performed. Here d_a, d_b
and d_c are the changes in cell lengths, while d_alpha, d_beta and
d_gamma are the changes in cell angles. It is recommend that this
option be only used for either constant volume calculations or that
it is used in conjunction with the ocell keyword when the cell is
being varied. The number of steps is given by nstep (each step
will change cell parameter a by d_a/nstep, for example)
Note that the translate and scan_cell options are mutually exclusive.
NB A value for the change in cell parameters that causes the cell
to go negative is not allowed.
If strain is specified after the option then the input values will
be taken as strains (e1-e6) rather than angles. Here zero means
that no strain will be applied to that component.
See also cell vectors ocell translate strain

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

scmaxsearch

Type Option
Format scmaxsearch <value>
Units None
Default 2.0
Use For free energy minimisation, this parameter sets the maximum
search range for pairs of atoms interacting via the same many
body term that gives a contribution to the third derivatives.
The value is a multiple of the density cut-off value for the
EAM model. In principle, the range can be up to 3 times the
density pairwise cut-off. However, this makes free energy
minimisation very expensive. In practice, a value of around
2 will give almosts identical results, depending on the system,
with a dramatic increase in speed. However, if precise gradients
are needed then a value of 3.0 should be used to check
the influence. Negative values and values greater than 3.0 are
disallowed as being stupid!
See also free zsisa manybody eam_functional eam_density lowest_mode

screened_coulomb

Type Option
Format screened_coulomb <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 epsilon_sat r_me sigma_e <rmin> rmax <3*flags>
Units r_me, sigma_e, rmin and rmax in Angs; sigma_e has no units
Default None
Use Specifies the parameters for a distance-dependent screened Coulomb potential
using the approach of Lenart et al, J. Chem. Phys., 126, 044509 (2007).
To use this potential, first set the bulk dielectric constant (epsilon_r) using the
option "dielectric_constant" (i.e. the long-range limit). This potential
then uses a switching function to unscreen the interactions in the short-range
limit to the saturation value, epsilon_sat. The parameter epsilon_sat for
water is usually 5.2. The form of the equations is:
E = qi*qj/(4*pi*epsilon_0*epsilon_r*r)*[(epsilon_0/epsilon_d) - 1]
where epsilon_d is a distance-dependent term:
epsilon_d(r) = 0.5*(epsilon_sat + epsilon_r) +
0.5*(epsilon_r - epsilon_sat)*tanh[(r-r_me)/sigma_e]
NB: If using these to create a distance-dependent dielectric constant then the
cutoff (rmax) should be long enough to ensure that the potential has gone to a
very small value. As a rule of thumb, if rmax = N*sigma_e then the dielectric
constant will have converged to 1 x the bulk value to within (N-1) decimal places.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also c6 mm3buck slater

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 young poisson shear voigt bulk omega

seed

Type Option
Format seed q
Default -1
Use Initial pointer used in random number generation wherever random numbers are used.
Input value is an integer.

segmentsperatom

Type Option
Format segmentsperatom <no. of segments per atom> <no. per H atom>
Default 92 (dodecahedron) / 110 (octahedron)
Units None
Use Specifies the number of segments per atom for the
solvent-accessible surface in a COSMO calculation.
The points per atom are grouped together to form
the segments. Note it is possible to specify a
different value for H. However, if this is omitted
then it defaults to the same value as for other atoms.
See also cosmo pointsperatom solventepsilon solventradius
solventrmax vdw cosmoshape rangeforsmooth

sfinite

Type Option
Format sfinite deltaC deltaS
Default 0.00001 / 0.00001
Units Angstroms and none for deltaC and deltaS, respectively.
Use Sets the finite difference intervals to be used for the numerical
evaluation of properties by central finite differencing of the
analytic first derivatives. deltaC is used for the Cartesian
displacements while deltaS controls the change in strain.
See also numerical pfinite

sfractional

Type Option
Format sfractional <region <qm/mm> <rigid <xyz>>> <nonrigid>
at.sym. <species_type> x y z <charge> <occupancy> <radius> <3 x flags> <T/%>
Units Fractional for x and y, Angstroms for z and radius, and electrons
Default For region 2, rigid is the default.
Use Internal coordinates and charges for all species in the surface cell.
Either the atomic number or the symbol may be supplied, followed
by the species type. If the species type is omitted then it is
assumed to be a core. Individual charges may be supplied for each
ion or the charges for each type of species given using the
species option. If the charges are given, then optionally site
occupancies may also be specified. Similarly, if the charge and
occupancy are given, then the radius of a breathing shell may
also be present. Optimisation flags are only needed if cellonly,
conv, bulk, conp or shell are not specified.
If the "region" sub-option is specified, then this tells the program
to treat the atoms as a group where the collective coordinates can be
specified to be fixed or not in a given direction. By default, the
regions are treated as being for a surface calculation where region 1
is free to relax while region 2 is held fixed. Regions are numbered
according to the order in which they appear in the input.
If the "rigid" sub-option is also specified after "region" then the region
is created as a rigid body so that all atoms are constrained with respect
to each other. By specifying a string after this containing x, y and/or z,
the region may be allowed to move in particular directions. For example,
in an interface calculation, a region could be specified that is allowed
to only relax in the z direction by using:
sfrac region 3 rigid z
NB: The "region" sub-option must come before any of the other related
sub-options.
If a "T" is specified then the atom is marked for the translate option
If a "%" is specified then the atom is part of a growth slice if it
is in region 1 of a surface calculation.
See also scell sregion2

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 young poisson

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

shift

Type Option
Format shift energy_shift <ev/au/kcal/kjmol-1>
Units eV (default), au, kcal or kJmol-1
Default 0.0 eV
Use Shifts energy by this amount - mainly for use in fitting
ab initio energy surfaces. Shift is applied to all subsequent
configurations until the value of shift is changed by another
shift directive. Shift can also appear in the variables section
as a command to cause the shift to be fitted.
See also sshift ashift

shrink

Type Option
Format shrink <origin> 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.
By default the k point grid generated avoids the origin of the
Brillouin zone since this is the best choice for thermodynamic properties.
The grid position can be centred on the origin by specifying the
origin sub-option:
shrink origin 4 4 4
See also phonon dispersion kpoints noksym msd

siginc

Type Option
Format siginc atomic_nnumber <siginc>
Units Angstrom2 (=108 Barns)
Use Used within element option input block, overwrites the default bound
incoherent neutron scattering cross-section (siginc) for a specified element.
(at. no. or symbol may be used)
See also coreinfo element bbar xray

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

slater

Type Option
Format slater <inter/intra> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <ener/grad> <scale14> <type_of_bond>
atom1 atom2 A B <rmin> rmax <2*flags>
Units A in eV, B in Angs**-1
If kcal is given : A in kcal, B in Angs**-1
If kjmol is given: A in kJmol-1, B in Angs**-1
Default none
Use Specifies a Slater two-body potential that arises from the overlap of
two spherical atomic densities that decay exponentially.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = A.[((B*r)**2/3) + B*r + 1]*exp(-B*r)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
The words energy or gradient may be
given on the first line resulting in energy or gradient offsets being
applied such that the specified quantity goes to zero at the cutoff
distance.
See also c6 mm3buck buckingham

slower

Type Option
Format slower <value> <+1/-1>
Units None
Default 0.001 +1
Use This is the scale factor by which the eigenvectors will be
multiplied when attempting to lower the symmetry along an
imaginary mode direction. When applying the lower operation
the phonon eigenvectors can be applied in one of two directions
depending on the sign. By specifying "-1" this change the direction
of displacement.
See also lower_symmetry

smelectronegativity

Type Option
Format smelectronegativity
<Atomic_symbol/atomic_number> chi mu zeta Znuc <Q0> <E0> <4 x flags>
or
smelectronegativity <qrange/qmin/qmax>
<Atomic_symbol/atomic_number> chi mu zeta Znuc <Q0> <E0> <qmin> <qmax> <4 x flags>
Units Chi, mu, and E0 in eV, Znuc in a.u., zeta in Angstroms**-1, Q0, qmin, qmax in a.u.
Default Q0 = 0.0, E0 = 0.0
Use Allows the user to specify the parameters needed for the
Streitz and Mintmire electronegativity equalisation method
for determining charges. Note that if the flags are not
specified they are assumed to be zero.
Q0 is the charge about which the electronegativity equations
are quadratic. In most methods this is zero, but need not be.
For example, the EQeq method assigns values of Q0 not equal
to zero.
E0 is an additive constant for the energy of an atom. This is
only really needed when using multiple q ranges to ensure
energy matching.
The sub-options qrange, qmin, and qmax control whether the
values apply for a given value of charge. By default the values
apply to all values of charge (q). If qmin is specified then
they are only applied to charges larger than qmin, while if qmax
is given the they are applied when q is less than qmax. When
qrange is specified then the values apply for qmin =< q < qmax.
NB: If no parameters are input then the default values will be
used for all charge values. However, if parameters are input
then this will override the default values and the user must
set parameters for all relevant ranges of charge.
See also sm eem electronegativity qeq qelectronegativity noqeem external_potential
eembond qeqradius

solventepsilon

Type Option
Format solventepsilon <dielectric constant OR solvent_name>
Default 1.0
Units None
Use Specifies the dielectric constant of the solvent to
be used in a COSMO solvation energy calculation. Note
that values must be greater than 1.0!
The values of the dielectric constant for use in
COSMO are known for the following solvents :
solvent_name dielectric_constant
------------ -------------------
water 78.400
acetone 20.700
benzene 2.274
chlorobenzene 5.621
chloroform 4.806
cyclohexane 2.015
ethylether 4.335
methanol 32.630
tetrachloromethane 2.228
conductor 1000.000
See also cosmo pointsperatom segmentsperatom solventradius
solventrmax vdw

solventradius

Type Option
Format solventradius <Rsolv> <deltaRsolv>
Defaults 1.0 / 0.1 Angstroms
Units Angstroms
Use Specifies the radius of the solvent molecule, Rsolv,
and the distance of the screening centre from the
molecular centre, deltaRsolv, for use in a COSMO
screening calculation. Note that these two values
are the parameters for each solvent that must be
determined in order to obtain accurate solvation
energies.
See also cosmo pointsperatom segmentsperatom solventepsilon
solventrmax vdw

solventrmax

Type Option
Format solventrmax <maximum distance> <smoothing range>
Defaults 10.0 / 1.0 Angstroms
Units Angstroms
Use Maximum distance parameter used by COSMO solvation
model. Below this value, elements of the A matrix
are evaluated at the level of sub-points, while
beyond this they are evaluated between segments,
which is more approximate. The smoothing range
is used to taper the two sides of the cut-off
together continuously to avoid problems during
optimisation.
See also cosmo pointsperatom segmentsperatom solventepsilon
solventradius vdw

spacegroup

Type Option
Format space group no. or Hermann-Maugain symbol
Note: symbol must be in capital letters with spaces between them
e.g. for MgO => 225 or F M -3 M
Units none
Default no symmetry => P1
Use Specifies symmetry information by space group. Either the standard
symbol may be used or the extended symbol for specifying alternative
settings. When giving extended symbols only the first line in
International Tables should be given i.e. the 4th operator/qualifier
after the centring symbol should be omitted. For example, in order
specify the non-standard P 21/A setting of P 21/C the input should be:
space
P 1 21/A 1
See also origin valid_spacegroups symmetry_operator

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 will overwrite the charges of ions that
are specified individually on the coordinate input line unless the
preserve_Q keyword is specified.
See also library preserve_Q polarisability spin

spin

Type Option
Format spin symbol <spin>
Units None
Default Spin is equal to zero.
Use Allows species spins to be set. Note that species symbols can
also be used for the spin to set different spins for different
species of the same element:
element
spin O1 0.5
spin O2 -0.5
end
or the older form of using the atomic number can be used:
element
spin 8 0.5
end
The spin can then contribute to an Ising Hamiltonian via the
j2 and j3 potentials. NB: This is currently not implemented
for the Mott-Littleton method.
Command is part of element section.
See also element j2 j3

spline

Type Option
Format spline <cubic> <reverse> <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <type_of_bond>
atom1 atom2 <shift> <rmin> rmax <1*flag>
energy_1 distance_1
energy_2 distance_2
: :
energy_n distance_n
Units Energies in eV, distances in Angs
Default rational function spline, shift = 0.0
Use Spline potential - flag for fitting (0/1) of shift.
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
If the option "reverse" is specified then the spline information
will be read as distance then energy, ie the reverse order to
normal.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded, potential cutoffs are omitted from input.

split

Type Option
Format split <number of species to be varied>
list of cores whose charges are to be varied
Units none
Default charges fixed
Use Allows split of core-shell to be varied during fitting while
maintaining the initial total charge.
This directive must be part of the variables section.
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.

spring

Type Option
Format spring <kcal/kjmol>
atom1 k2 <k4> <flags>
Eqn E = (1/2)*k2*r**2 + (1/24)*k4*r**4
Units k2 in eV/Angs*2, k4 in eV/Angs**4
Default k4 = 0.0
Use Core-shell spring potential - optimisation flags for fitting.
Spring potential does not need cutoffs as the maximum is set by cuts
and the minimum is zero.
Only atom1 needs to be specified as this potential is specifically
for core shell pairs. Atom1 can be given either by atomic number
or symbol which in the latter case can be followed by a species
type. If no species type is given then type is assumed to be core.
See also cosh-spring

sqomega

Type Option
Format sqomega filename.sqw <weight>
Units Arbitrary
Default No S(Q,omega) data to be fitted
Use This option enables fitting of S(Q,omega) data. The S(Q,omega)
data is read from a .sqw file specified on this line.
The parameters that control the grid for S(Q,omega) are
specified by the commands for scattering and must match those
present in the .sqw file.
See also elastic sdlc hfdlc weight srefractive hfrefractive piezo
bornq monopoleq qreaxff fbond fangle relax reaction

squaredharmonic

Type Option
Format squaredharmonic <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <grad> <scale14> <type_of_bond>
atom1 atom2 k2 r0 <coul> <rmin> rmax <2*flags>
Units k2 in eV*Angs**-4, r0 in Angs, coul in none
Use GROMOS bonded potential - optimisation flags for fitting.
coul = 1.0 => Coulomb subtracted
atom1 and atom2 may be specified either by atomic number or symbol
which in the latter case can be followed by a species type. If
no species type is given then type is assumed to be core.
E = 1/4 K2*(r**2 - r0**2)**2 - coul*qi*qj/r
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
When specified as bonded potential, cutoffs are omitted from input.
See also spring harmonic

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 weight

sregion2

Type Option
Format sregion2 atom_number
Units none
Use Specifies the first atom in the slab that is in region 2. Region 2
is the region that contains the fixed atoms that represent the
bulk in a surface calculation. Atoms in region 2 will automatically
be fixed during geometry optimisation and the self-energy of the
region will be excluded from the surface energy of the slab - i.e.
the surface energy calculated will be for one side, that of region 1.
See also sfrac scell sbulkenergy

srglue

Type Option
Format srglue <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 d rmin rmax
a14 a13 a12 a11 a10
a26 a25 a24 a23 a22 a21 a20
Units eV and Angstroms
Default none
Use Input for the Short-Range part of the Glue model:
if r < d:
E = a14*(r-d)**4 + a13*(r-d)**3 + a12*(r-d)**2 + a11*(r-d) + a10
if d < r =< rmax:
E = a26*(r-d)**6 + a25*(r-d)**5 + a24*(r-d)**4 + a23*(r-d)**3 +
a22*(r-d)**2 + a21*(r-d) + a20
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then potential will only act between bonded
atoms. x12 => exclude 1-2 interaction and x13 => exclude 1-2 and 1-3
interaction. x14 implies x13 and scale14 = 0 (i.e. no 1-4 interactions)
See also eam_functional eam_density

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

start

Type Option
Use Causes program to skip the rest of the input file and begin execution.

static dielectric

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

stepmx

Type Option
Format stepmx <opt/fit/rfo> <real value>
Units fractional
Default 1.0 for opt / 1000.0 for fit / 100.0 for rfo
Use Maximum step size in optimisation/fitting/rfo.
Value may appear on same line as option or on the following line.
If opt/fit is not supplied then value is applied to both.
See also maxcyc optimise fit rfo switch_stepmx

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.

strain_derivative

Type Option
Format strain_derivative
strain_no strain_derivative_value <weight>
Units eV
Default all fitted strain derivatives are zero
Use Subsection of observables, used for specifying the strain derivative
components for fitting to. Here the strain_no is as follows:
1 => xx 2 => yy 3 => zz 4 => yz 5 => xz 6 => xy
Note that strains are dependent on the cell orientation and so take
care when specifying.
NB: This keyword currently implies that symmetry will be turned off
since there is no guarantee that the strains or cell orientation will
be compatible with the symmetry-adapted algorithms.
See also observables gradients stress

stress

Type Option
Format stress
stress_no stress_value <weight>
Units GPa
Default all fitted stresses are zero
Use Subsection of observables, used for specifying the stress
components for fitting to. Here the stress_no is as follows:
1 => xx 2 => yy 3 => zz 4 => yz 5 => xz 6 => xy
Note that stresses are dependent on the cell orientation
and so take care when specifying.
See also observables gradients strain_derivative

supercell

Type Option
Format supercell <xyz/zyx> (ncells in x) (ncells in y) (ncells in z)
Default 1 1 1 (i.e. no supercell), xyz
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. The options xyz and zyx specify the order in which
the atom list is built when looping over the supercell indices with
the first letter being the outer loop and the last the inner.
NB: If generating results for use with phonopy or ShengBTE the
supercell should be specified with zyx:
e.g. super zyx 3 3 3
See also ghost_supercell

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.
NB: For non-periodic systems there is no need to specify vectors
See also scell cell vectors pcell pvector

sw2

Type Option
Format sw2 <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A rho B rmin rmax <3*flags>
Units A in eV, B in Angs**4, rho in Angs
Use Stillinger-Weber's two-body potential with cutoff smoothing such that potential goes to zero at rmax:
E = A.exp(rho/(r-rmax)).(B/r**4 - 1)
See also sw3 sw2jb sw3jb sw2gen

sw2gen

Type Option
Format sw2gen <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14> <type_of_bond>
atom1 atom2 A sigma B p q rmin rmax <5*flags>
Units A in eV, sigma in Angs, B, p and q are unitless
Use Stillinger-Weber's two-body potential in a more general for with cutoff smoothing such
that potential goes to zero at rmax:
E = A.exp(sigma/(r-rmax)).(B*(sigma/r)**p - (sigma/r)**q)
with p = 4 and q = 1 this is essentially the same as the sw2 potential.
See also sw3 sw2jb sw3jb sw2

sw2jb

Type Option
Format sw2jb <intra/inter> <bond/x12/x13/x14/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 A rho B Q <rmin> rmax <4*flags>
Units A in eV, B in Angs**4, rho in Angs, Q in a.u.
Use Jiang and Brown's variant of Stillinger-Weber's two-body potential
which includes charge dependent bond softening
E = A.exp(rho/(r-rmax)).(B/r**4 - 1)*F(qi,qj)
F(qi,qj) = exp(1/Q)exp(1/(qi + qj - Q)) if qi+qj < Q
F(qi,qj) = 0 if qi+qj > Q
See Chem. Eng. Sci., 49, 2991 (1994) for more details.
See also sw3 sw2 sw3jb

sw3

Type Option
Format sw3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23>
rmax23 <4*flags>
or
sw3 modified <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K theta0 rho1 rho2 C <rmin12> rmax12 <rmin13> rmax13 <rmin23>
rmax23 <5*flags>
or
sw3 garofalini <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K theta0 rho1 rho2 C <rmin12> rmax12 <rmin13> rmax13 <rmin23>
rmax23 <5*flags>
Units K in eV, theta in degrees, rho1 and rho2 in Angstroms
Use Stillinger-Weber's three-body potential with cutoff smoothing
E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*(cos-ct0)**2
where cos = cos(theta(jik)) and ct0 = cos(theta0)
If "modified" is specified then the functional form given in J. Appl. Phys.
101, 103515 (2007) is given:
E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*(cos-ct0)**2/(1 + C*(cos-ct0)**2)
If "garofalini" is specified then the functional form given in J. Phys. Chem.
100, 2201 (1996) is given:
E(three) = K * exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))*[(cos-ct0)*sin*cos]**2
intra/inter can also be specified for molecular calculations, as can
bond. Note that unlike most potentials, the specification of the
cut-off distances is still required when using the "bond" sub-option
since the values act as parameters to the model.
See also three-body angle exponential axilrod-teller bcross sw2 sw2jb urey-bradley
murrell-mottram bcoscross bacross hydrogen-bond equatorial sw3jb uff3
lin3 3coulomb bagcross j3 ppp3body

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 Stillinger-Weber's three-body potential with
charge-dependent softening
E(three) = K*F12*F13*exp(rho1/(r12-rmax12) + rho2/(r13-rmax13))(cos-ct0)**2
where cos = cos(theta(jik)) and ct0 = cos(theta0)
F12(q1,q2) = exp(1/Q)exp(1/(q1 + q2 - Q)) if q1+q2 < Q
F12(q1,q2) = 0 if q1+q2 > Q
F13(q1,q3) = exp(1/Q)exp(1/(q1 + q3 - Q)) if q1+q3 < Q
F13(q1,q3) = 0 if q1+q3 > Q
See Chem. Eng. Sci., 49, 2991 (1994) for more details.
intra/inter can also be specified for molecular calculations, as can
bond. Note that unlike most potentials, the specification of the
cut-off distances is still required when using the "bond" sub-option
since the values act as parameters to the model.
See also three-body angle exponential axilrod-teller bcross sw2 sw2jb urey-bradley
murrell-mottram bcoscross bacross hydrogen-bond equatorial sw3 lin3
uff3 bagcross j3 ppp3body

switch_minimiser

Type Option
Format switch_minimiser <minimiser> <cycle/gnorm/lower> <criterion>
Use This option allows the minimiser to be changed part
way through an optimisation when the given criterion
is satisfied. The criterion can be either the number
of cycles of optimisation or when the gradient norm
drops below a certain value. This option is particularly
useful for cases where the RFO minimiser is needed to
accelerate the end game convergence. However it is
inefficient and unstable a long way from the minimum.
Valid minimisers are:
bfgs (default)
rfo (rational function optimisation)
unit (bfgs, but starting from a unit Hessian)
nume (bfgs, but starting from numerical diagonal Hessian)
conj (conjugate gradients)
Examples:
switch rfo cycle 10
=> Change to rfo method after 10 cycles of optimisation.
Note that the order of words after switch is irrelevant
and additional words can be inserted to make the line more
readable. For example this line could be written as:
switch to rfo method after 10 cycles of optimisation
switch conj gnorm 0.123
=> Change to conjugate gradient method when Gnorm is less
than 0.123. Note that if cycle and gnorm are omitted then
GULP assumes gnorm as a default.
switch rfo lower
=> Change to rfo method if restarting optimisation after
the lower option has been applied.
See also optimise rfo unit conj optlower switch_stepmx

switch_stepmx

Type Option
Format switch_stepmx new_step_max <cycle/gnorm> <criterion>
Use This option allows the minimiser to change the maximum
step size to a value new_step_max from the current one
when a given criterion is met.
Examples:
switch_stepmx 0.1 cycle 10
=> Change to a maximum step size of 0.1 after 10 cycles
of optimisation.
switch 0.1 gnorm 0.123
=> Change to maximum step size of 0.1 when Gnorm is less
than 0.123. Note that if cycle and gnorm are omitted then
GULP assumes gnorm as a default.
See also stepmx switch_minimiser

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.
See also element

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

symmetry_number

Type Option
Format symmetry_number value
Default 1
Use This option allows the user to specify the symmetry number for use
in calculating the rotational partition function.
See also property temperature pressure

symmetry_operator

Type Option
Format symmetry_operator
r(1,1) r(1,2) r(1,3) t(1)
r(2,1) r(2,2) r(2,3) t(2)
r(3,1) r(3,2) r(3,3) t(3)
Units None / Fractional
Use Specifies the symmetry operators for a 3-D system manually. The
matrix r specifies the rotational matrix and the vector t specifies
the translational component of the roto-translational operator. Note
that the identity operator is always present and should not be given
again. If specified, this option causes any spacegroup specified to
be ignored.
See also spacegroup origin symmetry_cell

synciterations

Type Option
Format synciterations <maximum_number>
Default 1000
Use Specifies the maximum number of iterations for minimization
of the force norm during each step of a syncrhonous transit run.
See also neb syncsteps synctolerance synchronous
nebreplica fcartesian ffractional fcell fvectors

syncsteps

Type Option
Format syncsteps <maximum_number>
Default 1000
Use Specifies the maximum number of steps during a syncrhonous
transit run. Each consists of a move of one image towards the other
followed by minimisation of that image while the force remains
orthogonal to the vector between the images.
See also neb syncsteps synctolerance synchronous
nebreplica fcartesian ffractional fcell fvectors

synctolerance

Type Option
Format synctolerance <tolerance_value>
Default 0.0001
Use Specifies the convergence criteria for a synchronous transit
run in terms of the residual force norm.
See also neb syncsteps synciterations synchronous
nebreplica fcartesian ffractional fcell

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 Specifies the relaxation time for the barostat if the integrator is
set to type "stochastic".
See also integrator md tau_thermostat

tau_thermostat

Type Option
Format tau_thermostat tau <s/ns/ps/fs>
Units s, ns, ps or fs; default is ps
Default 1 ps
Use Specifies the relaxation time for the thermostat if the integrator is
set to type "stochastic".
See also integrator md tau_barostat

td_external_force

Type Option
Format td_external_force
atomnumber direction forceA forceB forceC
Units forceA in eV/Angstrom, forceB in 1/ps, & forceC in fraction
of 2*pi
Default No time dependent force
Use Specifies that a time-dependent force is applied to selected
atoms during a molecular dynamics simulation. This force can
be specified separately for each Cartesian direction and takes
the form of;
F = forceA*cos[2*pi*(t*forceB + forceC)]
where t is the time within the simulation.
Example 1:
1 z 3.5 0.5 0.5
3 z 3.5 0.5 0.0
Example 2:
1 z -3.5 0.5 0.0
3 z 3.5 0.5 0.0
Note: both of the other examples would cause the atoms to
oscillate exactly out of phase with each other and are
equivalent. The maximum force experienced would be +/-
3.5 eV/Angstrom
See also external_force

td_field

Type Option
Format td_field magnitude <direction> B C
Units magnitude in eV/(Ang.a.u.), B in 1/ps, & C in fraction of 2*pi
Default No time dependent force
Use Specifies that a time-dependent field is applied to the system.
For details of how to specify the field direction see the time-independent
field option. The time-dependence is then given by:
F = magnitude*cos[2*pi*(t*B + C)]
where t is the time within the simulation.
Multiple time-dependent fields can be applied to each configuration.
NB: This option only influences MD simulations.
See also field delay_field end_field dipole delta_dipole initial_coordinates

temperature

Type Option
Format temperature <multi> value_of_temperature <C/F/K> <step> <no. of steps> <step0>
Units Kelvin (or Centigrade if C added, or Fahrenheit if F added)
Default 0 K, no steps (for phonons) 100 K for simulated annealing.
Use Specifies temperature of a structure for use in the calculation of
phonon properties, such as the entropy, free energy and heat capacity.
Also specifies the temperature for molecular dynamics and Monte Carlo
runs, including annealing.
Temperature can optionally be followed by an increment, a number of steps,
(and a first step for MD).
Phonons
If a range is given, then the phonon properties will be calculated at each
temperature value over the range. Note that if present during a free energy
calculation this will result in the last temperature being used for the
run. For CPU time reasons a range should not be used during a free energy
minimisation.
Molecular dynamics / Monte Carlo
Here the option is used to set the temperature of the run or the schedule
of temperatures for an anneal. For example, if the initial temperature is
to be 298 K for the first 300 steps and then is to increase to 398 K over
a 1000 steps, the input would look like:
temperature 298 0.1 1000 300
If the "multi" sub-option is specified then a more complex temperature
profile can be created using multiple variable temperature steps. For example,
to hold the temperature at 398 K in the above example for 500 steps and then
increase it by a further 100 K using the same rate the input would be:
temperature multi 298 0.1 1000 300
0.1 1000 500
As many temperature ramps as necessary can be included.
See also phonon free predict anneal ftol factor ttol

terse

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

tether

Type Option
Format tether n1-n2 or n1,n2, ... or any combination of both
Use Specifies atoms to keep fixed during a molecular dynamics calculation.
These atoms create forces on other atoms, but do not move themselves.
n1, n2 ... is the number of the atom in the input file, e. g. if
atoms 2, 3, 4, and 7 shall be kept fixed tether 2-4,7 will do that.
NB: The line continuation character should not be used with the tether
option. Instead multiple tether lines can be used.
e.g.
tether 1-3, 121- 123, 127 - 129
tether 143 - 146, 150, 152, 181 - 183, 10, 11, 12
See also md

three-body

Type Option
Format three <exponential/vessal/cosine> <k3> <k4> <nbeq/nbne nbond> <intra/inter> <bond/mol> <kcal/kjmol/degree>
atom1 atom2 atom3 k <k3> <k4> theta0 <rmin(1-2)> rmax(1-2) <rmin(1-3)> rmax(1-3) &
<rmin(2-3)> rmax(2-3) <2-4 flags>
Units k in eVrad**-2, k3 in eVrad**-3, k4 in eVrad**-4 (for standard)
k in eVrad**-2 (for exponential/vessal)
k, k3 and k4 in eV (for cosine)
theta0 in degrees, rmin & rmax in Angs
Default none
Use Three-body potentials about atom1. k is force constant and theta0
the equilibrium angle. Optional flags are for fitting. Atom 1 is
the middle atom of the triad about which the force acts.
E(three) = 1/2 * k * (theta-theta0)**2
Exponentially decaying form is also available:
E(three) = 1/2 * k * (theta-theta0)**2.exp(-r12/rho1).exp(-r13/rho2)
Format:
three exponential
atom1 atom2 atom3 k theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags>
Exponentially decaying form is also available in Vessal form:
E(three) = 1/4*A*(B**2).exp(-r12/rho1).exp(-r13/rho2)
A = k/(2*(theta0-pi)**2)
B = (theta0-pi)**2 - (theta-pi)**2
Format:
three vessal
atom1 atom2 atom3 k theta0 rho1 rho2 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags>
k3 and k4 terms can also be included:
E(three) = 1/2*k*(theta-theta0)**2 + 1/6*k3*(theta-theta0)**3
+ 1/24*k4*(theta-theta0)**4
Formats:
three k3
atom1 atom2 atom3 k k3 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <3xflags>
three k4
atom1 atom2 atom3 k k4 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <3xflags>
three k3 k4
atom1 atom2 atom3 k k3 k4 theta0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <4xflags>
NB: k3 and k4 terms can only be specified with the standard threebody or cosine forms
Cosine of theta can also be used instead of theta, if the cosine
option is used :
E(three) = 1/2*k*(cos(theta)-cos(theta0))**2
k3 and k4 terms can also be included for the cosine form:
E(three) = 1/2*k*(cos(theta)-cos(theta0))**2 + 1/6*k3*(cos(theta)-cos(theta0))**3
+ 1/24*k4*(cos(theta)-cos(theta0))**4
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
The order of the bond type options matches the order of the pivot atom
- end atom pairs. For example, if a potential acts for the triad
S - C - O, where the C-S bond is a regular bond and the C-O is an
exocyclic double bond then the input would look like:
three bond single regular double exocyclic
C core S core O core ...... etc
Conditions can also be placed on a potential to check the number of bonds
associated with the pivot atom (e.g. if a potential is designed for a 90
degree angle it might be necessary to check that the number of bonds is
four or six for square planar or octahedral). The conditions are placed
using one or more instances of "nbeq" or "nbne" followed by an integer.
Here "nbeq" imples no. of bonds must equal and "nbne" number of bonds must
not equal. Hence, "nbeq 4" would require the pivot to have 4 bonds. When
multiple terms are used, the logic of nbeq is concatenated with "or", whereas
that of nbne is joined by "and". Therefore "nbne 4 nbne 6" would apply to
an atom with 3 bonds, but not one with 4 or 6.
NB It's important to specify the first bond as being of "regular" type so
that the "exocyclic" attribute is correctly assigned to the second bond
since the first term is assumed to apply to the first bond, whereas the
second applies to the second bond.
See also axilrod-teller angle stillinger-weber exponential bcross uff3
urey-bradley murrell-mottram bacross lin3 hydrogen-bond equatorial
3coulomb exp2 bagcross mm3angle j3 ppp3body

threshold

Type Option
Format threshold min_fc3_ij min_fc3
Default 0.0000001 / 0.00001
Units eV/Angs**3
Use Sets thresholds for the smallest values of third order force constants that
are considered non-zero. Because third order force constants can contain
numerical error, especially when using finite differences, many of the
resulting force constants contain noise. This allows some of this to be
removed. There are two threshold values:
min_fc3_ij: If an individual force constant is below this value then it is set
to zero.
min_fc3 : If all force constants within a block are below this value then the
: whole block is set to zero.
See also num3 output

time

Type Option
Format time time_limit <seconds/minutes/hours>
Units seconds (default), minutes or hours
Default Infinity!
Use Specifies time limit for calculation.

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 delay_force end_force momentum_correct

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

torangle

Type Option
Format torangle <intra/bond/improper> <kcal/kjmol> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 K theta0 theta0' rmax(1-2) rmax(2-3) rmax(3-4) <3 x flags>
Units K in eV/rad**2, theta0 & theta0' in degrees
Default none
Use Specifies a torsional - angle cross potential. The form of the potential is:
E = K.cos(phi).(theta - theta0).(theta' - theta0')
where theta is the angle between 1-2-3 & theta' is between 2-3-4
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torharm torexp outofplane uff4 torcosangle no4duplicates

torcosangle

Type Option
Format torcosangle <intra/bond/improper> <kcal/kjmol> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 K theta0 theta0' rmax(1-2) rmax(2-3) rmax(3-4) <3 x flags>
Units K in eV/rad**2, theta0 & theta0' in degrees
Default none
Use Specifies a torsional - cosine angle cross potential. The form of the potential is:
E = K.cos(phi).(cos(theta) - cos(theta0)).(cos(theta') - cos(theta0'))
where theta is the angle between 1-2-3 & theta' is between 2-3-4
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torharm torexp outofplane uff4 torangle no4duplicates

torexp

Type Option
Format torexp <bond/improper/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 k <+/->nphase <phi0> rho12 rho23 rho34 rmax(1-2)
rmax(2-3) rmax(3-4) rmax(4-1) <4 x flags>
or if esff option is specified
atom1 atom2 atom3 atom4 k1 k2 <+/->nphase rho12 rho23 rho34 rmax(1-2) rmax(2-3)
rmax(3-4) rmax(4-1) <5 x flags>
Units k/k1/k2 in eV, isign is +1 or -1 according to the sign of nphase,
rho12/23/34 and rmax in Angstroms, phi0 in degrees
Default if phi0 is not given it is assumed to be zero
Use Specifies an exponentially decaying torsional potential of the form:
E = k*(1+isign*cos(nphase*phi-phi0))*exp(-r12/rho12)*exp(-r23/rho23)*exp(-r34/rho34)
ESFF :
E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)]*
*exp(-r12/rho12)*exp(-r23/rho23)*exp(-r34/rho34)
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torharm outofplane torexp uff4 no4duplicates

torharm

Type Option
Format torharm <bond/improper/intra/inter> <kcal/kjmol> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 K <phi0> rmax(1-2) rmax(2-3) rmax(3-4) <rmax(1-4)> <2 x flags>
Units K in eV/rad**2, phi0 in degrees
Default none, phi0 = 0 if omitted, rmax(1-4) = 0.0
Use Specifies a harmonic torsional potential. Note that this is not a sensible
choice for a convenientional torsional potential, but is used by some
forcefields for an improper torsional angle. The form of the potential is:
E = 1/2 K(phi - phi0)**2
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torangle torexp outofplane uff4 no4duplicates

torsion

Type Option / Keyword
Format torsion <intra/inter> <bond/improper> <esff> <dreiding> <kcal/kjmol> <type_of_bond>
atom1 atom2 atom3 atom4 k <+/->n <phi0> rmax(1-2) rmax(2-3)
rmax(3-4) rmax(4-1) <1 x flag>
or if esff option is specified
atom1 atom2 atom3 atom4 k1 k2 <+/->n rmax(1-2) rmax(2-3)
rmax(3-4) rmax(4-1) <2 x flags>
Eqn Normal :
E = k*(1+isign*cos(n*phi-phi0))
ESFF :
E = k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)
Units k/k1/k2 in eV, isign is +1 or -1 according to the sign of n,
rmax in Angstroms, phi0 in degrees
Default if phi0 is not given it is assumed to be zero
Use Torsional potential about atoms 2 and 3. k is half the barrier
and nphase is the periodicity. The optional flag is for fitting of k.
If rmax(4-1) is input as zero then rmax(4-1) is set to infinity.
Note that when rmax(4-1) is not zero then atoms 1 and 4 cannot be
the same atom for a valid torsional term.
When used as a keyword, torsion causes a list of valid torsion terms
to be output before and after any optimisation/calculation.
See also Ryckaert for an alternative form of torsion potential.
four is an alternative valid name for this potential type.
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given then no cutoffs are required as the potential
will act only when i-j, j-k and k-l are bonded. If improper is given
then again no cutoffs are required, but the atoms must now be bonded
i-j, j-k, j-l to make an improper torsion about atom j.
if the option esff is specified after torsion then the potential takes
the ESFF form. Here the potential becomes dependent on the two angles
involved in the torsional angle so that it smoothly goes to zero when
the torsional angle becomes indeterminate. Strictly the two coefficients
k1 and k2 should be related by :
k1 = K / (sin10**2.sin20**2) k2 = K / (sin10**n.sin20**n)
where sin10 and sin20 are the sines of the equilibrium values of angles
1 and 2 respectively. Here they are just input as coefficients for
generality.
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also ryckaert outofplane torexp tortaper torangle uff4 no4duplicates

tortaper

Type Option
Format tortaper <bond/improper/intra/inter> <kcal/kjmol> <esff> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 k <+/->nphase <phi0> rtaper rmax(1-2)
rmax(2-3) rmax(3-4) rmax(4-1) <1 x flags>
or if esff option is specified
atom1 atom2 atom3 atom4 k1 k2 <+/->nphase rtaper rmax(1-2) rmax(2-3)
rmax(3-4) rmax(4-1) <2 x flags>
Units k/k1/k2 in eV, isign is +1 or -1 according to the sign of nphase,
rtaper and rmax in Angstroms, phi0 in degrees
Default if phi0 is not given it is assumed to be zero
Use Specifies a torsional potential with tapering of the cut-offs over rtaper of the form:
E = k*(1+isign*cos(nphase*phi-phi0))*f(r12)*f(r23)*f(r34)
ESFF :
E = [k1*(sin1**2)*(sin2**2)+isign*k2*(sin1**n)*(sin2**n)*cos(n*phi)]
*f(r12)*f(r23)*f(r34)
where f(r) is a cosine tapering function.
If the sub-option dreiding is specified then the force constant is divided
by the number of torsional interactions for each central j-k pair to
ensure a constant torsional barrier for the j-k bond.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torharm outofplane torexp torangle uff4 no4duplicates

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

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 the optimisation is stuck in a local minimum
then, if stepsize non-zero, tournament is reset to <initial>.
See also genetic anneal gexp

tpxo

Type Option
Default Use one point crossover
Use Part of ga options section.
See also crossover

translate

Type Option
Default none
Units dmax in Angstroms
Use Repeats the requested calculation type automatically for
a series of points in which a subset of atoms are shifted
by a translation vector. This option is useful for mapping
out energy surfaces at the moment in one dimension.
The input format is:
translate x y z nstep <noise fmax> <thermal dmax>
where x, y, z are the components of the vector between the
the initial and final positions of the atoms. If the
system is three-dimensional then x, y and z are assumed
to be in fractional units. If the system is a cluster
then they are assumed to be in angstroms. nstep is the
number of points to be sampled along the translation
vector (this leads to nstep+1 calculations including
the first and last points).
The subset of atoms to which the translation is to be
applied is defined by adding a "T" flag to the end of the
coordinate lines of these atoms. If the flag "T-" is used
then the atoms are translated in the opposite direction to
the vector input.
If "noise" is also specified with a value then random displacements
are added to the coordinates of the atoms in non-rigid regions
after each translation step to prevent trapping in local high
symmetry states. The magnitude of the displacement is given by a
random number between -1 and 1 times the step size during translate
scaled by fmax. Therefore fmax should usually be a small value << 1.
If "thermal" is specified with a value then random displacements
are added to the coordinates of all atoms in non-rigid regions,
regardless of whether they were displaced or not in the translation.
The magnitude of the displacement is given by a Gaussian random value with
mean of zero and a standard deviation of dmax (in Angstroms).
Note that the translate and scan_cell options are mutually exclusive.
See also nofirst_point scan_cell

trap

Type Option
Format trap <fc> <value>
Default Don't trap / value = 1000
Units none
Use This option allows the user specify things for the code to
trap that may be undesirable.
At present there is a single option:
fc - trap changes in the energy during optimisation where
the energy alters by more than a factor of "value".

tscale

Type Option
Format tscale value <freq> <s/ns/ps/fs>
Units s, ns, ps or fs; default is ps.
Use Controls how long in simulation time the temperature
scaling is to be applied for. By default this is set
equal to the length of the equilibration phase of
the run. Optionally the frequency of scaling can be
specified, which normally defaults to the timestep.
See also md equilibration production timestep sample write
nolist temperature delay_force end_force momentum_correct

tsuneyuki

Type Option
Format tsuneyuki <form2> <inter/intra/bond> <x12/x13/x14/mol/o14/g14> <type_of_bond>
atom1 atom2 Q1 Q2 zeta <rmin> rmax <1*flag>
Units Q1 & Q2 in a.u., zeta in Angstroms**-1
Defaults form1
Use Specifies the short-range Coulomb correction described by Tsuneyuki et al
PRL, 61, 869 (1988). Note that the role of the charges is inverted relative
to the paper in order that charge neutrality is achieved in the long-range
limit. It is assumed that this was a typo. The correction to the Coulomb
term is given by:
U = [Q1.Q2 - q1.q2]g(r)/r
where q1 & q2 are the regular charges specified elsewhere, and g(r) is:
Form1: g(r) = (1+z.r)exp(-2z.r)
Form2: g(r) = (1 + 11(z.r)/8 + 3(z.r)**2/4 + (z.r)**3/6)exp(-2z.r)
where z is used as a short-hand for zeta

ttol

Type Option
Format ttol Tmin
Default Tmin=0.01
Use Temperature tolerence for simulated annealing routine.

twist

Type Option
Format twist <+/->n
Units None
Defaults n = 0, or if twist is specified then +1
Use Takes the coordinates of a 1-D periodic system and introduces
a twist angle about the central axis in the repeat direction.
The periodicity will be set so that the twist completes over
a single cell. Longer periods can be created by first creating
a supercell, while n specifies the number of complete twists
in a single cell. By specifying -n then the phase is reversed.
See also pcell

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

uff3

Type Option
Format uff3 <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K theta0 rmin(1-2) rmax(1-2) rmin(1-3) rmax(1-3)
rmin(2-3) rmax(2-3) <flag>
Units K in eV, theta0 in degrees, rmin and rmax in Angstroms
Default none
Use UFF non-linear three-body form :
E(three) = K * (C0 + C1*cos(theta) + C2*cos(2*theta))
Here the coefficients are related to theta0 by:
C2 = 1/(2*sin(theta0))**2
C1 = - 4*C2*cos(theta0)
C0 = C2*(2*(cos(theta0))**2 + 1)
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species were 1-2, 2-3 and 1-3 are bonded.
See also axilrod-teller angle stillinger-weber exponential bcross lin3
urey-bradley murrell-mottram bacross three hydrogen-bond equatorial
3coulomb bagcross j3

uff4

Type Option
Format uff4 <bond/improper/intra/inter> <kcal/kjmol> <dreiding> <type_of_bond>
atom1 atom2 atom3 atom4 K n <phi0> rmax(1-2) rmax(2-3) rmax(3-4) rmax(4-1) <1 x flag>
Units K in eV, phi0 in degrees
Default none, phi0 = 0 if omitted
Use Specifies a torsional potential of the UFF form:
E = 1/2 K*(1 - cos(n.phi0)*cos(n.phi))
n is an integer and there is only a flag for K
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion torangle torexp outofplane torharm no4duplicates

uff_bondorder

Type Option
Format uff_bondorder bond_type bond_order
Units None
Default
double => bond_order = 2.0
treble => bond_order = 3.0
quadruple => bond_order = 4.0
resonant => bond_order = 1.5
amide => bond_order = 1.41
half => bond_order = 0.5
quarter => bond_order = 0.25
third => bond_order = 1/3
custom => bond_order = 1.0
Use Allows the user to change the default bond orders for use in UFF.
NB: The single bond order is fixed at 1.0 and cannot be changed.
See also connect

uffoop

Type Option
Format uffoop <intra/inter/bond/mol> <only3> <kcal/kjmol>
atom1 atom2 atom3 atom4 k C0 C1 C2 rmax(1-2) rmax(1-3) rmax(1-4) <4 x flags>
Units k in eV, C0, C1, C2 are unitless
Default none
Use Out of plane energy - energy penalty for atom 1 lying
out of the plane of atoms 2, 3 and 4. This form uses the
Universal Force Field expression:
E = k.(C0 + C1*cos(phi) + C2*cos(2*phi))
where phi is the angle between the plane of the centre atom and two
others with the bond from the centre atom to the third atom.
Note that because phi depends on which of the 3 different angles is
chosen, GULP computes the contribution for all 3 cases and takes the
average.
If the only3 sub-option is specified then the potential applies where
an atom has exactly 3 bonds present.
See also torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane

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 optimise transition_state cello noexclude fix_atom

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.

units

Type Option
Format units <kcaltoev/evtoangs> value
Default The default values for unit conversion factors are:
kcaltoev = 4.3364432032d-2
angstoev = 14.3997584
Use The default values of unit conversion factors can be changed either
by editing the values in modules.f90 before compilation or by setting
this value in the input.
NB: This should be placed after the keyword line otherwise any use
of the conversion factor before this command will use the default
value.
See also

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.

urey-bradley

Type Option
Format urey-bradley <intra/inter> <bond> <nbeq/nbne nbond> <kcal/kjmol>
atom1 atom2 atom3 K r0 <rmin12> rmax12 <rmin13> rmax13 <rmin23> rmax23 <2*flags>
Units K in eV/Angs**2, r0 in Angstroms
Use Harmonic distance potential between atoms which are 1-3
E(three) = 1/2 * K * (r - r0)**2
intra/inter can also be specified for molecular calculations, as can
bond. If bond is given no cutoff is required as the potential will
only act between species where 1-2 and 1-3 are bonded.
See also three-body angle exponential axilrod-teller stillinger bcross lin3
murrell-mottram bacross hydrogen-bond equatorial uff3 3coulomb j3
ppp3body

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

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

vbo_twobody

Type Option
Format vbo_twobody
atom1 atom2 c gamma R0 delta <4xflags>
Units c in eV; R0 and delta in Angstroms; gamma is unitless
Default None
Use Twobody potential of a form suitable for use as part of VBO model of Truhlar et al.
E = N.exp(-gamma/(1-sqrt(r/delta))) for r < delta & E = 0 for r >= delta
NB: Because the potential goes to zero at delta there is no rmax or rmin for this
potential (i.e. rmax = delta).
The normalisation constant N is given by:
N = 2*exp(gamma/(1-sqrt(R0/delta)))
NB: The factor of two in N comes from the translation of how the two-body sum is
expressed in the papers by Truhlar to how it is implemented in GULP.
See also eam_functional eam_density

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.
Can be species specific for use with COSMO/COSMIC
e.g. to change the VDW radius of all oxygens to 1.5 Ang:
element
vdw O 1.5
end
e.g. to change the VDW radius of 2 different types of oxygen:
element
vdw O2 1.3
vdw O4 1.5
end
See also element

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 optimisation flags appear on last line.
NB: For non-periodic systems there is no need to specify vectors
See also cell primitive_vectors scell svectors pcell pvector

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

volume

Type Option
Format volume vol <weight>
Units Angstroms**3
Default Volume is not fitted, weight = 1
Use Subsection of observables, used for specifying that the volume
is fitted. Usually the cell parameters of a system are fitted
and so this constrains the volume. This option allows the
volume to be targetted instead.
See also observables elastic sdlc hfdlc piezo energy stress

weight

Type Option
Format weight <number of weights to be changed>
list of observable numbers whose weights are to be changed
list of new weights in order
Units none
Default 1.0
Use Subsection of observables, allows weighting factors to changed.
Number of weights = 0 causes default to be
changed for subsequent observables.
See also default_weight

wmax

Type Option
Format wmax <n>
Units THz
Default None: must be specified.
Use Used within the "pdf" input block for "PDFcut" or "PDFkeep" calculations.
Sets the maximum phonon frequency to be used in calculating PDFs.
Units can be changed using 'unit freq'
See also PDFkeep PDFcut units wmin

wmin

Type Option
Format wmin <n>
Units THz
Default None: must be specified.
Use Used within the "pdf" input block for "PDFcut" or "PDFkeep" calculations.
Sets the minimum phonon frequency to be used in calculating PDFs.
Units can be changed using 'unit freq'
See also PDFkeep PDFcut units wmax

write

Type Option
Format write value <s/ns/ps/fs>
Units s, ns, ps or fs - if integer, then value is by default
a multiple of the timestep or if non-integer then by
default is the time in picoseconds.
Use Determines how often the program writes to the molecular
dynamics dumpfile during the production phase of the
run for subsequent analysis.
See also md timestep equilibration production temperature
tscale sample nolist delay_force end_force

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(1-2) rmax(1-3) rmax(1-4) <6 x flag>
Units All k in eV*rad**-2 and all theta0 in degrees
Default none
Use Angle-angle cross potential for all angles about a central atom, atom 1:
E = k(213/4)*(theta(213) - theta0(213))*(theta(214) - theta0(214)) +
k(312/4)*(theta(312) - theta0(312))*(theta(314) - theta0(314)) +
k(412/3)*(theta(412) - theta0(412))*(theta(413) - theta0(413))
See also torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane
uffoop xcosangleangle

xcosangleangle

Type Option
Format xcosangleangle <inter/intra> <bond> <kcal/kjmol>
atom1 atom2 atom3 atom4 k(213/4) k(312/4) k(412/3) theta0(213) theta0(214) theta0(314) &
rmax(1-2) rmax(1-3) rmax(1-4) <6 x flag>
Units All k in eV and all theta0 in degrees
Default none
Use Angle cosine - angle cosine cross potential for all angles about a central atom, atom 1:
E = k(213/4)*(cos(theta(213)) - cos(theta0(213)))*(cos(theta(214)) - cos(theta0(214))) +
k(312/4)*(cos(theta(312)) - cos(theta0(312)))*(cos(theta(314)) - cos(theta0(314))) +
k(412/3)*(cos(theta(412)) - cos(theta0(412)))*(cos(theta(413)) - cos(theta0(413)))
See also torsion ryckaert torangle torharm torexp xoutofplane inversion outofplane
uffoop xangleangle

xoutofplane

Type Option
Format xoutofplane <intra/inter/bond/mol> <kcal/kjmol> <type_of_bond>
atom1 atom2 atom3 atom4 atom5 atom6 k rmax(1-2) rmax(1-3) rmax(1-4) rmax(2-5) rmax(2-6) <1 x flag>
Units k in eV*Angs**-2
Default none
Use Specifies an cross - out of plane potential of form:
E = k.d1.d2
where d1 is the out of plane distance of atom 1 from the plane of atoms 2/3/4
and d2 is the out of plane distance of atom 2 from the plane of atoms 1/5/6. This
functional form is used in the CVFF forcefield. This is a six-body potential.
The type of bond sub-option can be used to control which bonded atoms the
potential applies to. For a three-body potential, the bond type for the
two bonds connected to the pivot atom can be supplied and then checked
before applying the potential. Valid type of bond options are: single,
double, triple, quadruple, resonant, amide, custom, half, quarter, and third.
In addition a bond may specified as regular (default), cyclic or exocyclic.
See also torsion ryckaert torangle torharm torexp outofplane uffoop

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.
See also gdcrit gtol gmax ftol

youngs_modulus

Type Option
Format youngs_modulus <n>
<x/y/z> youngs_modulus <weight>
Units GPa
Default no Youngs moduli to be fitted
Use Subsection of observables, used for specifying values of
Young's moduli for fitting.
Example To fit a Young's modulus of 240.0 GPa in the x direction
with a weight of 1.0:
young 1
x 240.0 1.0
NB: The Young's moduli are computed assuming that the
material is linear elastic orthotropic.
See also elastic sdlc hfdlc weight srefractive hfrefractive bornq
piezoelectric poisson shear voigt bulk

zbl

Type Option
Format zbl <intra/inter> <bond/x12/x13/x14/mol/o14/g14> <kcal/kjmol> <scale14>
atom1 atom2 <b1 c1 b2 c2 b3 c3 b4 c4 d n> <rmin> rmax <9*flags>
Units d, n, b1-4 are unitless, c1-4 are in Ang**-1
Default d = 0.46850, n=0.23, b1=0.18175, b2=0.50986, b3=0.28022, b4=0.02817
c1=3.19980, c2=0.94229, c3=0.40290, c4=0.20162
Use Specifies the use of the ZBL potential, as widely used in simulations
of radiation cascades.
E = (1/(4*pi*epsilon0)) * Zi*Zj*e**2*phi(rij/a)/rij
where Zi & Zj are the atomic numbers of the elements. The constant a
is given by;
a = d/(Zi**n + Zj**n)
and phi(x) by:
phi(x) = sum(i=1,4) bi*exp(-ci*x)
See also general

14_scale

Type Information
Info Many organic forcefields require the scaling of 1-4 two body
interactions. Typically a factor of a 1/2 is used. This can
be achieved in GULP. Nearly all two-body potentials allow a
scale factor to be specified on the same line as the potential
option word which has this effect. Similarly Coulomb interactions
can be scaled by using the Coulomb subtract potential which
already has a coefficient and can be specified to act only for
1-4 interactions.

Ctrl_C

Type Information
Use The control C key sequence can be used to exit a fitting
process or optimisation cleanly at the end of the current
cycle. If control C is executed twice then the program
will terminate.

line_continuation

Type Information
Info To continue a line onto further lines the character
"&" can be given at the end of the line.
e.g. the following input could be given in the two
following ways:
buck
Si core O shel 1280.0 0.3 0.0 0.0 12.0 1 0 0
or
buck
Si core O shel &
1280.0 0.3 0.0 0.0 12.0 &
1 0 0

scale14

Type Information
Info Many organic forcefields require the scaling of 1-4 two body
interactions. Typically a factor of a 1/2 is used. This can
be achieved in GULP. Nearly all two-body potentials allow a
scale factor to be specified on the same line as the potential
option word which has this effect. Similarly Coulomb interactions
can be scaled by using the Coulomb subtract potential which
already has a coefficient and can be specified to act only for
1-4 interactions.

stillinger-weber

Type Information
Info The 2 and 3 body potentials of Stillinger-Weber are
available using the potential types sw2 and sw3,
respectively.
See also sw2 sw2jb sw3 sw3jb

trajectory_format

Type    : Information
Written once only for each run :
        write(31)version
        write(31)numat,ndimensions
Written for every configuration :
  Version = 3.4:
        write(31)timesofar,ekin,fc,temp
        write(31)(xalat(i),i=1,numat)
        write(31)(yalat(i),i=1,numat)
        write(31)(zalat(i),i=1,numat)
        write(31)(velx(i),i=1,numat)
        write(31)(vely(i),i=1,numat)
        write(31)(velz(i),i=1,numat)
        if (lconp) then
          write(31)(xcell(i),i=1,9)
          write(31)(velc(i),i=1,nstrains)
        endif
  Version = 4.0 onwards:
        write(31)timesofar,ekin,fc,temp
        write(31)(xalat(i),i=1,numat)
        write(31)(yalat(i),i=1,numat)
        write(31)(zalat(i),i=1,numat)
        write(31)(velx(i),i=1,numat)
        write(31)(vely(i),i=1,numat)
        write(31)(velz(i),i=1,numat)
        write(31)(xdrv(i),i=1,numat)
        write(31)(ydrv(i),i=1,numat)
        write(31)(zdrv(i),i=1,numat)
        write(31)(esite(i),i=1,numat)
        if (lconp) then
          write(31)(xcell(i),i=1,9)
          write(31)(velc(i),i=1,nstrains)
        endif
Meaning of variables :
version (real*8)    = version number of GULP
numat   (integer*4) = total number of atoms including shells
timesofar (real*8)  = elapsed time of simulation for this frame (ps)
ekin    (real*8)    = kinetic energy for this frame (eV)
fc      (real*8)    = potential energy for this frame (eV)
temp    (real*8)    = temperature for this frame (Kelvin)
xalat   (real*8)    = x Cartesian coordinates of atoms (Angstroms)
yalat   (real*8)    = y Cartesian coordinates of atoms (Angstroms)
zalat   (real*8)    = z Cartesian coordinates of atoms (Angstroms)
velx    (real*8)    = x component of velocities (Angstroms/ps)
vely    (real*8)    = y component of velocities (Angstroms/ps)
velz    (real*8)    = z component of velocities (Angstroms/ps)
xdrv    (real*8)    = x component of first derivatives (eV/Angstroms) -> negative force
ydrv    (real*8)    = y component of first derivatives (eV/Angstroms) -> negative force
zdrv    (real*8)    = z component of first derivatives (eV/Angstroms) -> negative force
esite   (real*8)    = energy contribution of each atom (eV)
lconp   (logical)   = .true. for NPT calculation, otherwise .false.
xcell   (real*8)    = Cartesian components of cell vectors (Angstroms)
velc    (real*8)    = velocities of cell components (Angstroms)

valid_spacegroups

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