List of Keywords

Keywords

AMD	ATOMLABEL	AUTO	BADER	BASINPLOT	BENCHMARK
BONDFACTOR	BUNDLEPLOT	BZ	CLEAR	COMPARE	COMPAREVC
COORD	COUNT	CPREPORT	CRYSTAL	CUBE	ECHO
ECON	EDIT	END	ENVIRON	EWALD	EXIT
FLUXPRINT	GRDVEC	HIRSHFELD	IDENTIFY	INTEGRABLE	INTEGRALS
INT_RADIAL	ISOSURFACE	KPOINTS	LIBRARY	LIBXC	LINE
LIST	LOAD	MAKEMOLSNC	MAX	MEAN	MESHTYPE
MIN	MOLCALC	MOLCELL	MOLECULE	MOLMOVE	MOLREORDER
NCIPLOT	NEWCELL	NOSYM/NOSYMM	ODE_MODE	PACKING	PLANE
POINT	POINTPROP	POLYHEDRA	POWDER	PRECISECUBE	PRUNE_DISTANCE
Q/QAT	QTREE	RADII	RDF	REFERENCE	RESET
ROOT	RUN	SETFIELD	SIGMAHOLE	SPG	SPHEREINTEGRALS
STANDARDCUBE	STM	SUM	SYM/SYMM	SYSTEM	UNITS
UNLOAD	VDW	VORONOI	WRITE	XDM	XRPD
YT

Notation

• Keywords are in CAPS (except POSCAR, CONTCAR, etc.)
• .s: strings, .i: integers, .r: real numbers, expr.s: arithmetic expressions.
• Arithmetic expressions can be given between single quotes (‘’), double quotes (“”), or without quoting as long as there are no spaces. They can be used in most places that a real or integer can. An expression input:

  expression.r
  

  prints the value of the expression to the output. The list of functions that can be used in arithmetic expressions is below.

• Variables can be used almost everywhere. Variables are assigned:

  variable.s = value.r
  

• Fields are accessed using the $ symbol and modified with an optional colon and field modifier ($field:modifier). See below for a list of field modifiers.
• Structural variables are accessed using the @ symbol, and they can be used to incorporate position-dependent quantities to the expression. See below for a list of structural variables.
• In non-quiet mode (no -q argument), a copy of each input line is written to the output after a ‘%%’ prefix.
• Comment prefix: #.
• Continuation symbol: \.

List of Keywords

In the entries below, we use:

• nat.i: atom integer ID from the nonequivalent list (asymmetric unit).
• ncp.i: critical point integer ID from the non-equivalent list (asymmetric unit).
• at.i: atom integer ID from the complete list (unit cell).
• cp.i: critical point integer ID from the complete list (unit cell).
• at.s: atomic symbol.
• id.s: field identifier (string or integer ID).

AMD

Calculate the average minimum distances vector.

AMD [nnmax.i]

ATOMLABEL

Relabel the atoms in the current structure.

ATOMLABEL template.s

AUTO

Determine the position and properties of the critical points.

AUTO [GRADEPS eps.r] [CPEPS eps.r] [NUCEPS neps.r] [NUCEPSH nepsh.r]
   [EPSDEGEN edeg.r] [CHK] [DRY] [SEEDOBJ]
AUTO ... [TYPES {nbrc}]
AUTO ... [DISCARD [TYPES {nbrc}] expr.s] [DISCARD ...] ...
AUTO ... [CLIP CUBE x0.r y0.r z0.r x1.r y1.r z1.r]
AUTO ... [CLIP SPHERE x0.r y0.r z0.r rad.r]
AUTO ... [SEED ...] [SEED ...] ...
AUTO SEED WS [DEPTH depth.i] [X0 x0.r y0.r z0.r] [RADIUS rad.r]
AUTO SEED OH [DEPTH depth.i]  [X0 x0.r y0.r z0.r] [RADIUS rad.r]
           [NR nr.r]
AUTO SEED SPHERE [X0 x0.r y0.r z0.r] [RADIUS rad.r] [NTHETA ntheta.i]
               [NPHI nphi.i] [NR nr.r]
AUTO SEED PAIR [DIST dist.r] [NPTS n.i]
AUTO SEED TRIPLET [DIST dist.r]
AUTO SEED LINE [X0 x0.r y0.r z0.r] [X1 x0.r y0.r z0.r] [NPTS n.i]
AUTO SEED POINT [X0 x0.r y0.r z0.r]
AUTO SEED MESH

BADER

Integrate the attraction (atomic) basins of a field defined on a grid using Henkelman et al.’s method.

BADER [NNM] [NOATOMS] [WCUBE] [BASINS [OBJ|PLY|OFF] [ibasin.i]] [RATOM ratom.r]
    [DISCARD expr.s] [JSON file.json] [ONLY iat1.i iat2.i ...]

BASINPLOT

Three-dimensional plots of the attraction basins.

BASINPLOT [CUBE [lvl.i] | TRIANG [lvl.i] | SPHERE [ntheta.i nphi.i]]
        [OFF|OBJ|PLY|BASIN|DBASIN [npts.i]}]
        [CP cp.i] [PREC delta.r] [VERBOSE] [MAP id.s|"expr"]

BENCHMARK

Run a benchmark test to measure the evaluation cost of the reference field. Mostly for debug purposes.

BENCHMARK nn.i

BONDFACTOR

Two atoms are considered covalently bonded if their distance is less than the sum of their covalent radii times BONDFACTOR.

BONDFACTOR bondfactor.r

BUNDLEPLOT

Three-dimensional plot of a primary bundle.

BUNDLEPLOT x.r y.r z.r
         [CUBE [lvl.i] | TRIANG [lvl.i] | SPHERE [ntheta.i nphi.i]]
         [OFF|OBJ|PLY|BASIN|DBASIN [npts.i]}]
         [ROOT root.s] [PREC delta.r] [VERBOSE] [MAP id.s|"expr"]

BZ

Print the geometry of the Brillouin zone.

BZ

CLEAR

Clear the value of one or more variables.

CLEAR {var1.s var2.s ...|ALL}

COMPAREVC

Compare two crystal structures allowing for cell deformations.

COMPAREVC {.|file1.s} {.|file2.s} [SP|LOCAL|GLOBAL] [SAFE|QUICK] [ALPHA alpha.r]
        [LAMBDA lambda.r] [WRITE] [MAXFEVAL maxfeval.i] [BESTEPS besteps.r]
        [MAXELONG maxelong.r] [MAXANG maxang.r]
COMPAREVC VCPWDF {.|file1.s} {.|file2.s} [THR thr.r] [WRITE] [NOH] [MAXELONG me.r]
        [MAXANG ma.r] [MAXVOL mv.r]

COMPARE

Compare two or more crystal or molecular structures.

COMPARE {.|file1.s} {.|file2.s} [{.|file3.s} ...]
COMPARE ... [MOLECULE|CRYSTAL]
COMPARE ... [REDUCE eps.r] [NOH]
COMPARE ... [GPWDF|POWDER|RDF|AMD|EMD] [XEND xend.r] [LAMBDA l.r] [SIGMA sigma.r] [NORM 1|2|INF] ## crystals
COMPARE ... [SORTED|RDF|ULLMANN|UMEYAMA]  ## molecules

COORD

Calculate the pair and triplet coordination numbers.

COORD [DIST dist.r] [FAC fac.r]

COUNT

Count the number of nodes of a field defined on a grid that are greater than a certain value.

COUNT id.s eps.r

CPREPORT

Print additional information (including three-dimensional plots) about the critical point list.

CPREPORT {SHORT|LONG|VERYLONG|SHELLS [n.i]}
CPREPORT file.{xyz,gjf,cml,vmd} [SPHERE rad.r [x0.r y0.r z0.r]]
       [CUBE side.r [x0.r y0.r z0.r]] [BORDER] [ix.i iy.i iz.i]
       [MOLMOTIF] [ONEMOTIF] [ENVIRON dist.r]
       [NMER nmer.i]
CPREPORT file.{obj,ply,off} [SPHERE rad.r [x0.r y0.r z0.r]]
       [CUBE side.r [x0.r y0.r z0.r]] [BORDER] [ix.i iy.i iz.i]
       [MOLMOTIF] [ONEMOTIF] [CELL] [MOLCELL]
CPREPORT file.scf.in
CPREPORT file.tess
CPREPORT file.cri|file.incritic
CPREPORT {[file.]POSCAR|[file.]CONTCAR|file.vasp}
CPREPORT file.abin
CPREPORT file.elk
CPREPORT file.gau
CPREPORT file.cif
CPREPORT file.m
CPREPORT file.gin
CPREPORT file.lammps
CPREPORT file.fdf
CPREPORT file.STRUCT_IN
CPREPORT file.hsd
CPREPORT file.gen
CPREPORT file.json
CPREPORT file.test
CPREPORT [...] [GRAPH]

CRYSTAL

Load a crystal structure.

CRYSTAL/MOLECULE # molecule..endmolecule can be used to input a molecule.
CRYSTAL file.cif [datablock.s]
CRYSTAL file.res
CRYSTAL file.ins
CRYSTAL file.16
CRYSTAL file.21
CRYSTAL file.dmain
CRYSTAL file.cube
CRYSTAL file.bincube
CRYSTAL file.struct
CRYSTAL [file.]{POSCAR,CONTCAR,vasp,CHGCAR,CHG,ELFCAR,AECCAR0,AECCAR1,AECCAR2} [at1.s at2.s ...|POTCAR]
CRYSTAL file_{DEN|PAWDEN|ELF|POT|VHA|VHXC|VXC|VCLMB|VPSP|GDEN1|GDEN2|GDEN3|LDEN|KDEN}
CRYSTAL file.OUT # (GEOMETRY.OUT, elk)
CRYSTAL file.out [istruct.i] # (file.scf.out, quantum espresso output)
CRYSTAL file.pwo [istruct.i]
CRYSTAL file.out # (file.out, crystal output)
CRYSTAL file.out # (file.out, FPLO output)
CRYSTAL file.in # (file.scf.in, quantum espresso input)
CRYSTAL file.pwi
CRYSTAL file.STRUCT_IN
CRYSTAL file.STRUCT_OUT
CRYSTAL file.gen
CRYSTAL file.xsf
CRYSTAL file.axsf [istruct.i [xnudge.r]]
CRYSTAL file.pwc
CRYSTAL file.{in,in.next_step} # (geometry.in, FHIaims input)
CRYSTAL file.{out,own} # (FHIaims output)
CRYSTAL file.frac
CRYSTAL file.cell
CRYSTAL file.geom
CRYSTAL [CIF|SHELX|21|CUBE|BINCUBE|WIEN|ABINIT|ELK|QE_IN|QE_OUT|CRYSTAL|XYZ|WFN|WFX|
       FCHK|MOLDEN|GAUSSIAN|SIESTA|FPLO|XSF|GEN|VASP|PWC|AXSF|DAT|PGOUT|ORCA|DMAIN|
       FHIAIMS_IN|FHIAIMS_OUT|FRAC|CELL|GEOM] ...
CRYSTAL
 SPG [hall.i|ita.i HM|spg.s]
 CELL a.r b.r c.r alpha.r beta.r gamma.r [ANG|ANGSTROM|BOHR|AU]
 CARTESIAN [scal.r]
 [BOHR/AU]
 [ANGSTROM/ANG]
 x1.r y1.r z1.r
 x2.r y2.r z2.r
 x3.r y3.r z3.r
 ENDCARTESIAN/END
 NEQ x.r y.r z.r at.s [ANG|ANGSTROM] [BOHR|AU]
 atom.s x.r y.r z.r [ANG|ANGSTROM] [BOHR/AU]
 atnumber.i x.r y.r z.r [ANG|ANGSTROM] [BOHR/AU]
 ...
 SYMM exprx.s, epxry.s, exprz.s
ENDCRYSTAL/END
CRYSTAL LIBRARY label.s

CUBE

Write a file containing the values of a field on a three-dimensional grid.

CUBE x0.r y0.r z0.r x1.r y1.r z1.r nx.i ny.i nz.i [FILE file.s] [FIELD id.s/"expr"]
   [F,GX,GY,GZ,GMOD,HXX,HXY,HXZ,HYY,HYZ,HZZ,LAP] [HEADER] [ORTHO]
CUBE x0.r y0.r z0.r x1.r y1.r z1.r bpp.r ...
CUBE CELL {bpp.r|nx.i ny.i nz.i} ...
CUBE GRID [SHIFT ix.i iy.i iz.i] ...
CUBE MLWF ibnd.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE WANNIER ibnd.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE UNK ibnd.i ik.i [SPIN ispin.i] ...
CUBE PSINK ibnd.i ik.i nRx.i nRy.i nRz.i [SPIN ispin.i] ...
CUBE ... FILE CHGCAR
CUBE ... FILE bleh.cube
CUBE ... FILE bleh.bincube
CUBE ... FILE bleh.xsf

ECHO

Write a message to the critic2 output.

ECHO echooo.s

ECON

Calculate the effective coordination number (ECON).

ECON

EDIT

Edit the molecular or crystal structure.

EDIT
DELETE {ATOM|ATOMS} id1.i id2.i ...
DELETE {MOLECULE|MOLECULES} id1.i id2.i ...
DELETE {HYDROGEN|HYDROGENS}
MOVE id.i x.r y.r z.r [BOHR|ANG] [RELATIVE]
CELLMOVE {A|B|C|ALPHA|BETA|GAMMA|V|VOL|VOLUME} r.r [BOHR|ANG] [RELATIVE] [FRACTION]
ENDEDIT

END

Terminates the critic2 run. Same as EXIT.

END

ENVIRON

Calculate the nearest neighbors of the atoms in the crystal structure.

ENVIRON [DIST dist.r] [POINT x0.r y0.r z0.r|ATOM at.s/iat.i|CELATOM iat.i]
[BY by.s/iby.i] [SHELLS]

EWALD

Calculate the electrostatic energy by performing an Ewald summation.

EWALD

EXIT

Terminates the critic2 run. Same as END.

EXIT

FLUXPRINT

Three-dimensional representations of the current field’s gradient paths.

FLUXPRINT
POINT {1|-1|0} x.r y.r z.r
NCP cp.i ntheta.i nphi.i [LVEC x.i y.i z.i]
BCP cp.i 1 [LVEC x.i y.i z.i]
BCP cp.i {0|-1} n.i [LVEC x.i y.i z.i] [BRAINDEAD|QUOTIENT|DYNAMICAL]
RCP cp.i -1 [LVEC x.i y.i z.i]
RCP cp.i {0|1} n.i [LVEC x.i y.i z.i] [BRAINDEAD|QUOTIENT|DYNAMICAL]
CCP cp.i ntheta.i nphi.i [LVEC x.i y.i z.i]
GRAPH igraph.i
COLOR r.i g.i b.i
TEXT|TESSEL|TESS|OBJ|PLY|OFF|CML
SHELLS ishl.i
NOSYM
ENDFLUXPRINT/END

GRDVEC

Two-dimensional representations of the reference field, comprising contour lines, gradient paths, or a combination of the two.

GRDVEC
 {FILES|ROOT|ONAME} rootname.s
 PLANE x0.r y0.r z0.r x1.r y1.r z1.r x2.r y2.r z2.r
 SCALE sx.r sy.r
 EXTENDX zx0.r zx1.r
 EXTENDY zy0.r zy1.r
 OUTCP sx.r sy.r
 HMAX hmax.r
 ORIG x.r y.r z.r atr.i up.i down.i
 CP id.i up.i down.i
 CPALL
 BCPALL up.i down.i
 RBCPALL bup.i bdown.i rup.i rdown.i
 CHECK
    x.r y.r z.r
    ...
 ENDCHECK/END
 CONTOUR {F,GX,GY,GZ,GMOD,HXX,HXY,HXZ,HYY,HYZ,HZZ,LAP}
 nptsu.i nptsv.i {LIN niso.i [cini.r cend.r]|
 LOG niso.i [zmin.r zmax.r]|ATAN niso.i [zmin.r zmax.r]|
 BADER|i1.i i2.i...}
ENDGRDVEC/END

HIRSHFELD

Calculate the Hirshfeld (stockholder) atomic properties.

HIRSHFELD [WCUBE] [ONLY iat1.i iat2.i ...]

IDENTIFY

Identify the position of an atom or a critical point given in crystallographic or Cartesian coordinates.

IDENTIFY [ANG|ANGSTROM|BOHR|AU|CRYST]
x y z [ANG|ANGSTROM|BOHR|AU|CRYST]
...
file.xyz
ENDIDENTIFY/END
IDENTIFY file.xyz

INTEGRABLE

Mark a field as a property to be integrated in the attraction basins.

INTEGRABLE id.s {F|FVAL|GMOD|LAP|LAPVAL} [NAME name.s]
INTEGRABLE id.s {MULTIPOLE|MULTIPOLES} [lmax.i]
INTEGRABLE id.s DELOC [WANNIER] [PSINK] [NOU] [NOSIJCHK] [NOFACHK] [NORESTART] [WANCUT wancut.r]
              [DI3 [atom1.i [atom2.i [ix.i iy.i iz.i]]]]
INTEGRABLE "expr.s"
INTEGRABLE DELOC_SIJCHK file-sij.s
INTEGRABLE DELOC_FACHK file-fa.s
INTEGRABLE CLEAR
INTEGRABLE ... [NAME name.s]

INTEGRALS

Integrate the basins of the reference field by bisection.

INTEGRALS {GAULEG ntheta.i nphi.i|LEBEDEV nleb.i}
        [CP ncp.i] [RWINT] [VERBOSE]

INT_RADIAL

Radial integration method used in bisection.

INT_RADIAL [TYPE {GAULEG|QAGS|QNG|QAG}] [NR nr.i] [ABSERR err.r]
         [RELERR err.r] [ERRPROP prop.i] [PREC prec.r]

ISOSURFACE

Integration of regions bound by isosurfaces.

ISOSURFACE {HIGHER|LOWER} isov.r [WCUBE] [BASINS [OBJ|PLY|OFF] [ibasin.i]]
         [DISCARD expr.s]

KPOINTS

Calculate the dimensions of uniform k-point grids.

KPOINTS [rk.r] [RKMAX rkmax.r]

LIBRARY

Define the path to the library file.

LIBRARY {CRYSTAL|MOLECULE} path.s

LIBXC

List and give information about the functionals available in the libxc library.

LIBXC [REF|REFS] [NAME|NAMES] [FLAGS] [ALL]

LINE

Calculate the values of a field on a line.

LINE x0.r y0.r z0.r x1.r y1.r z1.r npts.i [FILE file.s] [FIELD id.s/"expr"]
   [GX,GY,GZ,GMOD,HXX,HXY,HXZ,HYY,HYZ,HZZ,LAP]

LIST

List all defined variables and named fields.

LIST

LOAD

Load a scalar field.

LOAD file.cube
LOAD file.bincube
LOAD file_{DEN|PAWDEN|ELF|ELF|POT|VHA|VHXC|VXC|GDEN1|
         GDEN2|GDEN3|LDEN|KDEN}
LOAD [file.]{CHGCAR|CHG|AECCAR0|AECCAR1|AECCAR2} [block.i|RHO|SPIN|MAGX|MAGY|MAGZ]
LOAD {[file.]ELFCAR} [block.i|RHO|SPIN|MAGX|MAGY|MAGZ]
LOAD file.qub
LOAD file.xsf
LOAD file_fmt
LOAD file.grid
LOAD file.{clmsum|clmup|clmdn} file.struct
LOAD file.{RHO,BADER,DRHO,LDOS,VT,VH}
LOAD file.001
LOAD file.OUT
LOAD STATE.OUT GEOMETRY.OUT
LOAD STATE.OUT GEOMETRY.OUT OTHER.OUT
LOAD file1.ion {nat1.i/at1.s} file2.ion ...
LOAD file.xml file.bin file.hsd
LOAD file.wfn
LOAD file.wfx
LOAD file.fchk [READVIRTUAL]
LOAD file.molden [READVIRTUAL] [ORCA|PSI4]
LOAD file.molden.input [READVIRTUAL]
LOAD file.pwc [file.chk [filedn.chk]] [SPIN spin.i] [KPT k1.i k2.i...]
            [BAND b1.i b2.i ...] [ERANGE emin.r emax.r]
LOAD COPY id.s [TO id2.s]
LOAD PROMOLECULAR
LOAD PROMOLECULAR [FRAGMENT file.xyz]
LOAD [WIEN|ELK|PI|CUBE|BINCUBE|ABINIT|VASP|VASPNOV|QUB|XSF|ELKGRID|SIESTA|FPLO|DFTB|
    WFN|WFX|MOLDEN|MOLDEN_ORCA|MOLDEN_PSI4|FCHK|PWC] file
LOAD ... [NEAREST|TRILINEAR|TRISPLINE|TRICUBIC|SMOOTHRHO [NENV nenv.i] [FDMAX fdmax.r]]
       [EXACT|APPROXIMATE] [RHONORM|VNORM] [NOCORE] [NUMERICAL|ANALYTICAL]
       [TYPNUC {-3,-1,1,3}] [NORMALIZE n.r] [{NAME|ID} id.s]
       [NOTESTMT] [ZPSP at1.s q1.r...]
LOAD AS "expression.s" [n1.i n2.i n3.i|SIZEOF id.s|GHOST]
LOAD AS PROMOLECULAR {n1.i n2.i n3.i|SIZEOF id.s}
      [FRAGMENT file.xyz]
LOAD AS CORE {n1.i n2.i n3.i|SIZEOF id.s} {ZPSP at1.s q1.r ...}
LOAD AS FFT [GX|GY|GZ|HXX|HXY|HXZ|HYY|HYZ|HZZ|GMOD|LAP|POT] id.s
LOAD AS RESAMPLE id.s n1.i n2.i n3.i
LOAD AS CLM {ADD id1.s id2.s|SUB id1.s id2.s}

MAKEMOLSNC

Write a mols file for DMACRYS/NEIGHCRYS.

MAKEMOLSNC file_fort.21.s file_mols.s

MAX

Find the maximum value of a field defined on a grid.

MAX [id.s]

MEAN

Find the average of a field defined on a grid.

MEAN [id.s]

MESHTYPE

Type and quality of the molecular integration mesh.

MESHTYPE {BECKE|FRANCHINI} [SMALL|NORMAL|GOOD|VERYGOOD|AMAZING]

MIN

Find the minimum value of a field defined on a grid.

MIN [id.s]

MOLCALC

Calculate molecular properties using molecular/mesh integrations.

MOLCALC
MOLCALC expr.s
MOLCALC PEACH
mo1a [->] mo1r k1
mo2a [->] mo2r k2
[...]
ENDMOLCALC/END
MOLCALC HF
MOLCALC ... [ASSIGN var.s]

MOLCELL

Define the molecular cell.

MOLCELL [border.r]

MOLECULE

Load a molecular structure.

MOLECULE file.xyz [border.r] [CUBIC|CUBE]
MOLECULE file.mol2 [border.r] [CUBIC|CUBE] [name.s]
MOLECULE file.pdb [border.r] [CUBIC|CUBE]
MOLECULE file.wfn [border.r] [CUBIC|CUBE]
MOLECULE file.wfx [border.r] [CUBIC|CUBE]
MOLECULE file.fchk [border.r] [CUBIC|CUBE]
MOLECULE file.molden [border.r] [CUBIC|CUBE]
MOLECULE file.log [border.r] [CUBIC|CUBE]
MOLECULE file.{gjf,com} [border.r] [CUBIC|CUBE]
MOLECULE file.zmat [border.r] [CUBIC|CUBE]
MOLECULE file.dat [border.r] [CUBIC|CUBE]
MOLECULE file.pgout [border.r] [CUBIC|CUBE]
MOLECULE file.gen [border.r] [CUBIC|CUBE]
MOLECULE file.cube
MOLECULE file.bincube
MOLECULE file.{in,in.next_step} # (geometry.in, FHIaims input)
MOLECULE file.{out,own} # (FHIaims output)
MOLECULE file.cif
MOLECULE ...
MOLECULE [CIF|SHELX|21|CUBE|BINCUBE|WIEN|ABINIT|ELK|QE_IN|QE_OUT|CRYSTAL|XYZ|MOL2|WFN|WFX|
        FCHK|MOLDEN|GAUSSIAN|SIESTA|XSF|GEN|VASP|PWC|AXSF|DAT|PGOUT|ORCA|DMAIN|
        FHIAIMS_IN|FHIAIMS_OUT|FRAC] ...
MOLECULE
 NEQ x.r y.r z.r atom.s [ANG/ANGSTROM] [BOHR/AU]
 atom.s x.r y.r z.r [ANG/ANGSTROM] [BOHR/AU]
 atnumber.i x.r y.r z.r [ANG/ANGSTROM] [BOHR/AU]
 CUBIC|CUBE
 BORDER border.r
ENDMOLECULE/END
MOLECULE LIBRARY label.s

MOLMOVE

Move atoms inside a molecular crystal to match a set of molecular structures.

MOLMOVE mol1.s mol2.s ... target.s new.s

MOLREORDER

Reorder the atoms in a molecule or molecular crystal to match a template.

MOLREORDER template.s target.s [WRITE file.s] [MOVEATOMS] [INV] [UMEYAMA|ULLMANN]

NCIPLOT

Make a non-covalent interaction plot.

NCIPLOT
ONAME root.s
CUTOFFS rhocut.r dimcut.r
RHOPARAM rhoparam.r
RHOPARAM2 rhoparam2.r
CUTPLOT rhoplot.r dimplot.r
SRHORANGE srhomin.r srhomax.r
VOID void.r
RTHRES rthres.r
INCREMENTS x.r y.r z.r
NSTEP nx.i ny.i nz.i
ONLYNEG
NOCHK
CUBE x0.r y0.r z0.r x1.r y1.r z1.r
CUBE file1.xyz file2.xyz ...
MOLMOTIF
FRAGMENT file.xyz
FRAGMENT
 x.r y.r z.r # (in angstrom, use it with xyz)
 ...
ENDFRAGMENT/END
ENDNCIPLOT/END

NEWCELL

Change the cell setting of the current crystal structure by defining a new unit cell.

NEWCELL {x1.r y1.r z1.r x2.r y2.r z2.r x3.r y3.r z3.r|n1.i n2.i n3.i} [INV|INVERSE]
      [ORIGIN x0.r y0.r z0.r]
NEWCELL [{PRIMSTD|STANDARD|PRIMITIVE} [REFINE]]
NEWCELL [NIGGLI|DELAUNAY]
NEWCELL NICE [inice.i]

NOSYMM/NOSYM

Deactivate the use of the symmetry module that lets critic2 determine the space group operations of a crystal structure.

NOSYMM|NOSYM

ODE_MODE

Choose the numerical method for gradient path tracing.

ODE_MODE [METHOD {EULER|HEUN|BS|RKCK|DP}] [MAXSTEP maxstep.r] [MAXERR maxerr.r] [GRADEPS gradeps.r]

PACKING

Calculate the packing ratio of the current crystal structure.

PACKING {COV|VDW|} [PREC prec.r]

PLANE

Write a file containing the values of a field on a plane and, optionally, make a contour plot.

PLANE x0.r y0.r z0.r x1.r y1.r z1.r x2.r y2.r z2.r nx.i ny.i
    [SCALE sx.r sy.r] [EXTENDX zx0.r zx1.r] [EXTENDY zy0.r zy1.r]
    [FILE file.s] [FIELD id.s/"expr"]
    [F,GX,GY,GZ,GMOD,HXX,HXY,HXZ,HYY,HYZ,HZZ,LAP]
          [CONTOUR {LOG niso.i [zmin.r zmax.r]|ATAN niso.i [zmin.r zmax.r]|
    BADER|LIN niso.i [rini.r rend.r]|i1.r i2.r ...}] [COLORMAP [LOG|ATAN]]
    [RELIEF zmin.r zmax.r] [LABELZ labelz.r]

POINT

Write the properties (value, derivatives, related quantities) of one or more fields at a given point or set of arbitrary points.

POINT [x.r y.r z.r|file.s] [ALL] [FIELD {id.s/"expr"}]

POINTPROP

Defines the list of properties to be calculated at critical points (AUTO) and through the use of the POINT keyword.

POINTPROP name.s expr.s
POINTPROP CLEAR
POINTPROP

POLYHEDRA

Calculate coordination polyhedra.

POLYHEDRA atcenter.s atvertex.s [[rmin.r] rmax.r]

POWDER

Calculate the powder diffraction pattern of the current crystal structure.

POWDER [TH2INI t2i.r] [TH2END t2e.r] [{L|LAMBDA} l.r]
     [FPOL fpol.r] [NPTS npts.i] [SIGMA sigma.r]
     [ROOT root.s] [HARD|SOFT]

PRECISECUBE

Extra precision in output cube files.

PRECISECUBE|STANDARDCUBE

PRUNE_DISTANCE

Prune gradient paths for lighter output.

PRUNE_DISTANCE prune.r

Q/QAT

Define the atomic charges.

Q/QAT at1.s q1.r [at2.s q2.r] ...

QTREE

Integrate the attractor basins using the qtree method.

QTREE [maxlevel.i [plevel.i]] [MINL minl.i] [GRADIENT_MODE gmode.i]
    [QTREE_ODE_MODE omode.i] [STEPSIZE step.r] [ODE_ABSERR abserr.r]
    [INTEG_MODE level.i imode.i] [INTEG_SCHEME ischeme.i] [KEASTNUM k.i]
    [PLOT_MODE plmode.i] [PROP_MODE prmode.i] [MPSTEP inistep.i]
    [QTREEFAC f.r] [CUB_ABS abs.r] [CUB_REL rel.r] [CUB_MPTS mpts.i]
    [SPHFACTOR {ncp.i fac.r|at.s fac.r}] [SPHINTFACTOR atom.i fac.r]
    [DOCONTACTS] [WS_ORIGIN x.r y.r z.r] [WS_SCALE scale.r]
    [NOKILLEXT] [AUTOSPH {1|2}] [CHECKBETA] [NOPLOTSTICKS]
    [COLOR_ALLOCATE {0|1}] [SETSPH_LVL lvl.i] [VCUTOFF vcutoff.r]

RADII

Sets the covalent and van der Waals radii of atoms.

RADII {COV|VDW|} [at1.s|z1.i] rad1.r [[at2.s|z2.i] rad2.r ...]

RDF

Calculate the radial distribution function of atoms in a molecule or crystal.

RDF [RINI t2i.r] [REND t2e.r] [SIGMA sigma.r] [NPTS npts.i]
  [ROOT root.s] [PAIR is1.s is2.s [PAIR is1.s is2.s ...]]
  [HARD|SOFT]

REFERENCE

Mark a field as the reference field.

REFERENCE id.s

RESET

Restart the critic2 run by clearing all structural and field information.

RESET

ROOT

Change the default prefix for the files generated by critic2.

ROOT {root.s}

RUN

Run an external command.

RUN command.s

SETFIELD

Change field flags after the field was loaded.

SETFIELD [id.s] [NEAREST|TRILINEAR|TRISPLINE|TRICUBIC] [EXACT|APPROXIMATE]
              [RHONORM|VNORM] [NOCORE] [NUMERICAL|ANALYTICAL]
              [TYPNUC {-3,-1,1,3}] [NORMALIZE n.r] [ZPSP at1.s q1.r...]

SIGMAHOLE

Calculate the properties of a $\sigma$-hole in a molecule

SIGMAHOLE ib.i ix.i [NPTS nu.i nv.i] [ISOVAL rho.r] [MAXANG ang.r]

SPG

List the space group types known to critic2.

SPG

SPHEREINTEGRALS

Integrate fields on a sphere.

SPHEREINTEGRALS {GAULEG [ntheta.i nphi.i]|LEBEDEV [nleb.i]}
              [NR npts.i] [R0 r0.r] [REND rend.r] [CP ncp.i]

STANDARDCUBE

Normal precision in output cube files.

PRECISECUBE|STANDARDCUBE

STM

Make scanning tunneling microscopy plots.

STM [CURRENT [curr.r]|HEIGHT [hei.r]] [TOP top.r]
  [{CELL|CELLS} nx.i ny.i] [NPTS n1.i n2.i]
  [LINE x0.r y0.r x1.r y1.r npts.i]

SUM

Sum of the values of a field defined on a grid.

SUM [id.s]

SYMM/SYM

Activates the use of symmetry and controls the symmetry level.

{SYMM|SYM}
{SYMM|SYM} [-1|0|1]
{SYMM|SYM} eps.r
{SYMM|SYM} CLEAR
{SYMM|SYM} RECALC
{SYMM|SYM} ANALYSIS
{SYMM|SYM} REFINE
{SYMM|SYM} WHOLEMOLS

SYSTEM

Run an external command.

SYSTEM command.s

UNITS

Change the default units used in the input and output.

UNITS {BOHR|AU|A.U.|ANG|ANGSTROM}

UNLOAD

Unload a field.

UNLOAD {id.s|ALL}

VDW

Calculate the van der Waals volume of a crystal or molecule.

VDW [PREC prec.r]

VORONOI

Calculate atomic properties integrated in the atomic Voronoi regions.

VORONOI [BASINS [OBJ|PLY|OFF] [ibasin.i]] [ONLY iat1.i iat2.i ...]

WRITE

Write the crystal structure to an external file.

WRITE file.{xyz,gjf,cml} [SPHERE rad.r [x0.r y0.r z0.r]]
    [CUBE side.r [x0.r y0.r z0.r]] [BORDER] [ix.i iy.i iz.i]
    [MOLMOTIF] [ONEMOTIF] [ENVIRON dist.r]
    [NMER nmer.i]
WRITE file.{obj,ply,off} [SPHERE rad.r [x0.r y0.r z0.r]]
    [CUBE side.r [x0.r y0.r z0.r]] [BORDER] [ix.i iy.i iz.i]
    [MOLMOTIF] [ONEMOTIF] [CELL] [MOLCELL]
WRITE file.scf.in [rklength.r]
WRITE file.pwi [rklength.r]
WRITE file.tess
WRITE file.cri|file.incritic
WRITE {[file.]POSCAR|[file.]CONTCAR|file.vasp}
WRITE file.abin
WRITE file.elk
WRITE file.gau
WRITE file.cif [NOSYM|NOSYMM]
WRITE file.d12 [NOSYM|NOSYMM] [NOEXTERNAL]
WRITE file.res [NOSYM|NOSYMM]
WRITE file.m
WRITE file.db
WRITE file.gin
WRITE file.lammps
WRITE file.cell [rklength.r]
WRITE file.fdf
WRITE file.STRUCT_IN
WRITE file.hsd
WRITE file.gen
WRITE file.pyscf
WRITE file.in [rklength.r] ## FHIaims geometry.in
WRITE file.frac

XDM

Calculate the XDM dispersion energy and derivatives.

XDM GRID [RHO irho.s] [TAU itau.s] [ELF ielf.s]
  [PDENS ipdens.s] [CORE icor.s] [LAP ilap.s]
  [GRAD igrad.s] [RHOAE irhoae.s] [XB ib.s]
  [XA1 a1.r] [XA2 a2.r] [ONLYC] [UPTO {6|8|10}]
XDM [QE|POSTG] [FILE file.s] [BETWEEN at1.i at1.i ... AND at1.i at2.i ...]
     [NOC6] [NOC8] [NOC10] [SCALC6 s6.r] [SCALC8 s8.r] [SCALC10 s10.r]
     [C9] [SCALC9 s9.r]
     [DAMP a1.r a2.r] [DAMP3 a3.r a4.r] [DAMP3BJN 3|6|sqrt6]
XDM a1.r a2.r chf.s

XRPD

Fit experimental X-ray powder diffraction pattern profile and background.

XRPD BACKGROUND source_xy.s outbckgnd_xy.s [nknot.i]
XRPD FIT source_xy.s [ymax_peakdetect.r] [nadj.i]
XRPD REFIT source_xy.s source_peaks.s

YT

Integrate the attraction (atomic) basins of a field defined on a grid using Yu and Trinkle’s method.

YT [NNM] [NOATOMS] [WCUBE] [BASINS [OBJ|PLY|OFF] [ibasin.i]] [RATOM ratom.r]
 [DISCARD expr.s] [JSON file.json] [ONLY iat1.i iat2.i ...]

List of Functions Used in Arithmetic Expressions

Basic arithmetic functions

abs, exp, sqrt, floor, ceil, ceiling, round, log, log10, sin, asin, cos, acos, tan, atan, atan2, sinh, cosh, erf, erfc, min, max.

gtf(id) [gtf]

Thomas-Fermi kinetic energy density.

vtf(id) [vtf]

Thomas-Fermi potential energy density (uses local virial).

htf(id) [htf]

Thomas-Fermi total energy density (uses local virial).

gtf_kir(id) [gtf_kir]

Thomas-Fermi ked with Kirzhnits gradient correction.

vtf_kir(id) [vtf_kir]

Thomas-Fermi potential energy density with Kirzhnits gradient correction (uses local virial).

htf_kir(id) [htf_kir]

Thomas-Fermi total energy density with Kirzhnits gradient correction (uses local virial).

gkin(id) [gkin]

Kinetic energy density, g-version (grho * grho).

kkin(id) [kkin]

Kinetic energy density, k-version (rho * laprho).

lag(id) [lag]

Lagrangian density (-1/4 laprho).

elf(id) [elf]

Electron localization function.

vir(id) [vir]

Electronic potential energy density (virial field).

stress [stress]

Schrodinger stress tensor (for the reference field only).

he(id) [he]

Electronic energy density, gkin+vir.

lol(id) [lol]

Localized-orbital locator.

lol_kir(id) [lol_kir]

Localized-orbital locator, with Kirzhnits k.e.d.

brhole_a1(id), brhole_a2(id), brhole_a(id)

BR hole, A prefactor (spin up, down, and average).

brhole_b1(id), brhole_b2(id), brhole_b(id)

BR hole, hole-reference distance (spin up, down, and average).

brhole_alf1(id), brhole_alf2(id), brhole_alf(id)

BR hole, exponent (spin up, down, and average).

xhcurv1(id), xhcurv2(id), xhcurv(id)

Curvature of the exchange hole at the reference point (spin up, down, and average).

dsigs1(id), dsigs2(id), dsigs(id)

Same-spin pair density leading coefficient (Dsigma) (spin up, down, and average).

xhole(id,x,y,z)

Exchange hole with reference point at x,y,z.

stress [STRESS]

Schrodinger stress tensor (only for the reference field).

mep(id)

Molecular electrostatic potential (requires libcint).

uslater(id)

Slater potential (requires libcint).

nheff(id)

Reverse-BR effective hole normalization (requires libcint).

xc(…,idx)

Exchange-correlation energy density (requires libxc).

List of Field Modifiers ($field:modifier)

:v

Valence-only value of the field.

:c

Core-only value of the field.

:x, :y, :z

First derivatives of the field

:xx, :xy, :yx, :xz, :zx, :yy, :yz, :zy, :zz

Second derivatives.

:g

Norm of the gradient.

:l

Laplacian.

:lv

Valence Laplacian.

:lc

Core Laplacian.

:<n>

Value of MO number n. (only for molecular wavefunctions)

:HOMO

Highest-occupied molecular orbital (RHF). (only for molecular wavefunctions)

:LUMO

Lowest-unoccupied molecular orbital (RHF). (only for molecular wavefunctions)

:A<n>

Alpha MO number n. (only for molecular wavefunctions)

:B<n>

Beta MO number n. (only for molecular wavefunctions)

:AHOMO

Alpha highest-occupied molecular orbital (UHF). (only for molecular wavefunctions)

:ALUMO

Alpha lowest-unoccupied molecular orbital (UHF). (only for molecular wavefunctions)

:BHOMO

Beta highest-occupied molecular orbital (UHF). (only for molecular wavefunctions)

:BLUMO

Beta lowest-unoccupied molecular orbital (UHF). (only for molecular wavefunctions)

:up, :dn, :sp

Alpha, beta, spin density. (only for molecular wavefunctions)

List of Structural Variables (@strucvar)

@dnuc

Distance to the closest nucleus. If used as @dnuc:n, the distance to the closest nucleus with ID n from the complete list.

@xnucx

x of the closest nucleus (crystallographic). If used as @xnuc:n, the x coordinate of the closest nucleus with ID n from the complete list.

@ynucx

y of the closest nucleus (crystallographic). If used as @ynuc:n, the y coordinate of the closest nucleus with ID n from the complete list.

@znucx

z of the closest nucleus (crystallographic). If used as @znuc:n, the z coordinate of the closest nucleus with ID n from the complete list.

@xnucc

x of the closest nucleus (Cartesian). If used as @xnucc:n, the x coordinate of the closest nucleus with ID n from the complete list.

@ynucc

y of the closest nucleus (Cartesian). If used as @ynucc:n, the y coordinate of the closest nucleus with ID n from the complete list.

@znucc

z of the closest nucleus (Cartesian). If used as @znucc:n, the z coordinate of the closest nucleus with ID n from the complete list.

@xx

x of the evaluation point (crystallographic).

@yx

y of the evaluation point (crystallographic).

@zx

z of the evaluation point (crystallographic).

@xc

x of the evaluation point (Cartesian).

@yc

y of the evaluation point (Cartesian).

@zc

z of the evaluation point (Cartesian).

@xm

x of the evaluation point (Cartesian molecular).

@ym

y of the evaluation point (Cartesian molecular).

@zm

z of the evaluation point (Cartesian molecular).

@xxr

x of the evaluation point (reduced crystallographic).

@yxr

y of the evaluation point (reduced crystallographic).

@zxr

z of the evaluation point (reduced crystallographic).

@idnuc

Complete-list id of the closest nucleus.

@nidnuc

Non-equivalent-list id of the closest nucleus.

@rho0nuc

Atomic density contribution from the closest nucleus. If used as @rho0nuc:n, the atomic density contribution of the closest nucleus with ID n from the complete list.

@spcnuc

Species id of the closest nucleus.

@zatnuc

Atomic number of the closest nucleus.