Structural tools
Relabel the Atoms in the Structure (ATOMLABEL)
The ATOMLABEL keyword can be used to change the atomic labels for the atoms in the current structure:
ATOMLABEL template.s
The template string (template.s) is used to build the new atomic
names. The format specifiers for this template are:
-
%aid: the index for the atom in the non-equivalent atom list. -
%id: the index for the atom in the non-equivalent atom list, counting only the atoms of the same type. -
%S: the atomic symbol, derived from the current atomic number. -
%s: same as%S, but lowercase. -
%l: the current atom label.
Powder Diffraction (POWDER)
The keyword POWDER calculates the powder diffraction pattern for 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]
Only the range from t2i.r (default: 5 degrees) to
t2e.r (default: 90 degrees) will be plotted. The wavelength of the
incident radiation is given by l.r (in angstrom, default: 1.5406
angstrom, corresponding to Cu-Kα). The polarization of the X-ray
radiation affects the treatment of the resulting intensities. The
default is fpol.r = 0, unpolarized light. For synchrotron radiation,
use fpol.r = 0.95. npts.i is the number of points in the generated
spectrum (default: 10001). Gaussian broadening is used on the observed
peaks, with width parameter sigma.r (default: 0.05 degrees).
By default, two files are generated: <root>_xrd.dat, containing the
versus intensity data, and <root>_xrd.gnu, the gnuplot
script to plot it. The name of these files can be changed using the
ROOT keyword. The Miller indices of the peaks are written to the
standard output.
The HARD and SOFT keywords control how peaks right outside the
plot range are treated. In a HARD powder diffraction pattern, the
peaks outside the plot range are not computed, and therefore their
tails will not appear on the plot even if the corresponding peak is so
close that the contribution to the RDF would be significant. In a
SOFT powder diffraction pattern, all peaks are computed and
represented, even if the maximum is outside the plot range. Default:
SOFT.
Radial Distribution Function (RDF)
The RDF keyword calculates the radial distribution function (RDF) for the current crystal or molecular structure:
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]
The definition of RDF is similar to the one found in Willighagen et al., Acta Cryst. B 61 (2005) 29, but where the atomic charges are replaced by the square root of the atomic number. Each pair of atoms A and B at a distance in the system will create a peak in the RDF with a Gaussian shape: \begin{equation} I_{AB}(r) = \sqrt{Z_AZ_B}\times \exp\left(-\frac{(r-d_{AB})^2}{2\sigma^2}\right) \end{equation} The RDF is constructed from the sum of all functions from all unique atom pairs by doing: \begin{equation} {\rm RDF}(r) = \sum_{A<B} \frac{I_{AB}(r)}{r^2N_{\rm cell}} \end{equation} where is the number of atoms in the unit cell.
The RDF is plotted from an initial distance t21.r (default: 0) up to
a maximum distance t2e.r (default: 25 bohr) using npts.i points in
that interval (default: 10001). Gaussian broadening is used with sigma
equal to sigma.r (default: 0.05 bohr). The default units of RINI,
REND, and SIGMA are bohr in crystals and angstrom in molecules
(this can be changed with the
UNITS keyword).
Two files are generated: <root>_rdf.dat, containing the RDF versus
distance data, and <root>_rdf.gnu, the gnuplot script to plot
it. The name of these files can be changed using the ROOT keyword. If
PAIR is given, only the distances between atoms of type is1.s and
is2.s will contribute to the RDF. Multiple PAIR keywords can be
used. The is1.s and is2.s must be the name of an atomic species in
the system.
The HARD and SOFT keywords control how peaks right outside the
plot range are treated. In a HARD RDF, the peaks outside the plot
range are not computed, and therefore their tails will not appear on
the plot even if the corresponding peak is so close that the
contribution to the RDF would be significant. In a SOFT RDF, all
peaks are computed and represented, even if the maximum is outside the
plot range. Default: SOFT.
Average Minimum Distances (AMD)
The AMD keyword calculates the average minimum distances vector. Element i in this vector corresponds to the average of all the i-th nearest-neighbor distances in the crystal or molecule. The AMD has been proposed as a way to compare crystal structures in Widdowson et al., Match. Commun. Math. Comput. Chem., 87 (2022) 529.
AMD [nnmax.i]
The AMD is calculate up to a maximum number of nearest-neighbors equal
to nnmax.i (default: 100). In a molecule, nnmax.i is capped at the
number of atoms in the molecule minus one.
Compare Crystal and Molecular Structures (COMPARE)
The COMPARE keyword compares two or more structures:
COMPARE {.|file1.s} {.|file2.s} [{.|file3.s} ...]
COMPARE ... [MOLECULE|CRYSTAL]
COMPARE ... [REDUCE eps.r] [NOH]
COMPARE ... [POWDER|RDF|AMD|EMD] [XEND xend.r] [SIGMA sigma.r] [NORM 1|2|INF] ## crystals
COMPARE ... [SORTED|RDF|ULLMANN|UMEYAMA] ## molecules
At least two structures are required for the comparison. The
structures can be given as external files (file1.s,
file2.s,…). The behavior regarding the input format is the same as
in CRYSTAL and MOLECULE: the file format is identified using the file
extension or its contents if the extension is not enough. If a dot
(“.”) is used instead of a file name, the current structure
(previously loaded with CRYSTAL/MOLECULE) is used. A file with
extension .peaks can also be given to provide powder diffraction
peak information directly (see below).
There are two distinct modes of operation in COMPARE, depending on whether a molecular or crystal comparison is carried out. If the structures are all molecules or if the MOLECULE keyword is used, then the structures are compared as molecules. If any one of the structures is a crystal or if the CRYSTAL keyword is used, a crystal comparison is done.
If the NOH keyword is used, either with molecules or crystals, the hydrogen atoms are stripped from the structures before running the comparison.
If more than two structures are used in COMPARE, critic2 will compare
each pair of structures and present the resulting similarity
matrix. Alternatively, if the REDUCE keyword is used, a threshold
(eps.r) is applied to determine whether two structures are equal or
not. Critic2 then prints a list of unique structures and repeated
structures in the output.
The COMPARE keyword does not require a previous CRYSTAL or MOLECULE keyword. Hence, valid critic2 inputs would be:
COMPARE bleh1.scf.in bleh2.cif
COMPARE bleh1.xyz bleh2.wfx
provided the files exist.
Examples of how to carry out structure comparisons in crystals and molecules are given in the corresponding example.
Crystal Comparison
There are several ways of calculating a comparison between crystals:
based on radial distribution functions
(RDF keyword), powder
diffraction patterns (POWDER
keyword), average minimum distances
(AMD keyword), or powder
diffraction patterns compared with the earth mover’s distance (EMD).
The default is POWDER. In all cases, COMPARE finds the measure of
similarity (DIFF) based on the corresponding functions (RDF,
diffractogram, AMD). Two crystal structures are exactly equal if
DIFF = 0. Maximum dissimilarity occurs when DIFF = 1. In the case
of RDF and POWDER, the crystal similarity measure is calculated using
the cross-correlation functions defined in
de Gelder et al., J. Comput. Chem., 22 (2001) 273,
with the triangle weight. In AMD, the dissimilarity is calculated by
default as the infinite-norm of the two AMD vectors (the maximum of
the absolute values of the differences). This can be change to the
1-norm (the sum of the absolute values) or the 2-norm (the Euclidean
distance) using the NORM keyword. The AMD dissimilarity is in atomic
units (bohr). In EMD, discrete powder diffraction patterns are
compared using the earth mover’s distance.
Powder diffraction patterns for POWDIFF and EMD are calculated from
up to xend.r (XEND keyword, default: 50). Radial
distribution functions are calculated from zero up to xend.r bohr
(XEND keyword, default: 25 bohr). SIGMA is the Gaussian broadening
parameter for the powder diffraction or RDF peaks. AMD vectors are
calculated up to a maximum of 100 nearest neighbors.
If a file with extension .peaks is given and the POWDER or EMD
crystal comparisons are used, read the diffraction peak info from the
file. The file must give one peak per line in the format:
2*theta Intensity
where is given in degrees and the intensity corresponds to the peak area. The powder diffraction pattern for the POWDER comparison is synthesized from this information by placing Gaussian functions at the peak positions with the same parameters as for the other structures.
Molecular Comparison
For the molecular comparison, there are several options. If the SORTED keyword is used, the atomic sequence in each molecule is assumed to be the same. In this case, COMPARE finds the translation and rotation that brings the molecules into closest agreement with each other and reports the resulting root-mean-square (RMS) of the atomic positions. The molecular rotation is calculated using Walker et al.’s quaternion algorithm (Walker et al., CVGIP-Imag. Understan. 54 (1991) 358). For the comparison to work correctly, it is necessary that the two molecules have the same number of atoms and that the atoms are in the same sequence.
If the molecules have the same atomic connectivity (the same molecular diagram) but the atomic sequences are not equivalent, i.e. the atoms are disordered, then the ULLMANN or UMEYAMA methods can be used. The Umeyama approach (keyword: UMEYAMA) uses a weighted graph matching method based on the algorithm proposed in Umeyama, S., IEEE PAMI, 10 (1988) 695-703. Umeyama’s method is non-iterative, but approximate. If there are significant differences between the structures being compared, or if they are highly symmetric, UMEYAMA may find the wrong atomic permutation, so it is a good idea to always check that the RMS in the output is reasonable. The Ullmann approach (keyword: ULLMANN) uses a modified version of Ullmann’s subgraph matching algorithm (Ullmann, J. R., J. ACM 23 (1976) 31-42). This method finds all possible matching sequences based on graph connectivity alone, then selects the sequence with lowest RMS upon molecular rotation. It is more reliable than UMEYAMA but may become expensive for larger molecules.
The ULLMANN method is the default if the number and types of atoms in the molecules being compared are the same. If this is not the case, or if the RDF keyword is used, then radial distribution functions are employed and the comparison is similar to how RDF works in crystals.
Compare Crystal Structures Allowing Cell Deformations (COMPAREVC)
The COMPAREVC keyword (variable-cell compare) is used to compare two crystal structures allowing one of them to have its lattice deformed to match the lattice of the other. This is useful when comparing structures that have very similar motifs but slightly mismatched lattices as a result of, for instance, deformations caused by temperature or pressure effects. In particular, COMPAREVC can be used to compare calculated equilibrium structures with experimental structures.
The COMPAREVC method works by exploring the set of lattice basis changes that transform the reduced cell of the first crystal into the reduced cell of the second crystal. For each transformation, the cell parameters are then forced to be equal, and the similarity is calculated using a cross-correlation function (the POWDIFF option in the COMPARE keyword). The lowest POWDIFF found in this way is the calculated variable-cell similarity measure (VC-POWDIFF). The algorithm is described in detail in Mayo et al., CrystEngComm (2022). The COMPAREVC keyword corresponds to the VC-PWDF (variable-cell POWDIFF) described in the article.
The syntax of the COMPAREVC keyword is:
COMPAREVC {.|file1.s} {.|file2.s} [THR thr.r] [WRITE] [NOH] [MAXELONG me.r] [MAXANG ma.r]
[MAXVOL mv.r]
The structures contained in file1.s and file2.s are compared using
the variable-cell comparison algorithm. The behavior regarding the
input format is the same as in CRYSTAL and MOLECULE: the file format
is identified using the file extension or its contents if the
extension is not enough. If a dot (“.”) is used instead of a file
name, the current structure (previously loaded with CRYSTAL/MOLECULE)
is used.
There are several optional keyword to COMPAREVC. If THR is given, stop the comparison if the calculated similarity measure (VC-POWDIFF) is lower than thr.r. This is useful for speeding up calculations in which we set a threshold below which we accept two crystal structures are equal. If WRITE, write the transformed structure to a SHELX file. If NOH, remove the hydrogens from both structures before comparing. The MAXELONG, MAXANG, and MAXVOL options control the maximum elongation, maximum angle change, and maximum volume change allowed for the cell deformation. By default, they are 30% (0.3), 20 degrees, and 50% (0.5) respectively.
Transform the Unit Cell (NEWCELL)
The NEWCELL keyword transforms the unit cell used to describe the current crystal structure to a new 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]
The new unit cell is given by the vectors (x1.r y1.r z1.r),
(x2.r y2.r z2.r), and (x3.r y3.r z3.r) in
crystallographic coordinates relative to the old unit cell. The x1,
x2, x3 vectors must be pure translations of the old cell; either
lattice vectors, centering vectors, or combinations of the
two. Alternatively, if three integers are given (n1.i n2.i n3.i),
NEWCELL builds a supercell with n1.i cells in the a direction,
n2.i cells in the b direction, and n3.i cells in the c direction.
NEWCELL unloads all fields (except the promolecular density) and
clears the critical point list. If the INV (or INVERSE) keyword is
used, the input vectors correspond to the crystallographic coordinates
of the old cell in the new coordinate system. A NEWCELL transformation
is the inverse of the same transformation using the INV keyword.
Optionally, if an ORIGIN vector is given, (x0.r y0.r z0.r), the
cell origin is translated to x0. The units of x0 are crystallographic
coordinates of the original cell.
The NEWCELL keyword is useful for building supercells or for performing routine but tedious crystallographic transformations. For instance, given a face-centered cubic lattice and the conventional cubic cell one can find the primitive (rhombohedral) cell by doing:
CRYSTAL LIBRARY mgo
NEWCELL 1/2 1/2 0 1/2 0 1/2 0 1/2 1/2
Likewise, if the current cell is rhombohedral, the same NEWCELL order but including the INVERSE keyword transforms to the cubic. That is:
CRYSTAL LIBRARY mgo
NEWCELL 1/2 1/2 0 1/2 0 1/2 0 1/2 1/2
NEWCELL 1/2 1/2 0 1/2 0 1/2 0 1/2 1/2 INVERSE
gives a unit cell and crystal structure description that is equivalent to the initial one read from the library.
NEWCELL also admits specific keywords that perform common transformations to certain cells of interest. The cell can be transformed to:
-
STANDARD: standard (canonical) unit cell.
-
PRIMITIVE: standard primitive unit cell. Does not transform the cell if the unit cell is already primitive.
-
PRIMSTD: standard primitive unit cell. Does the transformation even if the current unit cell is primitive.
-
NIGGLI: Niggli-reduced cell for the current lattice. Use a NEWCELL PRIMITIVE first to get the primitive Niggli cell.
-
DELAUNAY: Delaunay-reduced cell for the current lattice. Use a NEWCELL PRIMITIVE first to get the primitive Delaunay cell.
The origin is not translated by any of these keywords. The REFINE keyword can be used in combination with STANDARD, PRIMITIVE, or PRIMSTD. If REFINE is used, then the atomic positions are idealized according to the space group symmetry operations. For instance, an atomic coordinate of 0.333 may become 0.3333333… in a hexagonal space group. These transformations use the spglib library. Please consult the spglib manual for more information.
The keyword NICE can be used to activate a mode of operation of
NEWCELL that does not effect any cell transformation. Instead,
NICE examines all possible supercells of the currently loaded cell
containing a number of cells up to inice.i (default: 64). For a
given integer n between 1 and inice.i, all supercells with size
n (i.e. comprising n current cells) are examined and the
transformation to the “nicest” supercell is reported. The niceness of
a supercell is a number between 0 and 1 determined by the size of the
largest sphere it can contain (higher is nicer). The nicest supercell
possible is cubic and has a niceness of 1. In the output of NEWCELL
NICE, the NEWCELL transformations for all supercells with sizes
between 1 and inice.i are reported, together with their niceness and
the radius of the largest sphere they can contain.
Calculate Atomic Environments (ENVIRON)
The ENVIRON keyword prints lists of neighbor atoms:
ENVIRON [DIST dist.r] [POINT x0.r y0.r z0.r|ATOM at.s/iat.i|CELATOM iat.i]
[BY by.s/iby.i] [SHELL|SHELLS]
If POINT is given, print the atomic neighbors around the point with
coordinates (x0.r y0.r z0.r) in crystallographic coordinates
(crystal) or or molecular Cartesian coordinates (molecule, default
units: angstrom). Instead, if ATOM is given, print the neighbors
around atom iat.i from the non-equivalent atom list or around every
atom with atomic symbol at.s (converted internally to atomic
number). If CELATOM is used, then print the environment around atom
iat.i from the complete list. If neither POINT nor ATOM nor CELATOM
are given, print the environments of all non-equivalent atoms in the
unit cell.
By default, the environments extend up to 5 angstrom from the central
point. The DIST keyword can be used to change this value (by default,
dist.r is in bohr in crystals and angstrom in molecules). The BY
keyword allows filtering the neighbor list to print only certain kinds
of atoms. If iby.i is given, print only atoms whose non-equivalent ID
is the same as iby.i. If by.s is given, print only atoms with the same
atomic symbol as by.s (converted internally to atomic number). If
SHELLS (or SHELL) is given, group the neighbors in shells by distance
(1e-2 atomic distance threshold for atoms in the same shell) and
non-equivalent ID.
Calculate Coordination Polyhedra (POLYHEDRA)
The POLYHEDRA keyword calculates the coordination polyhedra in a periodic solid:
POLYHEDRA atcenter.s atvertex.s [[rmin.r] rmax.r]
The polyhedra are built with atom atcenter.s as the center and
atvertex.s as the vertices. These strings can refer to an atomic
species, if such species exists in the current structure. If not, then
the symbols are converted to atomic numbers, and these are used
instead. By default, the distance range to consider the central and
vertex atom are coordinated is from zero to the sum of covalent radii
times the BONDFACTOR. If a
single number (rmax.r) is indicated at the end of the POLYHEDRA
command, then the distance range goes from zero to rmax.r. If two
numbers are indicated, then the distance range goes from rmax.r to
rmin.r.
The output of the POLYHEDRA keyword contains a list of non-equivalent
atoms of type atcenter.s that have a coordination polyhedron. The
number of vertices, minimum and maximum vertex-center distance, number
of faces, and polyhedron volume are printed.
Effective Coordination Number (ECON)
The coordination number of an atom is typically defined as the number of neighbors that are closest to that atom. This definition can be unsatisfactory for situations where there is a range of bond lengths around the central atom. To address these complex cases, the calculation of an effective coordination number (ECoN) was introduced by Hoppe in 1979. The ECoN of a given atom is calculated by assigning to each atom around it a weight based on their distance. The original procedure is described in Hoppe, Z. Kristallogr. 150 (1979) 23 and examined in detail in Nespolo, Acta Cryst. B, 72 (2016) 51.
The implementation of ECoN in critic2 is slightly different from those two references in that we do not require the user to define coordination polyhedra for the calculation. Instead, the ECoN in critic2 is calculated as a formula that takes into account the distances from the central atom to all other atoms in the crystal. There are two variants of ECoN: iterative, calculated using a self-consistent procedure, and non-iterative.
For a given atom, the ECoN is defined as: \begin{equation} {\rm ECoN} = \sum_{i} w_{i} \end{equation} where the sum runs over all the atoms in the environment of the chosen central atom (or a subset of atoms belonging to a certain species, see below). The weight of the ith atom () is defined as: \begin{equation} w_{i} = \exp\left[1-\left(\frac{d_{i}}{d_{\rm av}}\right)^6\right] \end{equation} with the distance to atom . In the non-iterative variant of ECoN, is the weighted average distance, defined as: \begin{equation} d_{\rm av} = \frac{\sum_{i} d_{i}\exp\left[1-\left(\frac{d_{i}}{d_{\rm min}}\right)^6\right]} {\sum_{i}\exp\left[1-\left(\frac{d_{i}}{d_{\rm min}}\right)^6\right]} \end{equation} where is the shortest distance to the central atom for the considered atomic species. In contrast, the iterative variant of ECoN calculates the weighted average distance by solving the non-linear equation: \begin{equation} d_{\rm av}^{\rm it} = \frac{\sum_{i} d_{i}\exp\left[1-\left(\frac{d_{i}}{d_{\rm av}^{\rm it}}\right)^6\right]} {\sum_{i}\exp\left[1-\left(\frac{d_{i}}{d_{\rm av}^{\rm it}}\right)^6\right]} \end{equation} which is done using a self-consistent iterative procedure.
A typical output for the ECoN keyword is:
# nid->spc name(nid)->name(spc) econ 1econ nd 1nd
1 -> * Ti -> * 5.9754 5.9743 3.6805 3.6804
1 -> 1 Ti -> Ti 4.8730 4.7197 5.8587 5.8302
1 -> 2 Ti -> O 5.9754 5.9742 3.6805 3.6804
2 -> * O -> * 3.2704 3.2170 3.7153 3.7056
2 -> 1 O -> Ti 2.9877 2.9871 3.6805 3.6804
2 -> 2 O -> O 7.9476 6.4604 5.1286 4.9802
where nid represents the non-equivalent atom ID of the central atom
for which the ECoN is calculated and the values corresponding to
different spc are obtained by considering the distances to atoms
belonging to those atomic species only (spc=1, 2, etc.) or to all
atoms regardless of species (spc=*). Critic2 reports the
iterative ECoN (econ), non-iterative ECoN (1econ), iterative
weighted average distance (nd, ), and
non-iterative weighted average distance (1nd, ).
Pair and Triplet Coordination Numbers (COORD)
The COORD keyword calculates pair and triplet coordination numbers:
COORD [DIST dist.r] [FAC fac.r]
By default two atoms are coordinated if they are within fac.r times
the sum of their covalent radii. By default, fac.r is equal to the
BONDFACTOR and the internal
list of covalent radii is used (see the
RADII keyword). The value of fac.r
can be changed with the FAC keyword. The atomic radii for atomic
species can be changed with using the RADII keyword.
If the DIST keyword is used, all atoms within a distance dist.r are
coordinated.
On output, COORD will list the number of coordinated pairs per atom in the unit cell and per atomic species. In addition, it will also list all coordinated triplets X-Y-Z, where Y runs over all atoms in the unit cell and over all atomic species.
Packing Ratio (PACKING)
The PACKING keyword computes the packing ratio of the crystal.
PACKING {COV|VDW|} [PREC prec.r]
With VDW, use the van der Waals radii. With COV, use the covalent radii. If neither VDW nor COV are used, use half of the nearest neighbor distance (in this case, the spheres would not overlap).
In the VDW and COV cases, the calculation is done using a Monte-Carlo
sampling of the unit cell. The PREC keyword allows controlling the
precision of this calculation. PREC corresponds to the standard
deviation in the van der Waals volume divided by the volume
itself. The default prec.r is 0.01. The van der Waals and covalent
radii can be changed using the RADII
keyword.
Van der Waals Volume (VDW)
The VDW keyword calculates the van der Waals volume of a crystal or molecule.
VDW [PREC prec.r]
The calculation is done using a Monte-Carlo sampling of the unit cell
or the molecular volume. The PREC keyword allows controlling the
precision of this calculation. PREC corresponds to the standard
deviation in the van der Waals volume divided by the volume
itself. The default prec.r is 0.01. The van der Waals radii are
taken from the internal tables, and they can be changed using the
RADII keyword.
Identify Atoms in the Structure Given Their Coordinates (IDENTIFY)
The IDENTIFY keyword identifies the coordinates in the user input by matching them against the internal list of atoms and critical points:
IDENTIFY [ANG|ANGSTROM|BOHR|AU|CRYST]
x.r y.r z.r [ANG|ANGSTROM|BOHR|AU|CRYST]
...
file.xyz
ENDIDENTIFY/END
IDENTIFY file.xyz
If a coordinate is close (1e-4 bohr) to an atom or CP, the
corresponding indices as well as the coordinates are written to the
output. The input can come as either the coordinates of the points
themselves or a filename pointing to an .xyz file. IDENTIFY can be
used in environment mode (IDENTIFY/ENDIDENTIFY, with several lines of
input) or as a single command when applying it to a single .xyz
file.
The default units are crystallographic coordinates in crystals and
molecular Cartesian coordinates in molecules (default unit:
angstrom). However, these units can be modified with one of the
keywords that follow the IDENTIFY command. For specific points, the
unit can be changed by specifying the same keywords after the three
coordinates. The units in the .xyz file are angstrom (the xyz file
also has to have the usual syntax, with the number of atoms in the
first line and the title, or a blank line, in the second line).
In addition to the identity of the points, if any, critic2 also provides the vertices of the cube that encompasses all the points in the list that did match an atom or CP.
Point-Charge Electrostatic Energy (EWALD)
The EWALD keyword calculates the electrostatic energy of the lattice of point charges using Ewald’s method:
EWALD
The atomic charges are defined using the Q keyword.
Reorder Atoms in a Molecule or Molecular Crystal (MOLREORDER)
The MOLREORDER keyword reorders the atoms in a target molecule or all the molecules in a target molecular crystal to have the same atomic sequence as in a template molecule. The syntax is:
MOLREORDER {.|template.s} {.|target.s} [WRITE file.s] [MOVEATOMS] [INV] [UMEYAMA|ULLMANN]
The template molecule is in file template.s. The target structure
file target.s must contain either a molecule or a molecular
crystal. If target.s is a molecule, it must contain the same number
and types of atoms as the template. If target.s is a molecular
crystal, its asymmetric unit must have an integer number of molecules
(Z’, see the WHOLEMOLS option in
SYMM/SYM). In addition, all
molecular fragments in the target crystal must have the same number
and atom types as the template. On output, the atoms in structure
target.s are reordered such that they are in the same sequence as
template.s. A dot (“.”) given as either the template (template.s)
or target (target.s) files instructs critic2 to use the currently
loaded structure (with a previous CRYSTAL/MOLECULE command).
MOLREORDER can use two different algorithms to solve the atomic sequence reordering problem:
-
The Umeyama approach (keyword: UMEYAMA) uses a weighted graph matching method based on the algorithm proposed in Umeyama, S., IEEE PAMI, 10 (1988) 695-703. Umeyama’s method is non-iterative, but approximate. If there are significant differences between the structures being compared, or if they are highly symmetric, UMEYAMA may find the wrong atomic permutation, so it is a good idea to always check that the RMS in the output is small.
-
The Ullmann approach (keyword: ULLMANN) uses a modified version of Ullmann’s subgraph matching algorithm (Ullmann, J. R., J. ACM 23 (1976) 31-42). This method finds all possible matching sequences based on graph connectivity alone, then selects the sequence with lowest RMS upon molecular rotation. It is more reliable than UMEYAMA but may become expensive for larger molecules. This is the default.
Once the atoms are in the correct sequence, the RMS is obtained by calculating the rotation matrix that yields the best match, in the least squares sense, between the template and the reordered structure(s). The MOLREORDER keyword does not require having any molecular or crystal structure loaded.
If WRITE is used followed by a file name file.s, the output
structure with its atoms in the same order as the template is written
to that file. In addition, if MOVEATOMS is used, the atoms in the
structure written to file.s are moved to match the structure of the
template molecule. If INV is used, inversion operations are allowed.
Move Atoms in a Molecular Crystal to Match Molecules (MOLMOVE)
The MOLMOVE keyword is used to modify the atomic positions in a
molecular crystal in such a way that the structures of its fragments
are identical to a set of molecules provided by the user. This is
useful when the molecules in a molecular crystal are extracted (with
the NMER 1 ONEMOTIF options of the WRITE
command), then their structure is modified, most commonly by running a
geometry relaxation in the gas-phase, and then the new molecular
structures need to be re-packed back into the crystal structure. The
syntax for the MOLMOVE keyword is:
MOLMOVE mol1.s mol2.s ... moln.s target.s new.s
The molecular crystal that needs to be modified (target.s) must be
composed of n fragments, and n molecular structures have to be
given first (mol1.s to moln.s). The molecular structures can be
given in any order, but their centers of mass and atomic sequence must
be the same as the fragments in the target molecular crystal. Using
the NMER 1 ONEMOTIF options to WRITE the molecules in a molecular
crystal ensures that the order and centers of mass of the molecular
fragments are correct. The file name where the repacked molecular
structure will be written must be given at the end of the command
(new.s).
Calculate Dimensions of Uniform k-Point Grids (KPOINTS)
The KPOINTS keyword:
KPOINTS [rk.r] [RKMAX rkmax.r]
calculates the number of k-points in each direction (nk1, nk2, nk3) of
a uniform k-point grid with density given by length parameter
(rk.r). More k-points are allocated in short directions of the
crystal according to VASP’s formula:
\begin{equation}
n_i = \text{int}\left[\text{max}\left(1,R_k |{\rm b}_i| + \frac{1}{2}\right)\right]
\end{equation}
where is the number of k-points in direction i and is the length of the ith reciprocal lattice vector.
If the KPOINTS keyword is used without any further input, critic2
lists all the distinct uniform k-point grids for values of rk.r from
zero up to a value equal to rkmax.r, which can be modified with the
optional RKMAX keyword (default: 100 bohr). If a number rk.r follows
KPOINTS, the k-point grid dimensions are calculated only for that value.
Print the Brillouin Zone Geometry (BZ)
The BZ keyword:
BZ
calculates and prints the geometry of the Brillouin cell for the currently loaded crystal.
Edit the structure (EDIT)
This keyword can be used to edit the currently loaded molecular or crystal structure. The syntax of the EDIT environment is:
EDIT
DELETE [ATOM|ATOMS] id1.i id2.i ...
DELETE [MOLECULE|MOLECULES] id1.i id2.i ...
ENDEDIT
Each line in the EDIT environment carries out an edit in the
structure. The list of possible editing actions includes:
-
DELETE [ATOM|ATOMS] id1.i id2.i ...: delete cell atoms with IDsid1.i,id2.i, etc. After the atoms are deleted, recalculate the symmetry operations and bond connectivity. -
DELETE [MOLECULE|MOLECULES] id1.i id2.i ...: delete molecules with IDsid1.i,id2.i, etc. After the molecules are deleted, recalculate the symmetry operations and bond connectivity.