Exporting the Structure

Introduction

Critic2 can be used as a converter between different crystal structure file formats. For instance, to convert a cif file to a QE input, we can use:

CRYSTAL myfile.cif
WRITE myfile.scf.in

Sometimes, it is also necessary to create a finite representation of a crystal by taking the crystal motif, perhaps extended with some of atoms in the neighboring unit cells. The simplest way of doing this is by writing an xyz file:

CRYSTAL myfile_DEN
WRITE myfile.xyz

The MOLMOTIF keyword writes all atoms in the unit cell and completes the molecules by using atoms in the neighboring cells. One of the important aims of WRITE is to write template input files for different programs. The particular keywords used in those templates (calculation level, basis set, etc.) are mostly meaningless but the structure is correct. It is up to the user to adapt these templates to suit their needs.

In critic2, the main keyword to export the molecular or crystal structure, or a transformation of those structures, is the WRITE keyword.

Writing the Structure (WRITE)

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

The WRITE keyword writes the currently loaded structure to a file. A number of file formats can be written by critic2. As in CRYSTAL and MOLECULE, the type of file is detected by the extension (.xyz, .in, .cri, etc.).

Molecular File Formats (xyz, gjf, cml)

With this command:

WRITE file.{xyz,gjf,cml} [ix.i iy.i iz.i] [BORDER]
      [SPHERE rad.r [x0.r y0.r z0.r]] [CUBE side.r [x0.r y0.r z0.r]]
      [MOLMOTIF] [ONEMOTIF] [ENVIRON dist.r] [NMER nmer.i]

WRITE generates an xyz file containing a finite piece of the crystal (if the structure was loaded with CRYSTAL) or the molecule (resp. MOLECULE). Alternatively, if the .gjf extension is used, a template for a Gaussian input file is written. If cml is used, a Chemical Markup Language file (xml-style) is created, containing the same molecular fragment (see below). The number of cells used in each direction is given by ix.i, iy.i, and iz.i (default: 1, 1, 1). For the purpose of its graphical representation, it is sometimes convenient to include atoms that are almost exactly at the edge of the cell. For instance, the NaCl crystal is:

CRYSTAL
  SPG f m -3 m
  CELL 5.64 5.64 5.64 90 90 90 ANG
  NEQ 0. 0. 0. na
  NEQ 1/2 1/2 1/2 cl
ENDCRYSTAL
WRITE nacl.xyz

Critic2 will (correctly) generate a list of 4 Na and 4 Cl atoms, representing 1/8th of the conventional cell, because the atoms at (1, 0, 0), (1, 1/2, 0), etc. are repetitions of the atoms in the main cell. However, this does not look good when the unit cell is represented because many of the atoms in the cubic cell are “missing”. The BORDER keyword instructs critic2 to include atoms that are (almost) exactly at the edge of the cell.

The SPHERE keyword writes all atoms inside a sphere of radius rad.r (bohr) and centered around the crystallographic coordinates (x0.r, y0.r, z0.r). In molecules, the default units for both the center and radius of the sphere are Cartesian in angstrom. If no center is given, (0,0,0) is used in both cases. The similar keyword CUBE writes all atoms inside a cube of side side.r centered around (x0.r, y0.r, z0.r) (default: (0,0,0)).

The keyword MOLMOTIF is used in molecular crystals. All atoms in the requested crystal fragment (indicated by the optional ix.i,… integers) are written to the xyz file. Then, the molecules in the fragment are completed by including atoms from outside the fragment. Critic2 detects whether the atomic connectivity using a distance criterion (see the BONDFACTOR and RADII keywords).

The ONEMOTIF and ENVIRON keywords are also used in molecular crystals. ONEMOTIF writes all atoms in the unit cell, translated by lattice vectors so that the resulting fragment has whole molecules only. ENVIRON writes the molecular environment of the unit cell origin up to a distance renv.r (bohr in crystals, angstrom in molecules). All molecules whose center of mass is at a distance less than renv.r are written in their entirety, even if some of their atoms exceed the renv.r distance from the origin.

The NMER keyword is used in molecular systems as well, and in combination with ONEMOTIF, MOLMOTIF, or ENVIRON. When NMER is given, the fragment of the system selected with either of those three keywords is split into its component molecules. Then, all monomers, dimers, trimers,… are written to separate files. All n-mers are written from monomers up to n-mers, where n is equal to nmer.i. In NMER is used with ENVIRON, the first molecule in all n-mers except for those with n = nmer.i is always part of the Wigner-Seitz cell, which is useful when generating molecular environments of the crystal for calculations using incremental methods.

There is an important application of the xyz-format WRITE keyword: the coordinates written to the xyz file are consistent with the transformation to Cartesian coordinates in critic2, so it is possible to bring back all or part of these coordinates to critic2 in order to represent a subset of the atoms in a crystal. This is very useful when generating fragments for an NCIPLOT calculation (see the FRAGMENT keyword) and in some LOAD options to obtain the promolecular density of a subset of the atoms. Whether the contents of an xyz file are recognized by critic2 as atoms belonging to the current system or not can be determined using the IDENTIFY keyword.

The CML (Chemical Markup Language) format has the same options as the xyz output format. In the CML format, an XML-style file is written containing the selected crystal fragment. If the system is a crystal (loaded with the CRYSTAL keyword), then the cell geometry is written to the CML file as well. The CML output format is specially tailored for being easy to read by avogadro and its underlying engine, openbabel.

Graphical File Formats (obj, ply, off)

The following keyword also writes finite molecular representations of the structure:

WRITE file.{obj,ply,off} [ix.i iy.i iz.i] [BORDER]
      [SPHERE rad.r [x0.r y0.r z0.r]] [CUBE side.r [x0.r y0.r z0.r]]
      [MOLMOTIF] [ONEMOTIF] [CELL] [MOLCELL]

In this case, however, the generated files are graphical representations.

The OBJ output is the Wavefront OBJ format. The OBJ format is a three-dimensional model representation, that is, it uses vertices and faces instead of atoms. This file format is understood by many visualizers such as view3dscene, meshlab, blender, and others. The keywords have the same meaning as in the xyz format. The additional CELL keyword instructs critic2 to write a stick representation of the unit cell. In a molecular structure, the MOLCELL keyword can be used to represent the molecular cell. The similarly popular PLY (polygon file format or Stanford triangle format) and OFF (Geomview) file formats can be used as well, with the same options.

Quantum ESPRESSO (scf.in)

Quantum ESPRESSO inputs can be written using the extension .scf.in. This conversion is especially useful in the case of low-symmetry crystals (e.g. monoclinic in a non-conventional setting) where the conversion from other formats, such as CIF, can be tricky. The QE input generation works by first determining the Bravais lattice from the symmetry operations. Critic2 uses ‘ibrav=0’ always, and writes a CELL_PARAMETERS block containing the crystallographic-to-Cartesian transformation matrix. QE is particular about how this matrix should written in order for its own symmetry module to work. If the crystal setting matches any of those covered in the QE manual, then that particular matrix is used. Otherwise, critic2 uses its own internal CELL_PARAMETERS matrix, which may result in Quantum ESPRESSO failing to recognize the crystal symmetry. By default, the crystal cell used by critic2 is written to the QE input template. To reduce the cell to a primitive, use NEWCELL with the PRIMITIVE keyword before writing the file. The optional parameter to the QE input writer (rklength.i) is the length parameter (rk-length) that determines the density of the k-point grid (using VASP’s formula).

Tessel (tess)

A tessel input file (extension .tess) can be written. Tessel is a program for graphical representations of crystals, available upon request.

Critic2 (cri, incritic)

A critic2 input file can be written using the .cri or .incritic extensions. The input file contains the description of the molecular or crystal structure using the CRYSTAL/MOLECULE environment.

VASP (POSCAR, CONTCAR)

A VASP POSCAR (or CONTCAR) is generated by using the POSCAR or CONTCAR extension or name. The list of atomic types is written to the critic2 output. This list is necessary to build the corresponding POTCAR. The atoms are always ordered in increasing atomic number.

abinit (abin)

An abinit input file containing the input structure can be written by using the .abin extension.

elk (elk)

An elk input template can be written using the .elk extension.

Crystallographic Information File (cif)

A simple cif file is generated if the .cif extension is used. If NOSYM (or NOSYMM) is used, the cif file is written without symmetry (i.e. in the P1 space group).

SHELX (res)

The .res extension writes a SHELX file in res format. If NOSYM (or NOSYMM) is used, the cif file is written without symmetry (i.e. in the P1 space group).

Crystal (d12)

A template input file for crystal14 and crystal17 can be written with the extension .d12. If the crystal structure is written without symmetry (by using the NOSYM or NOSYMM keywords), then the .d12 file contains the complete structure specification. Otherwise, the .d12 file uses the EXTERNAL keyword to specify the geometry, and an additional .fort.34 file with the same root is created. This file contains the symmetry operations as well as the crystal geometry, and it should be renamed to just fort.34 before the crystal calculation is run. Note that the .d12 file contains only a keyword to run the geometry test - there is no basis set specification or any of the other relevant keywords.

Crystal17 (and probably earlier versions) has different tolerance values for detecting and accepting symmetry operations than critic2. It is strongly recommenteded that you use SYM REFINE before writing a .d12 file with symmetry in order to recalculcate the atomic positions in the detected space group.

Gaussian (periodic, gau)

A Gaussian input file for calculations under periodic boundary conditions can be written using the .gau extension. For a template corresponding to a finite molecule, use .gjf (see above).

Escher/Octave (m)

The octave script file (extension .m) contains the structure in octave format, to be read using the escher library.

DCP database (db)

The db file format is intended for a set of automated input generation octave scripts, the dcp package.

Gulp (gin)

A simple GULP template input file containing the structure (and EEM as the first line) can be written using the .gin extension. No resonant carbon atoms are detected. The GULP writer is experimental, so please exercise care and double-check the templates.

LAMMPS (lammps)

For file names with an extension .lammps, critic2 writes a simple LAMMPS data file containing one unit cell (length units are angstrom). Only orthogonal cells are supported for now. The LAMMPS writer is experimental, so please exercise care and double-check the templates.

SIESTA (fdf, STRUCT_IN)

Two types of siesta inputs can be generated. The .fdf extension writes a template for a proper functional siesta input template containing the crystal structure. The STRUCT_IN extension or name writes files that can be read using the MD.UseStructFile option.

DFTB+ (gen, hsd)

Two inputs types for DFTB+ may be written. The .gen format contains only the structure and is meant to be used with the GenFormat method in Geometry. The .hsd writes a full input template, including the structure.

pyscf (pyscf)

The .pyscf extension writes a template python script for using with pyscf. The script creates an instance of a Mole object (in the case of a molecule) or a Cell object (if it is a crystal).

FHIaims (fhi)

A geometry.in input file for FHIaims can be generated using the .fhi extension. The file then needs to be renamed to geometry.in. The appropriate selection of keywords is used depending on whether the current structure is a crystal or a molecule.

TINKER frac files (frac)

A .frac file can be generated in TINKER format. The .frac file always contains the cell lengths and angles (even if a molecule is written) and the atomic connectivity calculated by critic2. The force field atom types in the file correspond to the “tiny” force field parameters in the TINKER distribution (tiny.prm).

Writing a .mols File for DMACRYS/NEIGHCRYS (MAKEMOLSNC)

MAKEMOLSNC file_fort.21.s file_mols.s

The MAKEMOLSNC keyword is used to write .mols files for NEIGHCRYS, the companion program to DMACRYS. DMACRYS is a program for the calculation of lattice energies and their derivatives using rigid molecules and the distributed multipole approach. The atomic multipoles are calculated from a gas-phase molecular wavefunction using the GDMA program

The NEIGHCRYS program is used to help in the preparation of input files for DMACRYS. Sometimes, NEIGHCRYS has difficulty generating the .mols file, a file that contains the local frame of reference for the calculation of the multipoles for every molecule in the crystal. (See also SYM WHOLEMOLS.)

The MAKEMOLSNC keyword is intended to be a replacement for this function in NEIGHCRYS. MAKEMOLSNC reads the NEIGHCRYS output (a fort.21 file) and generates the corresponding mols file with name file_mols.s. MAKEMOLSNC does not work if the molecules are linear because NEIGHCRYS does not work with them either. The use of MAKEMOLSNC does not require a molecular or crystal structure being loaded.