- Download the executables: full license (serial and parallel versions) (max 10000 atoms/cell)/ demo license (serial version) (max 20 atoms/cell)
- Download the scripts to run the programs
- Download the graphical package Crgra2006 (check your postscript viewer)
- Install the package following the instructions
- crystal compute wave function - optimize geometry, if requested
- properties compute one electron properties
- runcry09 compute wave function (and properties, if input data exist)
- runprop09 wave function analysis and one electron properties
File name extension are interpreted by the scripts according to the following rules:
| .d12 | wave function calculation input (program crystal) |
| .out | wf calculation printed output file (it may be modified by setting environment variable $OUTFILE) |
| .d3 | properties calculation input (program properties) |
| .outp | properties calculation output file (it may be modified by setting environment variable) |
| .ps | postscript file - written by one of the programs of the package Crgra2006 |
| .maps | maps06 control file (see Crgra2006) |
| .band | band06 control file (see Crgra2006) |
| .doss | doss06 control file (see Crgra2006 |
Variables that must be defined (source the shell cry2k9.cshrc or cry2k9.bashrc):
variable name meaning value in the example CRY2K9_ROOT CRYSTAL09 root directoy $HOME/CRYSTAL09 CRY2K9_ARCH ARCH string to identify the executable Linux-ifort CRY2K9_SCRDIR temporary directory for scratch files $HOME CRY2K9_EXEDIR binaries directory
The default path to "crystal" and "properties" binaries is:
$CRY2K9_ROOT/bin/$CRY2K9_ARCH/std/The directory for scratch files is defined as:
$CRY2K9_SCRDIR/tmp$$
Variables that can be defined:
variable name meaning default value OUTFILE suffix of output files out VERSION version of the executable std CRY2K9_INP "crystal" input files directory $here CRY2K9_PROP "properties" input files directory $here CRY2K9_F9 wave function data directory $hereThe output directory is always $here
runcry09
Usage:runcry09 inpfilename [wf_filename]
This script controls a CRYSTAL runThe program crystal is executed for wave function and total energy calculation (and geometry optimization, if required).
If execution is successful, and an input file with the same name of the crystal input file (inpfilename.d12), but extension d3 (inpfilename.d3), is present, the program properties is executed.
| inpfilename.d12 | crystal HF/KS wave function calculation input deck |
| [wf_filename.f9] (optional) | wave function data from a previous run - see "SCF", keyword GUESSP, RESTART |
| [inpfilename.d3] (optional) | properties input deck |
| inpfilename.out | printed output file |
The following files (if they exist) are saved in the current directory at the end of the calculation (fort.9 is binary, all other files are formatted):
| program | saved as | data stored | keyword | |
| fort.9 | crystal | inpfilename.f9 | binary wave function | default, if SCF successful |
| fort.98 | crystal | inpfilename.f98 | formatted w-f | default, if SCF successful |
| GAUSS98.DAT | crystal | inpfilename.gjf | input for Gaussian98 | GAUSS98 |
| fort.33 | crystal | inpfilename.xyz | atoms coordinates | COORPRT |
| FINDSYM.DAT | crystal | inpfilename.FINDSYM | input for findsym | FINDSYM |
| fort.34 | crystal | inpfilename.gui | GUI - crystal structure | EXTPRT |
| HESSOPT.DAT | crystal | inpfilename.hessopt | Hessian | OPTGEOM |
| OPTINFO.DAT | crystal | inpfilename.optinfo | info for opt restart | OPTGEOM |
| FREQINFO.DAT | crystal | inpfilename.freqinfo | info for frequencies restart | FREQCALC |
| HESSFREQ.DAT | crystal | Hessian | FREQCALC | |
| REFLECTANCE.DAT | crystal | inpfilename.reflectance | reflectance data to plot | FREQCALC/REFLECTANCE |
| EOSINFO.DAT | crystal | inpfilename.eosinfo | Equation of State | EOS |
| ELASINFO.DAT | crystal | inpfilename.elasinfo | elastic constants | ELASTCON |
runprop09
This script controls a properties run, for the calculation of one electron properties and wave function analysis.The examples in the tutorials read wave function data from binary files, but it is possible to start from formatted w-f data. See CRYSTAL09 User's Manual, keyword RDFMWF.
Usage
runprop09 inpfilename [wf_filename]
| inpfilename.d3 | properties input file |
| inpfilename.f9 (default) | crystal SCF wave function data |
| [wf_filename.f9] (optional) | crystal SCF wave function data |
| inpfilename_wf_filename.outp | printed output file |
The program properties is executed, reading input from inpfilename.d3, and wave function from inpfilename.f9, or wf_filename.f9, if different from inpfilename.f9. Results are written in : inpfilename_wf_filename.outp.
Wave function data can be read from file fort.98 (saved as inpfilename.f98 at the end of SCF), by inserting the keyword RDFMWF in the first record of properties input stream.
Example:
runprop09 mgo
the program properties is executed. Input is read from file mgo.d3, the wave function is read from mgo.f9, output is written in mgo_mgo.out6p
runprop09 band mgo
the program properties is executed. Input is read from file band.d3, the wave function is read from mgo.f9, output is written inband_mgo.out6p. This allows computing from the same wave function, stored in wf_filename.f9, different properties in different runs, using inpfilename.d3 as input.
Files with extensions .f9 are not modified by properties.
The following files (if they exist) are saved, formatted, in the current directory at the end of the calculation:
| saved as | data stored | keyword | |
| fort.98 | inpfilename.f98 | formatted wave function | FMWF |
| fort.33 | inpfilename.xyz | atoms coordinates - xyz format | COORPRT |
| fort.25 | inpfilename.f25 | data for visualization | BAND,DOSS,ECHG,POTM |
| fort.31 | inpfilename_dat.prop3d | 3D charge (spin) density/potential | ECH3/POT3 |
| fort.32 | inpfilename_dat.info3d | information on 3D grid | ECH3/POT3 or GRID3D |
| fort.34 | inpfilename.gui | GUI - crystal structure | EXTPRT |
| SYMMINFO.DAT | inpfilename.sym | symmetry information | SYMMINFO |
| BAND.DAT | inpfilename_dat.BAND | band structure | BAND |
| DOSS.DAT | inpfilename_dat.DOSS | density of states | DOSS |
| RHOLINE.DAT | inpfilename_dat.RHOLINE | electron density profile | ECHG |
| POTC.DAT | inpfilename_dat.POTC | exact electrostatic potential | POTC (FIELD in geometry input) |
| EMDL.DAT | inpfilename_dat.EMDL | Electron Momentum distribution | EMDL |
| BIDIDI.DAT | inpfilename.BDIDI | B(r) | BIDIERD |
| GRED.DAT | inpfilename.GRED | BS, geom,direct lattice reducible data | CRYAPI_OUT |
| KRED.DAT | inpfilename.KRED | eigenvectors in full BZ | CRYAPI_OUT |
The files GRED.DAT, KRED.DAT are read by an external program, cryapi_inp.f, distributed as source file.
Visualization of data
Geometry
Coordinates of the atoms in the primitive cell are written in xyz format in fort.33, saved as inpfilename.xyz. (keyword COORPRT; always written when OPTGEOM, geometry optimization, is active).
The program MOLDEN allows visualization of the structure. The atoms in the cell are treated as atoms in a molecule, translational symmetry is not recognized. For a better visualization the keyword SUPERCEL can be used for visualizing larger fragments of the crystal structure.
The program MOLDRAW (run on MS-Windows only - free download from the web site) imports the printed output. It allows visualization of the cell. A number of facilities help in understanding crystal structure.
The package DLV, developed at Daresbury Laboratory, is also interfaced to the CRYSTAL package, and allows geometry and properties visualization.
The package XCrysDen, developed by A. Kokalj, is also interfaced to the CRYSTAL package, and allows geometry and properties visualization. A number of facilities help in understanding crystal structure.
Properties
The program properties writes data for visualization in fort.25, saved as inpfilename.f25. Data are in a format read by the programs of the package Crgra2006.
Crgra2006 allows plotting of bands (keyword BAND), density of states (DOSS), and to draw contour line maps of charge density (ECHG) and electrostatic potential (POTM, CLAS).
Three different programs are used to plot the three quantities, band06, doss06, maps06; each one selects the appropriate data in the file fort.25. They need the data file and a control file, read as standard input (see Crgra2006 User's Manual l).
The scripts band06, doss06, maps06 adopt the following convention:
| command | argument | control file | name of the postscript file | properties | |
| band06 | $1[.f25] | $1.band | $1_band06.ps | Band structure | |
| doss06 | $1[.f25] | $1.doss | $1_doss06.ps | Density of states | |
| maps06 | $1[.f25] | $1.maps | $1_maps06.ps | Isovalue contour maps (charge, elect. pot.) |
When fort.25 is present and not empty, scripts runcry09 and runprop09 execute maps06, doss06, band06 automatically.
Default control files are supplied for a first test.
See Crgra2006 User's Manual and Appendix F in CRYSTAL09 User's Manual.
Postscript files are generated, with filenames filename_maps06.ps, filename_doss06.ps, filename_band06.ps.In the scripts there is a call to a generic postscript-viewer "gv". Edit this call or alias it according to the proper application.
Unit of measure and constantsAll constants and conversion factors from "NIST reference on constants, units, uncertainty".
Reference: http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/
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