.TH xcrysden 1 "February 7, 2012" "XCrySDen" "XCrySDen" .SH NAME xcrysden \- crystalline and molecular structure visualizer .SH SYNOPSIS .B xcrysden .RI [ special-options ] .br .B xcrysden .RI [ special-options ] \fIformat-options\fR \fIfile\fR|\fIdirectory\fR .SH DESCRIPTION \fBXCrySDen\fR is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. .SH SPECIAL OPTIONS .TP 4 \fB\-h .PD 0 .TP \fB\-\-help Display help message. .TP \fB\-v .PD 0 .TP \fB\-\-version Display program version information. .TP \fB\-u \fIid\fR .PD 0 .TP \fB\-\-use\fR \fIid\fR Load XCrySDen embedded into container window with window-ID=\fIid\fR. .TP \fB\-r \fIdim .PD 0 .TP \fB\-\-reducedim \fIdim\fR Reduce periodic dimension of XSF file to \fIdim\fR. Must be specified before \fB\-\-xsf\fR option, e.g., \fBxcrysden \-r\fR 2 \fB\-\-xsf \fIfile\fR. .TP \fB\-c \fIfile\fR .PD 0 .TP \fB\-\-custom \fIfile\fR Load custom\-definitions from a specified file (the syntax is that of \fB~/.xcrysden/custom\-definitions\fR). .TP \fB\-a \fIfile\fR .PD 0 .TP \fB\-\-attributes \fIfile\fR Load attributes from file. The format of the attributes file is the following: \fBELEMENTCOLOR \fIatomic-number1 red1 blue1 green1 atomic-number2 red2 blue2 green2 \fR... \fBELEMENTRADIUS \fIatomic-number1 radius1 atomic-number2 radius2 \fR... .TP \fB\-l \fIfile\fR .PD 0 .TP \fB\-\-lights \fIfile\fR Load lights parameters from XCrySDen's lights formatted file. .SH FORMAT OPTIONS .TP 4 \fB\-\-xsf \fIfile\fR Load structure from XCrySDen's-Structure-File (XSF) formatted file. .TP \fB\-\-animxsf \fIfile\fR .PD 0 .TP \fB\-\-axsf \fIfile\fR Load structres from Animated-XCrySDen's-Structure-File (AXSF) formatted file. .TP .PD 1 \fB\-\-bxsf \fIfile\fR Load bands from BXSF (Band-XSF) file and visualize Fermi Surface. .TP \fB\-\-xmol \fIfile\fR .PD 0 .TP \fB\-\-xyz \fIfile\fR Load structure from XYZ formatted file. .TP \fB\-\-pdb \fIfile\fR Load structure from PDB formatted file. .TP \fB\-\-gzmat \fIfile\fR Load structure from Gaussian Z-matrix (requires Open-Babel program). .TP \fB\-\-gaussian_out \fIfile\fR .PD 0 .TP \fB\-\-gXX_out \fIfile\fR .PD 0 .TP \fB\-\-g98_out \fIfile\fR Load structure from Gaussian output file. Only single point calculation and optimization run is supported so far. For the optimization run it is possible to render all the structures that were produced during the run. .TP \fB\-\-cube \fIfile\fR .PD 0 .TP \fB\-\-gXX_cube \fIfile\fR .PD 0 .TP \fB\-\-g98_cube \fIfile\fR Load structure from Gaussian cube file. The cube file should be produced with the Cube=Cards option. Only scalar cube files are supported, that is, Cube=(Cards,Density) or Cube=(Cards,Orbitals) or Cube=(Cards,Potential). Refer to GAUSSIAN manual for the meaning of this keywords. .TP \fB\-\-crystal_inp \fIfile\fR Load structure from CRYSTAL (\fIhttp://http://www.crystal.unito.it/\fR) input file. .TP\fB \-\-crystal_f9 \fIfile\fR Load structure from CRYSTAL (\fIhttp://http://www.crystal.unito.it/\fR) fortran unit 9. .TP \fB\-\-wien_struct \fIfilehead\fR|\fIfile\fR|\fIdirectory\Fr Load structure from WIEN2k (\fIhttp://www.wien2k.at/\fR) struct-file, where: \fIfilehead\fR = name of struct file without \fB.struct\fR extension, \fIfile\fR = filename, \fIdirectory\fR = name of case directory. .TP \fB\-\-wien_kpath \fIdirectory\fR|\fIstruct-file\fR Read \fIstruct\fR file and render first Brillouin zone with special k-points. K-path can be selected interactively by mouse-clicking the special k-points. User must specify \fIEMIN\fR and \fIEMAX\fR energies and total number of k-points along the path. This number is merely an estimation of total number of k-points, since XCrySDen tries to get very uniform sampling of k-points along the path (don't specify WIEN2k maximum allowed number of k-points, since XCrySDen maight generate few points more). .TP \fB\-\-wien_renderdensity \fIdirectory\fR Read \fIstruct\fR, \fIoutput\fR, and \fIrho\fR files and renders crystalline structure and precomputed charge density. .TP \fB\-\-wien_density \fIdirecory\fR Either 2D or 3D region for charge density calculation is interactively chosen by mouse-clicking. XCrySDen generates \fIin5\fR file(s), calculates and renders charge density either as isolines/colorplanes (2D) or isosurfaces (3D). .TP \fB\-\-wien_fermisurface \fIdirectory\fR Pop-up a task window for Fermi surface creation. After several steps the Fermi surface is (hopefully) drawn as 3D isosurface. .TP \fB\-\-fhi_inpini \fIfile\fR Load structure from FHI98MD \fBinp.ini\fP formated file. .TP \fB\-\-fhi_coord \fIfile\fR Load structure from FHI98MD \fBcoord.out\fR formated file. .TP \fB\-\-pwi .PD 0 .TP \fB\-\-pw_inp \fIfile\fR Load structure from \fBpw.x input\fR file. \fBpw.x\fR is a pseudopotential planewave program of the Quantum-ESPRESSO distribution (\fIhttp://www.quantum-espresso.org/\fR). .TP \fB\-\-pwo .PD 0 .TP \fB\-\-pw_out \fIfile\fR Load structure from \fBpw.x output\fR file. \fBpw.x\fR is a pseudopotential planewave program of the Quantum-ESPRESSO distribution (\fIhttp://www.quantum-espresso.org/\fR). .TP \fB\-s \fIscript\fR .PD 0 .TP \fB\-\-script \fIscript\fR Load script from file containing Tcl script. .SH "SEE ALSO" Fore more information about \fBXCrySDen\fR, see: .br \fIhttp://www.xcrysden.org/\fR. Further documentation is available at: .br \fIhttp://www.xcrysden.org/Documentation.html\fR. .SH "COPYRIGHT" Copyright (C) 1996--2012 Anton Kokalj This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.