XCrySDen
can be customized to some extent. For this reason the
~/.xcrysden directory exists. Therein reside
the following two files: custom-definitions
and Xcrysden_defaults. The former file is
used for setting some definitions, such as the image
conversion program (for example the
convert program of ImageMagick), which
is used for conversion between different graphics
formats while printing to a file (this enables to
print to various formats such as JPG/PNG/GIF/TIFF).
In the second file the X-resources for XCrySDen are
specified, such as fonts and colors.
If the
CRYSTAL program is installed on
the computer, and one would prefer to enable its use in
XCrySDen,
then the
system(c95_exist) variable should be
set to 1, and the location of
CRYSTAL modules
should be defined. Here is an example:
# ------------------------------------------------------------------------
# do we have CRYSTAL package
# ------------------------------------------------------------------------
set system(c95_exist) 1
# ------------------------------------------------------------------------
# CRYSTAL modules
# ------------------------------------------------------------------------
set system(c95_integrals) /home/tone/bin/crystal
set system(c95_scf) /home/tone/bin/crystal
set system(c95_properties) /home/tone/bin/properties
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In case the
CRYSTAL program is
not present, or its use should be disabled, then the
system(c95_exist) variable should be set to 0,
and the definition of
CRYSTAL modules should
be left undefined (or commented with #). For
CRYSTAL03, the
integrals and
scf modules are the same: namely, the module
is named as
crystal, hence the two variables
should be set to the same value.
XCrySDen is able to
visualize molecular structures from GAUSSIAN input
files, when and only when molecular coordinates are
specified by Z-matrix. For this purpose the
BABEL
program is required. To enable the use of BABEL in
XCrySDen add
the following definition:
# ------------------------------------------------------------------------
# BABEL program
# ------------------------------------------------------------------------
set xcMisc(babel) $env(HOME)/bin/babel
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The BABEL program requires the
BABEL_DIR environmental variable to be
defined. If this variable is not defined in your shell
profile, then you should add the following definition
to
~/.xcrysden/custom-definitions file:
# this is the same as environmental BABEL_DIR. When BABEL_DIR is
# defined this is not needed
set xcMisc(babel_dir) $env(HOME)/lib/babel
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The print command can be defined as:
# ------------------------------------------------------------------------
# print command
# ------------------------------------------------------------------------
set xcMisc(printCommand) {lpr -h}
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To enable the printing to graphics format
such as PNG/JPG/GIF/TIFF, the image converting program
that will convert the PPM to these formats should be
specified. A convenient choice is the
convert
program of ImageMagick (
http://www.imagemagick.org/).
Here is an example:
# ------------------------------------------------------------------------
# An image conversion program: we need PPM to PNG/JPG/GIF/... conversion.
# The "convert" program of ImageMagick (http://www.imagemagick.org/) is
# a convinient choice.
#
# It is possible to specify the command-line options. For example:
#
# set xcMisc(ImageMagick.convert) "/usr/bin/convert \
# -quality 90 -border 3x3 -bordercolor black"
#
# Instead one can also use something like:
#
# set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \
# -blur 1x1 -trim -bordercolor white \
# -border 20x20 -bordercolor black -border 3x3"
# ------------------------------------------------------------------------
set xcMisc(ImageMagick.convert) /usr/bin/convert
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XCrySDen can also create
an
Animated GIF or even the
MPEG
movies for the animation of chemical structures. In
this case the corresponding programs that will create
Animated GIF or
MPEG should be
defined. An example is the
whirlgif program
for creating the
Animated GIF. For creating
the
MPEG movies
XCrySDen requires the
mpeg_encode program. Here is the example for
corresponding definitions:
# ------------------------------------------------------------------------
# With "whirlgif" program XCRYSDEN can create an Animated-GIF image
# ------------------------------------------------------------------------
set xcMisc(whirlgif) /usr/bin/whirlgif
# ------------------------------------------------------------------------
# MPEG_ENCODE for creating the MPEG movies
# ------------------------------------------------------------------------
set xcMisc(mpeg_encode) /usr/bin/mpeg_encode
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Custom atomic radii and colors can be defined by
setting the
atmRad and
atmCol arrays,
respectively. Below is an example (I hope it is self
explanatory). Read the comments in the example.
# ------------------------------------------------------------------------
# Custom setting of the atomic radii. The syntax is:
#
# set atmRad(atomic_number) radius
#
# Example:
#
# set atmRad(1) 0.5; # custom radius for Hydrogen
# set atmRad(8) 1.2; # custom radius for Oxygen
# ------------------------------------------------------------------------
set atmRad(1) 0.5
# ------------------------------------------------------------------------
# Custom setting of the atomic colors. The syntax is:
#
# set atmCol(atomic_number) {red gren blue}
#
# The components (red,gren,blue) must be in range [0,1]
#
# Example:
#
# set atmCol(1) {0.5 0.5 0.5}; # custom color for Hydrogen
# set atmRad(8) {0.0 1.0 0.0}; # custom color for Oxygen
# ------------------------------------------------------------------------
set atmCol(1) {0.5 0.5 0.5}
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Not only atomic colors and radii but also other
display parameters can be customized. The
myParam array serves this purpose (see example
below). One can customize the parameters such as
ball-factors, specefill scale factors, tessellation
factor, background of the main display window, etc.
Below the corresponding part of
custom-definitions file is shown. If one would
like to customize a particular parameter, then
uncomment the appropriate line and set the value
according to current needs. In below example each
individual
myParam array element is preceded
by a short description (i.e. comment).
# -------------------------------------------------------------------------
# Custom setting for a variety of molecular display parameters, such as
# ball-factors, specefill scale factors, tessellation factors, etc.
#
# Below are the default values. If you would like to change the
# default for a particular parameter, then uncomment the appropriate
# line and set the value according to your needs.
# ------------------------------------------------------------------------
## spacefill scale factor
#set myParam(ATRAD_SCALE) 1.40
#
## tesselation factor
#set myParam(TESSELLATION) 15.0
#
## RGB color of unibonds (each compoenent must be within [0,1])
#set myParam(UNIBONDCOLOR) {1.00 1.00 1.00}
#
## Perspective Fovy, Front and Back parameters. The smaller the Fovy
## the larger the perception of perspective. Front and Back parameters
## determine the front and back clipping planes. The smaller the Back
## parameter the more the structure is clipped from the back side. The
## Front parameter is counter-intuitive, meaning the smaller it is the
## more the structure is clipped from the front side.
#
#set myParam(PERSPECTIVEFOVY) 2.5
#set myParam(PERSPECTIVEFRONT) 0.65
#set myParam(PERSPECTIVEBACK) 3.0
#
## ball-factor
#set myParam(BALLF) 0.29
#
## rod-factor
#set myParam(RODF) 0.6
#
## line-width of wireframe display-mode (in pixels)
#set myParam(WFLINEWIDTH) 1
#
## line-width of pointline display-mode (in pixels)
#set myParam(PLLINEWIDTH) 1
#
## line-width of crystal cell's frames
#set myParam(FRAMELINEWIDTH) 1
#
## Lighting-Off outline width
#set myParam(OUTLINEWIDTH) 1
#
## Lighting-On wire line width
#set myParam(WF3DLINEWIDTH) 1
#
## point-size of pointline display-mode (in pixels)
#set myParam(PLRADIUS) 6
#
## chemical connectivity factor
#set myParam(COV_SCALE) 1.05
#
## RGB color of crystal frame (each compoenent must be within [0,1])
#set myParam(FRAMECOL) {0.88 1.00 0.67}
#
## line-width of crystal frame
#set myParam(FRAMELINEWIDTH) 1
#
## rod-factor of crystal frame
#set myParam(FRAMERODF) 0.1
#
## RGB background of XCRYSDEN display window
## (each compoenent must be within [0,1])
#set myParam(BACKGROUND) {0.00 0.00 0.00}
#
## maximum number of cells per direction for CRYSTALs
#set myParam(CRYSTAL_MAXCELL) 10
#
## maximum number of cells per direction for SLABs
#set myParam(SLAB_MAXCELL) 20
#
## maximum number of cells for POLYMERs
#set myParam(POLYMER_MAXCELL) 50
#
## default atomic-label font (in X11 XLFD format)
#set myParam(ATOMIC_LABEL_FONT) \
# -adobe-helvetica-medium-r-normal--12-120-75-75-p-67-iso8859-1
#
# default atomic-label bright and dark color (in clamped-float RGB format)
#set myParam(ATOMIC_LABEL_BRIGHTCOLOR) {1.0 1.0 1.0}
#set myParam(ATOMIC_LABEL_DARKCOLOR) {0.0 0.0 0.0}
#
#
## this are the parameters for the \"mpeg_encode\" program:
##--BEGIN::
#set myParam(MPEG_ENCODE_PARAM_FILE) {
#PATTERN IBBPBBPBBPBBPBBP
#OUTPUT \$output_file
#BASE_FILE_FORMAT PPM
#INPUT_FORMAT UCB
#\$input_convert
#GOP_SIZE 16
#SLICES_PER_FRAME 1
#INPUT_DIR \$input_dir
#INPUT
#\$input_files
#END_INPUT
#PIXEL FULL
#RANGE 10
#PSEARCH_ALG LOGARITHMIC
#BSEARCH_ALG CROSS2
#IQSCALE 8
#PQSCALE 10
#BQSCALE 25
#REFERENCE_FRAME ORIGINAL
#BIT_RATE 1000000
#BUFFER_SIZE 327680
#FRAME_RATE 30
#}
##--END
#
# ------------------------------------------------------------------------
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To enable the printing of debugging messages to
stdout/stderr, define the
xcMisc(debug)
variable and set it to 1. The debbuging output is very
chaotic, therefore this option should not be
interesting for the majority of users.
# ------------------------------------------------------------------------
# enable/disable the printing of debugging to stdout/stderr
# ------------------------------------------------------------------------
set xcMisc(debug) 1
|
If the visualization of chemical structures from
some format that is unknown to
XCrySDen is desired,
then it is possible to add a new command line option.
In this case one should provide a filter program that
will convert this format to
XSF
format. The usage of such program should be
myformat2xsf myfile. The program should read
the
myfile file (
myfile being the
name of any file in that format) and write the XSF file
to standard output. Here is an example (i.e. a
template) converting filter program written in
FORTRAN77 (the template can be downloaded from here:
myformat2xsf.f).
c ******************************************************
program MyFormat2XSF
c Usage: myformat2xcr myformat_file
c
c The program reads the myformat file from myformat_file
c and writes the XSF file to standard output
c ******************************************************
implicit none
integer MAXATOMS
PARAMETER (MAXATOMS = 1000)
character*256 my_file
real*8
$ primvec(3,3), ! primitive lattice vectors
$ convvec(3,3), ! conventional lattice vectors
$ coor(3,MAXATOMS) ! atomic coordinates
integer
$ iargc,
$ nat(MAXATOMS), ! atomic numbers
$ iat, i, j, len ! counters
if (iargc().ne.1)
$ stop 'Usage: myformat2xcr myformat_infile'
call getarg(1,my_file)
len = index(my_file,' ') - 1
open(unit=1, file=my_file(1:len), status='old')
c ***
c *** READ MyFormat file
c ***
... insert code here ...
c ***
c *** WRITE XSF file
c ***
c *** lets suppose it is a CRYSTAL structure
c *** other posibilites are (SLAB,POLYMER,MOLECULE)
write(*,*) 'CRYSTAL'
write(*,*) 'PRIMVEC'
write(*,1000) primvec
write(*,*) 'CONVVEC'
write(*,1000) convvec
write(*,*) 'PRIMCOORD'
write(*,*) iat, 1
do i=1,iat
write(*,1001) nat(i), (coor(j,i), j=1,3)
enddo
1000 format(2(3(F15.9,2X),/),3(F15.9,2X))
1001 format(I5,3(F15.9,2X))
END
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To add an option for the above example to
xcrysden, add the following entry to
~/.xcrysden/custom-definitions file.
#
# ------------------------------------------------------------------------
# Here go custom user-specified options
# ------------------------------------------------------------------------
# In order to add an --unknown option (i.e "unknown" stands for new
# format to add) to the XCRYSDEN allowed options, do the following:
#
# Usage:
# addOption option converterProgram description
#
# Arguments:
# option ... option to add to XCRYSDEN options
#
# converterProgram ... program that converts from an "unknown"
# to XSF format; this program must be
# supplied by the user !!!
#
# description ... description of the options that will
# appear in the help message
# (i.e. xcrysden --help).
#
# Example: (suppose the format is "myformat")
#
# addOption --myformat $env(HOME)/utils/myformat2xsf {
# load structure from myformat file format
# }
#
# Example Note: the converting program is myformat2xsf, and
# /path/to/myformat2xsf is the full pathname for the
# converting program.
addOption --myformat /path/to/myformat2xsf {
load structure from myformat file format
}
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Now you can load the
myformat
files as:
xcrysden --myformat file.myformat,
where
file.myformat is the appropriate
filename.
In this file the X-resources for
XCrySDen, such as fonts
and colors, are specified. Worth mentioning are two
options. The first is the
*palette. It will
set the palette, that is the master color-scheme for
XCrySDen
widgets (i.e. buttons, frames, menus, etc.). If you
want, for example,
XCrySDen to be red, then
set
*palette: #ff0000. The second option is
the
*font. If fonts of
XCrySDen appear to be
too big, then you can set the master font at the end of
the file using this option. A simple and useful setting
is
*font: fixed. Currently, the
Xcrysden_defaults file looks as:
# ------------------------------------------------------------------------
# if you have problems with fonts see the end of this file
# ------------------------------------------------------------------------
# ----------------------------
# here you can set palette
# ----------------------------
#*palette: #777
#---------------
# MenuBar
#---------------
*MenuBar.relief: raised
*MenuBar.borderWidth: 2
*MenuBar*activeBackground: #007d8d
*MenuBar*activeForeground: #ffffff
*Viewer*activeBackground: #007d8d
*Viewer*activeForeground: #ffffff
# ----------------------------
# this is STANDARD !!!
# ----------------------------
*Button.font: -*-helvetica-medium-r-normal-*-14-*-*-*-*-*-*-
*Menubutton.font: -*-helvetica-bold-r-normal-*-14-*-*-*-*-*-*-
*Entry.background: #daa
*SilentEntry*Entry.background: #ddd
*Text.background: #daa
*Listbox.background: #daa
*RaisedFrame.relief: raised
*RaisedFrame.borderWidth: 2
*GrooveFrame.relief: groove
*GrooveFrame.borderWidth: 2
# ------------------------------------------------------------------------
# stressed color
# ------------------------------------------------------------------------
*ctrl*Button.background: #b5a266
*ctrl*Button.foreground: #000000
*ctrl*Button.highlightBackground: #000
*close*Button.background: #b5a266
*close*Button.highlightBackground: #000
*close*Button.foreground: #000000
*StressText*Message.background: #b5a266
*StressText*Label.background: #b5a266
*Fileselect*Message.background: #b5a266
# ------------------------------------------------------------------------
# datagrid widgets
# ------------------------------------------------------------------------
*DataGridBlock*Frame.background: #ffce61
*DataGridBlock*Label.background: #ffce61
*DataGridBlock*Radiobutton.background: #ffce61
*DataGridSubBlock*Frame.background: #ffff9d
*DataGridSubBlock*Label.background: #ffff9d
*DataGridSubBlock*Entry.background: #daa
*DataGridSubBlock*Checkbutton.background: #99ddaa
*DataGridSubBlock*Checkbutton.selectColor: #000099
# ------------------------------------------------------------
# if you have problems with fonts uncomment the line below
# ------------------------------------------------------------
#*font:fixed
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![[Figure]](img/xcrysden-picture-small-new.jpg)