XCrySDen --
(X-Window) CRYstalline Structures and DENsities

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  Democritos scientific codes

 
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XCrySDen's Installation Instructions

Table of Contents

Installation Instructions
    How to Install the Compiled Package (for newer versions)
    How to Install the Compiled Package (for older versions)
        FOR IMPATIENT: minimal installation instructions
        A Bit Longer Installation Instructions
        What xcConfigure does?
    How to Install the Source Package
        Trouble Shooting

Installation Instructions

How to Install the Compiled Package (for newer versions)

For newer versions of xcrysden, the installation of compiled package is fairly simple:
  • unpack the xc-version.tar.gz package file as:
    tar zxvf xc-version.tar.gz
    or:
    gunzip -c xc-version.tar.gz | tar xvf -
  • cd into the so-created directory (i.e., cd xcrysden-version/)

  • and try: ./xcrysden

If this works then add the root directory of just installed xcrysden package (i.e., /full/path/to/xcrysden-version) to your PATH.

The use of XCRYSDEN_TOPDIR environmental variable is optional for newer versions. Optionally also the XCRYSDEN_SCRATCH environmental variable can be defined. It is the place where XCrySDen writes scratch (temporary) files. If this variable is not defined then either the value of TMPDIR (or TMP) environmental variable (if defined) or the /tmp will be used as the XCrySDen's scratch area.

BEWARE: If an older XCrySDen version is already installed then you need to manually unset (or update) the XCRYSDEN_TOPDIR variable definition in your profile !!!

How to Install the Compiled Package (for older versions)

FOR IMPATIENT: minimal installation instructions

  1. Unpack the *.tar.gz archive-file.
  2. Define the XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH environmental variables (XCRYSDEN_TOPDIR should point to XCrySDen root directory).
  3. Create the XCRYSDEN_SCRATCH directory (if it does not already exist).
  4. Run the program as xcrysden.
  5. From time to time clean the $XCRYSDEN_SCRATCH directory. For example, use the xc_cleanscratch utility.
BEWARE: it is recomemded to run the "./xcConfigure" script instead !!! [READ BELOW]

A Bit Longer Installation Instructions

After unpacking the *.tar.gz archive-file, each user should define two environmental variables: XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH. This can be facilitated by the xcConfigure script which in addition asks some questions and configures the package accoring to user's wishes. From XCrySDen root directory execute:
  • ./xcConfigure
The xcConfigure script modifies your profile (.bashrc or .profile or .cshrc, depending on the shell). It defines the two environmental variables (XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH), and modifies the PATH variable by including the $XCRYSDEN_TOPDIR to the path. Then you should source the corresponding profile in order to load the newly-added definitions. If you are using the csh- or tcsh-shell then execute:
  • source ~/.cshrc
For for sh-shell execute:
  • . ~/.profile
For bash-shell execute:
  • . ~/.bashrc
Then you can lanuch the program as:
  • xcrysden
From time to time clean the scratch directory ($XCRYSDEN_SCRATCH). This can be done by xc_cleanscratch utility.

BEWARE: If an older XCrySDen version is already installed, then you should manually update the XCRYSDEN_TOPDIR variable definition in your profile to point to the new place !!!

What xcConfigure does?

It creates the $HOME/.xcrysden directory and add the custom-definitions and Xcrysden_defaults files. The former file is used for setting some definitions, like 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 like JPG/PNG/GIF/TIFF). In the second file the X-resources for XCrySDen are specified, like fonts and colors. (read more)

How to Install the Source Package

Software requirements: The compilation of XCrySDen requires the following software: Tcl/Tk >= 8.3, and OpelGL (or Mesa). The compilation requires not just the Tcl/Tk + OpenGL library-files, but also their header files !!!
  • The Tcl/Tk can be downloaded from here.
  • The Mesa can be downloaded from here.
To compile the source package the file Make.sys should be present in the package root directory. Templates can be find in ./system/ subdirectory. Copy an appropriate template file:
  • cp ./system/Make.MY-SISTEM Make.sys
Now edit the file Make.sys to suit your needs. Then if you are impatient simply try:
  • make all
  • ./xcConfigure
See also How to install the compiled package section for the description of xcConfigure script. The xcConfigure will modify your profile (.bashrc or .profile or .cshrc, depending on the shell). Then you should source the corresponding profile in order to load the newly-added definitions.

Trouble Shooting

If the installation has failed for some reason, then read a few hints that are described below.

First, please read careful the instructions inside Make.sys and edit the file according to your needs. Basically you have two possibilities in Make.sys:

  • To use the included sources of external libraries, i.e., tcl8.3, tk8.3, Mesa-4.0 (for xc1.X.Ysource-all.tar.gz package only). In this case the flag COMPILE_LIBRARIES must be set to yes, which will enable the compilation of the libraries, and the corresponding section of Make.sys should be uncommented (it is already uncommented by default).
  • To use your own libraries. In this case the flag COMPILE_LIBRARIES must be set to no. The COMPILE_LIBRARIES = yes section should be commented, and COMPILE_LIBRARIES = no section uncommented.
If you are using the xc1.X.Ysource-all.tar.gz package, which contains also the required external libraries (Tcl, Tk, Mesa), then check if the error occurred during the compilation of external libraries. If this is the case, try to compile the library manually, i.e., do cd external/src/LIB, where LIB is the corresponding library directory, and read the installation instructions therein.

If you are using the xc1.X.Ysource-nolibs.tar.gz package this means that the error occurred during the XCrySDen compilation. Possibly you can correct the error by editing the ./Make.sys file.


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This document was last modified on Thu Jun 26 17:19:45 CEST 2014