Difference between revisions of "JUSTUS2/Software/Molden"
m (→Version-Specific Information) |
m |
||
Line 83: | Line 83: | ||
</pre> |
</pre> |
||
or from the [http://www.cmbi.ru.nl/molden/command.html website]. |
or from the [http://www.cmbi.ru.nl/molden/command.html website]. |
||
+ | <br> |
||
+ | |||
+ | == Molden-Specific Environments == |
||
+ | To see a list of all Molden environments set by the 'module load chem/molden/version'-command, |
||
+ | use 'env | grep MOLDEN' |
||
+ | Or try the command 'module show 'chem/molden/version'. |
||
+ | <pre> |
||
+ | $ module load chem/molden |
||
+ | $ env | grep MOLDEN |
||
+ | MOLDEN_VERSION=5.2.1 |
||
+ | MOLDEN_AMB_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/ambfor |
||
+ | MOLDEN_BIN_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin |
||
+ | MOLDEN_UTL_DIR=/opt/bwhpc/common/chem/molden/5.2.1/utils |
||
+ | MOLDEN_SRF_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/surf |
||
+ | $ |
||
+ | </pre> |
||
<br> |
<br> |
||
Revision as of 18:22, 30 November 2015
Description | Content |
---|---|
module load | chem/molden |
Availability | bwUniCluster | BwForCluster_Chemistry |
License | Free. See: Copyright CMBI |
Citing | Molden-Reference |
Links | Homepage | Documentation |
Graphical Interface | Yes |
Contents
1 Description
Molden is a software package for displaying molecular coordinates, molecular orbitals, electron densities from various quantum chemical software packages and supports contour and 3-D grid plots. Moreover, Molden supports many output formats including postscript, povray, OpenGL and hpgl.
2 Versions and Availability
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
Cluster Information System CIS
{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/molden |width=99% |height=200 |border=1 }}
Open the above links by using the right mouse button and select "open in a new window" or "open in a new tab".
On the command line interface of any bwHPC cluster, a list of the available versions using
'module avail chem/molden/version'.
$ module avail chem/molden ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/molden/5.2.1
3 Usage
3.1 Loading the module
You can load the default version of Molden with the command
$ module load chem/molden
If you wish to load a specific (older) version of Molden, you can do so using e.g.
$ module load chem/molden/5.1
to load the version 5.1
3.2 Software Binaries
3.2.1 Command-Line
Once the module Molden is loaded, the binaries molden and gmolden can be directly executed:
$ molden
3.2.2 Graphical User Interface (GUI)
$ gmolden &
3.2.3 Binary options
Available binary options can be taken from the binary help:
$ molden -h
or from the website.
4 Molden-Specific Environments
To see a list of all Molden environments set by the 'module load chem/molden/version'-command, use 'env | grep MOLDEN' Or try the command 'module show 'chem/molden/version'.
$ module load chem/molden $ env | grep MOLDEN MOLDEN_VERSION=5.2.1 MOLDEN_AMB_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/ambfor MOLDEN_BIN_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin MOLDEN_UTL_DIR=/opt/bwhpc/common/chem/molden/5.2.1/utils MOLDEN_SRF_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/surf $
5 Examples
To visualize the cartesian coordinates of one molecule stored in the file molecule.xyz without automatic conversion to Z-matrix, execute:
$ molden -a molecule.xyz
6 Version-Specific Information
For specific information about a special version , see the information available via the module system with the command
$ module help chem/molden/version