Connecting Infrastructure, Connecting Research

CASTEP

Description
	CASTEP is a software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules. CASTEP can give information about total energies, forces and stresses on an atomic system, as well as calculating optimum geometries, band structures, optical spectra, phonon spectra and much more. It can also perform molecular dynamics simulations. Further information on the features and functionality available in CASTEP can be found on the CASTEP web site.
Site	Version (Latest: v5.5.1)	Notes
ngs.rl.ac.uk	v5.5.1 (v5.0.1, 4.3,4.2)	64 bit
ngs.leeds.ac.uk	v5.0.1(v4.3)	64 bit
vidar.ngs.manchester.ac.uk	v5.0.1(v4.3)	64bit

License

If you are a UK academic then you qualify to use the free academic version of CASTEP after registering with UKCP where all the license files can be downloaded. Users on the NGS are required to demonstrate that they are covered by an existing 2007 Version of the Accelrys/UKCP Castep agreement. Email the NGS helpdesk with your UKCP agreement details (Your Institution, the name of your group or department and the person who signed the agreement) and your eScience certificate DN, if you wish to use the code. Your NGS id will then be added to the castep group so that you can access the program on the NGS. CASTEP FAQ page.

Running CASTEP on the NGS (general)

There a multiple ways in which jobs can be launched on the NGS. The examples below all use example files which can be found and copied from:

gsiftp://ngs.rl.ac.uk:2811/apps/castep/example

Submission Using the UI/WMS
To submit a Castep job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

glite-wms-job-submit -o jobIDs -a castep.jdl
```
Type = "Job";
JobType = "mpich";
Executable = "/usr/ngs/CASTEP";
Arguments = "CastepTest";
CpuNumber = 16;
StdOutput = "CastepTest.out";
StdError = "CastepTest.err";
InputSandbox = {"CastepTest.param","CastepTest.cell"};
InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/castep";
OutputSandbox = {"CastepTest.out",
                 "CastepTest.err",
                 "CastepTest.bands",
                 "CastepTest.castep",
                 "CastepTest.castep_bin",
                 "CastepTest.check",
                 "CastepTest.cst_esp",
                 "pseudopotentials/F_00.recpot",
                 "pseudopotentials/H_04.recpot",
                 "pseudopotentials/Na_00.recpot"
};
OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/castep/outputs";
#
# Forces to job to run on any site with CASTEP installed.
Requirements = (
     member("NGS-UEE-CASTEP", other.GlueHostApplicationSoftwareRunTimeEnvironment)
);
Rank = other.GlueCEStateFreeCPUs;
ShallowRetryCount = -1;
```
Notes:
1. The input files (.cell and .param) are assumed to be in your /home/ngsxxxx/castep directory on the UI. The files can be copied from the gsiftp URL above or you can substiute the gsiftp URL above into the JDL file replacing the InputSandBoxBaseURI. In which case they dont have to be in your /home/ngsxxxx/castep at the start of the job.
2. The /home/ngsxxxx/castep/outputs directory must exist before the job is submitted.
3. If you want to use the system default pseudopotential files, as in this example, they can always be found in the working directory of the job under the "pseudopotential" directory. You can reference these in your .cell files as in the example .cell file:
```
%BLOCK SPECIES_POT
F        pseudopotentials/F_00.recpot
H        pseudopotentials/H_04.recpot
Na       pseudopotentials/Na_00.recpot
%ENDBLOCK SPECIES_POT
```
4. The 3 pseudopotential files on the OutputSandBox list are only in the example to show how to retreive the system default files, should you need to view them. Normally you will either use On-The-Fly generation or upload your own pseudopotential files. In which case you would put them on the InputSandbox list, in the same directory as the .cell and .param files, or in a subdirectory other than "pseudopotentials". If you use a subdirectory called "pseudopotentials" for your own files, you wont also have access to the system default files.
5. The above JDL file runs the default version of Castep at the site the WMS submits it to. If you need to run a specific version of Castep, change the "Executable = " line to "/usr/ngs/CASTEP_5_0_1" and the "Requirements =" line to "NGS-UEE-CASTEP_5_0_1", to run v4.3 for example.
NGS Web Portal Submission

After logging in to the NGS Portal, select the "CASTEP" template under the " Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

Submission Using Globus
To run CASTEP there should be a .param and .cell input file and pseudopotential files, which can be copied or symbolically linked from /apps/castep/pseudopotentials.

Whilst running, CASTEP will generate a number of files that, by default, are named runName.<n>.err, where <n> is 1..#processors in the job. These will be deleted on a successful run, although they are kept if the job dies with an error.

In the job-example below the input files (CasteTest.param and CastepTest.cell) are already uploaded to your /home/ngsXXXX/castep directory and any required pseudopotential files are either in that directory or have symbolic links in that directory to the files in gsiftp:://ngs.rl.ac.uk:2811/apps/castep/pseudopotentials. An example may be copied from gsiftp:://ngs.rl.ac.uk:2811/apps/castep/example. The output files will be written to your working directory /home/ngsXXXX/castep.

To submit a CASTEP job on the NGS
- use the following command (one line excluding the backslashes) for a parallel job:
  
  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
  '&(executable=/usr/ngs/CASTEP)(jobtype=mpi)(count=8) \
  (directory=/home/ngsXXXX/castep) \
  (arguments=CastepTest)(stdout=/home/ngsXXXX/castep/CastepTest.stdout) \
  (stderr=/home/ngsXXXX/castep/CastepTest.stderr)'
Local submission

This should only be used as a last resort, if the UI-WMS, portal or Globus submission methods don't work. You can only submit to just the NGS site at RAL using this method, so this command should only be used for debugging your Castep run before submissino tothe NGS Grid via the UI-WMS. While logged onto ngs.rl.ac.uk: Rather than via the grid, you can use the run_castep_lsf script that is in your path to submit to the local batch system.

[ngs0xxx@ngs]# run_castep_lsf -h
Program usage: run_castep_lsf [-h] [-n x] -i runname

castep utility programs such as pdb2cell are available in your path after typing module load castep, or by using the CASTEPUTILS wrapper script e.g.: /usr/ngs/CASTEPUTILS pdb2cell

Compilation Information for ngs.rl.ac.uk

ngs.rl.ac.uk

v4.2 Linked to Scali MPI, fftw 3, GotoBLAS using PGI 6.2
v4.3 Linked to Scali MPI and FFTW3, BLAS from Intel MKL 10.2 using Intel Fortran 10.1.011

Further Information

CASTEP Home page
CASTEP mailing list.
UKCP Licensing (for academic License information).
CASTEP CCPForge site.

To request support for using CASTEP, please sign up to the Castep mailing list.

Primary links

CASTEP

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License

Running CASTEP on the NGS (general)

Compilation Information for ngs.rl.ac.uk

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