Difference between revisions of "BoltzTraP"
 
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= BoltzTraP =
== Description ==
== Description ==


''From the BoltzTraP homepage:'' Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients of materials from First Principles electronic band structures. The code uses a mesh of self-consistent band energies and is interfaced to the WIEN2k, AB-INIT, SIESTA, VASP and QuantumEspresso programs.
''From the BoltzTraP homepage:'' '''Boltzmann Transport Properties (BoltzTraP)''' is a program for calculating the semi-classic transport coefficients of materials from First Principles electronic band structures. The code uses a mesh of self-consistent band energies and is interfaced to the WIEN2k, AB-INIT, SIESTA, VASP and QuantumEspresso programs.


*[http://www.icams.de/boltztrap BoltzTraP Home Page]
{{AppStandardHeader|1.2.3|boltztrap}}
 
== Version ==
 
*1.2.3
 
== Authorized Users ==
 
*<code>CIRCE account holders</code>
 
== Platform ==
 
*<code>CIRCE cluster</code>


== Note to Users about using BoltzTraP ==
== Note to Users about using BoltzTraP ==
Line 25: Line 11:
*Madsen, G. K. H.* and Singh, D. J.; ''Comput. Phys. Commun.'' '''2006''' 175, 67
*Madsen, G. K. H.* and Singh, D. J.; ''Comput. Phys. Commun.'' '''2006''' 175, 67


== Running BoltzTraP on CIRCE via Web Apps ==
== Running BoltzTraP on CIRCE/SC via the Command Line ==
 
BoltzTraP is available to run on the cluster via [https://cwa.rc.usf.edu/cwa_applications/research-computing|Web Apps] by clicking [https://cwa.rc.usf.edu/cwa_applications/research-computing/43 here]. The application user’s guide can be downloaded at the bottom of this page.
 
== Running BoltzTraP on CIRCE via the Command Line ==
 
=== [[Modules]] ===
 
Before running a job, you must first set up your environment properly. Here are the required module files:
 
*apps/boltztrap/1.2.3
 
To run BoltzTraP on the cluster, ensure that you use ‘<code>module add</code>’ prior to using any BoltzTraP executables. See [[Modules]] for more information.


=== Submitting Jobs ===
=== Submitting Jobs ===


The BoltzTraP guide is essential to understanding the application and making the most of it. The guide and this page should be all you need to get started with your calculations. The user’s guide is located in the application directory on CIRCE listed below.
{{PleaseReadUserGuide}}
 
{{SLURMAppParams}}
*BoltzTraP User’s Guide: /apps/boltztrap/1.2.3/doc/UserGuide.pdf


If, for example, you have a BoltzTraP input file named BoltzTraP.def, you would set up a submit script like this:
If, for example, you have a BoltzTraP input file named BoltzTraP.def, you would set up a submit script like this:


* The script below (for testing, name it “boltztrap-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our [[SLURM Users|SLURM User’s Guide]]. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
* The script below (for testing, name it “boltztrap-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue..


<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
#!/bin/bash
#!/bin/bash
#
#
Line 59: Line 31:
#SBATCH --time=01:00:00
#SBATCH --time=01:00:00


#### Slurm 1 processor BoltzTraP test to run for 1 hour.
#### SLURM 1 processor BoltzTraP test to run for 1 hour.


module purge
module purge
Line 67: Line 39:
</pre>
</pre>


Creating a BoltzTraP.def file is outlined in the User Guide. There are a couple of ways to create one from the command line by either using the included ‘<code>x_trans</code>’ script using the “-f” flag with appropriate filename (sans extension) and “-d” flag:
Creating a BoltzTraP.def file is outlined in the [[BoltzTraP#Additional Documentation|User Guide]]. There are a couple of ways to create one from the command line by either using the included ‘<code>x_trans</code>’ script using the “-f” flag with appropriate filename (sans extension) and “-d” flag:


<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
[user@host jobdir]$ module load apps/boltztrap/1.2.3
[user@login0 jobdir]$ module load apps/boltztrap/1.2.3
[user@host jobdir]$ x_trans -f FileName -d BoltzTraP</pre>
[user@login0 jobdir]$ x_trans -f FileName -d BoltzTraP</pre>


or, by using the custom ‘<code>makedef</code>’ script:
or, by using the custom ‘<code>makedef</code>’ script:


<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#000000; color:white;">
[user@host jobdir]$ module load apps/boltztrap/1.2.3
[user@login0 jobdir]$ module load apps/boltztrap/1.2.3
[user@host jobdir]$ makedef FileName [opt1] [opt2] [opt3] [opt4]</pre>
[user@login0 jobdir]$ makedef FileName [opt1] [opt2] [opt3] [opt4]</pre>


Up to 4 additional options can be included as needed.
Up to 4 additional options can be included as needed.
 
&nbsp;<br>
Then, you can change to your job’s directory, and run the sbatch command to submit the job:
Next, you can change to your job’s directory, and run the sbatch command to submit the job:


<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
cd my/job/directory
[user@login0 ~]$ cd my/jobdir
sbatch ./boltztrap-test.sh</pre>
[user@login0 jobdir]$ sbatch ./boltztrap-test.sh</pre>


*You can view the status of your job with the “squeue -u <username>” command
*You can view the status of your job with the “squeue -u <username>” command


=== Examples ===
{{Documentation}}
 
*BoltzTraP Home Page
The following folder contains input parameters for known BoltzTraP benchmarks and tutorials:
**http://www.icams.de/boltztrap
*BoltzTraP User Guide
** /apps/boltztrap/1.2.3/doc/UserGuide.pdf


*/apps/boltztrap/1.2.3/tests
{{BKETOR}}
*BoltzTraP Known Tests
**/apps/boltztrap/1.2.3/tests


{{More Job Information}}
{{AppStandardFooter}}
{{Reporting Bugs}}

Latest revision as of 21:25, 20 February 2017

Description

From the BoltzTraP homepage: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients of materials from First Principles electronic band structures. The code uses a mesh of self-consistent band energies and is interfaced to the WIEN2k, AB-INIT, SIESTA, VASP and QuantumEspresso programs.

Version

  • 1.2.3

Authorized Users

  • CIRCE account holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

BoltzTraP requires the following module file to run:

  • apps/boltztrap/1.2.3

Note to Users about using BoltzTraP

Published results arising from use of the BoltzTraP code should acknowledge the program with an appropriate citation. The program has been documented in Computer Physics Communications.

  • Madsen, G. K. H.* and Singh, D. J.; Comput. Phys. Commun. 2006 175, 67

Running BoltzTraP on CIRCE/SC via the Command Line

Submitting Jobs

The BoltzTraP user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

If, for example, you have a BoltzTraP input file named BoltzTraP.def, you would set up a submit script like this:

  • The script below (for testing, name it “boltztrap-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue..
#!/bin/bash
#
#SBATCH --comment=boltztrap-test
#SBATCH --ntasks=1
#SBATCH --job-name=boltztrap-test
#SBATCH --output=output.%j.boltztrap-test
#SBATCH --time=01:00:00

#### SLURM 1 processor BoltzTraP test to run for 1 hour.

module purge
module load apps/boltztrap/1.2.3

boltztrap BoltzTraP.def

Creating a BoltzTraP.def file is outlined in the User Guide. There are a couple of ways to create one from the command line by either using the included ‘x_trans’ script using the “-f” flag with appropriate filename (sans extension) and “-d” flag: 

[user@login0 jobdir]$ module load apps/boltztrap/1.2.3
[user@login0 jobdir]$ x_trans -f FileName -d BoltzTraP

or, by using the custom ‘makedef’ script: 

[user@login0 jobdir]$ module load apps/boltztrap/1.2.3
[user@login0 jobdir]$ makedef FileName [opt1] [opt2] [opt3] [opt4]

Up to 4 additional options can be included as needed.  
Next, you can change to your job’s directory, and run the sbatch command to submit the job: 

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./boltztrap-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • BoltzTraP Known Tests
    • /apps/boltztrap/1.2.3/tests

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with BoltzTraP to the IT Help Desk: rc-help@usf.edu

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