dftbplus
Table of Content
About
DFTB+ is an implementation of the Density Functional based Tight Binding (DFTB) method, containing many extensions to the original method. The development is supported by various groups, resulting in a code which is probably the most versatile DFTB-implementation, with some unique features not available in other implementations so far.
Versions and Availability
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Module Names for dftbplus on qb
| Machine | Version | Module Name |
|---|---|---|
| qb2 | 19.1 | dftbplus/19.1/INTEL-18.0.1-MVAPICH2-2.2 |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
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Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Usage
Slater-Koster files
Note: The DFTB+ code needs parameterisation data (Slater-Koster files) in order to perform calculations. On QB2, the Slater-Koster files are available system-widely at /usr/local/packages/dftbplus/19.1/INTEL-18.0.1-MVAPICH2-2.2/recipes/slakos. Alternatively, you can download your own Slater-Koster files from DFTB.ORG.
Parallel usage of DFTB+
Please refer to the DFTB+ Manual about how to write parallelized DFTB+ code. There are two types of parallel computer that DFTB+ currently can make use of: OpenMP and MPI. DFTB+ can be used with both MPI and openMP parallelism combined (Hybrid parallelism).
Note:OpenMP threads must be explicitely enabled (i.e. "UseOmpThreads = Yes" in the Parallel session) in the DFTB+ code if more than one OpenMP-thread or MPI process is used.
OpenMP
OpenMP-threads can be changed by setting the OMP_NUM_THREADS environment variable in the shell. For example:
export OMP_NUM_THREADS=20 mpirun -np 1 dftb+ # Or just dftb+
MPI
mpirun -np 20 dftb+
Hybrid parallelism
export OMP_NUM_THREADS=10 mpirun -np 2 dftb+
Resources
Last modified: August 22 2019 15:01:09.