Created by Frank Schluenzen, last modified on Feb 01, 2022 18:17

Summary

Source: http://neel.cnrs.fr/spip.php?rubrique1007&lang=en

License: unknown

Code: Fortran90

Path:  /opt/xray/fdmnes_<version> 

Citations:

  • O. Bunau, Y. Joly: Self-consistent aspects of x-ray absorption calculations. J. Phys. : Condens. Matter 21, 345501 (2009).  

  • S. A. Guda, A. A. Guda, M. A. Soldatov, K. A. Lomachenko , A. L. Bugaev, C. Lamberti, W. Gawelda, C. Bressler, G. Smolentsev, A. V. Soldatov, Y. Joly: Optimized Finite Difference Method for the Full-Potential XANES Simulations : Application to Molecular Adsorption Geometries in MOFs and Metal-Ligand Intersystem Crossing Transients. J. Chem. Theory Comput. 11, 4512-4521 (2015).

  • please visit http://fdmnes.neel.cnrs.fr/download/ for more information



The aim of the FDMNES project is to supply to the community a user friendly code to simulate x-ray spectroscopies, linked to the real absorption (XANES, XMCD) or resonant scattering (RXD) of the synchrotron radiation. This ab initio approach, wants to eliminate all the methodological parameters. First mainly mono-electronic, using the functionnal density theory (DFT), it includes now multi-electronics advances with the use of the time dependant DFT (TD-DFT) for a better taking into account of the excited states linked to the photon-matter interaction. It includes also the Hubbard correction (LDA+U) for a better description of the so called correlated materials.

Using fdmnes v2020 or newer

[elx]% module avail fdmnes
[elx]% module load fdmnes            # load the current version
[elx]% module load fdmnes/version    # load a specific version
# alternatively just add /opt/xray/fdmnes_2020_10_08/bin to PATH

# running the serial version
[elx]% module load fdmnes
[elx]% fdmnes

# running the mpi parallel version. Be gentle on shared login nodes
[elx]% module load fdmnes
[elx]% mpirun_fdmnes -np 4

# when running as a batchjob use all physical cores
[elx]% module load fdmnes
[elx]% mpirun_fdmnes -np $(($(nproc)/2))

 

Using fdmnes v2015

fdmnes is available in 4 different variants and possibly a number of different versions. To initialize the environment use the module command:

[elx]% module avail
[elx]% module load fdmnes            # load the current version, gnu-compiled
[elx]% module load fdmnes-intel      # load the current version, intel-compiled (currently using intel 2013)
[elx]% module load fdmnes/version    # load a specific version (gnu-compiled & equivalent for the intel version)
 

Having prepared the environment three different commands are available to run fdmnes:

[elx]% fdmnes                        # single threaded fdmnes
[elx]% fdmnes_mpi                    # parallel fdmnes using openmpi (or openmpi-intel)
[elx]% fdmnes_par                    # a convenience wrapper used 1/4 of available cores on the local host:
                                     # mpirun -np $numc fdmnes_mpi  "$@"
#
#  To make full use of the HPC cluster running fdmnes on mulitple cores and hosts:
#
[it-hpc-wgs]% module load fdmnes
[it-hpc-wgs]% mpirun -np <number_of_cores> --hostfile <hostfile> fdmnes_mpi

Obsolete Patches

Older version of fdmnes prior to v2020 required the files xsect.dat and spacegroup.txt to be present in the folder from where fdmnes gets invoked. The installed versions have been patched to search for the files in the fdmnes installation path. It should not be necessary to copy over those files, unless you need to modify the files. Use the "folder_dat" directive in fdmnes input-files to specify a non-default location. Be aware that folder_dat has issues in the mpi-environment.