SkProgs

Package containing a few programs that are useful in generating Slater-Koster files for the DFTB-method.

NOTE: This packages comes with minimal documentation and with a currently rather fragile user interface. It is considered to be neither stable nor robust. Make sure, you check results as careful as possible. Use at your own risk!

Installation

Prerequisites

• Fortran 2003 compliant compiler
• CMake (>= 3.16)
• Python3 (>= 3.2)
• LAPACK/BLAS libraries (or compatible equivalents)
• libXC library with f03 interface (>=6.0.0)
• MpiFx (>=1.5, MPI-enabled build only)

Obtaining via Conda

The preferred way of obtaining SkProgs is to install it via the conda package management framework using Miniconda or Anaconda. Make sure to add/enable the conda-forge channel in order to be able to access SkProgs:

conda config --add channels conda-forge
conda config --set channel_priority strict

We recommend to set up a dedicated conda environment and to use the mamba solver

conda install -n base mamba
conda create -n skprogs
conda activate skprogs

to install the latest stable release of SkProgs (Fortran and Python components):

mamba install skprogs skprogs-python

Building from source

Follow the usual CMake build workflow:

• Configure the project, specify your compilers (e.g. gfortran), the install location (i.e. path stored in YOUR_SKPROGS_INSTALL_FOLDER, e.g. $HOME/opt/skprogs) and the build directory (e.g. _build):

  FC=gfortran cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=YOUR_SKPROGS_INSTALL_FOLDER -B _build .
  

  An MPI enabled build is obtained by additionally setting -DWITH_MPI=1 (default: -DWITH_MPI=0). At the moment only the two-center integration code sktwocnt is MPI parallelized and benefits from multiple processors.

  If libXC is installed in a non-standard location, you may need to specify either the CMAKE_PREFIX_PATH environment variable (if libXC was built with CMake) or the PKG_CONFIG_PATH environment variable (if libXC was built with autotools) in order to guide the library search:

  CMAKE_PREFIX_PATH=YOUR_LIBXC_INSTALL_FOLDER FC=gfortan cmake [...]
  
  PKG_CONFIG_PATH=FOLDER_WITH_LIBXC_PC_FILES FC=gfortran cmake [...]
  

• If the configuration was successful, build the code

  cmake --build _build -- -j
  

• After successful build, you should test the code by running

  pushd _build
  ctest -j
  popd
  

• If you want to test the MPI enabled binary with more than one MPI-process, you should set the TEST_MPI_PROCS variable in config.cmake accordingly, e.g.:

  set(TEST_MPI_PROCS "2" CACHE STRING "Nr. of processes used for testing")
  

  The TEST_MPI_PROCS cache variable can be updated or changed also after the compilation by invoking CMake with the appropriate -D option, e.g.:

  cmake -B _build -DTEST_MPI_PROCS=2 .
  pushd _build; ctest; popd
  

• If the tests were successful, install the package via

  cmake --install _build
  

Building libXC from source

Follow the usual CMake build workflow:

• Clone the official libXC repository and checkout the latest release tag, e.g. 6.2.2:

  git clone https://gitlab.com/libxc/libxc.git libxc
  cd libxc/
  git checkout 6.2.2
  

• Configure the project, specify your compilers (e.g. gfortran and gcc), the install location (i.e. path stored in YOUR_LIBXC_INSTALL_FOLDER, e.g. $HOME/opt/libxc) and the build directory (e.g. _build):

  FC=gfortran CC=gcc cmake -DENABLE_FORTRAN=True -DCMAKE_INSTALL_PREFIX=YOUR_LIBXC_INSTALL_FOLDER -B _build .
  

• If the configuration was successful, build the code

  cmake --build _build -- -j
  

• After successful build, you should test the code by running

  pushd _build
  ctest -j
  popd
  

• If the tests were successful, install the package via

  cmake --install _build
  

Advanced build configuration

Controlling the toolchain file selection

You can override the toolchain file, and select a different provided case, passing the -DTOOLCHAIN option with the relevant name, e.g.:

-DTOOLCHAIN=gnu

or

-DTOOLCHAIN=intel

or by setting the toolchain name in the SKPROGS_TOOLCHAIN environment variable. If you want to load an external toolchain file instead of one from the source tree, you can specify the file path with the -DTOOLCHAIN_FILE option

-DTOOLCHAIN_FILE=/path/to/myintel.cmake

or with the SKPROGS_TOOLCHAIN_FILE environment variable.

Similarly, you can also use an alternative build config file instead of config.cmake in the source tree by specifying it with the -DBUILD_CONFIG_FILE option or by defining the SKPROGS_BUILD_CONFIG_FILE environment variable.

Generating SK-files

The basic steps of generating the electronic part of the SK-tables are as follows:

• If you have build SkProgs from source, initialize the necessary environment variables by sourceing the skprogs-activate.sh script (provided you have BASH or a compatible shell, otherwise inspect the script and set up the environment variables manually):

  source <SKPROGS_INSTALL_FOLDER>/bin/skprogs-activate.sh
  

• Then create a file skdef.hsd containing the definitions for the elements and element pairs you wish to create. See the examples/ folder for some examples.

• Run the skgen script to create the SK-tables. For example, in order to generate the electronic part of the SK-tables for C, H and O with dummy (zero) repulsives added, issue

  skgen -o slateratom -t sktwocnt sktable -d C,H,O C,H,O
  

  For an MPI enabled binary, make sure to prepend any required information to the two-center binary, e.g.:

  skgen -o slateratom -t "mpirun -np 2 sktwocnt" sktable -d C C |& tee output
  

  The SK-files will be created in the current folder. See the help (e.g. skgen -h) for additional options.

Further documentation will be presented in a separate document later.

License

SkProgs is released under the GNU Lesser General Public License.

You can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. See the files COPYING and COPYING.LESSER for the detailed licensing conditions.