Download OpenMX package version 3.9.9 from http://www.openmx-square.org/download.html.

Install the dependent environment of the original OpenMX. Check that the original OpenMX can be installed successfully.

Install HDF5 1.12.1 for C language.

Apply the 'overlap only' patch. Copy patch files overlap_only_patch/openmx.c and overlap_only_patch/truncation.c to the source directory of the original OpenMX (openmx3.9/source).

Edit makefile in the source directory of the original OpenMX. Add -I${HDF5_path}/include -L${HDF5_path}/lib at the end of the CC in the original makefile, with ${HDF5_path} replaced by the HDF5 path; add -lhdf5 at the end of the LIB in the original makefile. Notice: depending on installation setup, the library path may be ${HDF5_path}/lib or ${HDF5_path}/lib64.

Run make command to install:

make clean
make all
make install

Executable file openmx can be found in the source directory.

Before running 'overlap only' OpenMX, the path to the HDF5 shared objects must be added to the runtime library search path. For example,

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5_path}/lib

with ${HDF5_path} replaced by the HDF5 path. Notice: depending on installation setup, the library path may be ${HDF5_path}/lib64 or ${HDF5_path}/lib64.

Perform the 'overlap only' program like the original OpenMX. For example, for overlap matrices of magic angle twisted bilayer graphene (MATBG), move to the directory examples of current repository, edit your path to the VPS and PAO (openmx3.9/DFT_DATA19) for DATA.PATH keyword in file MATBG.dat, and run:

mpirun -np 1 ${openmx_path} MATBG.dat > openmx.std

with ${openmx_path} replaced by the path of installed 'overlap only' OpenMX. The overlap matrices could be found in the output directory in the format of HDF5.