External Programs

Currently, the only way to enable MiMiC in the supported programs comes in the form of patches, which must be applied to the original source codes.

The following instructions mostly follow the compilation of the original software. Therefore, if you come across any problems unrelated to MiMiC, please consult their respective manuals.

Following the instructions for MiMiC, we will install the programs in the .local directory in the user’s home, but feel free to choose whichever location you prefer:

INSTALL_DIR=${HOME}/.local

Set the environment variables FC, CC, and CXX to your chosen Fortran, C, and C++ compilers, respectively. We will also use the same directory for the sources as in the instructions for MiMiC, but use whichever location you prefer:

SOURCE_DIR=${HOME}/mimic_sources

CPMD

In your ${SOURCE_DIR} directory, download and unpack CPMD 4.3:

cd ${SOURCE_DIR}
wget -O cpmd-4.3.tar.gz https://github.com/CPMD-code/CPMD/archive/refs/tags/4.3.tar.gz
tar -zxvf cpmd-4.3.tar.gz

Download the MiMiC patch for CPMD, copy it to the CPMD root directory, and apply the patch:

cp MiMiC_CPMD-4.3.sh ./CPMD-4.3/
cd CPMD-4.3
bash MiMiC_CPMD-4.3.sh

If you want to enable support for PLUMED in CPMD, then follow the instructions in Enabling support for PLUMED before continuing.

To make the install path available within CPMD’s configuration script you first have to export the INSTALL_DIR variable:

export INSTALL_DIR

Choose a configuration file from the configure directory that is most suitable for your target system (you may need to edit it to make it work). Append the following two lines to the selected configuration file:

FFLAGS=${FFLAGS}" -I${INSTALL_DIR}/include "
LFLAGS=${LFLAGS}" -L${INSTALL_DIR}/lib -L${INSTALL_DIR}/lib64 "

They should be the last two lines in the configuration file. If you use GCC then add also -fallow-argument-mismatch -ffree-line-length-none to FFLAGS.

Attention

Make sure that your selected configuration supports MPI, as this is required by MiMiC. There are no further checks and you would discover the incompatibility during runtime.

Now configure the build using the configure.sh script, switch to the build directory, and compile:

bash ./configure.sh -DEST=build -omp -mimic <configuration-file-name>
cd build
make

Optionally, as a final touch you can copy the CPMD executable to INSTALL_DIR:

mkdir -p ${INSTALL_DIR}/bin
cp ${SOURCE_DIR}/CPMD-4.3/build/bin/cpmd.x ${INSTALL_DIR}/bin/

Pseudopotentials

Pseudopotentials are not distributed with CPMD, so do not forget to download them either from the CPMD website or your favourite pseudopotential repository.

Enabling support for PLUMED

To enable support for PLUMED in CPMD, there are a few additional steps. First you need to have PLUMED installed. If you already have a working PLUMED installation, you can skip the PLUMED installation part.

Note

We have tested PLUMED v2.6.5, v2.7.4, v2.8.0, and v2.8.1, but it is likely that other versions of PLUMED 2 are also compatible with the CPMD patch provided in the MiMiC tarball.

Installing PLUMED

Here we provide a quick installation guide for PLUMED. For more detailed information please consult the official PLUMED documentation.

First move to the source directory, download PLUMED v2.8.1 from the official PLUMED website, and unpack it:

cd ${SOURCE_DIR}
wget https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-2.8.1.tgz
tar -zxvf plumed-2.8.1.tgz

Then enter the PLUMED source directory, configure, build, and install:

cd plumed-2.8.1
./configure CXX=<c++-mpi-wrapper> --prefix=${INSTALL_DIR}
make
make install

Finally, set the following environment variables:

export PATH=${INSTALL_DIR}/bin:${PATH}
export LIBRARY_PATH=${INSTALL_DIR}/lib:${LIBRARY_PATH}
export LD_LIBRARY_PATH=${INSTALL_DIR}/lib:${LD_LIBRARY_PATH}
export PLUMED_KERNEL=${INSTALL_DIR}/lib/libplumedKernel.so
export PLUMED_VIMPATH=${INSTALL_DIR}/lib/plumed/vim
export PYTHONPATH=${INSTALL_DIR}/lib/plumed/python:${PYTHONPATH}

First, ensure that the CPMD source has been patched with the MiMiC patch by following the instructions above. Then download the PLUMED patch for CPMD, copy it to the CPMD root directory, and apply it:

cp PLUMED_CPMD-4.3.sh ./CPMD-4.3/
cd CPMD-4.3
bash PLUMED_CPMD-4.3.sh

Next, use PLUMED to patch CPMD:

plumed patch -n CPMD-4.3
plumed patch -p -e CPMD-4.3

This step creates the Plumed.inc, Plumed.h, and Plumed.cmake files which are necessary to compile CPMD with PLUMED support.

Finally, add the -plumed option in the configuration step.

GROMACS

In your ${SOURCE_DIR} directory, download and unpack GROMACS 2021.6 from the official GROMACS website:

cd ${SOURCE_DIR}
wget -O gromacs-2021.6.tar.gz https://ftp.gromacs.org/gromacs/gromacs-2021.6.tar.gz
tar -zxvf gromacs-2021.6.tar.gz

Download the MiMiC patch for GROMACS, copy it to the GROMACS directory, and apply it:

cp MiMiC_GROMACS-2021.patch gromacs-2021.6/
cd gromacs-2021.6
patch -p1 < MiMiC_GROMACS-2021.patch

Create a build directory, enter it, configure the build by running CMake, build, and finally install:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DGMX_DOUBLE=ON -DGMX_MPI=ON -DGMX_MIMIC=ON \
      -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} -DCMAKE_PREFIX_PATH=${INSTALL_DIR} ..
make
make install

You are free to use any other flags, but those shown here are required for a successful build of MiMiC-enabled GROMACS.