Awesome
SOMD (A SIESTA Oriented Shitty Opinionated Molecular Dynamics Package)
SOMD is an ab-initio molecular dynamics (AIMD) package designed for the SIESTA DFT code. The SOMD code provides some common functionalities to perform standard Born-Oppenheimer molecular dynamics (BOMD) simulations, and contains a simple wrapper to the Neuroevolution Potential (NEP) package. The SOMD code may be used to automatically build NEPs by the mean of the active-learning methodology.
NOTE!
The SOMD code is designed to be maintained by one person, thus many important functionalities may be absent. Besides, the code should be considered EXPERIMENTAL since it has not been extensively tested. So if you would like to perform production runs with SOMD, please take your own risk.
INSTALLATION
SOMD only runs on GNU/Linux distros. The installation requires a working g++
compiler (with C++11 supports), a Python3 interpreter and four additional
Python3 libraries (cython
, h5py
, mdtraj
and toml
). You could install
SOMD by the following steps.
- Install the required dependencies with:
orconda config --add channels conda-forge conda install cython h5py mdtraj toml -c conda-forge
pip install cython h5py mdtraj toml
- Clone this repo:
Note: if you would like to proceed your installation with the tarball downloaded from GitHub, you should manually download the NEP_CPU package and put it in thegit clone https://www.github.com/initqp/somd cd somd git submodule update --init
somd/somd/potentials/src
directory. Besides, the version number of the installed package may be wrong. - Install SOMD:
orpython setup.py install
pip install .
- Start a
python
REPL and enter the following lines:
If the installation is successful, a version string should be printed. Likewise, you could enter the following command under your shell:>>> import somd >>> print(somd.__version__)
If the installation is successful, a version string should be printed as well.somd -v
- Compile the SIESTA code. SOMD could work with the 4.1.5 or the git master version of SIESTA. When compiling, you are suggested to link your binary against the ELPA library (and using ELPA as the diagonalization algorithm). This is because of one of the memory leakage bugs in SIESTA (read this page for details). The usage of the ELPA library could be found in the SIESTA documentation.
- If you would like to use DFTD3, DFTD4, TBLite and PLUMED with SOMD, you
should also install the corresponding packages:
orconda install dftd3-python dftd4-python tblite-python py-plumed -c conda-forge
Specifically, the above commands do not install the PLUMED kernel library for you. You should compile it separately and export thepip install dftd3 dftd4 plumed
PLUMED_KERNEL
environment variable before actually perform your PLUMED aided MD runs. - If you would like to use the MACE potential with SOMD, you should also install the MACE package. Read MACE's documentation for installation instructions.
TESTS
First, install the pytest
package with:
conda install pytest -c conda-forge
or
pip install pytest
Then, enter the somd/tests
directory and invoke this command (you need to
change the SIESTA_COMMAND
variable to the actual path of your siesta
binary):
SIESTA_COMMAND='/path/to/siesta' py.test
USAGE
SOMD has a naive command line interface, which reads the TOML format configure file. A typical input file looks like this (which defines a NVT run of a water molecule):
[system]
structure = "H2O.POSCAR"
[[group]]
atom_list = "all"
initial_temperature = 300.0
[[potential]]
type = "SIESTA"
siesta_options = """
xc.functional GGA
xc.authors PBE
PAO.BasisSize DZP
Mesh.Cutoff 300 Ry
"""
siesta_command = "mpirun -np 4 /path/to/siesta"
[[trajectory]]
format = "H5"
file_name = "traj.h5"
interval = 10
[[logger]]
format = "CSV"
file_name = "data.csv"
interval = 10
[integrator]
type = "BAOAB"
timestep = 0.0005
temperatures = 300.0
relaxation_times = 0.1
[run]
n_steps = 500
Based on this file (e.g., it is called input.toml
), you could run your
simulation via the following command:
somd -i input.toml
You may also invoke SOMD as a library and implement your own simulation protocols. For example, the above configure file equals to the following python script:
import somd
siesta_command = 'mpirun -np 4 /path/to/siesta'
siesta_options = r"""
xc.functional GGA
xc.authors PBE
PAO.BasisSize DZP
Mesh.Cutoff 300 Ry
"""
system = somd.core.systems.create_system_from_poscar('H2O.POSCAR')
g = {
'atom_list': list(range(0, system.n_atoms)),
'has_translations': False
}
system.groups.create_from_dict(g)
system.groups[0].add_velocities_from_temperature(300)
potential = somd.potentials.SIESTA(
range(0, system.n_atoms),
system,
siesta_options,
siesta_command
)
system.potentials.append(potential)
integrator = somd.core.integrators.baoab_integrator(
0.0005,
temperatures=[300],
relaxation_times=[0.1],
thermo_groups=[0]
)
trajectory = somd.apps.trajectories.H5WRITER(
'traj.h5',
write_forces=False,
interval=10
)
logger = somd.apps.loggers.DEFAULTCSVLOGGER('data.csv', interval=10)
simulation = somd.apps.simulations.SIMULATION(
system=system,
integrator=integrator,
trajectories=[trajectory],
loggers=[logger]
)
simulation.run(500)
Based on this script (e.g., it is called input.py
), you could run your
simulation via the following command:
python input.py
DOCUMENTATION
A problem-oriented documentation could be found here.
TUTORIALS
Tutorials of SOMD could be found here. Going through these tutorials is considered as an efficient way to get familiar with SOMD.
FAQ
-
Q: How to cite the code?
A: You don't. It's a toy.