You can install MDMC in broadly two ways. For non-expert users, it is strongly recommended that you use containers to run MDMC (option 1), as you will not have to separately install a supported molecular dynamics package (e.g. LAMMPS).
Container option: run MDMC in a container that already has all relevant external dependencies pre-installed, including molecular dynamics engines.
Two container technologies are supported: Docker and Singularity. Docker has more widespread usage, but Singularity is targeted for HPC hardware. These two container technologies are similar to operate, and once you are familiar with one, switching to the other should be relatively straightforward.
Containerless option: directly onto your favourite hardware and OS, e.g. Mac or Linux laptop or HPC hardware.
2.4. Installation Tests
Following installation, you can run installation tests to check that MDMC has installed correctly and which additional features are available (e.g. if the required dependencies are installed for LAMMPS to be used as the MD engine). These tests can either be run from within a Python environment or at the command line.
To run the installation tests from the command line:
To run the installation tests from a Python environment:
from MDMC.utilities import run_installation_tests run_installation_tests()
Either of these methods will print to screen whether the MDMC core has been correctly installed and whether the additional functionality can be used. If any of these tests fails, additional details will be given in the log file. Either of these methods will print to screen whether MDMC install components were correctly installed. If any of these tests fails, additional details will be given in the log file. Please note that all MDMC install components may not be required for your intended usage of MDMC or your operating system environment.
Source code is available from https://github.com/MDMCproject/MDMCv0.2_pilot and can be obtained using git with:
git clone https://github.com/MDMCproject/MDMCv0.2_pilot.git