D1.5: ClassicalMD E-CAMModules IV

David Swenson
2020 Zenodo  
In this report for Deliverable 1.5 of E-CAM, 9 software modules in classical dynamics are presented. These modules represent improvements and new features in response to the needs of users. The modules in this report include several based on OpenMM, OpenPathSampling (OPS) and n2p2. OpenMM is a powerful GPU-accelerated library, and the OpenMM-based modules gain their performance by using it. OpenPath-Sampling wraps around other dynamics engines, such as OpenMM, and leverages the performance that
more » ... is already developed in those. n2p2 is a software package supporting parallelization via Message Passing Interface (MPI) and OpenMulti-Processing (OpenMP). In addition, a Python interface to n2p2's underlying C++ libraries is provided. The presented modules based on n2p2 inherit and enhance the performance of the package. Another module presented here uses Python bindings for C++ code in order to provide the flexibility of Python while retaining the performance of C++. The 9 modules presented here are: 1. Gromacs engine for OPS 2. VisitAllStatesEnsemble for OPS 3. Interface-Constrained Shooting in OPS 4. Double-Well Test Systems in OpenMMTools 5. OpenMMPlectoneme 6. OpenMMCopolymer 7. pyscal 8. NNP-CG - Descriptor analysis 9. n2p2 - Symmetry FunctionMemory Footprint Reduction Each module is thoroughly tested, includes in-code documentation as well as external documentation, frequently in the form of Jupyter notebook examples.
doi:10.5281/zenodo.3699553 fatcat:kxxb773zinhjrjypqevkclbpky