├── .gitattributes ├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── black ├── doc ├── README.md ├── actice_learning.md ├── basics.md ├── cli.md ├── constraint.md ├── group.md ├── logo.png ├── system.md └── toml.md ├── pycodestyle ├── setup.cfg ├── setup.py ├── somd ├── __init__.py ├── _version.py ├── apps │ ├── __init__.py │ ├── barostats.py │ ├── cli.py │ ├── evaluation.py │ ├── loggers.py │ ├── parser.py │ ├── select.py │ ├── simulations.py │ ├── trajectories.py │ └── utils │ │ ├── __init__.py │ │ ├── backup.py │ │ └── post_step.py ├── core │ ├── __init__.py │ ├── groups.py │ ├── integrators.py │ ├── potential_base.py │ ├── snapshots.py │ ├── src │ │ ├── constants.h │ │ ├── constraints.cxx │ │ ├── constraints.h │ │ ├── constraints.pxd │ │ ├── constraints.pyx │ │ ├── lib.pyx │ │ ├── math_utils.cxx │ │ ├── math_utils.h │ │ ├── nhc.cxx │ │ ├── nhc.h │ │ ├── nhc.pxd │ │ └── nhc.pyx │ └── systems.py ├── potentials │ ├── __init__.py │ ├── _dftd3.py │ ├── _dftd4.py │ ├── _fake.py │ ├── _mace.py │ ├── _nep.py │ ├── _plumed.py │ ├── _siesta.py │ ├── _tblite.py │ └── src │ │ ├── nep.pxd │ │ ├── nep.pyx │ │ ├── nep_base.pyx │ │ └── nep_t.pyx └── utils │ ├── __init__.py │ ├── _rng.py │ ├── constants.py │ ├── defaults.py │ └── warning.py ├── tests ├── data │ ├── active_learning │ │ ├── msd.dat │ │ ├── nep.0.txt │ │ ├── nep.1.txt │ │ ├── nep.2.txt │ │ ├── nep.3.txt │ │ ├── topo.pdb │ │ └── traj.h5 │ ├── groups │ │ └── group_temperature.dat │ ├── integrators │ │ ├── integrators_baoab.dat │ │ ├── integrators_bdp.dat │ │ ├── integrators_cs4.dat │ │ ├── integrators_gbaoab.dat │ │ ├── integrators_gobabo │ │ ├── integrators_gobabo.dat │ │ ├── integrators_nhc.dat │ │ ├── integrators_obabo.dat │ │ └── integrators_vv.dat │ ├── parser │ │ ├── 1.toml │ │ └── 2.toml │ ├── potentials │ │ ├── Si.psf │ │ ├── nep.txt │ │ ├── plumed.inp │ │ ├── potential_dftd3.dat │ │ ├── potential_dftd4.dat │ │ ├── potential_nep.dat │ │ ├── potential_nep_t.dat │ │ ├── potential_plumed.dat │ │ ├── potential_plumed_cv.dat │ │ └── potential_siesta.dat │ ├── simulation │ │ ├── restart_1.h5 │ │ ├── restart_2.h5 │ │ └── restart_3.h5 │ └── system │ │ ├── model.pdb │ │ ├── model.poscar │ │ └── system_pressures.dat ├── harmonic.py ├── test_evaluation.py ├── test_groups.py ├── test_integrators.py ├── test_parser.py ├── test_potentials.py ├── test_select.py ├── test_simulation.py ├── test_system.py └── test_trajectories.py └── versioneer.py /.gitattributes: -------------------------------------------------------------------------------- 1 | *.h linguist-language=C++ 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/initqp/somd/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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