.gitignore
.readthedocs.yaml
LICENSE
README.rst
compile.sh
pyproject.toml
requirements.txt
setup.py
benchmark/Identify_SFs_TBs/SFTB_mdapy_ovito.py
benchmark/aja/aja_mdapy_ovito.py
benchmark/atomic_entropy/entropy_mdapy_ovito.py
benchmark/average_rdf/rdf_benchmark.gsd
benchmark/average_rdf/rdf_mdapy_mdanalysis_mdtraj.py
benchmark/cluster/cluster_mdapy_ovito.py
benchmark/cna/cna_mdapy_ovito.py
benchmark/csp/csp_mdapy_ovito.py
benchmark/lattice_maker/latticemaker_mdapy_freud.py
benchmark/msd/msd_mdapy_mdanalysis_mdtraj.py
benchmark/neighbor/neighbor_mdapy_ovito_freud.py
benchmark/neighbor_threads/neighbor_thread.py
benchmark/pair_distribution/pair_mdapy_ovito_freud.py
benchmark/polyhedra_template_match/ptm_mdapy_ovito.py
benchmark/steinhardt_order/steinhardt_mdapy_freud.py
doc/Makefile
doc/environment.yml
doc/make.bat
doc/source/conf.py
doc/source/index.rst
doc/source/mdapy.rst
doc/source/modules.rst
doc/source/gettingstarted/benchmark.ipynb
doc/source/gettingstarted/examples.rst
doc/source/gettingstarted/installation.rst
doc/source/gettingstarted/main_features.rst
doc/source/gettingstarted/quicklystart.ipynb
doc/source/gettingstarted/reading_and_saving_file.ipynb
doc/source/gettingstarted/use_mdapy_efficiently.ipynb
doc/source/images/mdapy_favico.ico
doc/source/images/mdapy_favico_white.ico
doc/source/images/mdapy_logo.png
doc/source/images/mdapy_logo_white.png
example/Al_DFT.eam.alloy
example/CoCuFeNiPd-4M.data
example/CoCuFeNiPd-4M.dump
example/CoNiFeAlCu.eam.alloy
example/FCC.data
example/ISF.dump
example/ISFsTBs.py
example/analyze_trajectories.py
example/calculate_eos.py
example/create_polycrystalline.py
example/get_WCP.py
example/solidliquid.dump
example/solidliquid.py
example/test_cpp_module.py
mdapy/__init__.py
mdapy/__main__.py
mdapy/ackland_jones_analysis.py
mdapy/calculator.py
mdapy/centro_symmetry_parameter.py
mdapy/cluser_analysis.py
mdapy/common_neighbor_analysis.py
mdapy/common_neighbor_parameter.py
mdapy/create_polycrystalline.py
mdapy/eam_average.py
mdapy/eam_generate.py
mdapy/entropy.py
mdapy/identify_SFs_TBs.py
mdapy/lattice_maker.py
mdapy/lindemann_parameter.py
mdapy/load_save_data.py
mdapy/main.py
mdapy/mean_squared_displacement.py
mdapy/nearest_neighbor.py
mdapy/neighbor.py
mdapy/pair_distribution.py
mdapy/pigz.py
mdapy/plotset.py
mdapy/polyhedral_template_matching.py
mdapy/potential.py
mdapy/replicate.py
mdapy/spatial_binning.py
mdapy/steinhardt_bond_orientation.py
mdapy/system.py
mdapy/temperature.py
mdapy/timer.py
mdapy/tool_function.py
mdapy/visualize.py
mdapy/void_distribution.py
mdapy/voronoi_analysis.py
mdapy/warren_cowley_parameter.py
mdapy.egg-info/PKG-INFO
mdapy.egg-info/SOURCES.txt
mdapy.egg-info/dependency_links.txt
mdapy.egg-info/entry_points.txt
mdapy.egg-info/not-zip-safe
mdapy.egg-info/requires.txt
mdapy.egg-info/top_level.txt
mdapy/cluster/_cluster.cpp
mdapy/neigh/_neigh.cpp
mdapy/ptm/_ptm.cpp
mdapy/rdf/_rdf.cpp
mdapy/voronoi/_voro.cpp
thirdparty/ptm/LICENSE
thirdparty/ptm/ptm_alloy_types.cpp
thirdparty/ptm/ptm_alloy_types.h
thirdparty/ptm/ptm_alt_templates.h
thirdparty/ptm/ptm_canonical_coloured.cpp
thirdparty/ptm/ptm_canonical_coloured.h
thirdparty/ptm/ptm_constants.cpp
thirdparty/ptm/ptm_constants.h
thirdparty/ptm/ptm_convex_hull_incremental.cpp
thirdparty/ptm/ptm_convex_hull_incremental.h
thirdparty/ptm/ptm_deformation_gradient.cpp
thirdparty/ptm/ptm_deformation_gradient.h
thirdparty/ptm/ptm_functions.h
thirdparty/ptm/ptm_fundamental_mappings.h
thirdparty/ptm/ptm_graph_data.cpp
thirdparty/ptm/ptm_graph_data.h
thirdparty/ptm/ptm_graph_tools.cpp
thirdparty/ptm/ptm_graph_tools.h
thirdparty/ptm/ptm_index.cpp
thirdparty/ptm/ptm_initialize_data.cpp
thirdparty/ptm/ptm_initialize_data.h
thirdparty/ptm/ptm_neighbour_ordering.cpp
thirdparty/ptm/ptm_neighbour_ordering.h
thirdparty/ptm/ptm_normalize_vertices.cpp
thirdparty/ptm/ptm_normalize_vertices.h
thirdparty/ptm/ptm_polar.cpp
thirdparty/ptm/ptm_polar.h
thirdparty/ptm/ptm_quat.cpp
thirdparty/ptm/ptm_quat.h
thirdparty/ptm/ptm_structure_matcher.cpp
thirdparty/ptm/ptm_structure_matcher.h
thirdparty/ptm/ptm_voronoi_cell.cpp
thirdparty/ptm/ptm_voronoi_cell.h
thirdparty/ptm/ptm_voronoi_config.h
thirdparty/voro++/LICENSE
thirdparty/voro++/README
thirdparty/voro++/c_info.hh
thirdparty/voro++/cell_2d.cc
thirdparty/voro++/cell_2d.hh
thirdparty/voro++/cell_3d.cc
thirdparty/voro++/cell_3d.hh
thirdparty/voro++/cmd_line.cc
thirdparty/voro++/common.cc
thirdparty/voro++/common.hh
thirdparty/voro++/config.hh
thirdparty/voro++/container_2d.cc
thirdparty/voro++/container_2d.hh
thirdparty/voro++/container_3d.cc
thirdparty/voro++/container_3d.hh
thirdparty/voro++/container_tri.cc
thirdparty/voro++/container_tri.hh
thirdparty/voro++/iter_2d.cc
thirdparty/voro++/iter_2d.hh
thirdparty/voro++/iter_3d.cc
thirdparty/voro++/iter_3d.hh
thirdparty/voro++/particle_list.cc
thirdparty/voro++/particle_list.hh
thirdparty/voro++/particle_order.hh
thirdparty/voro++/rad_option.hh
thirdparty/voro++/unitcell.cc
thirdparty/voro++/unitcell.hh
thirdparty/voro++/v_base_2d.cc
thirdparty/voro++/v_base_2d.hh
thirdparty/voro++/v_base_3d.cc
thirdparty/voro++/v_base_3d.hh
thirdparty/voro++/v_base_wl_2d.cc
thirdparty/voro++/v_base_wl_3d.cc
thirdparty/voro++/v_compute_2d.cc
thirdparty/voro++/v_compute_2d.hh
thirdparty/voro++/v_compute_3d.cc
thirdparty/voro++/v_compute_3d.hh
thirdparty/voro++/voro++.cc
thirdparty/voro++/voro++.hh
thirdparty/voro++/wall.cc
thirdparty/voro++/wall.hh
thirdparty/voro++/wall_2d.cc
thirdparty/voro++/wall_2d.hh
thirdparty/voro++/wall_3d.cc
thirdparty/voro++/wall_3d.hh
thirdparty/voro++/worklist_2d.hh
thirdparty/voro++/worklist_3d.hh