├── .gitignore ├── .gitlab-ci.yml ├── CMakeLists.txt ├── LICENSE ├── README.md ├── docs ├── mkdocs.yml └── source │ ├── authors.md │ ├── building.md │ ├── contributing.md │ ├── index.md │ ├── javascripts │ └── config.js │ ├── license.md │ ├── running.md │ └── technical.md ├── examples ├── README.md ├── ethane_water_charge_only │ ├── alchemy_example.py │ ├── equilibrated.pdb │ ├── equilibrated.xml │ ├── ethane_water.xml │ ├── recenter_for_vmd.py │ ├── run_ethane.py │ ├── solvated_ethane_from_openmm_setup.pdb │ ├── trajectory.dcd │ ├── trajectory.nc │ └── trajectory_recentered.dcd ├── parameters │ ├── convert_multipoles.py │ ├── swm4.xml │ ├── swm4_charmm.txt │ ├── swm6.xml │ └── tip3p.xml ├── water_dimer │ ├── mpidwater.xml │ ├── run_water_dimer.py │ ├── waterdimer.pdb │ └── waterdimer_aligned.pdb └── waterbox │ ├── restart.xml │ ├── run.py │ └── waterbox_31ang.pdb ├── openmmapi ├── include │ ├── OpenMMMPID.h │ └── openmm │ │ ├── MPIDForce.h │ │ ├── internal │ │ ├── MPIDForceImpl.h │ │ └── windowsExportMPID.h │ │ └── mpidKernels.h └── src │ ├── MPIDForce.cpp │ └── MPIDForceImpl.cpp ├── platforms ├── cuda │ ├── CMakeLists.txt │ ├── EncodeCUDAFiles.cmake │ ├── include │ │ └── MPIDCudaKernelFactory.h │ ├── src │ │ ├── CudaMPIDKernelSources.cpp.in │ │ ├── CudaMPIDKernelSources.h.in │ │ ├── MPIDCudaKernelFactory.cpp │ │ ├── MPIDCudaKernels.cpp │ │ ├── MPIDCudaKernels.h │ │ └── kernels │ │ │ ├── multipoleElectrostatics.cu │ │ │ ├── multipoleFixedField.cu │ │ │ ├── multipoleInducedField.cu │ │ │ ├── multipolePme.cu │ │ │ ├── multipoles.cu │ │ │ ├── pmeMultipoleElectrostatics.cu │ │ │ ├── sphericalMultipoles.cu │ │ │ └── vectorOps.cu │ └── tests │ │ ├── CMakeLists.txt │ │ └── TestCudaMPIDForce.cpp └── reference │ ├── CMakeLists.txt │ ├── include │ ├── MPIDReferenceKernelFactory.h │ └── windowsExportAmoebaReference.h │ ├── src │ ├── MPIDReferenceKernelFactory.cpp │ ├── MPIDReferenceKernels.cpp │ ├── MPIDReferenceKernels.h │ └── SimTKReference │ │ ├── MPIDReferenceForce.cpp │ │ ├── MPIDReferenceForce.h │ │ ├── jama_cholesky.h │ │ ├── jama_eig.h │ │ ├── jama_lu.h │ │ ├── jama_qr.h │ │ ├── jama_svd.h │ │ ├── tnt.h │ │ ├── tnt_array1d.h │ │ ├── tnt_array1d_utils.h │ │ ├── tnt_array2d.h │ │ ├── tnt_array2d_utils.h │ │ ├── tnt_array3d.h │ │ ├── tnt_array3d_utils.h │ │ ├── tnt_cmat.h │ │ ├── tnt_fortran_array1d.h │ │ ├── tnt_fortran_array1d_utils.h │ │ ├── tnt_fortran_array2d.h │ │ ├── tnt_fortran_array2d_utils.h │ │ ├── tnt_fortran_array3d.h │ │ ├── tnt_fortran_array3d_utils.h │ │ ├── tnt_i_refvec.h │ │ ├── tnt_math_utils.h │ │ ├── tnt_sparse_matrix_csr.h │ │ ├── tnt_stopwatch.h │ │ ├── tnt_subscript.h │ │ ├── tnt_vec.h │ │ └── tnt_version.h │ └── tests │ ├── CMakeLists.txt │ └── TestReferenceMPIDForce.cpp ├── python ├── CMakeLists.txt ├── header.i ├── mpidplugin.i └── setup.py └── serialization ├── include └── openmm │ └── serialization │ └── MPIDForceProxy.h ├── src ├── MPIDForceProxy.cpp └── MPIDSerializationProxyRegistration.cpp └── tests ├── CMakeLists.txt 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