Make axis_type and axis_indices setup right #10
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Now it is fully consistent with OpenMM-7.4.0
WangXinyan940
referenced
this pull request
in WangXinyan940/DMFF
Mar 28, 2022
* feat(classical): Support differentiable mscale & add test cases (#10) * Update PME code (#8) * get a preliminary result of point charge pme caclulation * correct gradient of coul * review api.py code * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add testcases for NoCutoff Coulomb potential and a large GAFF molecule * feat(classical): Support differentiable 1-4 scale Co-authored-by: Roy Kid <lijichen365@126.com> * formate code; add example XML section to parseElement docstring Co-authored-by: Roy Kid <lijichen365@126.com>
Ericwang6
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Apr 10, 2022
* fix(classical): fix import relationship * Update * feat(classical): make HarmonicBond and HarmonicAngle the same as GAFF * feat(classical): Support torsion force * fix(classical): use two attributes to save proper/improper dihedral separately * fix(classical): Jax the parameters when creating forces * fix(classical): fix a typo * fix(classical): use ndarray to save indexes * fix(classical): return sum of energies for torsion * feat(classical): support 4th order for torsion * feat(classical): Add UT for classical forcefields * fix(classical): Update PDB structures needed by test cases * fix(classical): Change atomtypes to be consistent with residues * feat(classical): add reference energies for test cases * fix(classical): decrease the decimal for energy comparision * feat(classical): Use the same way of openmm for dihedral typification * fix(classical): remove unused import * fix(classical): add order for impropers * fix(classical): use ndarray instead of list for index saving * fix(classical): Add import element * fix(classical): fix misusing between torsion.periodicity and torsion.phase * fix(classical): misusing between periodicity and phase * fix(classical): Correct bond connection in unit test pdb files * Fix pdb files in unittest * Update proper1.pdb * feat(classical): update reference energy for improper test * Update api.py * feat(classical): Add wildcard testcase for improper * set up LennardJones framework * feat(classical): Add test case for multiple dihedrals in one molecule * fix(classical): change the way of dihedral calculation * start to write LJ potential * feat(classical): Implement 12-6 potential without exclusion * feat(classical): Add exclusion pairs for LJ force * feat(classical): add simple test for LennardJonesForce * fix(classical): fix imp of nbfix * fix(classical): use more reasonable test case * fix(classical): add reference energy * draft for dev lj potential * fix Zonly typo in api.py:332 which not consistent with line 475 * reduce PME force to point charge calculation * get a preliminary result of point charge pme caclulation * feat(classical): support loading charge from residue card and NonbondedForce card * correct gradient of coul * feat(classical): Add setting for force switching * feat(classical): Add noPBC support on LJ potential * review api.py code * feat(classical): Use covalent map to generate exclusions * feat(classical): Call LJ in API * fix(classical): bug fix on misusing list and jnp.array * fix(classical): correctly support NoCutoff * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support * Update PME code (#8) * get a preliminary result of point charge pme caclulation * correct gradient of coul * review api.py code * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add testcases for NoCutoff Coulomb potential and a large GAFF molecule * feat(classical): Support differentiable 1-4 scale * Devel (#9) * feat(classical): Support differentiable mscale & add test cases (#10) * Update PME code (#8) * get a preliminary result of point charge pme caclulation * correct gradient of coul * review api.py code * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add testcases for NoCutoff Coulomb potential and a large GAFF molecule * feat(classical): Support differentiable 1-4 scale Co-authored-by: Roy Kid <lijichen365@126.com> * formate code; add example XML section to parseElement docstring Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add more GAFF2 test cases. * fix(classical): remove unnecessary lines Co-authored-by: Roy-Kid <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: Roy Kid <lijichen365@126.com>
KuangYu
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that referenced
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Apr 13, 2022
* fix(classical): fix import relationship * Update * feat(classical): make HarmonicBond and HarmonicAngle the same as GAFF * feat(classical): Support torsion force * fix(classical): use two attributes to save proper/improper dihedral separately * fix(classical): Jax the parameters when creating forces * fix(classical): fix a typo * fix(classical): use ndarray to save indexes * fix(classical): return sum of energies for torsion * feat(classical): support 4th order for torsion * feat(classical): Add UT for classical forcefields * fix(classical): Update PDB structures needed by test cases * fix(classical): Change atomtypes to be consistent with residues * feat(classical): add reference energies for test cases * fix(classical): decrease the decimal for energy comparision * feat(classical): Use the same way of openmm for dihedral typification * fix(classical): remove unused import * fix(classical): add order for impropers * fix(classical): use ndarray instead of list for index saving * fix(classical): Add import element * fix(classical): fix misusing between torsion.periodicity and torsion.phase * fix(classical): misusing between periodicity and phase * fix(classical): Correct bond connection in unit test pdb files * Fix pdb files in unittest * Update proper1.pdb * feat(classical): update reference energy for improper test * Update api.py * feat(classical): Add wildcard testcase for improper * set up LennardJones framework * feat(classical): Add test case for multiple dihedrals in one molecule * fix(classical): change the way of dihedral calculation * start to write LJ potential * feat(classical): Implement 12-6 potential without exclusion * feat(classical): Add exclusion pairs for LJ force * feat(classical): add simple test for LennardJonesForce * fix(classical): fix imp of nbfix * fix(classical): use more reasonable test case * fix(classical): add reference energy * draft for dev lj potential * fix Zonly typo in api.py:332 which not consistent with line 475 * reduce PME force to point charge calculation * get a preliminary result of point charge pme caclulation * feat(classical): support loading charge from residue card and NonbondedForce card * correct gradient of coul * feat(classical): Add setting for force switching * feat(classical): Add noPBC support on LJ potential * review api.py code * feat(classical): Use covalent map to generate exclusions * feat(classical): Call LJ in API * fix(classical): bug fix on misusing list and jnp.array * fix(classical): correctly support NoCutoff * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support * Update PME code (#8) * get a preliminary result of point charge pme caclulation * correct gradient of coul * review api.py code * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add testcases for NoCutoff Coulomb potential and a large GAFF molecule * feat(classical): Support differentiable 1-4 scale * Devel (#9) * feat(classical): Support differentiable mscale & add test cases (#10) * Update PME code (#8) * get a preliminary result of point charge pme caclulation * correct gradient of coul * review api.py code * feat(classical): Support more Coulomb potentials (#9) * fix(classical): fix misusing variables * feat(classical): add a testcase for two LJ molecules * fix(classical): correct setting of LJ case * feat(classical): add a testcase for large molecule (including 1-4) interactions * feat(classical): Add support for reaction-field and no-cutoff in Coulomb potential * imporve colvalent_map support Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add testcases for NoCutoff Coulomb potential and a large GAFF molecule * feat(classical): Support differentiable 1-4 scale Co-authored-by: Roy Kid <lijichen365@126.com> * formate code; add example XML section to parseElement docstring Co-authored-by: Roy Kid <lijichen365@126.com> * feat(classical): add more GAFF2 test cases. * fix(classical): remove unnecessary lines Co-authored-by: Roy-Kid <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: Roy Kid <lijichen365@126.com> Co-authored-by: Roy-Kid <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: Roy Kid <lijichen365@126.com>
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In this PR, the way to determine axis_type and axis_indices is changed. Now it is fully consistent with openmm. The previous implementation was incomplete for large organic molecules.