Update 4.3ADMPQeqForce.md #150
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WangXinyan940
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* Fix mbar example (#76) * Add requirement of mdtraj, optax and pymbar to the doc * Fix benzen demo (#75) * Add Gitee_mirror * Fix mirror CI/CD * Update ben-prm.xml Co-authored-by: Yingze Wang <ericwangyz@pku.edu.cn> Co-authored-by: Roy-Kid <lijichen365@126.com> Co-authored-by: KuangYu <windwhisper.yu@gmail.com> Co-authored-by: Jichen Li <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: crone <2223469329@qq.com> Co-authored-by: Yuzhi Zhang <529133328@qq.com> * Remove jax_md requirement to support high version of jax & tensorflow * Initialize topology information generator and its UT * Half way of detecting propers * Finish proper searching * Update topology.py * Update topology.py * Auto detect impropers * Update topology.py * Initialize template IO * Remove jax version limitation * Finish atom type matching with templates * Initialize UT for topology tools * Upload auto workflow for UT * Add issue templates for feature request and bug-report (#83) * Small update in issue template (#84) * Add issue templates for feature request and bug-report * Update issue template * Update initial version of frontend impl & unit tests * Modify new code to fit old parts * Make the structure clean * Update code * Finished adding vsite from template and smarts parsers * Support VSite IO in xml template * Support vsite in template matching * Add example * Add example of vsite addition * Try a better implementation * Implement a better Topology * Update bettertopology.py * Designed the usage of operators * Update our own Topology class * Update test_operators.py * Update test_operators.py * Implement VSite and AType operators * Create smartsvsite.py * Update am1charge.py * Update test_operators.py * Add AM1 charge OP * Add Coulomb Generator * supporting generators * Add method to find equivalent atoms (without vsites) * Let AM1 charge calculator use eqv info * Add full support of BCC charge * Support ambertools based typification * Update classical.py * Add LJ generator and an example * support LJ prms * Deal with atom classes in LJ * Add water example for interaction calculation * Update test_inter_water.py * Add support for loading BCC prms * Update classical.py * Finish BCC support * support type2 vsite * Make operators use the same initialization method * Support smirks patching on vsites. * Finished dimer energy example * Update classical.py * Update topology.py * Fix ParamSet to be a correct PyTree * Update paramset.py * Calculate test system by hand * Add test case for NoCutoff Coul and LJ energy * Support NBFix * Add Hamiltonian and its unittest. * Delete test.xml * update vsite positions in hamiltonian * replace Chem.SanitizeMol with topdata.regularize_aromaticity * fix N+ formal charge * Update .gitignore * Update topology.py * Support the way of updating paramset in optax * Update test_run_dimer_energy.py * Initialize generators before loading hamiltonian * add warmup and nesterov optimizer * fix 3fd vsite coordinates * Add mask generation * build vsites in multiple molecules separately * support dummy atom reading * fix vsite topologies and molecules * Init new example * Support Parmed LJ modifier * Update example for lennard jones optimization * Create simpler MBAR estimator * Add reweighting estimator * Update opt.ipynb * Update opt.ipynb * Update opt.ipynb * Add a simple example to calculate lennard-jones potential * Add openmm as reference * Pearl dingzhen patch 1 (#112) * Update classical.py Add NBFixPair support for LJ potential * Update inter.py add support for LJ nbfixpair * Update inter.py change eps_mat at (_map[1], _map[0]) * Update inter.py * Remove Jax-MD requirement * Fix Hamiltonian * Add HarmonicAngleGenerator * Add PeriodicTorsionGenerator * Update NonbondedForce * Correct the order of improper matching * Fix and update unittests. * Update unit-test workflow to fix requirement problem * Update test_compute.py * Update ut.yml * Update ut.yml * Add generator for ADMPPmeForce * Merge changes on devel branch * Update test_compute.py * Support LJ long range correction * Add generators for Slater type forces * Update ut.yml * Update ut.yml * Fix No-AxisType bug (#122) * add rules of local axis for NoAxisType * add test for NoAxisType --------- Co-authored-by: plumbum082 <gq0829@126.com> * qeq merge (#124) * add qeqforce and QeqQenerator, modify CoulmbGenerator * ethresh modified * add refresh in qeq.py * Add sGNN generator fixed a few problems in ADMPPmeGenerator * remove debugging codes * Add frontend for sGNN (#125) * Add sGNN generator fixed a few problems in ADMPPmeGenerator * remove debugging codes * Modified QEQ potential and add JIT support * Fix the two examples: * fluctuated_leading_term_waterff * peg_slater_isa Make map_atomtype and map_poltype available in generator * Add QEQ test * Add jaxopt requirement in github workflow * Update qeq.py * Fix the jupyter notebook * Support aux data for ADMP and QEQ * Clean the way of aux_data implementation * Add new unit test for QEQ with two residues. * Change jaxopt root finder to be jit-able * Update ut.yml * Explicit support nopbc calculation * Update admp.py * make the behavior of ADMP correct while using NoCutoff * Upload * Update pme.py * Add frontend for EANN (#127) * Change default scale setting of ADMP to reproduce MPID * Update pme.py * Fix optimizers for v1.0.0 * Fix nan problem while calculate power(0.0, 1/6) * Add esp calculator in ADMPPmeForce and CoulNoCutoffForce for noPBC systems * Fix the ADMP ESP calculator and add unit test * Update pme.py * Use std library warnings to handle import errors * Add eta to increase the numerical stability of QEQ * Fix the local frame axis setting in ADMP to be consistent with MPID * Correct local frame defination in unit test * Update fluctuated_leading_term_waterff and water_fullpol example * Save ADMP type mapping to potential.meta * Fix the ADMP examples, also improve the way map_atomtypes and map_poltypes are accessed. * Break a long line in code * Fix the ADMP aux test * docs_review * Fix examples (#130) * Add sGNN generator fixed a few problems in ADMPPmeGenerator * remove debugging codes * Fix the two examples: * fluctuated_leading_term_waterff * peg_slater_isa Make map_atomtype and map_poltype available in generator * Fix the jupyter notebook * Update fluctuated_leading_term_waterff and water_fullpol example * Fix the ADMP examples, also improve the way map_atomtypes and map_poltypes are accessed. * Break a long line in code * Fix the ADMP aux test * Update Installation.md * modifications to intro * Update introduction.md * Update index.md * Test modifying the MBAR.md file * Update MBAR doc * Update doc * Update 4.2ADMPPmeForce.md * Update 4.2ADMPPmeForce.md * Update 4.4MLForce.md * Update Optimization doc * Update 4.6MBAR.md * Update 4.5Optimization.md * Update 4.5Optimization.md * add nocutoff and noperioid nblist * Update 3.usage.md * Update 4.3ADMPQeqForce.md * update 4.3ADMPQeqForce.md * docs/examples fix (#140) * DMC_fix * udpate gitignore and delete .idea cache --------- Co-authored-by: Yingze Wang <ericwangyz@pku.edu.cn> * Update omm plugin and save_dmff2tf.py for aux (U_ind especially) compatible. (#135) * Add issue templates for feature request and bug-report * Add script for dmff model saving. * Remove issue template from devel branch. * debug workflow * remove debug * Update ut.yml. Install mdtraj by conda. * Add openmm dmff plugin to backend * Update .gitignore * Add test workflow for openmm dmff plugin * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Specific setuptools version in workflow yaml * Update tensorflow version * Enable double precision in test omm dmff plugin workflow * update nve assert checking in omm dmff plugin workflow * Fix no axis type bug (#120) * add rules of local axis for NoAxisType * add test for NoAxisType * Update omm plugin and save_dmff2tf.py for aux compatible. * Fix test issue. * Update test_openmm_dmff_plugin.yml --------- Co-authored-by: plumbum082 <54125554+plumbum082@users.noreply.github.com> * Delete docs/dev_guide/arch.md (#141) * review qeq docs and update the math display error (#139) Co-authored-by: WangXinyan940 <44082181+WangXinyan940@users.noreply.github.com> * Create 4.7OpenMMplugin.md * Update 4.3ADMPQeqForce.md * Update 4.3ADMPQeqForce.md (#150) * Update README.md (#147) * Update the doc for openmm dmff plugin usage. (#146) * Add issue templates for feature request and bug-report * Add script for dmff model saving. * Remove issue template from devel branch. * debug workflow * remove debug * Update ut.yml. Install mdtraj by conda. * Add openmm dmff plugin to backend * Update .gitignore * Add test workflow for openmm dmff plugin * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Specific setuptools version in workflow yaml * Update tensorflow version * Enable double precision in test omm dmff plugin workflow * update nve assert checking in omm dmff plugin workflow * Fix no axis type bug (#120) * add rules of local axis for NoAxisType * add test for NoAxisType * Update omm plugin and save_dmff2tf.py for aux compatible. * Fix test issue. * Update test_openmm_dmff_plugin.yml * Update the doc for openmm dmff plugin usage * Revision on the doc of DMFF plugin * Upload tf c directory. * Remove tf2.9.1_c.tar --------- Co-authored-by: plumbum082 <54125554+plumbum082@users.noreply.github.com> * add 2 notebooks in user guide (#145) * DMC_fix * udpate gitignore and delete .idea cache * Add files via upload * Update README.md * Update README.md * Add files via upload --------- Co-authored-by: Yingze Wang <ericwangyz@pku.edu.cn> * Fix bug when rendering xml files * Update the doc link in OpenMMPlugin doc (#151) * Add issue templates for feature request and bug-report * Add script for dmff model saving. * Remove issue template from devel branch. * debug workflow * remove debug * Update ut.yml. Install mdtraj by conda. * Add openmm dmff plugin to backend * Update .gitignore * Add test workflow for openmm dmff plugin * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Update workflow for openmm dmff plugin test. * Specific setuptools version in workflow yaml * Update tensorflow version * Enable double precision in test omm dmff plugin workflow * update nve assert checking in omm dmff plugin workflow * Fix no axis type bug (#120) * add rules of local axis for NoAxisType * add test for NoAxisType * Update omm plugin and save_dmff2tf.py for aux compatible. * Fix test issue. * Update test_openmm_dmff_plugin.yml * Update the doc for openmm dmff plugin usage * Revision on the doc of DMFF plugin * Upload tf c directory. * Remove tf2.9.1_c.tar * Update doc link in OpenMM plugin --------- Co-authored-by: plumbum082 <54125554+plumbum082@users.noreply.github.com> --------- Co-authored-by: Yingze Wang <ericwangyz@pku.edu.cn> Co-authored-by: Roy-Kid <lijichen365@126.com> Co-authored-by: KuangYu <windwhisper.yu@gmail.com> Co-authored-by: Jichen Li <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: crone <2223469329@qq.com> Co-authored-by: Yuzhi Zhang <529133328@qq.com> Co-authored-by: Ye Ding <charles.dingye@gmail.com> Co-authored-by: Ye Ding <dingye@westlake.edu.cn> Co-authored-by: Wang Xinyan <wangxy@dp.tech> Co-authored-by: Junhan Chang <1700011741@pku.edu.cn> Co-authored-by: pearlDingzhen <125740448+pearlDingzhen@users.noreply.github.com> Co-authored-by: plumbum082 <gq0829@126.com> Co-authored-by: Haichao Huang <100009402+gust-07@users.noreply.github.com> Co-authored-by: Junmin <72368464+Jeremydream@users.noreply.github.com> Co-authored-by: VINFeng <103423458+VINFeng@users.noreply.github.com> Co-authored-by: Zheng Cheng <mg1624011@smail.nju.edu.cn> Co-authored-by: Roy Kid <lijichen365@gmail.com> Co-authored-by: gust-07 <511714479@qq.com> Co-authored-by: plumbum082 <54125554+plumbum082@users.noreply.github.com> Co-authored-by: Taiping Hu <32788428+taipinghu@users.noreply.github.com>
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