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qeq merge #124

Merged
merged 3 commits into from
Oct 20, 2023
Merged

qeq merge #124

merged 3 commits into from
Oct 20, 2023

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gust-07
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@gust-07 gust-07 commented Oct 20, 2023

1.add qeq.py and QeqGenerator.py;
2.some functions and variables in classical were extracted for qeq calculation;
3. pme ethresh in classical.py is reduced to 5e-4 for memory consideration.

@WangXinyan940 WangXinyan940 merged commit 66d2eb9 into deepmodeling:wangxy/v1.0.0-devel Oct 20, 2023
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WangXinyan940 added a commit that referenced this pull request Nov 9, 2023
@WangXinyan940 @Ericwang6
@KuangYu @Roy-Kid @LanYang430 @AnguseZhang @dingye18 @TablewareBox @pearlDingzhen @plumbum082 @gust-07 @junminchen @VINFeng @zhengcheng233 @taipinghu
Merge 1.0.0-development branch to devel branch. (#129)
cfeffeb 
* 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 <[email protected]>
Co-authored-by: Roy-Kid <[email protected]>
Co-authored-by: KuangYu <[email protected]>
Co-authored-by: Jichen Li <[email protected]>
Co-authored-by: crone <[email protected]>
Co-authored-by: Yuzhi Zhang <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Delete docs/dev_guide/arch.md (#141)

* review qeq docs and update the math display error (#139)

Co-authored-by: WangXinyan940 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

---------

Co-authored-by: Yingze Wang <[email protected]>
Co-authored-by: Roy-Kid <[email protected]>
Co-authored-by: KuangYu <[email protected]>
Co-authored-by: Jichen Li <[email protected]>
Co-authored-by: crone <[email protected]>
Co-authored-by: Yuzhi Zhang <[email protected]>
Co-authored-by: Ye Ding <[email protected]>
Co-authored-by: Ye Ding <[email protected]>
Co-authored-by: Wang Xinyan <[email protected]>
Co-authored-by: Junhan Chang <[email protected]>
Co-authored-by: pearlDingzhen <[email protected]>
Co-authored-by: plumbum082 <[email protected]>
Co-authored-by: Haichao Huang <[email protected]>
Co-authored-by: Junmin <[email protected]>
Co-authored-by: VINFeng <[email protected]>
Co-authored-by: Zheng Cheng <[email protected]>
Co-authored-by: Roy Kid <[email protected]>
Co-authored-by: gust-07 <[email protected]>
Co-authored-by: plumbum082 <[email protected]>
Co-authored-by: Taiping Hu <[email protected]>
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@gust-07 @WangXinyan940