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enable use of CVs defined by PyTorch neural network models #570

Merged
merged 109 commits into from
Nov 14, 2024
Merged

enable use of CVs defined by PyTorch neural network models #570

merged 109 commits into from
Nov 14, 2024

Commits on May 13, 2022

  1. In the process of implementing torchann colvar

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  2. Merge branch 'master' of https://github.com/zwpku/colvars

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Commits on May 14, 2022

  1. Implementing torchann

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    zwpku committed May 14, 2022
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Commits on May 15, 2022

  1. Implemented calc_gradients and apply_forces

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Commits on May 16, 2022

  1. Start working

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Commits on May 20, 2022

  1. Handling periodicity; test torchANN with phi angle

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Commits on May 24, 2022

  1. Add output_index to specify the component of output layer that is used

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Commits on Feb 8, 2023

  1. update with upstream

    Zhang committed Feb 8, 2023
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Commits on Feb 9, 2023

  1. up

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Commits on Feb 10, 2023

  1. Update gromacs-2021.6 patch

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Commits on Feb 11, 2023

  1. modify patch files for namd to support LibTorch

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Commits on Mar 13, 2023

  1. Merge branch 'Colvars:master' into torchann

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Commits on Jul 20, 2023

  1. updated with upstream:master

    Zhang committed Jul 20, 2023
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Commits on Jul 21, 2023

  1. Add test for torchann

    Zhang committed Jul 21, 2023
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  2. Merge pull request #1 from zwpku/torchann1 

    Torchann1
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  3. minor changes

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Commits on Aug 2, 2023

  1. Modified test for torchann component

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    zwpku committed Aug 2, 2023
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  2. Add figures for AutoEncoder CV

    Zhang committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. Convert unit of atom coordinates to angstrom before feeding to torch … 

    …model
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  2. Bug fixed in gradient of torchann

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Commits on Aug 10, 2023

  1. Add Torch in lammps' cmake

    Zhang committed Aug 10, 2023
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Commits on Aug 14, 2023

  1. Added test files for torchann in NAMD

    Zhang committed Aug 14, 2023
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  2. Merge branch 'Colvars:master' into torchann

    @zwpku
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  3. Minor changes in torchann component

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Commits on Aug 15, 2023

  1. Updated patches for Gromacs 2020.x and 2022.x

    Zhang committed Aug 15, 2023
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  2. Updated torchann in header file; Removed test for torchann component

    Zhang committed Aug 15, 2023
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  3. Add tests for Gromacs and NAMD

    @zwpku
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  4. Add tests for Gromacs and NAMD

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  5. Updated torchann-namd test and references

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Commits on Aug 24, 2023

  1. Reimplement torchann as a derived class of LinearCombination

    @zwpku
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  2. declare torchann cvc as scalar

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Commits on Aug 25, 2023

  1. allocate memory of cv_force before use

    @zwpku
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  2. c++17 instead of c++14

    Zhang committed Aug 25, 2023
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  3. removed file to correct place

    Zhang committed Aug 25, 2023
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  4. removed file to correct place

    Zhang committed Aug 25, 2023
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Commits on Aug 26, 2023

  1. Minor correction in apply_force of torchann

    @zwpku
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  2. Add tests for gromacs and NAMD

    @zwpku
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  3. merged with master

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Commits on Aug 28, 2023

  1. Modified the definition of cv_force such that it contains the informa… 

    …tion on the size
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Commits on Aug 30, 2023

  1. Add option to set data type in torchann

    @zwpku
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  2. Add option to set data type in torchann

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Commits on Aug 31, 2023

  1. Enable GPU support; Further tests are needed.

    Zhang committed Aug 31, 2023
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Commits on Sep 1, 2023

  1. updated patch for gromacs-2021.x

    Zhang committed Sep 1, 2023
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  2. updated patch for gromacs-2022

    Zhang committed Sep 1, 2023
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  3. Updated patch for gromacs-2020.x

    Zhang committed Sep 1, 2023
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  4. Update namd config to support GPU

    Zhang committed Sep 1, 2023
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  5. Do not require libtorch in lammps by default

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Commits on Sep 2, 2023

  1. Minor changes (spaces/indent) in code; Removed tests for namd and gro… 

    …macs backend
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  2. update namd config patch to make namd3 work

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Commits on Sep 6, 2023

  1. Merge branch 'master' into torchann

    @zwpku
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  2. merge with master

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Commits on Sep 8, 2023

  1. Merge branch 'upmaster' into torchann

    Zhang committed Sep 8, 2023
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  2. updated patch for gromacs 2023 to support torchann

    Zhang committed Sep 8, 2023
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Commits on Sep 14, 2023

  1. Merge branch 'master' into torchann

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Commits on Oct 16, 2023

  1. merge torchann squash

    Zhang committed Oct 16, 2023
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  2. conflicts resolved

    Zhang committed Oct 16, 2023
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Commits on Oct 18, 2023

  1. Do not use GPU

    Zhang committed Oct 18, 2023
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  2. Merge branch 'upmaster' (early part) into torchann

    Zhang committed Oct 18, 2023
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Commits on Nov 3, 2023

  1. Merge branch 'master' into torchann

    @zwpku
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Commits on Nov 16, 2023

  1. Merge branch 'upmaster' into torchann

    Zhang committed Nov 16, 2023
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  2. merged with master and changed torchann class based on HanatoK's sugg… 

    …estions
    Zhang committed Nov 16, 2023
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  3. Merge branch 'github' into torchann

    Zhang committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. Added torchann tests for gromacs and namd (only when libtorch is linked)

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Commits on Nov 20, 2023

  1. Add torch option to library CMake file

    @jhenin
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Commits on Nov 27, 2023

  1. Merge branch 'master' into torchann

    @zwpku
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  2. Use the same code from distanceZ to handle nearest-image convection

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Commits on Dec 1, 2023

  1. Squash-merge of master branch

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  2. Integrate libTorch CMake recipe into GROMACS main

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Commits on Dec 11, 2023

  1. Fixed conflicts

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Commits on Dec 12, 2023

  1. Fixed Conflicts

    Zhang committed Dec 12, 2023
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  2. Fixed Conflicts

    Zhang committed Dec 12, 2023
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Commits on Dec 20, 2023

  1. Fix NAMD build dependencies

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Commits on Feb 22, 2024

  1. Merge branch 'master' into torchann

    @zwpku
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Commits on Jul 5, 2024

  1. Merge branch 'master' into torchann

    @giacomofiorin
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Commits on Jul 6, 2024

  1. Restore componentDisabled and make it more generally usable

    @giacomofiorin
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  2. Integrate cvc base class improvements with torchANN

    @giacomofiorin
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  3. Merge branch 'master' into torchann

    @giacomofiorin
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Commits on Sep 18, 2024

  1. Fix CMakeFile for Gromacs 2024 

    Also allow torchANN components to be declared as periodic to fix the regtest
    @jhenin
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Commits on Sep 20, 2024

  1. Set PRNG seed in Gromacs regtests

    @jhenin
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  2. Update patches for GMX CMake files 

    Had to make separate patch for the mdmodules version
    @jhenin
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  3. Add patch for gmxManageColvars.cmake

    @jhenin
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Commits on Sep 23, 2024

  1. Merge branch 'master' into torchann

    @jhenin
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Commits on Oct 4, 2024

  1. Use Clang and ccache more often when available

    @giacomofiorin
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  2. Find PyTorch through CMake and switch to -DCOLVARS_TORCH as macro

    @giacomofiorin
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  3. Update CentOS9-devel container recipe

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  4. Use libTorch from container when available

    @giacomofiorin
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  5. Remove pre-C++11 stuff

    @giacomofiorin
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  6. Add torchann test for standalone library

    @giacomofiorin
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  7. Disable torchann test when not building with libTorch

    @giacomofiorin
    giacomofiorin committed Oct 4, 2024
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  8. Enable Torch interface only when the requested C++ standard supports it

    @giacomofiorin
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  9. Raise the CMAKE_CXX_STANDARD to 17 if libtorch is used and 

    CMAKE_CXX_STANDARD is less than 17
    @HanatoK @giacomofiorin
    HanatoK authored and giacomofiorin committed Oct 4, 2024
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  10. Squash-merge of master branch

    @giacomofiorin
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  11. Remove patch files for old and unsupported GROMACS versions

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Commits on Oct 10, 2024

  1. Merge branch 'master'

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Commits on Oct 11, 2024

  1. - Isolated torch-related code 

    - Removed componentDisabled
    Zhang committed Oct 11, 2024
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  2. minor fix

    Zhang committed Oct 11, 2024
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  3. Add torch header file to dependence file of backends

    Zhang committed Oct 11, 2024
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  4. fixed bug when torch is not available

    Zhang committed Oct 11, 2024
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  5. Merge branch 'master'

    @giacomofiorin
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  6. Enable Torch in GROMACS builds when available from CI container

    @giacomofiorin
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Commits on Oct 19, 2024

  1. Do not duplicate libTorch C++ flags

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Commits on Oct 22, 2024

  1. Document apptainer push

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  2. Let GROMACS use the newer CMake when available

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Commits on Nov 7, 2024

  1. Squash-merge of master branch

    @giacomofiorin
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Commits on Nov 8, 2024

  1. Squash-merge of master branch

    @giacomofiorin
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Commits on Nov 13, 2024

  1. Set damping=0 in gromacs regtest for torchann class. 

    Updated reference files accordingly.
    Zhang committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. Updated references files generated by Gromacs with double precision

    Zhang committed Nov 14, 2024
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  2. Minor corrections in reference files.

    Zhang committed Nov 14, 2024
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  3. Squashed merge of master branch

    @giacomofiorin
    giacomofiorin committed Nov 14, 2024
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