Add new InterIntraMD Calculator to IPSuite #388

MrJulEnergy · 2025-02-16T10:48:53Z

I am proposing the new MD node InterIntraMD, which enables the reweighing of rotational, translational and vibrational forces acting on each molecule.

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PythonFZ · 2025-02-16T15:47:03Z

Do you think it might be possible to implement this as a modifier

IPSuite/ipsuite/calculators/ase_md.py

Lines 544 to 545 in b7ff045

    
               modifiers: list[Modifier] 
        
                   modifies e.g. temperature or cell during the simulation.

to allow for the usage of all other parts of the ASEMD node?

Or something like an


class InterIntraModelCalc(zntrack.Node):
    model: ... = zntrack.deps()
    ...


    def run(self): pass

    def get_calculator(self, **kwargs) -> ...

* rename `atoms` to `frames` * fix test

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Fix pre-commit.ci remarks

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Add a Bond Length Constraint Node

change typehint in langevin to float

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* introduce `GenericASECalculator` and `ApplyCalculator` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update abstraction * add `dump_rate` to apply * add deprecation warnings * introduce CP2KModel * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * working implementation * update CP2KModel * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add `TBLiteModel` * add `ORCAModel` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix typos * add docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use zntrack relase version * add MACEMP model as well as ApplyCalculator test using it. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix line length * move and rename `GenericASEModel` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * address comments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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* change python version requirements in pyproject * add PlumedCalculator to init files * draft basic plumed node and work on atoms dependency for the ase calc * kind of working now * Change params path to deps path * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix ruff problems * draft docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix the overwriting of model results when using plumed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * somehow a duplicate line keeps showing up and needs to be removed... * i seem to have missed a few things while merging * add a plumed example * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix minor mistakes * fix spelling * update plumded model * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove poetry references * refactor plumed calc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move files to output directory * add docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * inheret from ipsbase * remove plumed action imports * fix mutable defaults * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update units * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix units * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * lint * final lint --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fabian Zills <46721498+PythonFZ@users.noreply.github.com> Co-authored-by: Fabian Zills <fzills@icp.uni-stuttgart.de> Co-authored-by: PythonFZ <fabian.zills@web.de>

* small asemd refactoring to catch errors in the calculator * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix pbar * try .. except handling for plumed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * type hints * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add `time_step` and `temperature` * move checks to `dynamics` module * refactor `md`, `transformations`, `constraints` * refactor ASEMD * finish refactor of `ASEMD` * fix import path * account for missing laufband file * update tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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* introduced modifier step offset and test * change default status of checks * updated debugcheck * fix reset test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * check initialization in dynamics * add `modifier_step_offset` * ignore C901 * presumably fix the test * fix 0 / 1 indexing, add and adapt tests. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Moritz Schaefer <moritz.schaefer@pm.me> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fabian Zills <fzills@icp.uni-stuttgart.de>

* custom cp2k calculator * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add cp2koutput tes * update cp2k model parser * include pint, exclude cp2k-input-tools * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * precommit and keep legacy code * update packages * address comments * lint * bump Laufband * review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bugfix --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* re-introduce `TorchDFTD3` * add `implemented_properties` to always compute forces

MrJulEnergy and others added 21 commits May 6, 2024 10:14

start working on BondLength Constraint node

92c9506

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6d252b5

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try the most basic form of the class

79e09f0

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d424d57

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add class to init files

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Add Hookean Constraint Node

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cdcc38a

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dont make a new ipsuite object for every atom pair

754b3c1

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1e3a12e

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fix grammar

0513ae4

fix long line

379514b

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a1623b5

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change changelog

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add test for FixedBondLengthConstraint

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repair test

fa788b3

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fix example and variable name

f0d843d

switched xtb-python with tblite (#384)

b7ff045

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Add new InterIntraMD Calculator to IPSuite

fb7fad7

MrJulEnergy added the 🎉 new node Add a new and exciting node to IPSuite label Feb 16, 2025

pre-commit-ci bot and others added 3 commits February 16, 2025 10:49

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fix variable name map to mol_map

7f99cd2

fix missing mol_map

831b15d

PythonFZ and others added 4 commits February 17, 2025 17:47

rename atoms to frames (#385)

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* rename `atoms` to `frames` * fix test

fix ruff remarks

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pre-commit-ci bot and others added 30 commits March 31, 2025 18:05

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fix spelling

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bump ruff version

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Merge pull request #396 from zincware/fix_pre_commit_errors

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Fix pre-commit.ci remarks

merge main

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convert to dataclasses and fix test

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Merge pull request #294 from zincware/add_bond_constraint

08e631a

Add a Bond Length Constraint Node

change typehint in langevin to float

0f6f6b7

Merge pull request #397 from zincware/fix_typehint

a871da7

change typehint in langevin to float

use cp2k-output tools from source due to build issues with regex (#398)

8ada50d

bump version (#399)

bdcfd74

[pre-commit.ci] pre-commit autoupdate (#227)

400a5a0

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Update quickstart.rst

02a939b

Update packmol.py

8adc5c9

Update .readthedocs.yaml

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fix y lim (#413)

ab4afea

bump znh5md version (#414)

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Update pyproject.toml (#415)

cfcfeb1

fix tqdm disable (#417)

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pump version (#418)

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re-introduce TorchDFTD3 (#419)

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* re-introduce `TorchDFTD3` * add `implemented_properties` to always compute forces

Merge branch 'main' into InterIntraNode

48010b6

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MrJulEnergy commented Feb 16, 2025

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PythonFZ commented Feb 16, 2025 •

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