Increasing pyMBE interoperability (part I) - #151

Merged

pm-blanco merged 87 commits into

pyMBE-dev:mainfrom

jorch28:CheckThisFeature

Aug 14, 2026

Commits on Apr 8, 2026

Add engine factory and unfinished files for the espresso and lammps engines
jsd94
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93f8e93
Add engine factory to init method to instantiate the wanted engine class when the pymbe class is instantiated
jsd94
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d98eec9
Add particle_charge,particle_label,particle_position and particle_fix to ParticleInstance class
jsd94
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ec47aaa
Use attributes inst.particle_label, inst.particle_charge, inst.particle_position,inst._particle_fix to _get_instances_df method
jsd94
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7985bc7

Commits on Apr 9, 2026

Add tutorial
jsd94
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731e325

Commits on Apr 16, 2026

Add modifications to decouple the follwoing methods from espresso:
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802cac6
modify base classes to base engine. Delete engine factory
jsd94
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aa70a25
Add espresso engine methods
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dd74d6c
Add Espresso protocol classes to simulate the structure of the espresso system object
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08b2453
Modify manager _get_particle_instances to just add position and fix rows to the instance dataframe
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4d5163d
Modify pydantic validation for particle instances enabling arbitrary type in config class in order to be able to set the position as NDarrays
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10fa793
Add modifications to pymbe tutorial according to the decoupling of espresso from pymbe
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764c716

Commits on Apr 30, 2026

Adapt methods:
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43fdd35
Modify method add_instances_to_engine in order that takes into account the missing particles from pymbe DB and the particles that have not been transferred yet to espresso.
jsd94
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ae645c8
Add LammpsEngineProtocol
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914f74c
Add LammpsSimulation still to be build the code related to LammpsSimulation
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7b903b3
Add position and added to engine in pmb_type particle for _load_database_csv and _save_database_csv
jsd94
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7c57df5
Add into Manager class _update_instance method for pymbe type particle, particle_id,position and added_to_engine.
jsd94
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0fa66d4
Add attributes added_to_engine for both particleinstances and bond instances
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6c939ff
Adapt sample/branched_polyampholyte to changes related in decoupling pymbe
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fd4572d
Add modifications to tests.
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c1d3ea8
Add changes to peptide_cpH to account for the decouple of espresso
jsd94
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e815cea
various small revisions together with Jordi
Pablo
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edaabda

Commits on May 9, 2026

Add changes to decouple:
jsd94
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16a8263
Add pymbe warnings to send a deprecate warning for the use of certain handy functions
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02559f5
Add deprecation warnings to the use of handy functions
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267cbf8
Add to espresso engine:
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557971b
Add methods that might be useful for any engine:
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7d8294b
Add changes in save and load database functions to load and save arrays and lists into the instances dataframe
jsd94
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3a04e0a
Add methods to manager:
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d3930fe
Add changes:
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322bf3b
Add comment
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6aab5d1
set the simulation engine in order to use the pmb method to determine reservoir concentrations
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685a26e
set simulation engine before executing the tests
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5533abb
Set simulation engine before executing the tests remove espresso system from setup_lj interactions
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fc6fa7d
Add simulation engine in both tests
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282d215
Add simulation engine before executing the handy functions as now they are migrated to espresso_engine class
jsd94
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919afbf
Modify method to test column positions from the dataframe as it contains a numpy array that contains arrays. Thus, the approach that has worked is to loop through the array and compare them element…
jsd94
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64811b7

Commits on May 11, 2026

Adapt sample file to current version decoupling espresso
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7df1750
Adapt current sample files towards decoupling espresso
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2348bb4
remove espresso_system as an input from methods migrated from handy functions
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44aea18
Adapt test_handy_functions towards decoupling espresso
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861f03b
Adapt changes to decoupling espresso from pymbe
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337cf47

Commits on May 14, 2026

Add modifications to adapt sample script to espresso decoupling
jsd94
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c8d3f7d
Add changes to pymbe_tutorial
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1a9b961
Merge branch 'main' into CheckThisFeature
jsd94
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e7c1445
Decouple create_angular_potential,generate_angles_for_entity,
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73404f9
Add method add_angle, _create_angle_instance and _get_angle_instance.
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850ec76
include in io.py _load_database and _save_database added_to_engine for the pmb_type angle
jsd94
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4e28d5e
Adapt angle tests to decouple it from espresso
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2212e89
Add as pmb_type "angle" with attributes particle_id1,particle_id2 and particle_id3 and added_to_engine
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39ac794
Add added_to_engine in AngleInstance data class
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1b03f67
Adapt test hydrogel_builder_with_angles
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61625c4
Adapt test_lattice_setup
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72562ee
Adapt to decouple from espresso method test_io_instances
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27348fa

Commits on May 18, 2026

A commit
jsd94
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e273215

Commits on Jun 10, 2026

Add box_l argument to _create_hydrogel_chain
jorch28
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b1a99a9

Commits on Jun 22, 2026

Commits on Jun 24, 2026

Calculate the resulting quantity of the chain length in reduced units instead of using the magnitude
jorch28
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698afb2

Commits on Jun 30, 2026

Delete unused imports.
jorch28
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b5e4523
use np.prod(box_l) to replace box_l[0]*box_l[1]*box_l[2]

jorch28
and
jngrad
authored
7316798
Add Copyright Notes
jorch28
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2ca41b2
Clear pymbe_tutorial outputs
jorch28
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06560f8

Commits on Jul 1, 2026

Delete data.csv
jorch28
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858fe3e
Add DummyEngine with __getattr__ dunder method to raise RuntimeError
jorch28
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32289b7
Use __getattr__ to setup not ImplementedError for LammpsSimulationEngine
jorch28
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0dc430a
remove unused variable espresso_local_system
jorch28
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8f18d26
Add LammpsSimulationEngine that Raises a not ImplementedError
jorch28
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cface83
Add a DummyEngine instantiated by default in pyMBE.
jorch28
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807296f

Commits on Jul 2, 2026

added jordi to author list, update changelog
Pablo
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d8453bc
Merge branch 'main' into CheckThisFeature
Pablo
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ea58a8d
Add facade method to lammps engine to comply with the interface contract
jorch28
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d20e6b8
Delete files from titration simulations
jorch28
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bcbbaa4

Commits on Jul 3, 2026

Commits on Jul 10, 2026

Commits on Jul 16, 2026

LAMMPS testsuite
jngrad
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40ad03c

Commits on Aug 13, 2026

address review coments, minor code cosmetic changes
pmblanco
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bf42843
Remove duplicated functions
jngrad
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017f07d
remove all duplicated functions from handy functions, remove custom deprecation warnings, reach full coverage, add docs to tests
pmblanco
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cab9817
fix bug in centering molecules, remove unnecesary test
pmblanco
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f5effe7
fix issue in test
pmblanco
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bf9743c
Cleanup
jngrad
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028a1c5