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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
Commits on Apr 9, 2026
- Add tutorial
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Commits on Apr 16, 2026
- Add modifications to decouple the follwoing methods from espresso:
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- modify base classes to base engine. Delete engine factory
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- Add espresso engine methods
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- Add Espresso protocol classes to simulate the structure of the espresso system object
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- Modify manager _get_particle_instances to just add position and fix rows to the instance dataframe
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- 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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- Add modifications to pymbe tutorial according to the decoupling of espresso from pymbe
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Commits on Apr 30, 2026
- Adapt methods:
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- 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.
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- Add LammpsEngineProtocol
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- Add LammpsSimulation still to be build the code related to LammpsSimulation
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- Add position and added to engine in pmb_type particle for _load_database_csv and _save_database_csv
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- Add into Manager class _update_instance method for pymbe type particle, particle_id,position and added_to_engine.
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- Add attributes added_to_engine for both particleinstances and bond instances
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- Adapt sample/branched_polyampholyte to changes related in decoupling pymbe
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- Add modifications to tests.
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- Add changes to peptide_cpH to account for the decouple of espresso
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- various small revisions together with Jordi
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Commits on May 9, 2026
- Add changes to decouple:
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- Add pymbe warnings to send a deprecate warning for the use of certain handy functions
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- Add deprecation warnings to the use of handy functions
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- Add to espresso engine:
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- Add methods that might be useful for any engine:
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- Add changes in save and load database functions to load and save arrays and lists into the instances dataframe
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- Add methods to manager:
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- Add changes:
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- Add comment
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- set the simulation engine in order to use the pmb method to determine reservoir concentrations
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- set simulation engine before executing the tests
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- Set simulation engine before executing the tests remove espresso system from setup_lj interactions
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- Add simulation engine in both tests
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- Add simulation engine before executing the handy functions as now they are migrated to espresso_engine class
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- 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…
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Commits on May 11, 2026
- Adapt sample file to current version decoupling espresso
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- Adapt current sample files towards decoupling espresso
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- remove espresso_system as an input from methods migrated from handy functions
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- Adapt test_handy_functions towards decoupling espresso
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- Adapt changes to decoupling espresso from pymbe
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Commits on May 14, 2026
- Add modifications to adapt sample script to espresso decoupling
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- Add changes to pymbe_tutorial
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- Merge branch 'main' into CheckThisFeature
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- Decouple create_angular_potential,generate_angles_for_entity,
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- Add method add_angle, _create_angle_instance and _get_angle_instance.
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- include in io.py _load_database and _save_database added_to_engine for the pmb_type angle
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- Adapt angle tests to decouple it from espresso
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- Add as pmb_type "angle" with attributes particle_id1,particle_id2 and particle_id3 and added_to_engine
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- Add added_to_engine in AngleInstance data class
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- Adapt test hydrogel_builder_with_angles
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- Adapt test_lattice_setup
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- Adapt to decouple from espresso method test_io_instances
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Commits on May 18, 2026
- A commit
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Commits on Jun 10, 2026
- Add box_l argument to _create_hydrogel_chain
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Commits on Jun 22, 2026
- Fix box_l size to match a diamond lattice of monomer chains that contain mpc monomer + 2 nodes
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- Modify test so that the expected result is expressed in terms of magnitude instead of reduced length, because now the backbone vector in the polymeric chain between nodes is not normalized
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Commits on Jun 24, 2026
- Calculate the resulting quantity of the chain length in reduced units instead of using the magnitude
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Commits on Jun 30, 2026
- Delete unused imports.
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- use np.prod(box_l) to replace box_l[0]*box_l[1]*box_l[2]
  
  jorch28
  and
  jngrad
  authored
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- Add Copyright Notes
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- Clear pymbe_tutorial outputs
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Commits on Jul 1, 2026
- Delete data.csv
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- Add DummyEngine with __getattr__ dunder method to raise RuntimeError
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- Use __getattr__ to setup not ImplementedError for LammpsSimulationEngine
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- remove unused variable espresso_local_system
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- Add LammpsSimulationEngine that Raises a not ImplementedError
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- Add a DummyEngine instantiated by default in pyMBE.
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Commits on Jul 2, 2026
- added jordi to author list, update changelog
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- Merge branch 'main' into CheckThisFeature
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- Add facade method to lammps engine to comply with the interface contract
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- Delete files from titration simulations
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Commits on Jul 3, 2026
Commits on Jul 10, 2026
Commits on Jul 16, 2026
- LAMMPS testsuite
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Commits on Aug 13, 2026
- address review coments, minor code cosmetic changes
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- Remove duplicated functions
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- remove all duplicated functions from handy functions, remove custom deprecation warnings, reach full coverage, add docs to tests
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- fix bug in centering molecules, remove unnecesary test
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  f5effe7
- fix issue in test
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  bf9743c
- Cleanup
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Commits

Commits on Apr 8, 2026

Commits on Apr 9, 2026

Commits on Apr 16, 2026

Commits on Apr 30, 2026

Commits on May 9, 2026

Commits on May 11, 2026

Commits on May 14, 2026

Commits on May 18, 2026

Commits on Jun 10, 2026

Commits on Jun 22, 2026

Commits on Jun 24, 2026

Commits on Jun 30, 2026

Commits on Jul 1, 2026

Commits on Jul 2, 2026

Commits on Jul 3, 2026

Commits on Jul 10, 2026

Commits on Jul 16, 2026

Commits on Aug 13, 2026