Draft: add support for nanoparticle models#148

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pm-blanco wants to merge 84 commits intopyMBE-dev:mainfrom

pm-blanco:db_nanoparticles

Commits on Mar 11, 2025

Improve coverage of pymbe_library.get_particle_id_map() and make test unit for pymbe_library.get_radius_map()
pinedaps
committed

Commits on Mar 12, 2025

Modification of the test for get_particle_id and get_radius_map to make more robust. Remove unnecessary pieces of code in pyMBE (assign_molecule and get_type_map)
pinedaps
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Solving issues with unusued variable: used_molecules_id
pinedaps
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Added two unit test for the print statements in add_value_to_df()
pinedaps
committed

Commits on Mar 13, 2025

Commits on Mar 19, 2025

Merge branch 'pyMBE-dev:main' into main
pinedaps
authored

Commits on Nov 21, 2025

first draft
pmblanco
committed

Commits on Nov 25, 2025

Database with reactions and states disentangled
pmblanco
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first complete draft of the database for particles
pmblanco
committed

Commits on Nov 28, 2025

Merge branch 'pyMBE-dev:main' into main
pinedaps
authored

Commits on Dec 2, 2025

add all pmb_types
pmblanco
committed

Commits on Dec 3, 2025

clean up and document storage code
pmblanco
committed

Commits on Dec 4, 2025

start refactoring pyMBE to use the new database
pmblanco
committed

Commits on Dec 5, 2025

updated residue and bond management in pyMBE
Pablo
committed

Commits on Dec 6, 2025

finish refactoring of residues, molecules and peptides
Pablo
committed
updated create_protein
Pablo
committed

Commits on Dec 8, 2025

refactor hydrogels
Pablo
committed

Commits on Dec 9, 2025

Commits on Dec 17, 2025

update methods to work with the new database
Pablo
committed

Commits on Dec 23, 2025

Implementation of a simulation of Nanoparticles (NPs) with a uniform distribution of sites and two different kinds of sites (one main site and a secondary site)
Sebastian Pineda
committed

Commits on Dec 25, 2025

pmb.define_nanoparticle implemented, including sanity checks
Sebastian Pineda
committed

Commits on Dec 27, 2025

Improving pmb.define_nanoparticle() and start the development of pmd.create_nanoparticle(), specifically: reading data from pmb.df and creating the center of the nanoparticles
Sebastian Pineda
committed

Commits on Dec 30, 2025

Implementation of the Thomson-like iterative force‑based relaxation for uniformly distributing points on a sphere pmb.uniform_distribution_sites_on_sphere(). First draft of the fucntion create_patc…
Sebastian Pineda
committed

Commits on Dec 31, 2025

Running version of the function create_patch() for the distribution of main sites. Need to be fully tested and add the secondary sites to the output list
Sebastian Pineda
committed

Commits on Jan 2, 2026

Sanity check for overlapping between patches done!. Construction of the secondary patch implemented, but not working properly. Final report of the construction working.
Sebastian Pineda
committed

Commits on Jan 3, 2026

Construction of the secondary patch implemented and working properly. Implementation of the calculation of distances between sites and dipole and quadrupole moments. Improving docs of auxiliary fun…
Sebastian Pineda
committed

Commits on Jan 5, 2026

Polishing function pmb.create_patches()
Sebastian Pineda
committed

Commits on Jan 6, 2026

Creating core and sites particles in the function pmb.create_nanopartice()
Sebastian Pineda
committed

Commits on Jan 10, 2026

fix test for define and create molecules
Pablo
committed

Commits on Jan 11, 2026

modernize molecule tests, start cleaning lj tests
Pablo
committed

Commits on Jan 13, 2026

implement lj templates, fix tests
pmblanco
committed

Commits on Jan 16, 2026

add demo, add functions to load/save the database to the pyMBE API
pmblanco
committed

Commits on Jan 18, 2026

fix unit test
Pablo
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fix bug in create_counterions, fix unittest
Pablo
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update copyright
Pablo
committed

Commits on Jan 20, 2026

disentagle particle states from particle templates
pmblanco
committed

Commits on Jan 21, 2026

fix wrong handling of espresso types and acidity test
pmblanco
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fix molecule position test
pmblanco
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fix test
pmblanco
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fix seed test and load_interaction_parameters
pmblanco
committed

Commits on Jan 22, 2026

add metadata management, small cleanup
pmblanco
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clean up gcmc functional test
pmblanco
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fix bugs in setup bond, fix unittest
pmblanco
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fix net charge test
pmblanco
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fix parameter test
pmblanco
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Commits on Jan 23, 2026

Commits on Jan 24, 2026

fix protein framework and unit test
Pablo
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adapt cpH method
Pablo
committed

Commits on Jan 25, 2026

adapt reaction methods to the new database, fix docs
Pablo
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standarize docs
Pablo
committed

Commits on Jan 28, 2026

clean up repo, fix bug in setup of rigid object
pmblanco
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increase coverage
pmblanco
committed

Commits on Jan 29, 2026

improve coverage, clean docs
pmblanco
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Commits on Jan 30, 2026

add missing test
pmblanco
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increase coverage manager io, fix bug in lj
pmblanco
committed

Commits on Feb 4, 2026

remove dead ends in database io
Pablo
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improve docs
Pablo
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increase coverage of the database manager
Pablo
committed

Commits on Feb 6, 2026

reach full coverage
pmblanco
committed
solve issues detected by pylint
pmblanco
committed
fix bug
pmblanco
committed
solve dependency issues on the CI
pmblanco
committed
fix new bug in unit test
pmblanco
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lower requierements for pydantic to comply with current EESSI
pmblanco
committed

Commits on Feb 9, 2026

Commits on Feb 10, 2026

clean up tutorial
pmblanco
committed
update changelog
pmblanco
committed

Commits on Mar 5, 2026

Merge remote-tracking branch 'sebas/nanoparticles' into db_nanoparticles
pmblanco
committed
Start integrating nanoparticles into the new pyMBE database

pmblanco
and
pinedaps
committed

Commits on Mar 6, 2026

Add nanoparticle template and instance to the database

pmblanco
and
Sebastian Pineda
committed
Create np_aux.py with auxiliary functions for the creations of nanoparticles. Updating the code to the new database format of pyMBE

Pablo
and
Sebastian Pineda
committed
integrate create_nanoparticle into the pyMBE module, add nanoparticle instance logic

pmblanco
and
Sebastian Pineda
committed
Fix bugs in enable_motion_of_rigid_object and integrate it into create_nanoparticle

pmblanco
and
Sebastian Pineda
committed
Adapt sample script to run with molecular interactions, seems to be running fine

pmblanco
and
Sebastian Pineda
committed
Reach full coverage, make CI run

pmblanco
and
Sebastian Pineda
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add docs to the test

pmblanco
and
Sebastian Pineda
committed
add full coverage to the lattice function

pmblanco
and
Sebastian Pineda
committed

Commits on Mar 9, 2026

update changelog
pmblanco
committed