Draft: add support for nanoparticle models#148
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pm-blanco wants to merge 84 commits intopyMBE-dev:mainfrom
Open
Draft: add support for nanoparticle models#148pm-blanco wants to merge 84 commits intopyMBE-dev:mainfrom
pm-blanco wants to merge 84 commits intopyMBE-dev:mainfrom
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… unit for pymbe_library.get_radius_map()
…ke more robust. Remove unnecessary pieces of code in pyMBE (assign_molecule and get_type_map)
…emove verbose optional arguments
…distribution of sites and two different kinds of sites (one main site and a secondary site)
…create_nanoparticle(), specifically: reading data from pmb.df and creating the center of the nanoparticles
…or uniformly distributing points on a sphere pmb.uniform_distribution_sites_on_sphere(). First draft of the fucntion create_patches()
…f main sites. Need to be fully tested and add the secondary sites to the output list
…he secondary patch implemented, but not working properly. Final report of the construction working.
… Implementation of the calculation of distances between sites and dipole and quadrupole moments. Improving docs of auxiliary functions and readability of the code.
…emplates with nested residues, continue refactoring samples
Co-authored-by: pinedaps <sebastian.pineda_pineda@chem.lu.se>
Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
…rticles. Updating the code to the new database format of pyMBE Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
… instance logic Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
…e_nanoparticle Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
…unning fine Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
Co-authored-by: Sebastian Pineda <pinedaps@chem.lu.se>
Co-authored-by: Sebastian Pineda <pinedaps@chem.lu.se>
Co-authored-by: Sebastian Pineda <pinedaps@chem.lu.se>
4 tasks
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Closes #144
Added
NanoparticleTemplateandNanoparticleInstance.pmb.define_nanoparticleandpmb.create_nanoparticleto define and build nanoparticles with configurable core particles and surface site composition.pyMBE.lib.nanoparticle_toolsfor spherical site distribution, patch construction, and overlap checks.samples/nanoparticles_grxmc.pyto demonstrate nanoparticle setup and simulation workflows.testsuite/nanoparticle_unit_tests.py) and coverage for nanoparticle-related code paths.Changed
pmb.create_nanoparticle.Fixed