Draft: add support for nanoparticle models#148
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Co-authored-by: Sebastian Pineda <sebastian.pineda_pineda@chem.lu.se>
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…lt concentration Gradually grows the LJ offset of the nanoparticle core from zero to its Lorentz-Berthelot target value, relaxing the system after each increment. This prevents hard overlaps between the nanoparticle core and salt ions that arise when the full offset is applied immediately at high salt concentrations. Ion sigma and epsilon are now handled consistently through a general variable instead of being hardcoded in each particle definition. Also fixes a pre-existing bug where the Langevin thermostat was left OFF before the production MD loop. Unit tests for the new function are added to nanoparticle_unit_tests.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
thermostat.kT is not available in all ESPResSo versions; replace with thermostat.langevin.is_active which is stable across versions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…; rename template file Refactor the nanoparticle site definition from a float fraction to an integer count per patch, making the physical meaning more explicit and avoiding implicit conversions. The real fraction of primary sites is now a computed output shown by print_nanoparticle_properties() rather than an input parameter. Rename storage/templates/nanoparticle.py to patchy_nanoparticle.py to better reflect the patchy nanoparticle model. Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Store angle_between_patches in NanoparticleTemplate so it is part of the nanoparticle definition rather than a creation-time argument. create_nanoparticle now reads it from the template. The property is included in calculate_nanoparticle_properties only when number_of_patches == 2; for more than two patches the angle is irrelevant as patch centres are distributed at regular polyhedron vertices. This behaviour is documented in the sample script and covered by three new unit tests. Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
The test verified that relax_nanoparticle_overlaps leaves the thermostat off, which is a contract of relax_espresso_system rather than of the nanoparticle function itself. The ESPResSo thermostat API differs across versions, making a portable assertion impossible. Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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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