ISISNeutronMuon/MDMC

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A pilot version of the second iteration of MDMC to refine against simple datasets (e.g. water)

Stars: 4
Forks: 0
Open beginner issues: 0
Indexed issues: 156
Avg merge: 2d 4h
Merged PRs (30d): 5

Dominant language: Python
License: GPL-3.0
Last GitHub push: Sep 11, 2026
Latest indexed: Sep 17, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Open All

156 open issues indexed

Add time correlation control Open

enhancement needs more info P1

ISISNeutronMuon/MDMC#9 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Change trajectory format for test_SQw system test Open

P0 refactor

ISISNeutronMuon/MDMC#18 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Change SQw to accommodate ensembles other than NVE/NVT Open

enhancement P2

ISISNeutronMuon/MDMC#69 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Change implementation of Parameter tying Open

P1 refactor

ISISNeutronMuon/MDMC#87 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Extract all Interaction classes from MD.structural_unit Open

P2 refactor

ISISNeutronMuon/MDMC#125 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Exclude water from max number of bonds calculation Open

P1 refactor

ISISNeutronMuon/MDMC#127 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deepcopy Molecule results in different interaction order in Atom Open

bug P2

ISISNeutronMuon/MDMC#128 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Implement Listener pattern for Interaction updates Open

needs more info P1 refactor

ISISNeutronMuon/MDMC#133 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add disp.atoms to test_init_dispersion Open

P1 testing

ISISNeutronMuon/MDMC#134 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add error checking to LAMMPS kspace solver setting Open

enhancement P1

ISISNeutronMuon/MDMC#145 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Approximate SHAKE and RATTLE in LAMMPSEngine.minimize Open

enhancement P0

ISISNeutronMuon/MDMC#160 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add system test for LAMMPS trajectory conversion Open

P1 testing

ISISNeutronMuon/MDMC#162 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add log.lammps unit tests Open

enhancement P2 testing

ISISNeutronMuon/MDMC#165 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Extract convert_unit function out of lammps_engine.py into MD engine common module Open

enhancement P1

ISISNeutronMuon/MDMC#166 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
StructuralUnit Universe can be set during initialisation Open

enhancement P1

ISISNeutronMuon/MDMC#169 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Reorder properties, magic methods, public and private methods in classes Open

good first issue P1 refactor

ISISNeutronMuon/MDMC#202 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Inherit base class docstrings for properties and methods with different implementations Open

documentation enhancement P1

ISISNeutronMuon/MDMC#204 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Make obs automatically determine the file reader from the extension/file format Open

enhancement P2

ISISNeutronMuon/MDMC#206 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add in ID setting for StructuralUnit Open

enhancement P2

ISISNeutronMuon/MDMC#207 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Error thrown when trying to set charge to None of an Atom with charge None and Coulombic interaction. Open

bug P1

ISISNeutronMuon/MDMC#213 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Should num_density in Universe.fill() be consistent with density in Universe.solvate() ? Open

P0 question

ISISNeutronMuon/MDMC#221 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add delete_structural_unit method to Universe Open

enhancement P1

ISISNeutronMuon/MDMC#229 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Adding an Atom of atom_type that has already had a Coulombic interaction initialised should add that Atom to the universe's Coulombic interaction. Open

bug P3

ISISNeutronMuon/MDMC#234 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Should the user be able to pass just total (solute + solvent) density, or solvent density also as a parameter to Universe.solvate() ? Open

enhancement P1

ISISNeutronMuon/MDMC#243 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Change the relationship between fixed and tie attributes of Parameter Open

bug P3

ISISNeutronMuon/MDMC#245 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Automatically determine Minimizer max parameter change Open

enhancement P2

ISISNeutronMuon/MDMC#262 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Should MDMC use the unrestricted 'hybrid/overlay' pair_style command? Open

LAMMPS Interface P1 question

ISISNeutronMuon/MDMC#285 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add tests for LAMMPS pair_modify Open

LAMMPS Interface P1 testing

ISISNeutronMuon/MDMC#314 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Document which options can be used by which MD engine Open

documentation P1

ISISNeutronMuon/MDMC#335 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Sphinx can't generate html for static abstract propert docstring Open

bug documentation P0

ISISNeutronMuon/MDMC#416 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Wrong GUI visualistion from docker-Jupyter with different multiple monitors Open

bug P1

ISISNeutronMuon/MDMC#422 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Make building documentation on Windows easier Open

Maintenance P1

ISISNeutronMuon/MDMC#425 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
docstring code examples displayed incorrectly Open

bug documentation P3

ISISNeutronMuon/MDMC#458 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Redirect PyLammps stdout message Open

bug iceboxed LAMMPS Interface

ISISNeutronMuon/MDMC#471 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Dynamic plots increase in size after refinement completion in some environments Open

bug P2

ISISNeutronMuon/MDMC#472 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Doc page for: Onboarding new member Open

documentation good first issue P1

ISISNeutronMuon/MDMC#485 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Investigate and comment on huge deviation of pressure in systemtest Open

testing

ISISNeutronMuon/MDMC#490 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Test threading with MDMC on IDAaaS platform and compared to running on local PC Open

LAMMPS Interface P3 question testing

ISISNeutronMuon/MDMC#506 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Investigate size of MDMC logs Open

P2 question

ISISNeutronMuon/MDMC#511 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Use mdanalysis with MDMC in some way? Open

enhancement P1

ISISNeutronMuon/MDMC#560 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Handling of different temperatures, isotopes, pressure, instruments etc Open

enhancement P1

ISISNeutronMuon/MDMC#595 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add force field refinement test and nightly CI testing setup Open

good first issue P4 testing

ISISNeutronMuon/MDMC#598 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Verify / reproduce Argon results from MDMC Fortran version Open

P4 testing

ISISNeutronMuon/MDMC#621 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
LAMMPS with MDMC on GPU Open

enhancement P2

ISISNeutronMuon/MDMC#629 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Simulate / reproduce details of the A. A. van Well Argon dataset Open

P4 testing

ISISNeutronMuon/MDMC#636 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Remove relative links to some or all images in Jupyter tutorials Open

documentation P1

ISISNeutronMuon/MDMC#654 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
create ansible playbook for configuring dev environments Open

enhancement P3

ISISNeutronMuon/MDMC#659 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Add direnv support Open

enhancement P0

ISISNeutronMuon/MDMC#713 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Developer documentation for how to test for memory bugs Open

documentation P2

ISISNeutronMuon/MDMC#716 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
create roadmap for integrating clayff Open

enhancement iceboxed P1

ISISNeutronMuon/MDMC#734 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026

ISISNeutronMuon/MDMC

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