Fix return statement in _parse_coulombic
#744
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| def test_zero_charges(self): | ||
| compound = mb.load("CC", smiles=True) | ||
| com_box = mb.packing.fill_box(compound, box=[5, 5, 5], n_compounds=100) | ||
| base_units = { |
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Additional details and impacted files@@ Coverage Diff @@
## main #744 +/- ##
==========================================
+ Coverage 91.92% 91.95% +0.02%
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Files 67 67
Lines 6815 6815
==========================================
+ Hits 6265 6267 +2
+ Misses 550 548 -2
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emarinri
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Aug 11, 2023
* Add fixed angle support * Fix charge sign error (gmso-wide) * Update ring identification to handle fused systems (mbuild mosdef-hub#744) * Increase floating point accuracy * Increase element type length and atom type length * Correctly write atom indices for bonds/angles/dihedrals/impropers
daico007
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Sep 22, 2023
* Add fixed length bonds and angles to potential templates library. * Working to make MCF writer feature complete. Tests in progress. * Add fixed angle support * Fix charge sign error (gmso-wide) * Update ring identification to handle fused systems (mbuild #744) * Increase floating point accuracy * Increase element type length and atom type length * Correctly write atom indices for bonds/angles/dihedrals/impropers * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add dimensions to Fixed Bond and Angle templates * Update keys in OPLS dihedral parameters dict * Modify dihedral constant indexing from k0 to k3 to k1 to k4 in the OPLSTorsionPotential template. * Fix typed OPLS ethane test for MCF format * Updated from old Mie Xenon test to OPLS ethane. * Remove assertions related to n and m parameters of the Mie potential. * Fix floating point format issues in MCF writer. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add typed ethane test. This test is not complete yet. The 1/2 factor in the angles and OPLS dihedral is not accounted for. * Fix code style * Add fixture to parse mcf into sections * Support Pydantic v1 and v2 (#752) Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com> * Update MCF with GMSO builtin top site sorting * Use PotentialFilters to check for unique atomtypes * Add test to check charge neutrality * Add test for incompatible expressions * Test full MCF for Mie-Xe and LJ-Ar * Check charge neutrality in each molecule test * Add exception for not neutral system in MCF writer * Move parsing and neutrality check as utils * minor docstring/comment fixes, swap out simplify with symengine expand * [pre-commit.ci] pre-commit autoupdate (#763) updates: - [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Test for 0.5 factor of OPLS dihedral potential * Test to account for 0.5 factor in harmonic angles * Test for rigid angles using the TIP3P model * MCF writer test with topology with 10 argon mols * Tentative output of multiple MCF from one Topology * Change psi to phi and consts for ethylene xml test * Test for 0.5 factor in OPLS dihedrals * Add cassandra test for gmso * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test for two atom fragment * Test for molecule with one ring * Change nitrogen test to ethane ua * Add ethane rigid reference xml * Use Fourier dihedrals as MCF standard dihedrals. * Fix dihedral type output fourier to opls * Match MCF GMSO Angle header to mb Angle header * Add a test comparing gmso and mbuild mcf writers * Use the Fourier converter for ethylene dihedrals * Write atom type masses instead of atom masses to account for UA beads * Output correct case for dihedral styles in MCFs * Run an energy calculation to compare GMSO and mBuild MCF writers * Update gmso/tests/test_mcf.py * Update gmso/tests/test_mcf.py --------- Co-authored-by: Ryan S. DeFever <r.s.defever@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matt Thompson <mattwthompson@protonmail.com> Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com> Co-authored-by: Co Quach <daico007@gmail.com> Co-authored-by: CalCraven <nicholas.c.craven@vanderbilt.edu>
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This is a quick fix I noticed when using
convert_hoomd.pyon a topology with no charges._parse_coulombic()returnsNoneif none of the sites have a charge value. This causes an error since the function is called inside of anextendmethod:With lists, passing
Nonetoextend()givesTypeError: 'NoneType' object is not iterableReturning an empty list instead of
Noneseems like the simplest fix. I added a unit test that should have caught this as well.