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fixed error in verbose mode for missing dihedrals #335

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merged 3 commits into from
Jun 12, 2020
Merged

fixed error in verbose mode for missing dihedrals #335

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128a7e3
fixed error in verbose mode for missing dihedrals
chrisiacovella Jun 4, 2020
ec94649
Merge remote-tracking branch 'upstream/master' to fix other issues ad…
chrisiacovella Jun 11, 2020
a7c9ce4
merged in additional error messages from ray's PR
chrisiacovella Jun 11, 2020
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34 changes: 25 additions & 9 deletions foyer/forcefield.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,22 +310,38 @@ def _check_dihedrals(data, structure, verbose,
if verbose:
for omm_ids in data.propers:
missing_dihedral = True
for pmd_proper in proper_dihedrals:
pmd_ids = (pmd_proper.atom1.idx, pmd_proper.atom2.idx, pmd_proper.atom3.idx, pmd_proper.atom4.idx)
if pmd_ids == omm_ids:
missing_dihedral = False
for pmd_proper in structure.rb_torsions:
pmd_ids = (pmd_proper.atom1.idx, pmd_proper.atom2.idx, pmd_proper.atom3.idx, pmd_proper.atom4.idx)
if pmd_ids == omm_ids:
missing_dihedral = False
if missing_dihedral:
print('missing improper with ids {}'.format(pmd_ids))
print("Missing dihedral with ids {} and types {}.".format(
omm_ids, [structure.atoms[idx].type for idx in omm_ids]))

if data.propers and len(data.propers) != \
len(proper_dihedrals) + len(structure.rb_torsions):
msg = ("Parameters have not been assigned to all proper dihedrals. "
"Total system dihedrals: {}, Parameterized dihedrals: {}. "
"Note that if your system contains torsions of Ryckaert-"
"Bellemans functional form, all of these torsions are "
"processed as propers.".format(len(data.propers),
len(proper_dihedrals) + len(structure.rb_torsions)))
_error_or_warn(assert_dihedral_params, msg)
len(proper_dihedrals) + len(structure.rb_torsions):
if data.propers and len(data.propers) < \
len(proper_dihedrals) + len(structure.rb_torsions):
msg = ("Parameters have been assigned to all proper dihedrals. "
"However, there are more parameterized dihedrals ({}) "
"than total system dihedrals ({}). "
"This may be due to having multiple periodic dihedrals "
"for a single system dihedral.".format(len(proper_dihedrals) +
len(structure.rb_torsions),
len(data.propers)))
warnings.warn(msg)
else:
msg = ("Parameters have not been assigned to all proper dihedrals. "
"Total system dihedrals: {}, Parameterized dihedrals: {}. "
"Note that if your system contains torsions of Ryckaert-"
"Bellemans functional form, all of these torsions are "
"processed as propers.".format(len(data.propers),
len(proper_dihedrals) + len(structure.rb_torsions)))
_error_or_warn(assert_dihedral_params, msg)

improper_dihedrals = [dihedral for dihedral in structure.dihedrals
if dihedral.improper]
Expand Down