Open
Description
Description
Interchange instances created from a Topology containing any number of water molecules (including just 1) and from the SMIRNOFF TIP3P force field cannot be written to LAMMPS input/data files using Interchange.to_lammps(), "citing unsupported constraints in the LAMMPS writer".
Incidentally (unless I've misunderstood what's going on), Interchange creation does NOT use TIP3P library charges supplied by the FF, but rather assigns explicit AM1-BCC charges. This is evidenced by the telltale Resolved in #1144Warning: Cannot perform Hydrogen sampling with GPU-Omega: GPU-Omega disabled. log message generated by the OpenEye charge model when calling ForceField.create_interchange(...).
Reproduction
from openff.toolkit import Molecule, ForceField
offmol = Molecule.from_smiles('O')
offmol.generate_conformers(n_conformers=1)
ff = ForceField('tip3p.offxml')
inc = ff.create_interchange(offmol.to_topology())
inc.to_lammps(prefix='water')Output
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
Cell In[2], line 10
7 ff = ForceField('tip3p.offxml')
8 inc = ff.create_interchange(offmol.to_topology())
---> 10 inc.to_lammps(prefix='water')
File ~/miniconda3/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/components/interchange.py:474, in Interchange.to_lammps(self, prefix)
472 datafile_path = prefix + ".lmp"
473 self.to_lammps_datafile(datafile_path)
--> 474 self.to_lammps_input(
475 prefix + "_pointenergy.in",
476 datafile_path,
477 )
File ~/miniconda3/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/components/interchange.py:511, in Interchange.to_lammps_input(self, file_path, data_file)
508 data_file = Path(file_path).with_suffix(".lmp")
510 mdconfig = MDConfig.from_interchange(self)
--> 511 mdconfig.write_lammps_input(self, str(file_path), data_file=str(data_file))
File ~/miniconda3/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/components/mdconfig.py:271, in MDConfig.write_lammps_input(self, interchange, input_file, data_file)
250 return (
251 {
252 key
(...)
264 },
265 )
267 # zero-indexed here
268 (
269 constrained_bond_coeffs,
270 constrained_angle_coeffs,
--> 271 ) = _get_coeffs_of_constrained_bonds_and_angles(interchange)
273 # Construct the input file in memory so nothing is written to disk if an
274 # error is encountered.
275 with StringIO() as lmp:
File ~/miniconda3/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/components/mdconfig.py:238, in MDConfig.write_lammps_input.<locals>._get_coeffs_of_constrained_bonds_and_angles(interchange)
235 constraint_styles = {key.associated_handler for key in interchange["Constraints"].potentials}
237 if len(constraint_styles.difference({"Bonds", "Angles"})) > 0:
--> 238 raise NotImplementedError(
239 "Found unsupported constraints case in LAMMPS input writer.",
240 )
242 constrained_bond_smirks = {
243 key.id for key in interchange["Constraints"].potentials if key.associated_handler == "Bonds"
244 }
246 constrained_angle_smirks = {
247 key.id for key in interchange["Constraints"].potentials if key.associated_handler == "Angles"
248 }
NotImplementedError: Found unsupported constraints case in LAMMPS input writer.
Software versions
- OS: Ubuntu 20.04.6 LTS
- Interchange installed via mamba. Using openff.interchange 0.4.0 and openff.toolkit 0.16.7, running Python 3.11.11
- Output of
conda list:
# packages in environment at /home/timber/miniconda3/envs/nrel-polymers:
#
# Name Version Build Channel
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argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
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arpack 3.8.0 nompi_h0baa96a_101 conda-forge
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