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Add and update conversions for opls and fourier potentials #825

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4 changes: 2 additions & 2 deletions gmso/formats/mcf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
from gmso.lib.potential_templates import PotentialTemplateLibrary
from gmso.utils.compatibility import check_compatibility
from gmso.utils.conversions import (
convert_opls_to_ryckaert,
convert_fourier_to_ryckaert,
convert_ryckaert_to_fourier,
)

Expand Down Expand Up @@ -473,7 +473,7 @@ def _write_dihedral_information(mcf, top):
dihedral_style = "FOURIER"

if dihedral_style == "OPLS":
dihedral.connection_type = convert_opls_to_ryckaert(
dihedral.connection_type = convert_fourier_to_ryckaert(
dihedral.connection_type
)
dihedral.connection_type = convert_ryckaert_to_fourier(
Expand Down
10 changes: 5 additions & 5 deletions gmso/tests/test_internal_conversions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from gmso.lib.potential_templates import PotentialTemplateLibrary
from gmso.tests.base_test import BaseTest
from gmso.utils.conversions import (
convert_opls_to_ryckaert,
convert_fourier_to_ryckaert,
convert_ryckaert_to_fourier,
)

Expand Down Expand Up @@ -81,7 +81,7 @@ def test_invalid_connection_type(self, templates):
)

with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type)
ryckaert_connection_type = convert_fourier_to_ryckaert(opls_connection_type)

Check warning

Code scanning / CodeQL

Variable defined multiple times

This assignment to 'ryckaert_connection_type' is unnecessary as it is [redefined](1) before this value is used.

variables = opls_torsion_potential.independent_variables
expression = "k0+k1+k2+k3+k4+phi"
Expand All @@ -93,7 +93,7 @@ def test_invalid_connection_type(self, templates):
)

with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type)
ryckaert_connection_type = convert_fourier_to_ryckaert(opls_connection_type)

Check notice

Code scanning / CodeQL

Unused local variable

Variable ryckaert_connection_type is not used.

def test_ryckaert_to_fourier(self, templates):
# Pick some RB parameters at random
Expand Down Expand Up @@ -176,7 +176,7 @@ def test_opls_to_ryckaert(self, templates):
)

# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type)
ryckaert_connection_type = convert_fourier_to_ryckaert(opls_connection_type)

# Pick some angles to check
angles = [-2.38, -1.31, -0.44, 0.0, 0.26, 0.92, 1.84, 3.10]
Expand Down Expand Up @@ -231,7 +231,7 @@ def test_double_conversion(self, templates):
)

# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(opls_connection_type)
ryckaert_connection_type = convert_fourier_to_ryckaert(opls_connection_type)

# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_fourier(ryckaert_connection_type)
Expand Down
73 changes: 54 additions & 19 deletions gmso/utils/conversions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,7 @@

@lru_cache(maxsize=128)
def _constant_multiplier(pot1, pot2):
# TODO: Doc string
# TODO: Test outputs
# TODO: Check speed
"""Take two potentials and check for a difference of a constant multiplier between them."""
try:
constant = symengine.expand(pot1.expression / pot2.expression)
# constant = sympy.simplify(pot1.expression / pot2.expression)
Expand Down Expand Up @@ -70,9 +68,9 @@ def convert_topology_expressions(top, expressionMap={}):
# Apply from predefined conversions or easy sympy conversions
conversions_map = {
(
"OPLSTorsionPotential",
"FourierTorsionPotential",
"RyckaertBellemansTorsionPotential",
): convert_opls_to_ryckaert,
): convert_fourier_to_ryckaert,
(
"RyckaertBellemansTorsionPotential",
"OPLSTorsionPotential",
Expand All @@ -81,6 +79,10 @@ def convert_topology_expressions(top, expressionMap={}):
"RyckaertBellemansTorsionPotential",
"FourierTorsionPotential",
): convert_ryckaert_to_opls,
(
"OPLSTorsionPotential",
"FourierTorsionPotential",
): convert_opls_to_fourier,
} # map of all accessible conversions currently supported

for conv in expressionMap:
Expand Down Expand Up @@ -121,8 +123,8 @@ def convert_topology_expressions(top, expressionMap={}):


@lru_cache(maxsize=128)
def convert_opls_to_ryckaert(opls_connection_type):
"""Convert an OPLS dihedral to Ryckaert-Bellemans dihedral.
def convert_fourier_to_ryckaert(fourier_connection_type):
"""Convert a Foufourier dihedral to Ryckaert-Bellemans dihedral.

Equations taken/modified from:
http://manual.gromacs.org/documentation/2019/
Expand All @@ -133,31 +135,32 @@ def convert_opls_to_ryckaert(opls_connection_type):
phi_cis = 0 while RB torsions are defined as phi_trans = 0.
"""
# TODO: this function really converts the fourier torsion to rb, not opls
opls_torsion_potential = templates["FourierTorsionPotential"]
fourier_torsion_potential = templates["FourierTorsionPotential"]
valid_connection_type = False
if (
opls_connection_type.independent_variables
== opls_torsion_potential.independent_variables
fourier_connection_type.independent_variables
== fourier_torsion_potential.independent_variables
):
if (
sympy.simplify(
opls_connection_type.expression - opls_torsion_potential.expression
fourier_connection_type.expression
- fourier_torsion_potential.expression
)
== 0
):
valid_connection_type = True
if not valid_connection_type:
raise GMSOError(
"Cannot use convert_opls_to_ryckaert "
"Cannot use convert_fourier_to_ryckaert "
"function to convert a ConnectionType that is not an "
"OPLSTorsionPotential"
"FourierTorsionPotential"
)

f0 = opls_connection_type.parameters["k0"]
f1 = opls_connection_type.parameters["k1"]
f2 = opls_connection_type.parameters["k2"]
f3 = opls_connection_type.parameters["k3"]
f4 = opls_connection_type.parameters["k4"]
f0 = fourier_connection_type.parameters["k0"]
f1 = fourier_connection_type.parameters["k1"]
f2 = fourier_connection_type.parameters["k2"]
f3 = fourier_connection_type.parameters["k3"]
f4 = fourier_connection_type.parameters["k4"]

converted_params = {
"c0": (f2 + 0.5 * (f0 + f1 + f3)),
Expand All @@ -179,7 +182,8 @@ def convert_opls_to_ryckaert(opls_connection_type):
expression=expression,
independent_variables=variables,
parameters=converted_params,
member_types=opls_connection_type.member_types,
member_types=fourier_connection_type.member_types,
member_classes=fourier_connection_type.member_classes,
)

return ryckaert_connection_type
Expand Down Expand Up @@ -285,6 +289,37 @@ def convert_ryckaert_to_fourier(ryckaert_connection_type):
return fourier_connection_type


def convert_opls_to_fourier(opls_connection_type):
"""Convert opls dihedrals to Fourier.

NOTE: These only differ by the number of elements. Fourier style has a k0 term.
LAMMPS uses the opls style -> https://docs.lammps.org/dihedral_opls.html.
GROMACS uses the fourier style ->
https://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#proper-dihedrals-fourier-function.
"""

fourier_torsion_potential = templates["FourierTorsionPotential"]
converted_params = {
k: opls_connection_type.parameters.get(k, None)
for k in ["k1", "k2", "k3", "k4"]
}
converted_params["k0"] = 0 * u.kJ / u.mol
name = fourier_torsion_potential.name
expression = fourier_torsion_potential.expression
variables = fourier_torsion_potential.independent_variables

fourier_connection_type = gmso.DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=converted_params,
member_classes=opls_connection_type.member_classes,
member_types=opls_connection_type.member_types,
)

return fourier_connection_type


def convert_kelvin_to_energy_units(
energy_input_unyt,
energy_output_unyt_units_str,
Expand Down