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Support list of parameter values in Forcefield XML #681

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Jul 28, 2022
Merged

Support list of parameter values in Forcefield XML #681

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f990002
Support list of parameter values in Forcefield XML
umesh-timalsina Jul 25, 2022
4b60bbd
fix indentation for aesthetic purpose
daico007 Jul 28, 2022
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53 changes: 53 additions & 0 deletions gmso/tests/files/sequence_of_parameters_ff.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
<ForceField version="0.0.0" name="Flexible carbon">
<FFMetaData>
<Units energy="kJ/mol" distance="nm" mass="amu" charge="coulomb"/>
</FFMetaData>
<AtomTypes expression="4*epsilon*((sigma/r)**12 - (sigma/r)**6)">
<ParametersUnitDef parameter="sigma" unit="nm"/>
<ParametersUnitDef parameter="epsilon" unit="kJ/mol"/>
<AtomType name="C" element="C" charge="0.0" mass="12.011" definition="C" description="Generic sp2 carbon">
<Parameters>
<Parameter name="sigma" value="0.339966950842"/>
<Parameter name="epsilon" value="0.359824"/>
</Parameters>
</AtomType>
</AtomTypes>
<BondTypes expression="0.5 * k * (r-r_eq)**2">
<ParametersUnitDef parameter="r_eq" unit="nm"/>
<ParametersUnitDef parameter="k" unit="kJ/(mol*nm**2)"/>
<BondType name="BondType1" type1='C' type2='C'>
<Parameters>
<Parameter name='r_eq' value="0.1324"/>
<Parameter name='k' value="493460.96"/>
</Parameters>
</BondType>
</BondTypes>
<AngleTypes expression="0.5 * k * (theta-theta_eq)**2">
<ParametersUnitDef parameter="theta_eq" unit="radian"/>
<ParametersUnitDef parameter="k" unit="kJ/(mol*radian**2)"/>
<AngleType name="AngleType1" type1='C' type2='C' type3="C">
<Parameters>
<Parameter name='theta_eq' value="2.12598556185"/>
<Parameter name='k' value="584.42112"/>
</Parameters>
</AngleType>
</AngleTypes>
<DihedralTypes expression="k * (1 + cos(n * theta - theta_0))">
<ParametersUnitDef parameter="k" unit="kJ/mol"/>
<ParametersUnitDef parameter="n" unit="dimensionless"/>
<ParametersUnitDef parameter="theta_0" unit="radian"/>
<DihedralType name="DihedralType1" type1="" type2="C" type3="C" type4="">
<Parameters>
<Parameter name='k'>
<Value>38</Value>
<Value>45</Value>
</Parameter>
<Parameter name='n' value="2"/>
<Parameter name='theta_0'>
<Value>25</Value>
<Value>32</Value>
</Parameter>
</Parameters>
</DihedralType>
</DihedralTypes>
</ForceField>
8 changes: 8 additions & 0 deletions gmso/tests/test_forcefield.py
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Original file line number Diff line number Diff line change
Expand Up @@ -634,3 +634,11 @@ def test_write_xml(self, opls_ethane_foyer):
def test_write_not_xml(self, opls_ethane_foyer):
with pytest.raises(ForceFieldError):
opls_ethane_foyer.xml("bad_path")

def test_valid_sequence(self):
for j in range(10):
ff = ForceField(get_path("sequence_of_parameters_ff.xml"), "r")
dih_with_list = ff.dihedral_types["*~C~C~*"]
params = dih_with_list.get_parameters()
assert u.allclose_units(params["theta_0"], [25, 32] * u.radian)
assert u.allclose_units(params["k"], [38, 45] * u.kJ / u.mol)
20 changes: 19 additions & 1 deletion gmso/utils/ff_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import os
import re

import numpy as np
import unyt as u
from lxml import etree
from sympy import sympify
Expand Down Expand Up @@ -70,7 +71,24 @@ def _parse_params_values(parent_tag, units_dict, child_tag, expression=None):
)
param_name = param.attrib["name"]
param_unit = units_dict[param_name]
param_value = u.unyt_quantity(float(param.attrib["value"]), param_unit)
if param.attrib.get("value"):
param_value = u.unyt_quantity(
float(param.attrib["value"]), param_unit
)
else:
children = param.getchildren()
if len(children) == 0:
raise ForceFieldParseError(
f"Neither a single value nor a sequence of values "
f"is specified for parameter {param_name}, please specify "
f"either a single value as an attribute value or a sequence "
f"of values."
)
value_array = np.array(
[value.text for value in children], dtype=float
)
param_value = u.unyt_array(value_array, param_unit)

params_dict[param_name] = param_value
param_ref_dict = units_dict
if child_tag == "DihedralType":
Expand Down
5 changes: 4 additions & 1 deletion gmso/utils/schema/ff-gmso.xsd
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Original file line number Diff line number Diff line change
Expand Up @@ -193,8 +193,11 @@
<xsd:sequence>
<xsd:element name="Parameter" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="Value" minOccurs="0" maxOccurs="unbounded" type="xsd:float"/>
</xsd:sequence>
<xsd:attribute name="name" use="required" type="xsd:string"/>
<xsd:attribute name="value" use="required" type="xsd:float"/>
<xsd:attribute name="value" use="optional" type="xsd:float"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
Expand Down