Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Support list of parameter values in Forcefield XML #681

Merged
merged 2 commits into from
Jul 28, 2022
Merged

Support list of parameter values in Forcefield XML #681

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f990002
Support list of parameter values in Forcefield XML
umesh-timalsina Jul 25, 2022
4b60bbd
fix indentation for aesthetic purpose
daico007 Jul 28, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
54 changes: 54 additions & 0 deletions gmso/tests/files/sequence_of_parameters_ff.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
<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
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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