Cassandra gmso (#756)

* Add fixed length bonds and angles to potential templates library.

* Working to make MCF writer feature complete. Tests in progress.

* Add fixed angle support
* Fix charge sign error (gmso-wide)
* Update ring identification to handle fused systems (mbuild #744)
* Increase floating point accuracy
* Increase element type length and atom type length
* Correctly write atom indices for bonds/angles/dihedrals/impropers

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Add dimensions to Fixed Bond and Angle templates

* Update keys in OPLS dihedral parameters dict

* Modify dihedral constant indexing from k0 to k3
to k1 to k4 in the OPLSTorsionPotential template.

* Fix typed OPLS ethane test for MCF format

* Updated from old Mie Xenon test to OPLS ethane.
* Remove assertions related to n and m parameters of the Mie potential.
* Fix floating point format issues in MCF writer.

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Add typed ethane test.

This test is not complete yet. The 1/2 factor
in the angles and OPLS dihedral is not
accounted for.

* Fix code style

* Add fixture to parse mcf into sections

* Support Pydantic v1 and v2 (#752)

Co-authored-by: Co Quach <[email protected]>

* Update MCF with GMSO builtin top site sorting

* Use PotentialFilters to check for unique atomtypes

* Add test to check charge neutrality

* Add test for incompatible expressions

* Test full MCF for Mie-Xe and LJ-Ar

* Check charge neutrality in each molecule test

* Add exception for not neutral system in MCF writer

* Move parsing and neutrality check as utils

* minor docstring/comment fixes, swap out simplify with symengine expand

* [pre-commit.ci] pre-commit autoupdate (#763)

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Test for 0.5 factor of OPLS dihedral potential

* Test to account for 0.5 factor in harmonic angles

* Test for rigid angles using the TIP3P model

* MCF writer test with topology with 10 argon mols

* Tentative output of multiple MCF from one Topology

* Change psi to phi and consts for ethylene xml test

* Test for 0.5 factor in OPLS dihedrals

* Add cassandra test for gmso

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Add test for two atom fragment

* Test for molecule with one ring

* Change nitrogen test to ethane ua

* Add ethane rigid reference xml

* Use Fourier dihedrals as MCF standard dihedrals.

* Fix dihedral type output fourier to opls

* Match MCF GMSO Angle header to mb Angle header

* Add a test comparing gmso and mbuild mcf writers

* Use the Fourier converter for ethylene dihedrals

* Write atom type masses instead of atom masses to account for UA beads

* Output correct case for dihedral styles in MCFs

* Run an energy calculation to compare GMSO and mBuild MCF writers

* Update gmso/tests/test_mcf.py

* Update gmso/tests/test_mcf.py

---------

Co-authored-by: Ryan S. DeFever <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Matt Thompson <[email protected]>
Co-authored-by: Co Quach <[email protected]>
Co-authored-by: Co Quach <[email protected]>
Co-authored-by: CalCraven <[email protected]>

gmso/lib/jsons/FixedAnglePotential.json

@@ -0,0 +1,8 @@
+{
+  "name": "FixedAnglePotential",
+  "expression": "DiracDelta(theta-theta_eq)",
+  "independent_variables": "theta",
+  "expected_parameters_dimensions": {
+    "theta_eq": "angle"
+  }
+}

gmso/lib/jsons/FixedBondPotential.json

@@ -0,0 +1,8 @@
+{
+  "name": "FixedBondPotential",
+  "expression": "DiracDelta(r-r_eq)",
+  "independent_variables": "r",
+  "expected_parameters_dimensions": {
+    "r_eq": "length"
+  }
+}

gmso/tests/base_test.py

@@ -263,6 +263,14 @@ def typed_water_system(self, water_system):
         top = apply(top, ff)
         return top
 
+    @pytest.fixture
+    def typed_tip3p_rigid_system(self, water_system):
+        top = water_system
+        top.identify_connections()
+        ff = ForceField(get_path("tip3p-rigid.xml"))
+        top = apply(top, ff)
+        return top
+
     @pytest.fixture
     def foyer_fullerene(self):
         from foyer.tests.utils import get_fn

gmso/tests/files/ethane-rigid.xml

@@ -0,0 +1,23 @@
+<?xml version='1.0' encoding='UTF-8'?>
+ <ForceField name="nitrogen" version="0.0.1">
+   <FFMetaData electrostatics14Scale="0.0" nonBonded14Scale="0.0" combiningRule="lorentz">
+    <Units energy="kJ/mol" mass="amu" charge="elementary_charge" distance="nm"/>
+  </FFMetaData>
+  <AtomTypes expression="4*epsilon * ((sigma/r)**12 - (sigma/r)**6)">
+    <ParametersUnitDef parameter="epsilon" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="sigma" unit="nm"/>
+    <AtomType name="_CH3" atomclass="_CH3" element="_CH3" charge="0.0" mass="15.0" definition="[_CH3;X1]" description="UA carbon"> <Parameters>
+        <Parameter name="epsilon" value="0.814772"/>
+        <Parameter name="sigma" value="0.375"/>
+      </Parameters>
+    </AtomType>
+  </AtomTypes>
+  <BondTypes expression="DiracDelta(r-r_eq)">
+    <ParametersUnitDef parameter="r_eq" unit="nm"/>
+    <BondType name="BondType-Harmonic-1" type1="_CH3" type2="_CH3">
+      <Parameters>
+        <Parameter name="r_eq" value="0.154"/>
+      </Parameters>
+    </BondType>
+  </BondTypes>
+</ForceField>

gmso/tests/files/ethylene.xml

@@ -51,21 +51,21 @@
       </Parameters>
     </AngleType>
   </AngleTypes>
-  <DihedralTypes expression="c_0 + c_1 * cos(psi) + c_2 * cos(psi)**2 + c_3 * cos(psi)**3 + c_4 * cos(psi)**4 + c_5 * cos(psi)**5">
-    <ParametersUnitDef parameter="c_0" unit="kJ/mol"/>
-    <ParametersUnitDef parameter="c_1" unit="kJ/mol"/>
-    <ParametersUnitDef parameter="c_2" unit="kJ/mol"/>
-    <ParametersUnitDef parameter="c_3" unit="kJ/mol"/>
-    <ParametersUnitDef parameter="c_4" unit="kJ/mol"/>
-    <ParametersUnitDef parameter="c_5" unit="kJ/mol"/>
+  <DihedralTypes expression="c0 + c1 * cos(phi) + c2 * cos(phi)**2 + c3 * cos(phi)**3 + c4 * cos(phi)**4 + c5 * cos(phi)**5">
+    <ParametersUnitDef parameter="c0" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="c1" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="c2" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="c3" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="c4" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="c5" unit="kJ/mol"/>
     <DihedralType name="DihedralType-RyckaertBellemans-1" type1="opls_144" type2="opls_143" type3="opls_143" type4="opls_144">
       <Parameters>
-        <Parameter name="c_0" value="58.576"/>
-        <Parameter name="c_1" value="0.0"/>
-        <Parameter name="c_2" value="-58.576"/>
-        <Parameter name="c_3" value="0.0"/>
-        <Parameter name="c_4" value="0.0"/>
-        <Parameter name="c_5" value="0.0"/>
+        <Parameter name="c0" value="58.576"/>
+        <Parameter name="c1" value="0.0"/>
+        <Parameter name="c2" value="-58.576"/>
+        <Parameter name="c3" value="0.0"/>
+        <Parameter name="c4" value="0.0"/>
+        <Parameter name="c5" value="0.0"/>
       </Parameters>
     </DihedralType>
   </DihedralTypes>

gmso/tests/files/tip3p-rigid.xml

@@ -0,0 +1,38 @@
+<?xml version='1.0' encoding='UTF-8'?>
+ <ForceField name="TIP3P" version="0.0.1">
+   <FFMetaData electrostatics14Scale="0.5" nonBonded14Scale="0.5" combiningRule="lorentz">
+    <Units energy="kJ/mol" mass="amu" charge="elementary_charge" distance="nm"/>
+  </FFMetaData>
+  <AtomTypes expression="4*epsilon * ((sigma/r)**12 - (sigma/r)**6)">
+    <ParametersUnitDef parameter="epsilon" unit="kJ/mol"/>
+    <ParametersUnitDef parameter="sigma" unit="nm"/>
+    <AtomType name="opls_111" atomclass="OW" element="O" charge="-0.834" mass="16" definition="[O;X2]" description="water O">
+      <Parameters>
+        <Parameter name="epsilon" value="0.636386"/>
+        <Parameter name="sigma" value="0.315061"/>
+      </Parameters>
+    </AtomType>
+    <AtomType name="opls_112" atomclass="HW" element="H" charge="0.417" mass="1.011" definition="[H;X1]" description="water H">
+      <Parameters>
+        <Parameter name="epsilon" value="0.0"/>
+        <Parameter name="sigma" value="1.0"/>
+      </Parameters>
+    </AtomType>
+  </AtomTypes>
+  <BondTypes expression="DiracDelta(r-r_eq)">
+    <ParametersUnitDef parameter="r_eq" unit="nm"/>
+    <BondType name="BondType-Harmonic-1" type1="opls_111" type2="opls_112">
+      <Parameters>
+        <Parameter name="r_eq" value="0.09572"/>
+      </Parameters>
+    </BondType>
+  </BondTypes>
+  <AngleTypes expression="DiracDelta(theta-theta_eq)">
+    <ParametersUnitDef parameter="theta_eq" unit="radian"/>
+    <AngleType name="AngleType-Harmonic-1" type1="opls_112" type2="opls_111" type3="opls_112">
+      <Parameters>
+        <Parameter name="theta_eq" value="1.824218134"/>
+      </Parameters>
+    </AngleType>
+  </AngleTypes>
+</ForceField>