Cassandra gmso (mosdef-hub#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 mosdef-hub#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 (mosdef-hub#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 (mosdef-hub#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]>
chrisjonesBSU · Sep 22, 2023 · 7537899 · 7537899
1 parent ff94811
commit 7537899
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Showing 11 changed files with 834 additions and 234 deletions.
diff --git a/gmso/formats/mcf.py b/gmso/formats/mcf.py
diff --git a/gmso/lib/jsons/FixedAnglePotential.json b/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"
+  }
+}
diff --git a/gmso/lib/jsons/FixedBondPotential.json b/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"
+  }
+}
diff --git a/gmso/tests/base_test.py b/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

diff --git a/gmso/tests/files/ethane-rigid.xml b/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>
diff --git a/gmso/tests/files/ethylene.xml b/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>

diff --git a/gmso/tests/files/tip3p-rigid.xml b/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>