Cleanup TinkerReader, ForceField, and amoebaforces (#5080)

* Fresh branch refactoring the new AMOEBA code

* Finish cleaning up AmoebaAngleForce and AmoebaInPlaneAngleForce

* Cleanup AmoebaTorsionTorsionForce

* Cleanup AmoebaOutOfPlaneBend

* Cleanup AmoebaMultipoleForce

* Remove unnecessary gkForce

* Simplify usage of atomClasses in ForceField

* Formatting

* Fix type of class on WCA

* Simplify angle forces

* Add parsing of units to PiTorsion and StretchBond, and misc. formatting adjustments

* Update code per review feedback

* Clearly defined API for TorsionTorsion,  and correct matching for UB,

* Unindent break statements

* Raise ValueError if classes and types are mixed in a Urey-Bradley term definition

wrappers/python/tests/TestForceField.py

@@ -1958,12 +1958,12 @@ class AmoebaTestForceField(unittest.TestCase):
 
         # Compare to values computed with Tinker.
 
-        self.assertAlmostEqual(290.2445, energies['AmoebaBond'], 4)
-        self.assertAlmostEqual(496.4300, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4)
-        self.assertAlmostEqual(51.2913, energies['AmoebaOutOfPlaneBend'], 4)
-        self.assertAlmostEqual(5.7695, energies['AmoebaStretchBend'], 4)
+        self.assertAlmostEqual(290.2445, energies['AmoebaBondForce'], 4)
+        self.assertAlmostEqual(496.4300, energies['AmoebaAngleForce']+energies['AmoebaInPlaneAngleForce'], 4)
+        self.assertAlmostEqual(51.2913, energies['AmoebaOutOfPlaneBendForce'], 4)
+        self.assertAlmostEqual(5.7695, energies['AmoebaStretchBendForce'], 4)
         self.assertAlmostEqual(75.6890, energies['PeriodicTorsionForce'], 4)
-        self.assertAlmostEqual(19.3364, energies['AmoebaPiTorsion'], 4)
+        self.assertAlmostEqual(19.3364, energies['AmoebaPiTorsionForce'], 4)
         self.assertAlmostEqual(-32.6689, energies['AmoebaTorsionTorsionForce'], 4)
         self.assertAlmostEqual(383.8705, energies['AmoebaVdwForce'], 4)
         self.assertAlmostEqual(-1323.5640-225.3660, energies['AmoebaMultipoleForce'], 2)
@@ -1975,14 +1975,14 @@ class AmoebaTestForceField(unittest.TestCase):
 
         # Compare to values computed with Tinker.
 
-        self.assertAlmostEqual(749.6953, energies['AmoebaBond'], 4)
-        self.assertAlmostEqual(579.9971, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4)
-        self.assertAlmostEqual(10.6630, energies['AmoebaOutOfPlaneBend'], 4)
-        self.assertAlmostEqual(5.2225, energies['AmoebaStretchBend'], 4)
+        self.assertAlmostEqual(749.6953, energies['AmoebaBondForce'], 4)
+        self.assertAlmostEqual(579.9971, energies['AmoebaAngleForce']+energies['AmoebaInPlaneAngleForce'], 4)
+        self.assertAlmostEqual(10.6630, energies['AmoebaOutOfPlaneBendForce'], 4)
+        self.assertAlmostEqual(5.2225, energies['AmoebaStretchBendForce'], 4)
         self.assertAlmostEqual(166.7233, energies['PeriodicTorsionForce'], 4)
-        self.assertAlmostEqual(57.2066, energies['AmoebaPiTorsion'], 4)
-        self.assertAlmostEqual(-4.2538, energies['AmoebaStretchTorsion'], 4)
-        self.assertAlmostEqual(-5.0402, energies['AmoebaAngleTorsion'], 4)
+        self.assertAlmostEqual(57.2066, energies['AmoebaPiTorsionForce'], 4)
+        self.assertAlmostEqual(-4.2538, energies['AmoebaStretchTorsionForce'], 4)
+        self.assertAlmostEqual(-5.0402, energies['AmoebaAngleTorsionForce'], 4)
         self.assertAlmostEqual(187.1103, energies['AmoebaVdwForce'], 4)
         self.assertAlmostEqual(1635.1289-236.1484, energies['AmoebaMultipoleForce'], 3)
         self.assertAlmostEqual(3146.3046, sum(list(energies.values())), 3)

wrappers/python/tests/TestTinkerFiles.py

@@ -14,8 +14,6 @@ class TestTinkerFiles(unittest.TestCase):
             polarization="mutual",
             mutualInducedTargetEpsilon=1e-5,
             nonbondedMethod=NoCutoff,
-            constraints=None,
-            useDispersionCorrection=False,
         )
 
         # Compute the energy with OpenMM.
@@ -91,10 +89,10 @@ class TestTinkerFiles(unittest.TestCase):
         energies, _, _ = self.computeAmoebaEnergies(xyzFile, keyFiles)
 
         # Compare to values computed with Tinker.
-        self.assertEnergyEqual(1104.0455, energies["AmoebaBond"])
-        self.assertEnergyEqual(602.7082, energies["AmoebaAngle"] + energies["AmoebaInPlaneAngle"])
-        self.assertEnergyEqual(2.0572, energies["AmoebaOutOfPlaneBend"], 1e-4)
-        self.assertEnergyEqual(-0.1361, energies["AmoebaStretchBend"], 1e-3)
+        self.assertEnergyEqual(1104.0455, energies["AmoebaBondForce"])
+        self.assertEnergyEqual(602.7082, energies["AmoebaAngleForce"] + energies["AmoebaInPlaneAngleForce"])
+        self.assertEnergyEqual(2.0572, energies["AmoebaOutOfPlaneBendForce"], 1e-4)
+        self.assertEnergyEqual(-0.1361, energies["AmoebaStretchBendForce"], 1e-3)
         self.assertEnergyEqual(-0.8625, energies["PeriodicTorsionForce"], 1e-4)
         self.assertEnergyEqual(-33.8595, energies["HarmonicBondForce"])
         self.assertEnergyEqual(5908.1343, energies["AmoebaVdwForce"])
@@ -156,12 +154,12 @@ class TestTinkerFiles(unittest.TestCase):
                             'LYS', 'ARG'], f'Unexpected residues: {residues}'
 
         # Compare to values computed with Tinker.
-        self.assertEnergyEqual(19.6519, energies["AmoebaBond"])
-        self.assertEnergyEqual(58.2509, energies["AmoebaAngle"] + energies["AmoebaInPlaneAngle"])
-        self.assertEnergyEqual(1.9697, energies["AmoebaOutOfPlaneBend"], 1e-4)
-        self.assertEnergyEqual(-0.4384, energies["AmoebaStretchBend"], 1e-3)
+        self.assertEnergyEqual(19.6519, energies["AmoebaBondForce"])
+        self.assertEnergyEqual(58.2509, energies["AmoebaAngleForce"] + energies["AmoebaInPlaneAngleForce"])
+        self.assertEnergyEqual(1.9697, energies["AmoebaOutOfPlaneBendForce"], 1e-4)
+        self.assertEnergyEqual(-0.4384, energies["AmoebaStretchBendForce"], 1e-3)
         self.assertEnergyEqual(-2.3514, energies["PeriodicTorsionForce"], 1e-4)
-        self.assertEnergyEqual(1.2115, energies["AmoebaPiTorsion"], 1e-4)
+        self.assertEnergyEqual(1.2115, energies["AmoebaPiTorsionForce"], 1e-4)
         self.assertEnergyEqual(-3.2958, energies["AmoebaTorsionTorsionForce"])
         self.assertEnergyEqual(1509.1915, energies["AmoebaVdwForce"])
         self.assertEnergyEqual(-488.0403 - 110.9042, energies["AmoebaMultipoleForce"], 1e-3)
@@ -224,14 +222,14 @@ class TestTinkerFiles(unittest.TestCase):
                             'G', 'C', 'G', 'U', 'U', 'A', 'A', 'G', 'U', 'C', 'G', 'C', 'A'], f'Unexpected residues: {residues}'
 
         # Compare to values computed with Tinker.
-        self.assertEnergyEqual(749.6953, energies["AmoebaBond"])
-        self.assertEnergyEqual(579.9971, energies["AmoebaAngle"] + energies["AmoebaInPlaneAngle"])
-        self.assertEnergyEqual(10.6630, energies["AmoebaOutOfPlaneBend"])
-        self.assertEnergyEqual(5.2225, energies["AmoebaStretchBend"])
+        self.assertEnergyEqual(749.6953, energies["AmoebaBondForce"])
+        self.assertEnergyEqual(579.9971, energies["AmoebaAngleForce"] + energies["AmoebaInPlaneAngleForce"])
+        self.assertEnergyEqual(10.6630, energies["AmoebaOutOfPlaneBendForce"])
+        self.assertEnergyEqual(5.2225, energies["AmoebaStretchBendForce"])
         self.assertEnergyEqual(166.7233, energies["PeriodicTorsionForce"])
-        self.assertEnergyEqual(57.2066, energies["AmoebaPiTorsion"])
-        self.assertEnergyEqual(-4.2538, energies["AmoebaStretchTorsion"])
-        self.assertEnergyEqual(-0.0880, energies["AmoebaAngleTorsion"], 1e-4)
+        self.assertEnergyEqual(57.2066, energies["AmoebaPiTorsionForce"])
+        self.assertEnergyEqual(-4.2538, energies["AmoebaStretchTorsionForce"])
+        self.assertEnergyEqual(-0.0880, energies["AmoebaAngleTorsionForce"], 1e-4)
         self.assertEnergyEqual(187.1103, energies["AmoebaVdwForce"])
         self.assertEnergyEqual(1635.1289 - 236.1484, energies["AmoebaMultipoleForce"])
         self.assertEnergyEqual(3151.2568, sum(list(energies.values())))