Merge pull request #2 from peastman/ljpme

More updates to dispersion PME

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -690,7 +690,7 @@ class CharmmPsfFile(object):
             The parameter set to use to parametrize this molecule
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions. Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions.
         switchDistance : distance=0*nanometer
@@ -728,7 +728,7 @@ class CharmmPsfFile(object):
             added to a hydrogen is subtracted from the heavy atom to keep their
             total mass the same.
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if the nonbonded method is Ewald or PME.
+            The error tolerance to use if the nonbonded method is Ewald, PME, or LJPME.
         flexibleConstraints : bool=True
             Are our constraints flexible or not?
         verbose : bool=False
@@ -746,10 +746,10 @@ class CharmmPsfFile(object):
                 cutoff = cutoff.value_in_unit(u.nanometers)
 
         if nonbondedMethod not in (ff.NoCutoff, ff.CutoffNonPeriodic,
-                                   ff.CutoffPeriodic, ff.Ewald, ff.PME):
+                                   ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal value for nonbonded method')
         if not hasbox and nonbondedMethod in (ff.CutoffPeriodic,
-                                              ff.Ewald, ff.PME):
+                                              ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a '
                              'non-periodic system')
         if implicitSolvent not in (HCT, OBC1, OBC2, GBn, GBn2, None):
@@ -1009,6 +1009,8 @@ class CharmmPsfFile(object):
                 force.setNonbondedMethod(mm.NonbondedForce.Ewald)
             elif nonbondedMethod is ff.PME:
                 force.setNonbondedMethod(mm.NonbondedForce.PME)
+            elif nonbondedMethod is ff.LJPME:
+                force.setNonbondedMethod(mm.NonbondedForce.LJPME)
             else:
                 raise ValueError('Cutoff method is not understood')
 
@@ -1088,8 +1090,7 @@ class CharmmPsfFile(object):
                     mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
             cforce.addPerParticleParameter('type')
             cforce.setForceGroup(self.NONBONDED_FORCE_GROUP)
-            if (nonbondedMethod is ff.PME or nonbondedMethod is ff.Ewald or
-                        nonbondedMethod is ff.CutoffPeriodic):
+            if (nonbondedMethod in (ff.PME, ff.LJPME, ff.Ewald, ff.CutoffPeriodic)):
                 cforce.setNonbondedMethod(cforce.CutoffPeriodic)
                 cforce.setCutoffDistance(nonbondedCutoff)
                 cforce.setUseLongRangeCorrection(True)

wrappers/python/simtk/openmm/app/desmonddmsfile.py

@@ -165,11 +165,11 @@ class DesmondDMSFile(object):
         ----------
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if nonbondedMethod is Ewald or PME.
+            The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
         removeCMMotion : boolean=True
             If true, a CMMotionRemover will be added to the System
         hydrogenMass : mass=None
@@ -185,7 +185,7 @@ class DesmondDMSFile(object):
         boxSize = self.topology.getUnitCellDimensions()
         if boxSize is not None:
             sys.setDefaultPeriodicBoxVectors((boxSize[0], 0, 0), (0, boxSize[1], 0), (0, 0, boxSize[2]))
-        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a non-periodic system')
 
         # Create all of the particles
@@ -207,7 +207,8 @@ class DesmondDMSFile(object):
                      ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      ff.Ewald:mm.NonbondedForce.Ewald,
-                     ff.PME:mm.NonbondedForce.PME}
+                     ff.PME:mm.NonbondedForce.PME,
+                     ff.LJPME:mm.NonbondedForce.LJPME}
         nb.setNonbondedMethod(methodMap[nonbondedMethod])
         nb.setCutoffDistance(nonbondedCutoff)
         nb.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/forcefield.py

@@ -115,6 +115,11 @@ class PME(Singleton):
         return 'PME'
 PME = PME()
 
+class LJPME(Singleton):
+    def __repr__(self):
+        return 'LJPME'
+LJPME = LJPME()
+
 # Enumerated values for constraint type
 
 class HBonds(Singleton):
@@ -971,7 +976,7 @@ class ForceField(object):
             The Topology for which to create a System
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         constraints : object=None
@@ -2195,7 +2200,8 @@ class NonbondedGenerator(object):
                      CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      Ewald:mm.NonbondedForce.Ewald,
-                     PME:mm.NonbondedForce.PME}
+                     PME:mm.NonbondedForce.PME,
+                     LJPME:mm.NonbondedForce.LJPME}
         if nonbondedMethod not in methodMap:
             raise ValueError('Illegal nonbonded method for NonbondedForce')
         force = mm.NonbondedForce()
@@ -2307,7 +2313,7 @@ class LennardJonesGenerator(object):
         self.force.addTabulatedFunction('acoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, acoef))
         self.force.addTabulatedFunction('bcoef', mm.Discrete2DFunction(numLjTypes, numLjTypes, bcoef))
         self.force.addPerParticleParameter('type')
-        if nonbondedMethod in [CutoffPeriodic, Ewald, PME]:
+        if nonbondedMethod in [CutoffPeriodic, Ewald, PME, LJPME]:
             self.force.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
         elif nonbondedMethod is NoCutoff:
             self.force.setNonbondedMethod(mm.CustomNonbondedForce.NoCutoff)

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -552,7 +552,7 @@ class GromacsTopFile(object):
         ----------
         nonbondedMethod : object=NoCutoff
             The method to use for nonbonded interactions.  Allowed values are
-            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
         nonbondedCutoff : distance=1*nanometer
             The cutoff distance to use for nonbonded interactions
         constraints : object=None
@@ -570,7 +570,7 @@ class GromacsTopFile(object):
             The solvent dielectric constant to use in the implicit solvent
             model.
         ewaldErrorTolerance : float=0.0005
-            The error tolerance to use if nonbondedMethod is Ewald or PME.
+            The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
         removeCMMotion : boolean=True
             If true, a CMMotionRemover will be added to the System
         hydrogenMass : mass=None
@@ -589,7 +589,7 @@ class GromacsTopFile(object):
         boxVectors = self.topology.getPeriodicBoxVectors()
         if boxVectors is not None:
             sys.setDefaultPeriodicBoxVectors(*boxVectors)
-        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME):
+        elif nonbondedMethod in (ff.CutoffPeriodic, ff.Ewald, ff.PME, ff.LJPME):
             raise ValueError('Illegal nonbonded method for a non-periodic system')
         nb = mm.NonbondedForce()
         sys.addForce(nb)
@@ -877,7 +877,8 @@ class GromacsTopFile(object):
                      ff.CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                      ff.CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                      ff.Ewald:mm.NonbondedForce.Ewald,
-                     ff.PME:mm.NonbondedForce.PME}
+                     ff.PME:mm.NonbondedForce.PME,
+                     ff.LJPME:mm.NonbondedForce.LJPME}
         nb.setNonbondedMethod(methodMap[nonbondedMethod])
         nb.setCutoffDistance(nonbondedCutoff)
         nb.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -776,6 +776,8 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
             force.setNonbondedMethod(mm.NonbondedForce.Ewald)
         elif nonbondedMethod == 'PME':
             force.setNonbondedMethod(mm.NonbondedForce.PME)
+        elif nonbondedMethod == 'LJPME':
+            force.setNonbondedMethod(mm.NonbondedForce.LJPME)
         else:
             raise Exception("Cutoff method not understood.")
 
@@ -885,7 +887,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
             ii, jj, chg, sig, eps = force.getExceptionParameters(i)
             cforce.addExclusion(ii, jj)
         # Now set the various properties based on the NonbondedForce object
-        if nonbondedMethod in ('PME', 'Ewald', 'CutoffPeriodic'):
+        if nonbondedMethod in ('PME', 'LJPME', 'Ewald', 'CutoffPeriodic'):
             cforce.setNonbondedMethod(cforce.CutoffPeriodic)
             cforce.setCutoffDistance(nonbondedCutoff)
             cforce.setUseLongRangeCorrection(True)

wrappers/python/tests/TestAPIUnits.py

@@ -186,6 +186,8 @@ class TestAPIUnits(unittest.TestCase):
         self.assertTrue(force.usesPeriodicBoundaryConditions())
         force.setNonbondedMethod(NonbondedForce.PME)
         self.assertTrue(force.usesPeriodicBoundaryConditions())
+        force.setNonbondedMethod(NonbondedForce.LJPME)
+        self.assertTrue(force.usesPeriodicBoundaryConditions())
 
     def testCmapForce(self):
         """ Tests the CMAPTorsionForce API features """

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -21,12 +21,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
     """Test the AmberPrmtopFile.createSystem() method."""
 
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff,
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic,
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = prmtop1.createSystem(nonbondedMethod=method)
             forces = system.getForces()
@@ -37,7 +39,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = prmtop1.createSystem(nonbondedMethod=method,
                                           nonbondedCutoff=2*nanometer,
                                           constraints=HBonds)
@@ -51,7 +53,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
     def test_EwaldErrorTolerance(self):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
-        for method in [Ewald, PME]:
+        for method in [Ewald, PME, LJPME]:
             system = prmtop1.createSystem(nonbondedMethod=method,
                                           ewaldErrorTolerance=1e-6,
                                           constraints=HBonds)

wrappers/python/tests/TestDesmondDMSFile.py

@@ -14,12 +14,14 @@ class TestDesmondDMSFile(unittest.TestCase):
         self.dms = DesmondDMSFile(path)
     
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic, 
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = self.dms.createSystem(nonbondedMethod=method)
             forces = system.getForces()
@@ -30,7 +32,7 @@ class TestDesmondDMSFile(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = self.dms.createSystem(nonbondedMethod=method, 
                                             nonbondedCutoff=2*nanometer)
             cutoff_distance = 0.0*nanometer
@@ -43,7 +45,7 @@ class TestDesmondDMSFile(unittest.TestCase):
     def test_EwaldErrorTolerance(self):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
-        for method in [Ewald, PME]:
+        for method in [Ewald, PME, LJPME]:
             system = self.dms.createSystem(nonbondedMethod=method,
                                             ewaldErrorTolerance=1e-6)
             tolerance = 0

wrappers/python/tests/TestForceField.py

@@ -33,12 +33,14 @@ class TestForceField(unittest.TestCase):
 
 
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff,
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic,
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = self.forcefield1.createSystem(self.pdb1.topology,
                                                   nonbondedMethod=method)
@@ -62,7 +64,7 @@ class TestForceField(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = self.forcefield1.createSystem(self.pdb1.topology,
                                                    nonbondedMethod=method,
                                                    nonbondedCutoff=2*nanometer,
@@ -776,7 +778,7 @@ class AmoebaTestForceField(unittest.TestCase):
 
 
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test both options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:AmoebaMultipoleForce.NoCutoff,
                      PME:AmoebaMultipoleForce.PME}

wrappers/python/tests/TestGromacsTopFile.py

@@ -22,12 +22,14 @@ class TestGromacsTopFile(unittest.TestCase):
         self.top2 = GromacsTopFile('systems/implicit.top')
 
     def test_NonbondedMethod(self):
-        """Test all five options for the nonbondedMethod parameter."""
+        """Test all six options for the nonbondedMethod parameter."""
 
         methodMap = {NoCutoff:NonbondedForce.NoCutoff,
                      CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
                      CutoffPeriodic:NonbondedForce.CutoffPeriodic,
-                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+                     Ewald:NonbondedForce.Ewald,
+                     PME:NonbondedForce.PME,
+                     LJPME:NonbondedForce.LJPME}
         for method in methodMap:
             system = self.top1.createSystem(nonbondedMethod=method)
             forces = system.getForces()
@@ -52,7 +54,7 @@ class TestGromacsTopFile(unittest.TestCase):
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
-        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME]:
             system = self.top1.createSystem(nonbondedMethod=method,
                                                nonbondedCutoff=2*nanometer,
                                                constraints=HBonds)
@@ -66,7 +68,7 @@ class TestGromacsTopFile(unittest.TestCase):
     def test_EwaldErrorTolerance(self):
         """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
 
-        for method in [Ewald, PME]:
+        for method in [Ewald, PME, LJPME]:
             system = self.top1.createSystem(nonbondedMethod=method,
                                                ewaldErrorTolerance=1e-6,
                                                constraints=HBonds)