Merged upstream changes

plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu

@@ -599,14 +599,14 @@ extern "C" __global__ void computeFixedField(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu

@@ -337,14 +337,14 @@ extern "C" __global__ void computeInducedField(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu

@@ -321,14 +321,14 @@ extern "C" __global__ void computeElectrostatics(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

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

@@ -1107,6 +1107,8 @@ class NonbondedGenerator:
         force.setCutoffDistance(nonbondedCutoff)
         if 'ewaldErrorTolerance' in args:
             force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
+        if 'useDispersionCorrection' in args:
+            force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
         sys.addForce(force)
 
     def postprocessSystem(self, sys, data, args):
@@ -3037,7 +3039,7 @@ class AmoebaVdwGenerator:
             # dispersion correction
 
             if ('useDispersionCorrection' in args):
-                force.setUseDispersionCorrection(int(args['useDispersionCorrection']))
+                force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
 
             if (nonbondedMethod == PME):
                 force.setNonbondedMethod(mm.AmoebaVdwForce.CutoffPeriodic)

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

@@ -111,7 +111,7 @@ class GromacsTopFile(object):
                 if len(fields) < 2:
                     raise ValueError('Illegal line in .top file: '+line)
                 name = fields[1]
-                valueStart = stripped.find(name, len(command))+len(name)
+                valueStart = stripped.find(name, len(command))+len(name)+1
                 value = line[valueStart:].strip()
                 self._defines[name] = value
             elif command == '#ifdef':

wrappers/python/tests/TestForceField.py

@@ -19,6 +19,7 @@ class TestForceField(unittest.TestCase):
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
 
+        # alalnine dipeptide with implicit water
         self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
@@ -38,6 +39,18 @@ class TestForceField(unittest.TestCase):
                                 f.getNonbondedMethod()==methodMap[method] 
                                 for f in forces))
 
+    def test_DispersionCorrection(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for useDispersionCorrection in [True, False]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedCutoff=2*nanometer, 
+                                                   useDispersionCorrection=useDispersionCorrection)
+
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
+
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
 
@@ -133,6 +146,62 @@ class TestForceField(unittest.TestCase):
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
             self.assertTrue(norm(f1-f2) < 0.1)
 
+class AmoebaTestForceField(unittest.TestCase):
+    """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
+ 
+    def setUp(self):
+        """Set up the tests by loading the input pdb files and force field 
+        xml files.
+
+        """
+
+        self.pdb1 = PDBFile('systems/amoeba-ion-in-water.pdb')
+        self.forcefield1 = ForceField('amoeba2009.xml')
+        self.topology1 = self.pdb1.topology
+
+
+    def test_NonbondedMethod(self):
+        """Test all five options for the nonbondedMethod parameter."""
+
+        methodMap = {NoCutoff:AmoebaMultipoleForce.NoCutoff,
+                     PME:AmoebaMultipoleForce.PME}
+
+        for method in methodMap:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                  nonbondedMethod=method)
+            forces = system.getForces()
+            self.assertTrue(any(isinstance(f, AmoebaMultipoleForce) and
+                                f.getNonbondedMethod()==methodMap[method]
+                                for f in forces))
+    def test_Cutoff(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        cutoff_distance = 0.7*nanometer
+        for method in [NoCutoff, PME]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedMethod=method,
+                                                   nonbondedCutoff=cutoff_distance,
+                                                   constraints=None)
+
+            for force in system.getForces():
+                if isinstance(force, AmoebaVdwForce):
+                    self.assertEqual(force.getCutoff(), cutoff_distance)
+                if isinstance(force, AmoebaMultipoleForce):
+                    self.assertEqual(force.getCutoffDistance(), cutoff_distance)
+
+    def test_DispersionCorrection(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for useDispersionCorrection in [True, False]:
+            system = self.forcefield1.createSystem(self.pdb1.topology,
+                                                   nonbondedMethod=PME,
+                                                   useDispersionCorrection=useDispersionCorrection)
+
+            for force in system.getForces():
+                if isinstance(force, AmoebaVdwForce):
+                    self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
+
+
 if __name__ == '__main__':
     unittest.main()