resolved PR #2611 merge conflicts

tests/TestVerletIntegrator.h

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
@@ -254,6 +255,31 @@ void testInitialTemperature() {
     ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
 }
 
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -264,6 +290,7 @@ int main(int argc, char* argv[]) {
         testConstrainedClusters();
         testConstrainedMasslessParticles();
         testInitialTemperature();
+        testForceGroups();
         runPlatformTests();
     }
     catch(const exception& e) {

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

@@ -841,6 +841,7 @@ class ForceField(object):
                     newSite = deepcopy(site)
                     newSite.index = indexMap[site.index]
                     newSite.atoms = [indexMap[i] for i in site.atoms]
+                    newSite.excludeWith = indexMap[site.excludeWith]
                     newTemplate.virtualSites = [site for site in newTemplate.virtualSites if site.index != newSite.index]
                     newTemplate.virtualSites.append(newSite)
             return newTemplates

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

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2018 Stanford University and the Authors.
+Portions copyright (c) 2012-2020 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -139,8 +139,10 @@ class PDBFile(object):
                             element = elem.potassium
                         elif upper.startswith('ZN'):
                             element = elem.zinc
-                        elif( len( residue ) == 1 and upper.startswith('CA') ):
+                        elif len(residue) == 1 and upper.startswith('CA'):
                             element = elem.calcium
+                        elif upper.startswith('D') and any(a.name == atomName[1:] for a in residue.iter_atoms()):
+                            pass # A Drude particle
                         else:
                             try:
                                 element = elem.get_by_symbol(upper[0])
@@ -258,7 +260,7 @@ class PDBFile(object):
                 map[atom.attrib[id]] = name
 
     @staticmethod
-    def writeFile(topology, positions, file=sys.stdout, keepIds=False, extraParticleIdentifier=' '):
+    def writeFile(topology, positions, file=sys.stdout, keepIds=False, extraParticleIdentifier='EP'):
         """Write a PDB file containing a single model.
 
         Parameters
@@ -274,7 +276,7 @@ class PDBFile(object):
             rather than generating new ones.  Warning: It is up to the caller to
             make sure these are valid IDs that satisfy the requirements of the
             PDB format.  Otherwise, the output file will be invalid.
-        extraParticleIdentifier : string=' '
+        extraParticleIdentifier : string='EP'
             String to write in the element column of the ATOM records for atoms whose element is None (extra particles)
         """
         PDBFile.writeHeader(topology, file)
@@ -301,7 +303,7 @@ class PDBFile(object):
                     a*10, b*10, c*10, alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG), file=file)
 
     @staticmethod
-    def writeModel(topology, positions, file=sys.stdout, modelIndex=None, keepIds=False, extraParticleIdentifier=' '):
+    def writeModel(topology, positions, file=sys.stdout, modelIndex=None, keepIds=False, extraParticleIdentifier='EP'):
         """Write out a model to a PDB file.
 
         Parameters
@@ -321,7 +323,7 @@ class PDBFile(object):
             make sure these are valid IDs that satisfy the requirements of the
             PDB format.  No guarantees are made about what will happen if they
             are not, and the output file could be invalid.
-        extraParticleIdentifier : string=' '
+        extraParticleIdentifier : string='EP'
             String to write in the element column of the ATOM records for atoms whose element is None (extra particles)
         """
 

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

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012-2015 Stanford University and the Authors.
+Portions copyright (c) 2012-2020 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -250,7 +250,8 @@ class Simulation(object):
             if next[4]:
                 getEnergy = True
         state = self.context.getState(getPositions=getPositions, getVelocities=getVelocities, getForces=getForces,
-                                      getEnergy=getEnergy, getParameters=True, enforcePeriodicBox=periodic)
+                                      getEnergy=getEnergy, getParameters=True, enforcePeriodicBox=periodic,
+                                      groups=self.context.getIntegrator().getIntegrationForceGroups())
         for reporter, next in reports:
             reporter.report(self, state)
 

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -106,6 +106,33 @@ Parameters:
   }
 }
 
+%extend OpenMM::Integrator {
+  %pythoncode %{
+    def setIntegrationForceGroups(self, groups):
+        """Set which force groups to use for integration.  By default, all force groups are included.
+
+        Parameters
+        ----------
+        groups : set or int
+            a set of indices for which force groups to include when integrating the equations of motion.
+            Alternatively, the groups can be passed as a single unsigned integer interpreted as a bitmask,
+            in which case group i will be included if (groups&(1<<i)) != 0.
+        """
+        try:
+            # is the input integer-like?
+            groups_mask = int(groups)
+        except TypeError:
+            if isinstance(groups, set):
+                groups_mask = functools.reduce(operator.or_,
+                        ((1<<x) & 0xffffffff for x in groups))
+            else:
+                raise TypeError('%s is neither an int nor set' % groups)
+        if groups_mask >= 0x80000000:
+            groups_mask -= 0x100000000
+        _openmm.Integrator_setIntegrationForceGroups(self, groups_mask)
+    %}
+}
+
 %extend OpenMM::RPMDIntegrator {
   %pythoncode %{
     def getState(self,

wrappers/python/tests/TestForceField.py

@@ -1019,6 +1019,75 @@ END"""))
         # If the check is not done correctly, this will throw an exception.
         ff.createSystem(pdb.topology)
 
+    def test_CharmmPolar(self):
+        """Test the CHARMM polarizable force field."""
+        pdb = PDBFile('systems/ala_ala_ala_drude.pdb')
+        pdb.topology.setUnitCellDimensions(Vec3(3, 3, 3))
+        ff = ForceField('charmm_polar_2019.xml')
+        system = ff.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1.2*nanometers)
+        for i,f in enumerate(system.getForces()):
+            f.setForceGroup(i)
+            if isinstance(f, NonbondedForce):
+                f.setPMEParameters(3.4, 64, 64, 64)
+        integrator = DrudeLangevinIntegrator(300, 1.0, 1.0, 10.0, 0.001)
+        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context.setPositions(pdb.positions)
+
+        # Compare the energy to values computed by CHARMM.  Here is what it outputs:
+
+        # ENER ENR:  Eval#     ENERgy      Delta-E         GRMS
+        # ENER INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
+        # ENER CROSS:           CMAPs        PMF1D        PMF2D        PRIMO
+        # ENER EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
+        # ENER EWALD:          EWKSum       EWSElf       EWEXcl       EWQCor       EWUTil
+        #  ----------       ---------    ---------    ---------    ---------    ---------
+        # ENER>        0    102.83992      0.00000     13.06415
+        # ENER INTERN>       54.72574     40.21459     11.61009     26.10373      0.14113
+        # ENER CROSS>        -3.37113      0.00000      0.00000      0.00000
+        # ENER EXTERN>       22.74761    -24.21667      0.00000      0.00000      0.00000
+        # ENER EWALD>        56.14258  -7279.07968   7197.82192      0.00000      0.00000
+        #  ----------       ---------    ---------    ---------    ---------    ---------
+
+        # First check the total energy.
+        
+        energy = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        self.assertAlmostEqual(102.83992, energy, delta=energy*1e-3)
+
+        # Now check individual components.  CHARMM and OpenMM split them up a little differently.  I've tried to
+        # match things up, but I think there's still some inconsistency in where forces related to Drude particles
+        # are categorized.  That's why the Coulomb and bonds terms match less accurately than the other terms
+        # (and less accurately than the total energy, which agrees well).
+
+        coulomb = 0
+        vdw = 0
+        bonds = 0
+        angles = 0
+        propers = 0
+        impropers = 0
+        cmap = 0
+        for i,f in enumerate(system.getForces()):
+            energy = context.getState(getEnergy=True, groups={i}).getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+            if isinstance(f, NonbondedForce):
+                coulomb += energy
+            elif isinstance(f, CustomNonbondedForce) or isinstance(f, CustomBondForce):
+                vdw += energy
+            elif isinstance(f, HarmonicBondForce) or isinstance(f, DrudeForce):
+                bonds += energy
+            elif isinstance(f, HarmonicAngleForce):
+                angles += energy
+            elif isinstance(f, PeriodicTorsionForce):
+                propers += energy
+            elif isinstance(f, CustomTorsionForce):
+                impropers += energy
+            elif isinstance(f, CMAPTorsionForce):
+                cmap += energy
+        self.assertAlmostEqual(-24.21667+56.14258-7279.07968+7197.82192, coulomb, delta=abs(coulomb)*5e-2) # ELEC+EWKSum+EWSElf+EWEXcl
+        self.assertAlmostEqual(22.74761, vdw, delta=vdw*1e-3) # VDWaals
+        self.assertAlmostEqual(54.72574+11.61009, bonds, delta=bonds*2e-2) # BONDs+UREY-b
+        self.assertAlmostEqual(40.21459, angles, delta=angles*1e-3) # ANGLes
+        self.assertAlmostEqual(26.10373, propers, delta=propers*1e-3) # DIHEdrals
+        self.assertAlmostEqual(0.14113, impropers, delta=impropers*1e-3) # IMPRopers
+
 class AmoebaTestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
 

wrappers/python/tests/TestMetadynamics.py

@@ -17,7 +17,7 @@ class TestMetadynamics(unittest.TestCase):
         cv = CustomBondForce('r')
         cv.addBond(0, 1)
         bias = BiasVariable(cv, 0.94, 1.06, 0.00431, gridWidth=31)
-        meta = Metadynamics(system, [bias], 300*kelvin, 2.0, 5.0, 10)
+        meta = Metadynamics(system, [bias], 300*kelvin, 3.0, 5.0, 10)
         integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.001*picosecond)
         integrator.setRandomNumberSeed(4321)
         topology = Topology()

wrappers/python/tests/TestPdbFile.py

@@ -80,7 +80,7 @@ class TestPdbFile(unittest.TestCase):
         output = StringIO()
         PDBFile.writeFile(pdb.topology, pdb.positions, output)
         input = StringIO(output.getvalue())
-        pdb = PDBFile(input, extraParticleIdentifier = '')
+        pdb = PDBFile(input)
         for atom in pdb.topology.atoms():
             if atom.index > 2:
                 self.assertEqual(None, atom.element)

wrappers/python/tests/TestSimulatedTempering.py

@@ -35,7 +35,7 @@ class TestSimulatedTempering(unittest.TestCase):
         
         distances = [[] for i in range(10)]
         count = 0
-        for i in range(7000):
+        for i in range(20000):
             st.step(5)
             pos = simulation.context.getState(getPositions=True).getPositions().value_in_unit(nanometers)
             r = norm(pos[0]-pos[1])

wrappers/python/tests/systems/ala_ala_ala_drude.pdb

+REMARK   1 CREATED WITH OPENMM 7.5, 2020-06-04
+ATOM      1  N   ALA A   1       0.072  -0.034  -0.113  1.00  0.00           N  
+ATOM      2 DN   ALA A   1       0.024  -0.103  -0.101  1.00  0.00          EP  
+ATOM      3  H   ALA A   1      -0.396   0.850  -0.349  1.00  0.00           H  
+ATOM      4  H2  ALA A   1      -0.547  -0.623   0.444  1.00  0.00           H  
+ATOM      5  H3  ALA A   1       0.343  -0.509  -0.974  1.00  0.00           H  
+ATOM      6  CA  ALA A   1       1.286   0.359   0.692  1.00  0.00           C  
+ATOM      7 DCA  ALA A   1       1.247   0.375   0.636  1.00  0.00          EP  
+ATOM      8  HA  ALA A   1       0.730   0.825   1.494  1.00  0.00           H  
+ATOM      9  C   ALA A   1       1.986   1.606   0.031  1.00  0.00           C  
+ATOM     10 DC   ALA A   1       1.956   1.579   0.036  1.00  0.00          EP  
+ATOM     11  O   ALA A   1       1.230   2.563  -0.208  1.00  0.00           O  
+ATOM     12 DO   ALA A   1       1.219   2.525  -0.201  1.00  0.00          EP  
+ATOM     13 LPOA ALA A   1       0.996   2.412  -0.097  1.00  0.00          EP  
+ATOM     14 LPOB ALA A   1       1.458   2.722  -0.321  1.00  0.00          EP  
+ATOM     15  CB  ALA A   1       2.135  -0.773   1.297  1.00  0.00           C  
+ATOM     16 DCB  ALA A   1       2.057  -0.772   1.289  1.00  0.00          EP  
+ATOM     17  HB1 ALA A   1       2.779  -1.237   0.521  1.00  0.00           H  
+ATOM     18  HB2 ALA A   1       1.483  -1.559   1.736  1.00  0.00           H  
+ATOM     19  HB3 ALA A   1       2.788  -0.373   2.102  1.00  0.00           H  
+ATOM     20  N   ALA A   2       3.340   1.626  -0.172  1.00  0.00           N  
+ATOM     21 DN   ALA A   2       3.289   1.631  -0.202  1.00  0.00          EP  
+ATOM     22  H   ALA A   2       3.913   0.773  -0.267  1.00  0.00           H  
+ATOM     23  CA  ALA A   2       3.977   2.932  -0.230  1.00  0.00           C  
+ATOM     24 DCA  ALA A   2       3.990   2.909  -0.215  1.00  0.00          EP  
+ATOM     25  HA  ALA A   2       3.675   3.404   0.715  1.00  0.00           H  
+ATOM     26  C   ALA A   2       5.518   2.682  -0.121  1.00  0.00           C  
+ATOM     27 DC   ALA A   2       5.487   2.654  -0.128  1.00  0.00          EP  
+ATOM     28  O   ALA A   2       5.947   1.505  -0.133  1.00  0.00           O  
+ATOM     29 DO   ALA A   2       5.889   1.489  -0.137  1.00  0.00          EP  
+ATOM     30 LPOA ALA A   2       5.668   1.399  -0.158  1.00  0.00          EP  
+ATOM     31 LPOB ALA A   2       6.229   1.603  -0.108  1.00  0.00          EP  
+ATOM     32  CB  ALA A   2       3.712   3.828  -1.442  1.00  0.00           C  
+ATOM     33 DCB  ALA A   2       3.662   3.802  -1.434  1.00  0.00          EP  
+ATOM     34  HB1 ALA A   2       2.636   4.055  -1.572  1.00  0.00           H  
+ATOM     35  HB2 ALA A   2       4.080   3.339  -2.370  1.00  0.00           H  
+ATOM     36  HB3 ALA A   2       4.238   4.801  -1.334  1.00  0.00           H  
+ATOM     37  N   ALA A   3       6.281   3.795  -0.031  1.00  0.00           N  
+ATOM     38 DN   ALA A   3       6.275   3.733  -0.037  1.00  0.00          EP  
+ATOM     39  H   ALA A   3       5.825   4.723   0.051  1.00  0.00           H  
+ATOM     40  CA  ALA A   3       7.692   3.798   0.060  1.00  0.00           C  
+ATOM     41 DCA  ALA A   3       7.707   3.802   0.068  1.00  0.00          EP  
+ATOM     42  HA  ALA A   3       8.015   3.302  -0.864  1.00  0.00           H  
+ATOM     43  C   ALA A   3       8.044   5.364   0.125  1.00  0.00           C  
+ATOM     44 DC   ALA A   3       8.018   5.323   0.136  1.00  0.00          EP  
+ATOM     45  CB  ALA A   3       8.274   3.163   1.304  1.00  0.00           C  
+ATOM     46 DCB  ALA A   3       8.233   3.093   1.333  1.00  0.00          EP  
+ATOM     47  HB1 ALA A   3       8.009   2.087   1.363  1.00  0.00           H  
+ATOM     48  HB2 ALA A   3       7.899   3.666   2.221  1.00  0.00           H  
+ATOM     49  HB3 ALA A   3       9.384   3.230   1.300  1.00  0.00           H  
+ATOM     50  O   ALA A   3       7.074   6.193   0.135  1.00  0.00           O  
+ATOM     51 DOT1 ALA A   3       7.032   6.119   0.127  1.00  0.00          EP  
+ATOM     52  OXT ALA A   3       9.258   5.664   0.187  1.00  0.00           O  
+ATOM     53 DOT2 ALA A   3       9.219   5.692   0.188  1.00  0.00          EP  
+ATOM     54 LPT1 ALA A   3       7.196   6.521   0.158  1.00  0.00          EP  
+ATOM     55 LPT2 ALA A   3       6.769   6.022   0.114  1.00  0.00          EP  
+ATOM     56 LPT3 ALA A   3       9.295   6.011   0.208  1.00  0.00          EP  
+ATOM     57 LPT4 ALA A   3       9.454   5.374   0.178  1.00  0.00          EP  
+TER      58      ALA A   3
+END