Merge remote-tracking branch 'upstream/master' into vagrant

plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp

@@ -61,7 +61,7 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
     
     // Try moving each particle along each axis, and see if the energy changes by the correct amount.
     
-    double offset = 1e-3;
+    double offset = 1e-2;
     for (int i = 0; i < system.getNumParticles(); i++)
         for (int j = 0; j < 3; j++) {
             vector<Vec3> offsetPos = positions;
@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
 }
 
 void testSingleParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -92,9 +92,9 @@ void testSingleParticle() {
 }
 
 void testAnisotropicParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double a1 = 0.8;
     const double a2 = 1.1;
     const double k1 = k/a1;
@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
 }
 
 void testThole() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double thole = 2.5;
     System system;
     system.addParticle(1.0);
@@ -157,9 +157,9 @@ void testThole() {
 }
 
 void testChangingParameters() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     Platform& platform = Platform::getPlatformByName("CUDA");
     
     // Create the system.
@@ -184,9 +184,9 @@ void testChangingParameters() {
     
     // Modify the parameters.
     
-    const double k2 = 2.2;
+    const double k2 = ONE_4PI_EPS0*2.2;
     const double charge2 = 0.3;
-    const double alpha2 = charge2*charge2/k2;
+    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
     drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
     drude->updateParametersInContext(context);
     state = context.getState(State::Energy);

plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp

@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories();
 void testSinglePair() {
     const double temperature = 300.0;
     const double temperatureDrude = 10.0;
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double mass1 = 1.0;
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
@@ -132,7 +132,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp

@@ -85,7 +85,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp

@@ -131,9 +131,9 @@ void OpenCLCalcDrudeForceKernel::initialize(const System& system, const DrudeFor
             double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
             double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
             double a3 = 3-a1-a2;
-            double k3 = charge*charge/(polarizability*a3);
-            double k1 = charge*charge/(polarizability*a1) - k3;
-            double k2 = charge*charge/(polarizability*a2) - k3;
+            double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
+            double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
+            double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
             if (atoms[i][2] == -1) {
                 atoms[i][2] = 0;
                 k1 = 0;
@@ -202,9 +202,9 @@ void OpenCLCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context, c
             double a1 = (p2 == -1 ? 1 : aniso12);
             double a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34);
             double a3 = 3-a1-a2;
-            double k3 = charge*charge/(polarizability*a3);
-            double k1 = charge*charge/(polarizability*a1) - k3;
-            double k2 = charge*charge/(polarizability*a2) - k3;
+            double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
+            double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
+            double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
             if (p2 == -1)
                 k1 = 0;
             if (p3 == -1 || p4 == -1)

plugins/drude/platforms/opencl/src/kernels/drudePairForce.cl

@@ -13,7 +13,7 @@ real u = drudeParams.x*r;
 real screening = 1-(1+0.5f*u)*EXP(-u);
 real pairEnergy = drudeParams.y*screening*rInv;
 energy += pairEnergy;
-real4 f = delta*(pairEnergy*rInv*rInv);
+real4 f = delta*(drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
 force1 += f;
 force3 -= f;
 
@@ -26,7 +26,7 @@ u = drudeParams.x*r;
 screening = 1-(1+0.5f*u)*EXP(-u);
 pairEnergy = -drudeParams.y*screening*rInv;
 energy += pairEnergy;
-f = delta*(pairEnergy*rInv*rInv);
+f = delta*(-drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
 force1 += f;
 force4 -= f;
 
@@ -39,7 +39,7 @@ u = drudeParams.x*r;
 screening = 1-(1+0.5f*u)*EXP(-u);
 pairEnergy = -drudeParams.y*screening*rInv;
 energy += pairEnergy;
-f = delta*(pairEnergy*rInv*rInv);
+f = delta*(-drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
 force2 += f;
 force3 -= f;
 
@@ -52,6 +52,6 @@ u = drudeParams.x*r;
 screening = 1-(1+0.5f*u)*EXP(-u);
 pairEnergy = drudeParams.y*screening*rInv;
 energy += pairEnergy;
-f = delta*(pairEnergy*rInv*rInv);
+f = delta*(drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
 force2 += f;
 force4 -= f;

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp

@@ -61,7 +61,7 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
     
     // Try moving each particle along each axis, and see if the energy changes by the correct amount.
     
-    double offset = 1e-3;
+    double offset = 1e-2;
     for (int i = 0; i < system.getNumParticles(); i++)
         for (int j = 0; j < 3; j++) {
             vector<Vec3> offsetPos = positions;
@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
 }
 
 void testSingleParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -92,9 +92,9 @@ void testSingleParticle() {
 }
 
 void testAnisotropicParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double a1 = 0.8;
     const double a2 = 1.1;
     const double k1 = k/a1;
@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
 }
 
 void testThole() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double thole = 2.5;
     System system;
     system.addParticle(1.0);
@@ -157,9 +157,9 @@ void testThole() {
 }
 
 void testChangingParameters() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     Platform& platform = Platform::getPlatformByName("OpenCL");
     
     // Create the system.
@@ -184,9 +184,9 @@ void testChangingParameters() {
     
     // Modify the parameters.
     
-    const double k2 = 2.2;
+    const double k2 = ONE_4PI_EPS0*2.2;
     const double charge2 = 0.3;
-    const double alpha2 = charge2*charge2/k2;
+    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
     drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
     drude->updateParametersInContext(context);
     state = context.getState(State::Energy);

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp

@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories();
 void testSinglePair() {
     const double temperature = 300.0;
     const double temperatureDrude = 10.0;
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double mass1 = 1.0;
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
@@ -132,7 +132,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp

@@ -85,7 +85,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -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) 2011-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -136,9 +136,9 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
         RealOpenMM a1 = (p2 == -1 ? 1 : aniso12[i]);
         RealOpenMM a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34[i]);
         RealOpenMM a3 = 3-a1-a2;
-        RealOpenMM k3 = charge[i]*charge[i]/(polarizability[i]*a3);
-        RealOpenMM k1 = charge[i]*charge[i]/(polarizability[i]*a1) - k3;
-        RealOpenMM k2 = charge[i]*charge[i]/(polarizability[i]*a2) - k3;
+        RealOpenMM k3 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a3);
+        RealOpenMM k1 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a1) - k3;
+        RealOpenMM k2 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a2) - k3;
         
         // Compute the isotropic force.
         
@@ -188,6 +188,7 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
         int dipole2 = pair2[i];
         int dipole1Particles[] = {particle[dipole1], particle1[dipole1]};
         int dipole2Particles[] = {particle[dipole2], particle1[dipole2]};
+        RealOpenMM uscale = pairThole[i]/pow(polarizability[dipole1]*polarizability[dipole2], 1.0/6.0);
         for (int j = 0; j < 2; j++)
             for (int k = 0; k < 2; k++) {
                 int p1 = dipole1Particles[j];
@@ -195,10 +196,10 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
                 RealOpenMM chargeProduct = charge[dipole1]*charge[dipole2]*(j == k ? 1 : -1);
                 RealVec delta = pos[p1]-pos[p2];
                 RealOpenMM r = sqrt(delta.dot(delta));
-                RealOpenMM u = r*pairThole[i]/pow(polarizability[dipole1]*polarizability[dipole2], 1.0/6.0);
+                RealOpenMM u = r*uscale;
                 RealOpenMM screening = 1.0 - (1.0+0.5*u)*exp(-u);
                 energy += ONE_4PI_EPS0*chargeProduct*screening/r;
-                RealVec f = delta*(ONE_4PI_EPS0*chargeProduct*screening/(r*r*r));
+                RealVec f = delta*(ONE_4PI_EPS0*chargeProduct/(r*r))*(screening/r-0.5*(1+u)*exp(-u)*uscale);
                 force[p1] += f;
                 force[p2] -= f;
             }
@@ -461,4 +462,4 @@ void ReferenceIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double
     lbfgsfloatval_t fx;
     MinimizerData data(context, drudeParticles);
     lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams);
-}
+}
\ No newline at end of file

plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp

@@ -71,14 +71,14 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
             offsetPos[i][j] = positions[i][j]+offset;
             context.setPositions(offsetPos);
             double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-3);
+            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-5);
         }
 }
 
 void testSingleParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -92,9 +92,9 @@ void testSingleParticle() {
 }
 
 void testAnisotropicParticle() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double a1 = 0.8;
     const double a2 = 1.1;
     const double k1 = k/a1;
@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
 }
 
 void testThole() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double thole = 2.5;
     System system;
     system.addParticle(1.0);
@@ -157,9 +157,9 @@ void testThole() {
 }
 
 void testChangingParameters() {
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     Platform& platform = Platform::getPlatformByName("Reference");
     
     // Create the system.
@@ -184,9 +184,9 @@ void testChangingParameters() {
     
     // Modify the parameters.
     
-    const double k2 = 2.2;
+    const double k2 = ONE_4PI_EPS0*2.2;
     const double charge2 = 0.3;
-    const double alpha2 = charge2*charge2/k2;
+    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
     drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
     drude->updateParametersInContext(context);
     state = context.getState(State::Energy);

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
 void testSinglePair() {
     const double temperature = 300.0;
     const double temperatureDrude = 10.0;
-    const double k = 1.5;
+    const double k = ONE_4PI_EPS0*1.5;
     const double charge = 0.1;
-    const double alpha = charge*charge/k;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
     const double mass1 = 1.0;
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
@@ -132,7 +132,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp

@@ -85,7 +85,7 @@ void testWater() {
         system.addConstraint(startIndex, startIndex+3, 0.09572);
         system.addConstraint(startIndex+2, startIndex+3, 0.15139);
         system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
     }
     vector<Vec3> positions;
     for (int i = 0; i < gridSize; i++)

wrappers/python/CMakeLists.txt

@@ -55,12 +55,16 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.crd"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.par"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.str"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
     )

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

@@ -28,7 +28,7 @@ from desmonddmsfile import DesmondDMSFile
 from checkpointreporter import CheckpointReporter
 from charmmcrdfiles import CharmmCrdFile, CharmmRstFile
 from charmmparameterset import CharmmParameterSet
-from charmmpsffile import CharmmPsfFile
+from charmmpsffile import CharmmPsfFile, CharmmPSFWarning
 
 # Enumerated values
 

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

@@ -13,7 +13,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason M. Swails
 Contributors:
-Date: April 18, 2014
+Date: July 17, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -123,6 +123,8 @@ class CharmmParameterSet(object):
             elif arg.endswith('.str'):
                 strs.append(arg)
             elif arg.endswith('.inp'):
+                # Only consider the file name (since the directory is likely
+                # "toppar" and will screw up file type detection)
                 fname = os.path.split(arg)[1]
                 if 'par' in fname:
                     pars.append(arg)
@@ -436,11 +438,29 @@ class CharmmParameterSet(object):
                 try:
                     at1 = words[0]
                     at2 = words[1]
-                    emin = conv(words[2], float, 'NBFIX Emin')
+                    emin = abs(conv(words[2], float, 'NBFIX Emin'))
                     rmin = conv(words[3], float, 'NBFIX Rmin')
+                    try:
+                        emin14 = abs(conv(words[4], float, 'NBFIX Emin 1-4'))
+                        rmin14 = conv(words[5], float, 'NBFIX Rmin 1-4')
+                    except IndexError:
+                        emin14 = rmin14 = None
+                    try:
+                        self.atom_types_str[at1].add_nbfix(at2, rmin, emin,
+                                                           rmin14, emin14)
+                        self.atom_types_str[at2].add_nbfix(at1, rmin, emin,
+                                                           rmin14, emin14)
+                    except KeyError:
+                        # Some stream files define NBFIX terms with an atom that
+                        # is defined in another toppar file that does not
+                        # necessarily have to be loaded. As a result, not every
+                        # NBFIX found here will necessarily need to be applied.
+                        # If we can't find a particular atom type, don't bother
+                        # adding that nbfix and press on
+                        pass
                 except IndexError:
                     raise CharmmFileError('Could not parse NBFIX terms.')
-                self.nbfix_types[(min(at1, at2), max(at1, at2))] = (emin, rmin)
+                self.nbfix_types[(min(at1, at2), max(at1, at2))] = (rmin, emin)
         # Now we're done. Load the nonbonded types into the relevant AtomType
         # instances. In order for this to work, all keys in nonbonded_types
         # must be in the self.atom_types_str dict. Raise a RuntimeError if this

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

@@ -995,11 +995,25 @@ class CharmmPsfFile(object):
                             u.kilojoule_per_mole)
         ene_conv = dihe_frc_conv
       
-        # Create the system
+        # Create the system and determine if any of our atoms have NBFIX (and
+        # therefore requires a CustomNonbondedForce instead)
+        typenames = set()
         system = mm.System()
         if verbose: print('Adding particles...')
         for atom in self.atom_list:
+            typenames.add(atom.type.name)
             system.addParticle(atom.mass)
+        has_nbfix_terms = False
+        typenames = list(typenames)
+        try:
+            for i, typename in enumerate(typenames):
+                typ = params.atom_types_str[typename]
+                for j in range(i, len(typenames)):
+                    if typenames[j] in typ.nbfix:
+                        has_nbfix_terms = True
+                        raise StopIteration
+        except StopIteration:
+            pass
         # Set up the constraints
         if verbose and (constraints is not None and not rigidWater):
             print('Adding constraints...')
@@ -1240,9 +1254,85 @@ class CharmmPsfFile(object):
 
         # Add per-particle nonbonded parameters (LJ params)
         sigma_scale = 2**(-1/6) * 2
-        for i, atm in enumerate(self.atom_list):
-            force.addParticle(atm.charge, sigma_scale*atm.type.rmin*length_conv,
-                              abs(atm.type.epsilon*ene_conv))
+        if not has_nbfix_terms:
+            for atm in self.atom_list:
+                force.addParticle(atm.charge, sigma_scale*atm.type.rmin*length_conv,
+                                  abs(atm.type.epsilon*ene_conv))
+        else:
+            for atm in self.atom_list:
+                force.addParticle(atm.charge, 1.0, 0.0)
+            # Now add the custom nonbonded force that implements NBFIX. First
+            # thing we need to do is condense our number of types
+            lj_idx_list = [0 for atom in self.atom_list]
+            lj_radii, lj_depths = [], []
+            num_lj_types = 0
+            lj_type_list = []
+            for i, atom in enumerate(self.atom_list):
+                atom = atom.type
+                if lj_idx_list[i]: continue # already assigned
+                num_lj_types += 1
+                lj_idx_list[i] = num_lj_types
+                ljtype = (atom.rmin, atom.epsilon)
+                lj_type_list.append(atom)
+                lj_radii.append(atom.rmin)
+                lj_depths.append(atom.epsilon)
+                for j in range(i+1, len(self.atom_list)):
+                    atom2 = self.atom_list[j].type
+                    if lj_idx_list[j] > 0: continue # already assigned
+                    if atom2 is atom:
+                        lj_idx_list[j] = num_lj_types
+                    elif not atom.nbfix:
+                        # Only non-NBFIXed atom types can be compressed
+                        ljtype2 = (atom2.rmin, atom2.epsilon)
+                        if ljtype == ljtype2:
+                            lj_idx_list[j] = num_lj_types
+            # Now everything is assigned. Create the A-coefficient and
+            # B-coefficient arrays
+            acoef = [0 for i in range(num_lj_types*num_lj_types)]
+            bcoef = acoef[:]
+            for i in range(num_lj_types):
+                for j in range(num_lj_types):
+                    namej = lj_type_list[j].name
+                    try:
+                        rij, wdij, rij14, wdij14 = lj_type_list[i].nbfix[namej]
+                    except KeyError:
+                        rij = (lj_radii[i] + lj_radii[j]) * length_conv
+                        wdij = sqrt(lj_depths[i] * lj_depths[j]) * ene_conv
+                    else:
+                        rij *= length_conv
+                        wdij *= ene_conv
+                    acoef[i+num_lj_types*j] = sqrt(wdij) * rij**6
+                    bcoef[i+num_lj_types*j] = 2 * wdij * rij**6
+            cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;'
+                                             'a=acoef(type1, type2);'
+                                             'b=bcoef(type1, type2)')
+            cforce.addTabulatedFunction('acoef',
+                    mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef))
+            cforce.addTabulatedFunction('bcoef',
+                    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):
+                cforce.setNonbondedMethod(cforce.CutoffPeriodic)
+                cforce.setCutoffDistance(nonbondedCutoff)
+                cforce.setUseLongRangeCorrection(True)
+            elif nonbondedMethod is ff.NoCutoff:
+                cforce.setNonbondedMethod(cforce.NoCutoff)
+            elif nonbondedMethod is ff.CutoffNonPeriodic:
+                cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
+                cforce.setCutoffDistance(nonbondedCutoff)
+            else:
+                raise ValueError('Unrecognized nonbonded method')
+            if switchDistance and nonbondedMethod is not ff.NoCutoff:
+                # make sure it's legal
+                if switchDistance >= nonbondedCutoff:
+                    raise ValueError('switchDistance is too large compared '
+                                     'to the cutoff!')
+                    cforce.setUseSwitchingFunction(True)
+                    cforce.setSwitchingDistance(switchDistance)
+            for i in lj_idx_list:
+                cforce.addParticle((i - 1,)) # adjust for indexing from 0
 
         # Add 1-4 interactions
         excluded_atom_pairs = set() # save these pairs so we don't zero them out
@@ -1283,6 +1373,13 @@ class CharmmPsfFile(object):
                     continue
                 force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
         system.addForce(force)
+        # If we needed a CustomNonbondedForce, map all of the exceptions from
+        # the NonbondedForce to the CustomNonbondedForce
+        if has_nbfix_terms:
+            for i in range(force.getNumExceptions()):
+                ii, jj, q, eps, sig = force.getExceptionParameters(i)
+                cforce.addExclusion(ii, jj)
+            system.addForce(cforce)
 
         # Add GB model if we're doing one
         if implicitSolvent is not None:

wrappers/python/simtk/openmm/app/data/swm4ndp.xml

@@ -30,7 +30,7 @@
   <Atom type="swm4ndp-OD" charge="-1.71636" sigma="1" epsilon="0"/>
  </NonbondedForce>
  <DrudeForce>
-  <Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="7.040850e-6" thole="1.3"/>
+  <Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="0.000978253" thole="1.3"/>
  </DrudeForce>
 </ForceField>