Merge branch 'master' into amber-switching

 Conflicts:
	wrappers/python/simtk/openmm/app/amberprmtopfile.py

In fixing the merge conflict, I went ahead and fixed up the switchDistance logic
to match what I did in CharmmPsfFile.

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -111,6 +111,26 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("CustomNonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");
     }
+    // Check that all interaction groups only specify particles that have been defined.
+    for (int group = 0; group < owner.getNumInteractionGroups(); group++) {
+        set<int> set1, set2;
+        owner.getInteractionGroupParameters(group, set1, set2);
+        for (set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
+            if ((*it < 0) || (*it >= owner.getNumParticles())) {
+                stringstream msg;
+                msg << "CustomNonbondedForce: Interaction group " << group << " set1 contains a particle index (" << *it << ") "
+                    << "not present in system (" << owner.getNumParticles() << " particles).";
+                throw OpenMMException(msg.str());
+            }
+        for (set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
+            if ((*it < 0) || (*it >= owner.getNumParticles())) {
+                stringstream msg;
+                msg << "CustomNonbondedForce: Interaction group " << group << " set2 contains a particle index (" << *it << ") "
+                    << "not present in system (" << owner.getNumParticles() << " particles).";
+                throw OpenMMException(msg.str());
+            }
+    }
+
     kernel.getAs<CalcCustomNonbondedForceKernel>().initialize(context.getSystem(), owner);
 }
 

openmmapi/src/GBVIForceImpl.cpp

-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * 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) 2008 Stanford University and the Authors.           *
- * Authors: Peter Eastman                                                     *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/internal/GBVIForceImpl.h"
-#include "openmm/internal/ContextImpl.h"
-#include "openmm/OpenMMException.h"
-#include "openmm/kernels.h"
-#include <vector>
-#include <cmath>
-#include <cstdio>
-#include <sstream>
-
-using namespace OpenMM;
-using std::vector;
-
-GBVIForceImpl::GBVIForceImpl(const GBVIForce& owner) : owner(owner) {
-}
-
-void GBVIForceImpl::initialize(ContextImpl& context) {
-    kernel = context.getPlatform().createKernel(CalcGBVIForceKernel::Name(), context);
-    if (owner.getNumParticles() != context.getSystem().getNumParticles())
-        throw OpenMMException("GBVIForce must have exactly as many particles as the System it belongs to.");
-    
-    const System& system      = context.getSystem();
-    int     numberOfParticles = owner.getNumParticles();
-    int numberOfBonds         = owner.getNumBonds();
-
-    // load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
-    // numberOfBonds < 1, indicating they were not set by the user
-
-    if( numberOfBonds < 1 && numberOfParticles > 1 ){
-        (void) fprintf( stderr, "Warning: no covalent bonds set for GB/VI force!\n" ); 
-//        getBondsFromForces( context );
-//        numberOfBonds = owner.getNumBonds();
-    }
-
-    std::vector< std::vector<int> > bondIndices;
-    bondIndices.resize( numberOfBonds );
-
-    std::vector<double> bondLengths;
-    bondLengths.resize( numberOfBonds );
-
-    for (int i = 0; i < numberOfBonds; i++) {
-        int particle1, particle2;
-        double bondLength;
-        owner.getBondParameters(i, particle1, particle2, bondLength);
-        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
-            std::stringstream msg;
-            msg << "GBVISoftcoreForce: Illegal particle index: ";
-            msg << particle1;
-            throw OpenMMException(msg.str());
-        }
-        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
-            std::stringstream msg;
-            msg << "GBVISoftcoreForce: Illegal particle index: ";
-            msg << particle2;
-            throw OpenMMException(msg.str());
-        }
-        if (bondLength < 0 ) { 
-            std::stringstream msg;
-            msg << "GBVISoftcoreForce: negative bondlength: ";
-            msg << bondLength;
-            throw OpenMMException(msg.str());
-        }
-        bondIndices[i].push_back( particle1 );  
-        bondIndices[i].push_back( particle2 );
-        bondLengths[i] = bondLength;
-    }   
-    if (owner.getNonbondedMethod() == GBVIForce::CutoffPeriodic) {
-        Vec3 boxVectors[3];
-        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
-        double cutoff = owner.getCutoffDistance();
-        if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
-            throw OpenMMException("GBVIForce: The cutoff distance cannot be greater than half the periodic box size.");
-    }
-
-    vector<double> scaledRadii;
-    scaledRadii.resize(numberOfParticles);
-    findScaledRadii( numberOfParticles, bondIndices, bondLengths, scaledRadii);
-
-    kernel.getAs<CalcGBVIForceKernel>().initialize(context.getSystem(), owner, scaledRadii);
-}
-
-/*
-int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
-
-    // load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
-    
-    const System& system = context.getSystem();
-    for (int i = 0; i < system.getNumForces(); i++) {
-        if (dynamic_cast<const HarmonicBondForce*>(&system.getForce(i)) != NULL) {
-            const HarmonicBondForce& force = dynamic_cast<const HarmonicBondForce&>(system.getForce(i));
-            for (int j = 0; j < force.getNumBonds(); ++j) {
-                int particle1, particle2;
-                double length, k;
-                force.getBondParameters(j, particle1, particle2, length, k); 
-                owner.addBond( particle1, particle2, length );
-            }
-            break;
-        }
-    }   
-
-    // Also treat constrained distances as bonds if mass of one particle is < (2 + epsilon) (~2=deuterium) 
-
-    for (int j = 0; j < system.getNumConstraints(); j++) {
-        int particle1, particle2;
-        double distance;
-        system.getConstraintParameters(j, particle1, particle2, distance);
-        double mass1 = system.getParticleMass( particle1 );
-        double mass2 = system.getParticleMass( particle2 );
-        if( mass1 < 2.1 || mass2 < 2.1 ){
-            owner.addBond( particle1, particle2, distance );
-        }
-    }   
-
-    return 0;
-}
-*/
-
-void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
-                                     const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
-
-    // load 1-2 indicies for each atom 
-
-    std::vector<std::vector<int> > bonded12(numberOfParticles);
-
-    for (int i = 0; i < (int) bondIndices.size(); ++i) {
-        bonded12[bondIndices[i][0]].push_back(i);
-        bonded12[bondIndices[i][1]].push_back(i);
-    }
-
-    int errors = 0;
-
-    // compute scaled radii (Eq. 5 of Labute paper [JCC 29 p. 1693-1698 2008])
-
-    for (int j = 0; j < (int) bonded12.size(); ++j){
-
-        double charge;
-        double gamma;
-        double radiusJ;
-        double scaledRadiusJ;
-     
-        owner.getParticleParameters(j, charge, radiusJ, gamma); 
-
-        if(  bonded12[j].size() == 0 && numberOfParticles > 1 ){
-            (void) fprintf( stderr, "Warning GBVIForceImpl::findScaledRadii atom %d has no covalent bonds; using atomic radius=%.3f.\n", j, radiusJ );
-            scaledRadiusJ = radiusJ;
-//             errors++;
-        } else {
-
-            double rJ2    = radiusJ*radiusJ;
-    
-            // loop over bonded neighbors of atom j, applying Eq. 5 in Labute
-
-            scaledRadiusJ = 0.0;
-            for (int i = 0; i < (int) bonded12[j].size(); ++i){
-    
-               int index            = bonded12[j][i];
-               int bondedAtomIndex  = (j == bondIndices[index][0]) ? bondIndices[index][1] : bondIndices[index][0];
-              
-               double radiusI;
-               owner.getParticleParameters(bondedAtomIndex, charge, radiusI, gamma); 
-               double rI2           = radiusI*radiusI;
-    
-               double a_ij          = (radiusI - bondLengths[index]);
-                      a_ij         *= a_ij;
-                      a_ij          = (rJ2 - a_ij)/(2.0*bondLengths[index]);
-    
-               double a_ji          = radiusJ - bondLengths[index];
-                      a_ji         *= a_ji;
-                      a_ji          = (rI2 - a_ji)/(2.0*bondLengths[index]);
-    
-               scaledRadiusJ       += a_ij*a_ij*(3.0*radiusI - a_ij) + a_ji*a_ji*( 3.0*radiusJ - a_ji );
-            }
-    
-            scaledRadiusJ  = (radiusJ*radiusJ*radiusJ) - 0.125*scaledRadiusJ; 
-            if( scaledRadiusJ > 0.0 ){
-                scaledRadiusJ  = 0.95*pow( scaledRadiusJ, (1.0/3.0) );
-            } else {
-                scaledRadiusJ  = 0.0;
-            }
-        }
-        scaledRadii[j] = scaledRadiusJ;
-
-    }
-
-    // abort if errors
-
-    if( errors ){
-        throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
-    }
-}
-
-double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
-    if ((groups&(1<<owner.getForceGroup())) != 0)
-        return kernel.getAs<CalcGBVIForceKernel>().execute(context, includeForces, includeEnergy);
-    return 0.0;
-}
-
-std::vector<std::string> GBVIForceImpl::getKernelNames() {
-    std::vector<std::string> names;
-    names.push_back(CalcGBVIForceKernel::Name());
-    return names;
-}

openmmapi/src/Integrator.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -47,3 +47,19 @@ Integrator::~Integrator() {
         context->integratorDeleted();
     }
 }
+
+double Integrator::getStepSize() const {
+    return stepSize;
+}
+
+void Integrator::setStepSize(double size) {
+    stepSize = size;
+}
+
+double Integrator::getConstraintTolerance() const {
+    return constraintTol;
+}
+
+void Integrator::setConstraintTolerance(double tol) {
+    constraintTol = tol;
+}

platforms/cpu/CMakeLists.txt

@@ -12,9 +12,11 @@
 #   libOpenMMCPU_static.a
 #----------------------------------------------------
 
-IF(BUILD_TESTING)
+SET(OPENMM_BUILD_CPU_TESTS TRUE CACHE BOOL "Whether to build CPU platform test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_CPU_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_CPU_TESTS)
     SUBDIRS(tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_CPU_TESTS)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.

serialization/include/openmm/serialization/GBVIForceProxy.h → platforms/cpu/tests/TestCpuCompoundIntegrator.cpp

-#ifndef OPENMM_GBVIFORCE_PROXY_H_
-#define OPENMM_GBVIFORCE_PROXY_H_
-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -9,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,22 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/internal/windowsExport.h"
-#include "openmm/serialization/SerializationProxy.h"
-
-namespace OpenMM {
-
-/**
- * This is a proxy for serializing GBVIForce objects.
- */
-
-class OPENMM_EXPORT GBVIForceProxy : public SerializationProxy {
-public:
-    GBVIForceProxy();
-    void serialize(const void* object, SerializationNode& node) const;
-    void* deserialize(const SerializationNode& node) const;
-};
-
-} // namespace OpenMM
+#include "CpuTests.h"
+#include "TestCompoundIntegrator.h"
 
-#endif /*OPENMM_GBVIFORCE_PROXY_H_*/
+void runPlatformTests() {
+}

platforms/cuda/include/CudaContext.h

@@ -30,6 +30,7 @@
 #include <map>
 #include <queue>
 #include <string>
+#include <utility>
 #define __CL_ENABLE_EXCEPTIONS
 #ifdef _MSC_VER
     // Prevent Windows from defining macros that interfere with other code.
@@ -538,6 +539,11 @@ public:
      */
     void invalidateMolecules();
 private:
+    /**
+     * Compute a sorted list of device indices in decreasing order of desirability
+     */
+    std::vector<int> getDevicePrecedence();
+
     struct Molecule;
     struct MoleculeGroup;
     class VirtualSiteInfo;

platforms/cuda/include/CudaPlatform.h

@@ -121,7 +121,7 @@ public:
     ContextImpl* context;
     std::vector<CudaContext*> contexts;
     std::vector<double> contextEnergy;
-    bool removeCM, peerAccessSupported, useCpuPme;
+    bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme;
     int cmMotionFrequency;
     int stepCount, computeForceCount;
     double time;