Merge pull request #1 from peastman/ljpme

Cleanup to LJ PME code

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -208,4 +208,5 @@ ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const Expressio
 
 void CustomCompoundBondForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomCompoundBondForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/CustomExternalForceImpl.cpp

@@ -97,4 +97,5 @@ map<string, double> CustomExternalForceImpl::getDefaultParameters() {
 
 void CustomExternalForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomExternalForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/CustomGBForceImpl.cpp

@@ -126,4 +126,5 @@ map<string, double> CustomGBForceImpl::getDefaultParameters() {
 
 void CustomGBForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomGBForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/CustomHbondForceImpl.cpp

@@ -278,4 +278,5 @@ ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNo
 
 void CustomHbondForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomHbondForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/CustomIntegrator.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) 2011-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -63,6 +63,15 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
         if (contextRef.getParameters().find(name) != contextRef.getParameters().end())
             throw OpenMMException("The Integrator defines a variable with the same name as a Context parameter: "+name);
     }
+    set<std::string> globalTargets;
+    globalTargets.insert(globalNames.begin(), globalNames.end());
+    globalTargets.insert("dt");
+    for (map<string, double>::const_iterator iter = contextRef.getParameters().begin(); iter != contextRef.getParameters().end(); ++iter)
+        globalTargets.insert(iter->first);
+    for (int i = 0; i < computations.size(); i++) {
+        if (computations[i].type == ComputeGlobal && globalTargets.find(computations[i].variable) == globalTargets.end())
+            throw OpenMMException("Unknown global variable: "+computations[i].variable);
+    }
     context = &contextRef;
     owner = &contextRef.getOwner();
     kernel = context->getPlatform().createKernel(IntegrateCustomStepKernel::Name(), contextRef);

openmmapi/src/CustomManyParticleForceImpl.cpp

@@ -240,6 +240,7 @@ ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const Expressio
 
 void CustomManyParticleForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomManyParticleForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }
 
 void CustomManyParticleForceImpl::buildFilterArrays(const CustomManyParticleForce& force, int& numTypes, vector<int>& particleTypes, vector<int>& orderIndex, vector<vector<int> >& particleOrder) {

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -155,6 +155,7 @@ map<string, double> CustomNonbondedForceImpl::getDefaultParameters() {
 
 void CustomNonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomNonbondedForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }
 
 void CustomNonbondedForceImpl::calcLongRangeCorrection(const CustomNonbondedForce& force, const Context& context, double& coefficient, vector<double>& derivatives) {

openmmapi/src/CustomTorsionForceImpl.cpp

@@ -115,4 +115,5 @@ map<string, double> CustomTorsionForceImpl::getDefaultParameters() {
 
 void CustomTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcCustomTorsionForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/GBSAOBCForceImpl.cpp

@@ -69,4 +69,5 @@ std::vector<std::string> GBSAOBCForceImpl::getKernelNames() {
 
 void GBSAOBCForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcGBSAOBCForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/GayBerneForceImpl.cpp

@@ -126,4 +126,5 @@ std::vector<std::string> GayBerneForceImpl::getKernelNames() {
 
 void GayBerneForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcGayBerneForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/HarmonicAngleForceImpl.cpp

@@ -63,4 +63,5 @@ std::vector<std::string> HarmonicAngleForceImpl::getKernelNames() {
 
 void HarmonicAngleForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcHarmonicAngleForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/HarmonicBondForceImpl.cpp

@@ -73,4 +73,5 @@ vector<pair<int, int> > HarmonicBondForceImpl::getBondedParticles() const {
 
 void HarmonicBondForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcHarmonicBondForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp

@@ -34,6 +34,7 @@
 #include "openmm/internal/OSRngSeed.h"
 #include "openmm/Context.h"
 #include "openmm/kernels.h"
+#include "openmm/OpenMMException.h"
 #include <cmath>
 #include <vector>
 #include <algorithm>
@@ -51,6 +52,8 @@ MonteCarloAnisotropicBarostatImpl::MonteCarloAnisotropicBarostatImpl(const Monte
 }
 
 void MonteCarloAnisotropicBarostatImpl::initialize(ContextImpl& context) {
+    if (!context.getSystem().usesPeriodicBoundaryConditions())
+        throw OpenMMException("A barostat cannot be used with a non-periodic system");
     kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner);
     Vec3 box[3];

openmmapi/src/MonteCarloBarostatImpl.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,6 +34,7 @@
 #include "openmm/internal/OSRngSeed.h"
 #include "openmm/Context.h"
 #include "openmm/kernels.h"
+#include "openmm/OpenMMException.h"
 #include <cmath>
 #include <vector>
 #include <algorithm>
@@ -51,6 +52,8 @@ MonteCarloBarostatImpl::MonteCarloBarostatImpl(const MonteCarloBarostat& owner)
 }
 
 void MonteCarloBarostatImpl::initialize(ContextImpl& context) {
+    if (!context.getSystem().usesPeriodicBoundaryConditions())
+        throw OpenMMException("A barostat cannot be used with a non-periodic system");
     kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner);
     Vec3 box[3];

openmmapi/src/MonteCarloMembraneBarostatImpl.cpp

@@ -34,6 +34,7 @@
 #include "openmm/internal/OSRngSeed.h"
 #include "openmm/Context.h"
 #include "openmm/kernels.h"
+#include "openmm/OpenMMException.h"
 #include <cmath>
 #include <vector>
 #include <algorithm>
@@ -51,6 +52,8 @@ MonteCarloMembraneBarostatImpl::MonteCarloMembraneBarostatImpl(const MonteCarloM
 }
 
 void MonteCarloMembraneBarostatImpl::initialize(ContextImpl& context) {
+    if (!context.getSystem().usesPeriodicBoundaryConditions())
+        throw OpenMMException("A barostat cannot be used with a non-periodic system");
     kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner);
     Vec3 box[3];

openmmapi/src/NonbondedForce.cpp

@@ -106,6 +106,13 @@ void NonbondedForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz)
     nz = this->nz;
 }
 
+void NonbondedForce::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
+    alpha = this->dalpha;
+    nx = this->dnx;
+    ny = this->dny;
+    nz = this->dnz;
+}
+
 void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
     this->alpha = alpha;
     this->nx = nx;
@@ -113,10 +120,21 @@ void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
     this->nz = nz;
 }
 
+void NonbondedForce::setLJPMEParameters(double alpha, int nx, int ny, int nz) {
+    this->dalpha = alpha;
+    this->dnx = nx;
+    this->dny = ny;
+    this->dnz = nz;
+}
+
 void NonbondedForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
     dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
 }
 
+void NonbondedForce::getLJPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
+    dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getLJPMEParameters(alpha, nx, ny, nz);
+}
+
 int NonbondedForce::addParticle(double charge, double sigma, double epsilon) {
     particles.push_back(ParticleInfo(charge, sigma, epsilon));
     return particles.size()-1;

openmmapi/src/NonbondedForceImpl.cpp

@@ -151,7 +151,10 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
         kmaxz++;
 }
 
-void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize) {
+void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize, bool lj) {
+    if (lj)
+        force.getLJPMEParameters(alpha, xsize, ysize, zsize);
+    else
         force.getPMEParameters(alpha, xsize, ysize, zsize);
     if (alpha == 0.0) {
         Vec3 boxVectors[3];
@@ -277,8 +280,13 @@ double NonbondedForceImpl::calcDispersionCorrection(const System& system, const
 
 void NonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcNonbondedForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }
 
 void NonbondedForceImpl::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
     kernel.getAs<CalcNonbondedForceKernel>().getPMEParameters(alpha, nx, ny, nz);
 }
+
+void NonbondedForceImpl::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
+    kernel.getAs<CalcNonbondedForceKernel>().getLJPMEParameters(alpha, nx, ny, nz);
+}

openmmapi/src/PeriodicTorsionForceImpl.cpp

@@ -63,4 +63,5 @@ std::vector<std::string> PeriodicTorsionForceImpl::getKernelNames() {
 
 void PeriodicTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcPeriodicTorsionForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

openmmapi/src/RBTorsionForceImpl.cpp

@@ -63,4 +63,5 @@ std::vector<std::string> RBTorsionForceImpl::getKernelNames() {
 
 void RBTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
     kernel.getAs<CalcRBTorsionForceKernel>().copyParametersToContext(context, owner);
+    context.systemChanged();
 }

platforms/cpu/include/CpuCustomGBForce.h

 
-/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -254,15 +254,15 @@ public:
     std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
     std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
     std::vector<std::vector<Lepton::CompiledExpression> > valueParamDerivExpressions;
-    std::vector<int> valueIndex;
+    std::vector<double> value;
     std::vector<Lepton::CompiledExpression> energyExpressions;
     std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
     std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
     std::vector<std::vector<Lepton::CompiledExpression> > energyParamDerivExpressions;
-    std::vector<int> paramIndex;
-    std::vector<int> particleParamIndex;
-    std::vector<int> particleValueIndex;
-    int xindex, yindex, zindex, rindex;
+    std::vector<double> param;
+    std::vector<double> particleParam;
+    std::vector<double> particleValue;
+    double x, y, z, r;
     int firstAtom, lastAtom;
     // Workspace vectors
     std::vector<float> value0, dVdR1, dVdR2, dVdX, dVdY, dVdZ;