Merge master

openmmapi/include/openmm/GBSAOBCForce.h

@@ -100,9 +100,9 @@ public:
      * Get the force field parameters for a particle.
      *
      * @param index               the index of the particle for which to get parameters
-     * @param charge         the charge of the particle, measured in units of the proton charge
-     * @param radius         the GBSA radius of the particle, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the particle
+     * @param[out] charge         the charge of the particle, measured in units of the proton charge
+     * @param[out] radius         the GBSA radius of the particle, measured in nm
+     * @param[out] scalingFactor  the OBC scaling factor for the particle
      */
     void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
     /**

openmmapi/include/openmm/GBVIForce.h

@@ -110,9 +110,9 @@ public:
      * Get the force field parameters for a particle.
      *
      * @param index               the index of the particle for which to get parameters
-     * @param charge         the charge of the particle, measured in units of the proton charge
-     * @param radius         the GBSA radius of the particle, measured in nm
-     * @param gamma          the gamma parameter
+     * @param[out] charge         the charge of the particle, measured in units of the proton charge
+     * @param[out] radius         the GBSA radius of the particle, measured in nm
+     * @param[out] gamma          the gamma parameter
      */
     void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
     /**
@@ -138,9 +138,9 @@ public:
      * Get the parameters defining a bond
      *
      * @param      index     the index of the bond for which to get parameters
-     * @param particle1 the index of the first particle involved in the bond
-     * @param particle2 the index of the second particle involved in the bond
-     * @param distance  the distance between the two particles, measured in nm
+     * @param[out] particle1 the index of the first particle involved in the bond
+     * @param[out] particle2 the index of the second particle involved in the bond
+     * @param[out] distance  the distance between the two particles, measured in nm
      */
     void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
     /**

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -74,11 +74,11 @@ public:
      * Get the force field parameters for an angle term.
      *
      * @param      index     the index of the angle for which to get parameters
-     * @param particle1 the index of the first particle forming the angle
-     * @param particle2 the index of the second particle forming the angle
-     * @param particle3 the index of the third particle forming the angle
-     * @param angle     the equilibrium angle, measured in radians
-     * @param k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
+     * @param[out] particle1 the index of the first particle forming the angle
+     * @param[out] particle2 the index of the second particle forming the angle
+     * @param[out] particle3 the index of the third particle forming the angle
+     * @param[out] angle     the equilibrium angle, measured in radians
+     * @param[out] k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
     /**

openmmapi/include/openmm/HarmonicBondForce.h

@@ -73,10 +73,10 @@ public:
      * Get the force field parameters for a bond term.
      *
      * @param      index     the index of the bond for which to get parameters
-     * @param particle1 the index of the first particle connected by the bond
-     * @param particle2 the index of the second particle connected by the bond
-     * @param length    the equilibrium length of the bond, measured in nm
-     * @param k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
+     * @param[out] particle1 the index of the first particle connected by the bond
+     * @param[out] particle2 the index of the second particle connected by the bond
+     * @param[out] length    the equilibrium length of the bond, measured in nm
+     * @param[out] k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
      */
     void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
     /**

openmmapi/include/openmm/Integrator.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -61,30 +61,22 @@ public:
      *
      * @return the step size, measured in ps
      */
-    double getStepSize() const {
-        return stepSize;
-    }
+    virtual double getStepSize() const;
     /**
      * Set the size of each time step, in picoseconds.  If this integrator uses variable time steps,
      * the effect of calling this method is undefined, and it may simply be ignored.
      *
      * @param size    the step size, measured in ps
      */
-    void setStepSize(double size) {
-        stepSize = size;
-    }
+    virtual void setStepSize(double size);
     /**
      * Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
      */
-    double getConstraintTolerance() const {
-        return constraintTol;
-    }
+    virtual double getConstraintTolerance() const;
     /**
      * Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
      */
-    void setConstraintTolerance(double tol) {
-        constraintTol = tol;
-    }
+    virtual void setConstraintTolerance(double tol);
     /**
      * Advance a simulation through time by taking a series of time steps.
      * 
@@ -94,6 +86,7 @@ public:
 protected:
     friend class Context;
     friend class ContextImpl;
+    friend class CompoundIntegrator;
     ContextImpl* context;
     Context* owner;
     /**

openmmapi/include/openmm/NonbondedForce.h

@@ -201,10 +201,10 @@ public:
      * Get the parameters to use for PME calculations.  If alpha is 0 (the default), these parameters are
      * ignored and instead their values are chosen based on the Ewald error tolerance.
      *
-     * @param alpha   the separation parameter
-     * @param nx      the number of grid points along the X axis
-     * @param ny      the number of grid points along the Y axis
-     * @param nz      the number of grid points along the Z axis
+     * @param[out] alpha   the separation parameter
+     * @param[out] nx      the number of grid points along the X axis
+     * @param[out] ny      the number of grid points along the Y axis
+     * @param[out] nz      the number of grid points along the Z axis
      */
     void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
     /**
@@ -224,10 +224,10 @@ public:
      * See the manual for details.
      *
      * @param context      the Context for which to get the parameters
-     * @param alpha   the separation parameter
-     * @param nx      the number of grid points along the X axis
-     * @param ny      the number of grid points along the Y axis
-     * @param nz      the number of grid points along the Z axis
+     * @param[out] alpha   the separation parameter
+     * @param[out] nx      the number of grid points along the X axis
+     * @param[out] ny      the number of grid points along the Y axis
+     * @param[out] nz      the number of grid points along the Z axis
      */
     void getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const;
     /**
@@ -247,9 +247,9 @@ public:
      * Get the nonbonded force parameters for a particle.
      *
      * @param index          the index of the particle for which to get parameters
-     * @param charge    the charge of the particle, measured in units of the proton charge
-     * @param sigma     the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
-     * @param epsilon   the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
+     * @param[out] charge    the charge of the particle, measured in units of the proton charge
+     * @param[out] sigma     the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param[out] epsilon   the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
      */
     void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
     /**
@@ -284,11 +284,11 @@ public:
      * Get the force field parameters for an interaction that should be calculated differently from others.
      *
      * @param index           the index of the interaction for which to get parameters
-     * @param particle1  the index of the first particle involved in the interaction
-     * @param particle2  the index of the second particle involved in the interaction
-     * @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
-     * @param sigma      the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
-     * @param epsilon    the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
+     * @param[out] particle1  the index of the first particle involved in the interaction
+     * @param[out] particle2  the index of the second particle involved in the interaction
+     * @param[out] chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
+     * @param[out] sigma      the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param[out] epsilon    the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
      */
     void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
     /**

openmmapi/include/openmm/PeriodicTorsionForce.h

@@ -76,13 +76,13 @@ public:
      * Get the force field parameters for a periodic torsion term.
      *
      * @param index             the index of the torsion for which to get parameters
-     * @param particle1    the index of the first particle forming the torsion
-     * @param particle2    the index of the second particle forming the torsion
-     * @param particle3    the index of the third particle forming the torsion
-     * @param particle4    the index of the fourth particle forming the torsion
-     * @param periodicity  the periodicity of the torsion
-     * @param phase        the phase offset of the torsion, measured in radians
-     * @param k            the force constant for the torsion
+     * @param[out] particle1    the index of the first particle forming the torsion
+     * @param[out] particle2    the index of the second particle forming the torsion
+     * @param[out] particle3    the index of the third particle forming the torsion
+     * @param[out] particle4    the index of the fourth particle forming the torsion
+     * @param[out] periodicity  the periodicity of the torsion
+     * @param[out] phase        the phase offset of the torsion, measured in radians
+     * @param[out] k            the force constant for the torsion
      */
     void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const;
     /**

openmmapi/include/openmm/RBTorsionForce.h

@@ -79,16 +79,16 @@ public:
      * Get the force field parameters for a Ryckaert-Bellemans torsion term.
      *
      * @param index             the index of the torsion for which to get parameters
-     * @param particle1    the index of the first particle forming the torsion
-     * @param particle2    the index of the second particle forming the torsion
-     * @param particle3    the index of the third particle forming the torsion
-     * @param particle4    the index of the fourth particle forming the torsion
-     * @param c0           the coefficient of the constant term, measured in kJ/mol
-     * @param c1           the coefficient of the 1st order term, measured in kJ/mol
-     * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
-     * @param c3           the coefficient of the 3rd order term, measured in kJ/mol
-     * @param c4           the coefficient of the 4th order term, measured in kJ/mol
-     * @param c5           the coefficient of the 5th order term, measured in kJ/mol
+     * @param[out] particle1    the index of the first particle forming the torsion
+     * @param[out] particle2    the index of the second particle forming the torsion
+     * @param[out] particle3    the index of the third particle forming the torsion
+     * @param[out] particle4    the index of the fourth particle forming the torsion
+     * @param[out] c0           the coefficient of the constant term, measured in kJ/mol
+     * @param[out] c1           the coefficient of the 1st order term, measured in kJ/mol
+     * @param[out] c2           the coefficient of the 2nd order term, measured in kJ/mol
+     * @param[out] c3           the coefficient of the 3rd order term, measured in kJ/mol
+     * @param[out] c4           the coefficient of the 4th order term, measured in kJ/mol
+     * @param[out] c5           the coefficient of the 5th order term, measured in kJ/mol
      */
     void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const;
     /**

openmmapi/include/openmm/State.h

@@ -95,9 +95,9 @@ public:
     /**
      * Get the vectors defining the axes of the periodic box (measured in nm).
      *
-     * @param a      on exit, this contains the vector defining the first edge of the periodic box
-     * @param b      on exit, this contains the vector defining the second edge of the periodic box
-     * @param c      on exit, this contains the vector defining the third edge of the periodic box
+     * @param[out] a    the vector defining the first edge of the periodic box
+     * @param[out] b    the vector defining the second edge of the periodic box
+     * @param[out] c    the vector defining the third edge of the periodic box
      */
     void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
     /**

openmmapi/include/openmm/System.h

@@ -153,9 +153,9 @@ public:
      * Get the parameters defining a distance constraint.
      *
      * @param index     the index of the constraint for which to get parameters
-     * @param particle1 the index of the first particle involved in the constraint
-     * @param particle2 the index of the second particle involved in the constraint
-     * @param distance  the required distance between the two particles, measured in nm
+     * @param[out] particle1 the index of the first particle involved in the constraint
+     * @param[out] particle2 the index of the second particle involved in the constraint
+     * @param[out] distance  the required distance between the two particles, measured in nm
      */
     void getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const;
     /**
@@ -216,9 +216,9 @@ public:
      * created Context will have its box vectors set to these.  They will affect
      * any Force added to the System that uses periodic boundary conditions.
      *
-     * @param a      on exit, this contains the vector defining the first edge of the periodic box
-     * @param b      on exit, this contains the vector defining the second edge of the periodic box
-     * @param c      on exit, this contains the vector defining the third edge of the periodic box
+     * @param[out] a     the vector defining the first edge of the periodic box
+     * @param[out] b     the vector defining the second edge of the periodic box
+     * @param[out] c     the vector defining the third edge of the periodic box
      */
     void getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
     /**

openmmapi/src/CompoundIntegrator.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) 2015 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/CompoundIntegrator.h"
+#include "openmm/Context.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/kernels.h"
+#include <string>
+
+using namespace OpenMM;
+using namespace std;
+
+CompoundIntegrator::CompoundIntegrator() : currentIntegrator(0) {
+}
+
+CompoundIntegrator::~CompoundIntegrator() {
+    for (int i = 0; i < integrators.size(); i++)
+        delete integrators[i];
+}
+
+int CompoundIntegrator::getNumIntegrators() const {
+    return integrators.size();
+}
+
+int CompoundIntegrator::addIntegrator(Integrator* integrator) {
+    if (owner != NULL)
+        throw OpenMMException("addIntegrator() cannot be called after a CustomIntegrator is already bound to a context");
+    integrators.push_back(integrator);
+    return integrators.size()-1;
+}
+
+Integrator& CompoundIntegrator::getIntegrator(int index) {
+    ASSERT_VALID_INDEX(index, integrators);
+    return *integrators[index];
+}
+
+const Integrator& CompoundIntegrator::getIntegrator(int index) const {
+    ASSERT_VALID_INDEX(index, integrators);
+    return *integrators[index];
+}
+
+int CompoundIntegrator::getCurrentIntegrator() const {
+    return currentIntegrator;
+}
+
+void CompoundIntegrator::setCurrentIntegrator(int index) {
+    if (index < 0 || index >= integrators.size())
+        throw OpenMMException("Illegal index for setCurrentIntegrator()");
+    currentIntegrator = index;
+}
+
+double CompoundIntegrator::getStepSize() const {
+    return integrators[currentIntegrator]->getStepSize();
+}
+
+void CompoundIntegrator::setStepSize(double size) {
+    integrators[currentIntegrator]->setStepSize(size);
+}
+
+double CompoundIntegrator::getConstraintTolerance() const {
+    return integrators[currentIntegrator]->getConstraintTolerance();
+}
+
+void CompoundIntegrator::setConstraintTolerance(double tol) {
+    integrators[currentIntegrator]->setConstraintTolerance(tol);
+}
+
+void CompoundIntegrator::step(int steps) {
+    integrators[currentIntegrator]->step(steps);
+}
+
+void CompoundIntegrator::initialize(ContextImpl& context) {
+    if (integrators.size() == 0)
+        throw OpenMMException("CompoundIntegrator must contain at least one Integrator");
+    for (int i = 0; i < integrators.size(); i++)
+        integrators[i]->initialize(context);
+}
+
+void CompoundIntegrator::cleanup() {
+    for (int i = 0; i < integrators.size(); i++)
+        integrators[i]->cleanup();
+}
+
+vector<string> CompoundIntegrator::getKernelNames() {
+    vector<string> kernels;
+    for (int i = 0; i < integrators.size(); i++) {
+        vector<string> integratorKernels = integrators[i]->getKernelNames();
+        kernels.insert(kernels.end(), integratorKernels.begin(), integratorKernels.end());
+    }
+    return kernels;
+}
+
+double CompoundIntegrator::computeKineticEnergy() {
+    return integrators[currentIntegrator]->computeKineticEnergy();
+}

openmmapi/src/Context.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -114,21 +114,15 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
                 center *= 1.0/molecules[i].size();
 
                 // Find the displacement to move it into the first periodic box.
-
-                int xcell = (int) floor(center[0]/periodicBoxSize[0][0]);
-                int ycell = (int) floor(center[1]/periodicBoxSize[1][1]);
-                int zcell = (int) floor(center[2]/periodicBoxSize[2][2]);
-                double dx = xcell*periodicBoxSize[0][0];
-                double dy = ycell*periodicBoxSize[1][1];
-                double dz = zcell*periodicBoxSize[2][2];
+                Vec3 diff;
+                diff -= periodicBoxSize[0]*static_cast<int>(center[0]/periodicBoxSize[0][0]);
+                diff -= periodicBoxSize[1]*static_cast<int>(center[1]/periodicBoxSize[1][1]);
+                diff -= periodicBoxSize[2]*static_cast<int>(center[2]/periodicBoxSize[2][2]);
 
                 // Translate all the particles in the molecule.
-                
                 for (int j = 0; j < (int) molecules[i].size(); j++) {
                     Vec3& pos = positions[molecules[i][j]];
-                    pos[0] -= dx;
-                    pos[1] -= dy;
-                    pos[2] -= dz;
+                    pos -= diff;
                 }
             }
         }
@@ -207,6 +201,10 @@ void Context::setVelocitiesToTemperature(double temperature, int randomSeed) {
     impl->applyVelocityConstraints(1e-5);
 }
 
+const map<string, double>& Context::getParameters() const {
+    return impl->getParameters();
+}
+
 double Context::getParameter(const string& name) const {
     return impl->getParameter(name);
 }

openmmapi/src/CustomNonbondedForce.cpp

@@ -263,9 +263,9 @@ void CustomNonbondedForce::setFunctionParameters(int index, const std::string& n
 
 int CustomNonbondedForce::addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2) {
     for (set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
-        ASSERT_VALID_INDEX(*it, particles);
+        ASSERT(*it >= 0);
     for (set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
-        ASSERT_VALID_INDEX(*it, particles);
+        ASSERT(*it >= 0);
     interactionGroups.push_back(InteractionGroupInfo(set1, set2));
     return interactionGroups.size()-1;
 }

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/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/tests/TestCpuCompoundIntegrator.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) 2015 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 "CpuTests.h"
+#include "TestCompoundIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/cuda/include/CudaIntegrationUtilities.h

@@ -62,6 +62,14 @@ public:
     CudaArray& getStepSize() {
         return *stepSize;
     }
+    /**
+     * Set the size to use for the next step.
+     */
+    void setNextStepSize(double size);
+    /**
+     * Get the size that was used for the last step.
+     */
+    double getLastStepSize();
     /**
      * Apply constraints to the atom positions.
      *
@@ -154,6 +162,7 @@ private:
     CudaArray* vsiteLocalCoordsParams;
     int randomPos;
     int lastSeed, numVsites;
+    double2 lastStepSize;
     struct ShakeCluster;
     struct ConstraintOrderer;
 };

platforms/cuda/include/CudaKernels.h

@@ -592,7 +592,7 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
 public:
     CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
             cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
-            pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL),  pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), fft(NULL), pmeio(NULL) {
+            pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL),  pmeAtomRange(NULL), pmeAtomGridIndex(NULL), pmeEnergyBuffer(NULL), sort(NULL), fft(NULL), pmeio(NULL) {
     }
     ~CudaCalcNonbondedForceKernel();
     /**
@@ -657,6 +657,7 @@ private:
     CudaArray* pmeBsplineModuliZ;
     CudaArray* pmeAtomRange;
     CudaArray* pmeAtomGridIndex;
+    CudaArray* pmeEnergyBuffer;
     CudaSort* sort;
     Kernel cpuPme;
     PmeIO* pmeio;
@@ -1123,7 +1124,6 @@ public:
     double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
 private:
     CudaContext& cu;
-    double prevStepSize;
     CUfunction kernel1, kernel2;
 };
 
@@ -1354,7 +1354,7 @@ private:
     void recordChangedParameters(ContextImpl& context);
     bool evaluateCondition(int step);
     CudaContext& cu;
-    double prevStepSize, energy;
+    double energy;
     float energyFloat;
     int numGlobalVariables;
     bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;

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;

platforms/cuda/src/CudaIntegrationUtilities.cpp

@@ -106,21 +106,21 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
         vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL) {
     // Create workspace arrays.
 
+    lastStepSize = make_double2(0.0, 0.0);
     if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
         posDelta = CudaArray::create<double4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<double4> deltas(posDelta->getSize(), make_double4(0.0, 0.0, 0.0, 0.0));
         posDelta->upload(deltas);
         stepSize = CudaArray::create<double2>(context, 1, "stepSize");
-        vector<double2> step(1, make_double2(0.0, 0.0));
-        stepSize->upload(step);
+        stepSize->upload(&lastStepSize);
     }
     else {
         posDelta = CudaArray::create<float4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<float4> deltas(posDelta->getSize(), make_float4(0.0f, 0.0f, 0.0f, 0.0f));
         posDelta->upload(deltas);
         stepSize = CudaArray::create<float2>(context, 1, "stepSize");
-        vector<float2> step(1, make_float2(0.0f, 0.0f));
-        stepSize->upload(step);
+        float2 lastStepSizeFloat = make_float2(0.0f, 0.0f);
+        stepSize->upload(&lastStepSizeFloat);
     }
 
     // Record the set of constraints and how many constraints each atom is involved in.
@@ -650,6 +650,29 @@ CudaIntegrationUtilities::~CudaIntegrationUtilities() {
         delete vsiteLocalCoordsParams;
 }
 
+void CudaIntegrationUtilities::setNextStepSize(double size) {
+    if (size != lastStepSize.x || size != lastStepSize.y) {
+        lastStepSize = make_double2(size, size);
+        if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+            stepSize->upload(&lastStepSize);
+        else {
+            float2 lastStepSizeFloat = make_float2((float) size, (float) size);
+            stepSize->upload(&lastStepSizeFloat);
+        }
+    }
+}
+
+double CudaIntegrationUtilities::getLastStepSize() {
+    if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+        stepSize->download(&lastStepSize);
+    else {
+        float2 lastStepSizeFloat;
+        stepSize->download(&lastStepSizeFloat);
+        lastStepSize = make_double2(lastStepSizeFloat.x, lastStepSizeFloat.y);
+    }
+    return lastStepSize.y;
+}
+
 void CudaIntegrationUtilities::applyConstraints(double tol) {
     applyConstraints(false, tol);
 }