Merge branch 'master' into applecl

libraries/validate/src/ValidateOpenMMForces.cpp

@@ -68,7 +68,7 @@ ForceValidationResult::ForceValidationResult( const Context& context1, const Con
 ForceValidationResult::~ForceValidationResult(  ){
 }
 
-void ForceValidationResult::_calculateNorms( void ){
+void ForceValidationResult::_calculateNorms(){
 
 // ---------------------------------------------------------------------------------------
 
@@ -195,7 +195,7 @@ std::vector<double> ForceValidationResult::getForceNorms( int forceIndex  ) cons
    }
 }
 
-int ForceValidationResult::nansDetected( void ) const {
+int ForceValidationResult::nansDetected() const {
     return _nansDetected;
 }
 
@@ -203,7 +203,7 @@ void ForceValidationResult::registerInconsistentForceIndex( int index, int value
     _inconsistentForceIndicies[index] = value;
 }
 
-void ForceValidationResult::clearInconsistentForceIndexList( void ){
+void ForceValidationResult::clearInconsistentForceIndexList(){
     _inconsistentForceIndicies.clear();
 }
 
@@ -213,7 +213,7 @@ void ForceValidationResult::getInconsistentForceIndexList( std::vector<int>& inc
     }
 }
 
-int ForceValidationResult::getNumberOfInconsistentForceEntries( void ) const {
+int ForceValidationResult::getNumberOfInconsistentForceEntries() const {
     return  static_cast<int>(_inconsistentForceIndicies.size() );
 }
 
@@ -329,7 +329,7 @@ double ForceValidationResult::getMaxDotProduct( int* maxIndex  ) const {
     return maxDotProduct;
 }
 
-std::string ForceValidationResult::getForceName( void ) const {
+std::string ForceValidationResult::getForceName() const {
 
 // ---------------------------------------------------------------------------------------
 
@@ -376,7 +376,7 @@ void ForceValidationResult::compareForces( double tolerance ){
     std::vector<Vec3> forces2          = getForces( 1 );
     std::vector<double> forceNorms2    = getForceNorms( 1 );
 
-    clearInconsistentForceIndexList( );
+    clearInconsistentForceIndexList();
     for( unsigned int jj = 0; jj < forces1.size(); jj++ ){
         if( ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ||  ValidateOpenMM::isNanOrInfinity( forceNorms2[jj] ) ){
             registerInconsistentForceIndex( jj );
@@ -406,7 +406,7 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
     std::vector<double> forceNorms0    = getForceNorms( 0 );
     std::vector<double> forceNorms1    = getForceNorms( 1 );
 
-    clearInconsistentForceIndexList( );
+    clearInconsistentForceIndexList();
     for( unsigned int jj = 0; jj < forceNorms0.size(); jj++ ){
         if( ValidateOpenMM::isNanOrInfinity( forceNorms0[jj] ) || ValidateOpenMM::isNanOrInfinity( forceNorms1[jj] ) ){
             registerInconsistentForceIndex( jj );
@@ -420,11 +420,11 @@ void ForceValidationResult::compareForceNorms( double tolerance ){
     }
 }
 
-ValidateOpenMMForces::ValidateOpenMMForces( void ) {
+ValidateOpenMMForces::ValidateOpenMMForces() {
     _initialize();
 }
 
-void ValidateOpenMMForces::_initialize( void ){
+void ValidateOpenMMForces::_initialize(){
 
     _forceTolerance                               = 1.0e-02;
     _maxErrorsToPrint                             = 25;
@@ -450,7 +450,7 @@ void ValidateOpenMMForces::_initialize( void ){
     _forcesToBeExcluded[ANDERSEN_THERMOSTAT]      = 1;
 }
 
-ValidateOpenMMForces::~ValidateOpenMMForces( ){
+ValidateOpenMMForces::~ValidateOpenMMForces(){
 
     for( unsigned int ii = 0; ii < _forceValidationResults.size(); ii++ ){
          delete _forceValidationResults[ii];
@@ -459,7 +459,7 @@ ValidateOpenMMForces::~ValidateOpenMMForces( ){
     
 }
 
-double ValidateOpenMMForces::getForceTolerance( void ) const {
+double ValidateOpenMMForces::getForceTolerance() const {
     return _forceTolerance;
 }
 
@@ -706,7 +706,7 @@ double ValidateOpenMMForces::getForceTolerance( const std::string& forceName ) c
     return _forceTolerance;
 }
 
-int ValidateOpenMMForces::getMaxErrorsToPrint( void ) const {
+int ValidateOpenMMForces::getMaxErrorsToPrint() const {
     return _maxErrorsToPrint;
 }
 

olla/include/openmm/kernels.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:                                                              *
  *                                                                            *
@@ -103,11 +103,13 @@ public:
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed
      * @param groups        a set of bit flags for which force groups to include
+     * @param valid         the method may set this to false to indicate the results are invalid and the force/energy
+     *                      calculation should be repeated
      * @return the potential energy of the system.  This value is added to all values returned by ForceImpls'
      * calcForcesAndEnergy() methods.  That is, each force kernel may <i>either</i> return its contribution to the
      * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
      */
-    virtual double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) = 0;
+    virtual double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid) = 0;
 };
 
 /**
@@ -492,6 +494,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CMAPTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) = 0;
 };
 
 /**
@@ -1223,12 +1232,12 @@ public:
     virtual void initialize(int gridx, int gridy, int gridz, int numParticles, double alpha) = 0;
     /**
      * Begin computing the force and energy.
-     * 
-     * @param io               an object that coordinates data transfer
-     * @param periodicBoxSize  the size of the periodic box (measured in nm)
-     * @param includeEnergy    true if potential energy should be computed
+     *
+     * @param io                  an object that coordinates data transfer
+     * @param periodicBoxVectors  the vectors defining the periodic box (measured in nm)
+     * @param includeEnergy       true if potential energy should be computed
      */
-    virtual void beginComputation(IO& io, Vec3 periodicBoxSize, bool includeEnergy) = 0;
+    virtual void beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) = 0;
     /**
      * Finish computing the force and energy.
      * 

olla/src/Platform.cpp

@@ -134,7 +134,10 @@ int Platform::getNumPlatforms() {
 }
 
 Platform& Platform::getPlatform(int index) {
-    return *getPlatforms()[index];
+    if (index >= 0 && index < getNumPlatforms()) {
+        return *getPlatforms()[index];
+    }
+    throw OpenMMException("Invalid platform index");
 }
 
 Platform& Platform::getPlatformByName(const string& name) {

openmmapi/include/OpenMM.h

@@ -56,6 +56,7 @@
 #include "openmm/LocalEnergyMinimizer.h"
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/MonteCarloBarostat.h"
+#include "openmm/MonteCarloMembraneBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"

openmmapi/include/openmm/AndersenThermostat.h

@@ -35,6 +35,7 @@
 #include "Force.h"
 #include <string>
 #include "internal/windowsExport.h"
+#include "openmm/internal/OSRngSeed.h"
 
 namespace OpenMM {
 
@@ -113,10 +114,23 @@ public:
      * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
      * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
      * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
      */
     void setRandomNumberSeed(int seed) {
         randomNumberSeed = seed;
     }
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/BrownianIntegrator.h

@@ -49,7 +49,7 @@ public:
      * 
      * @param temperature    the temperature of the heat bath (in Kelvin)
      * @param frictionCoeff  the friction coefficient which couples the system to the heat bath, measured in 1/ps
-     * @param stepSize       the step size with which to integrator the system (in picoseconds)
+     * @param stepSize       the step size with which to integrate the system (in picoseconds)
      */
     BrownianIntegrator(double temperature, double frictionCoeff, double stepSize);
     /**
@@ -99,6 +99,10 @@ public:
      * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
      * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
      * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
      */
     void setRandomNumberSeed(int seed) {
         randomNumberSeed = seed;

openmmapi/include/openmm/CMAPTorsionForce.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -148,6 +148,26 @@ public:
      * @param b4    the index of the fourth particle forming the second torsion
      */
     void setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4);
+    /**
+     * Update the map and torsion parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
+     * to copy them over to the Context.
+     *
+     * The only information that can be updated with this method is the energy values for a map, and the map index
+     * for a torsion.  The size of a map and the set of particles involved in a torsion cannot be changed.  Also,
+     * new bonds and torsions cannot be added.
+     */
+    void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CMMotionRemover.h

@@ -61,6 +61,15 @@ public:
     void setFrequency(int freq) {
         frequency = freq;
     }
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/Context.h

@@ -182,8 +182,9 @@ public:
      * Set the vectors defining the axes of the periodic box (measured in nm).  They will affect
      * any Force that uses periodic boundary conditions.
      *
-     * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
-     * x, y, and z axes respectively.  Future releases may support arbitrary triclinic boxes.
+     * Triclinic boxes are supported, but the vectors must satisfy certain requirements.  In particular,
+     * a must point in the x direction, b must point "mostly" in the y direction, and c must point "mostly"
+     * in the z direction.  See the documentation for details.
      *
      * @param a      the vector defining the first edge of the periodic box
      * @param b      the vector defining the second edge of the periodic box

openmmapi/include/openmm/CustomAngleForce.h

@@ -65,7 +65,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  */
 
@@ -194,7 +194,7 @@ public:
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-angle parameters.
@@ -202,6 +202,15 @@ public:
      * the Context.  The set of particles involved in a angle cannot be changed, nor can new angles be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomBondForce.h

@@ -65,7 +65,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  */
 
@@ -191,7 +191,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-bond parameters.
@@ -199,6 +199,15 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -89,7 +89,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  *
  * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values.  You specify the function by
@@ -289,7 +289,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-bond parameters.
@@ -297,6 +297,15 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomExternalForce.h

@@ -68,7 +68,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  */
 
@@ -191,7 +191,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-particle parameters.
@@ -199,6 +199,15 @@ public:
      * the Context.  Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomGBForce.h

@@ -129,7 +129,7 @@ namespace OpenMM {
  * particular piece of the computation.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.  In expressions for
  * particle pair calculations, the names of per-particle parameters and computed values
  * have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles.  As seen in the above example,
@@ -515,7 +515,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-particle parameters.
@@ -523,6 +523,15 @@ public:
      * the Context.  Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return nonbondedMethod == CustomGBForce::CutoffPeriodic;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomHbondForce.h

@@ -89,7 +89,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  *
  * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values.  You specify the function by
@@ -435,7 +435,7 @@ public:
      * Update the per-donor and per-acceptor parameters in a Context to match those stored in this Force object.  This method
      * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
      * Simply call setDonorParameters() and setAcceptorParameters() to modify this object's parameters, then call
-     * updateParametersInState() to copy them over to the Context.
+     * updateParametersInContext() to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-donor and per-acceptor parameters.
      * All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only
@@ -443,6 +443,15 @@ public:
      * new donors or acceptors be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return nonbondedMethod == CustomHbondForce::CutoffPeriodic;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -474,7 +483,7 @@ public:
     GroupInfo() : p1(-1), p2(-1), p3(-1) {
     }
     GroupInfo(int p1, int p2, int p3, const std::vector<double>& parameters) :
-        p1(p1), p2(p2), p3(p3), parameters(parameters) {
+        parameters(parameters), p1(p1), p2(p2), p3(p3) {
     }
 };
 

openmmapi/include/openmm/CustomIntegrator.h

@@ -204,7 +204,7 @@ namespace OpenMM {
  * the force from a single force group, or a random number.
  * 
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.  An expression
  * may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
  */
@@ -302,6 +302,13 @@ public:
      * @return the current value of the variable
      */
     double getGlobalVariable(int index) const;
+    /**
+     * Get the current value of a global variable, specified by name.
+     *
+     * @param name    the name of the variable to get
+     * @return the current value of the parameter
+     */
+    double getGlobalVariableByName(const std::string& name) const;
     /**
      * Set the value of a global variable.
      * 
@@ -324,6 +331,14 @@ public:
      *                are stored into this
      */
     void getPerDofVariable(int index, std::vector<Vec3>& values) const;
+    /**
+     * Get the value of a per-DOF variable, specified by name.
+     *
+     * @param name    the name of the variable to get
+     * @param values  the values of the variable for all degrees of freedom
+     *                are stored into this
+     */
+    void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
     /**
      * Set the value of a per-DOF variable.
      * 
@@ -429,6 +444,10 @@ public:
      * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
      * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
      * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
      */
     void setRandomNumberSeed(int seed) {
         randomNumberSeed = seed;

openmmapi/include/openmm/CustomManyParticleForce.h

@@ -149,7 +149,7 @@ namespace OpenMM {
  * still only be evaluated once for each triplet, so it must still be symmetric with respect to p2 and p3.
  * 
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * The names of per-particle parameters have the suffix "1", "2", etc. appended to them to indicate the values for the multiple interacting particles.
  * For example, if you define a per-particle parameter called "charge", then the variable "charge2" is the charge of particle p2.
@@ -461,6 +461,15 @@ public:
      * the parameters of existing ones.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return nonbondedMethod == CustomManyParticleForce::CutoffPeriodic;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -120,7 +120,7 @@ namespace OpenMM {
  * frequently, the long range correction can be very slow.  For this reason, it is disabled by default.
  * 
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.  The names of per-particle parameters
  * have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles.  As seen in the above example,
  * the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
@@ -464,6 +464,15 @@ public:
      * the parameters of existing ones.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return nonbondedMethod == CustomNonbondedForce::CutoffPeriodic;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/CustomTorsionForce.h

@@ -65,7 +65,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  */
 
@@ -197,7 +197,7 @@ public:
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-torsion parameters.
@@ -205,6 +205,15 @@ public:
      * the Context.  The set of particles involved in a torsion cannot be changed, nor can new torsions be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

openmmapi/include/openmm/Force.h

@@ -78,6 +78,14 @@ public:
      * @param group    the group index.  Legal values are between 0 and 31 (inclusive).
      */
     void setForceGroup(int group);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions. This method should be overridden for all Force subclasses, or
+     * a OpenMM::OpenMMException will be thrown
+     *
+     * @return true if Force uses periodic boundaries or false if it does not
+     */
+    virtual bool usesPeriodicBoundaryConditions() const;
 protected:
     friend class ContextImpl;
     /**