Merged fork with latest original master

openmmapi/include/openmm/PeriodicTorsionForce.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) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -108,20 +108,24 @@ public:
      * in a torsion cannot be changed, nor can new torsions be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * 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;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class PeriodicTorsionInfo;
     std::vector<PeriodicTorsionInfo> periodicTorsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/RBTorsionForce.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) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -117,20 +117,24 @@ public:
      * in a torsion cannot be changed, nor can new torsions be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * 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;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class RBTorsionInfo;
     std::vector<RBTorsionInfo> rbTorsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/System.h

@@ -243,7 +243,7 @@ public:
      *
      * @return true if at least one force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions();
+    bool usesPeriodicBoundaryConditions() const;
 private:
     class ConstraintInfo;
     Vec3 periodicBoxVectors[3];

openmmapi/include/openmm/TabulatedFunction.h

@@ -40,10 +40,10 @@ namespace OpenMM {
 /**
  * A TabulatedFunction uses a set of tabulated values to define a mathematical function.
  * It can be used by various custom forces.
- * 
+ *
  * TabulatedFunction is an abstract class with concrete subclasses for more specific
  * types of functions.  There are subclasses for:
- * 
+ *
  * <ul>
  * <li>1, 2, and 3 dimensional functions.  The dimensionality of a function means
  * the number of input arguments it takes.</li>
@@ -69,7 +69,7 @@ class OPENMM_EXPORT Continuous1DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Continuous1DFunction f(x) based on a set of tabulated values.
-     * 
+     *
      * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
      *                       and max.  A natural cubic spline is used to interpolate between the tabulated values.
      *                       The function is assumed to be zero for x &lt; min or x &gt; max.
@@ -80,11 +80,11 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
-     *                       and max.  A natural cubic spline is used to interpolate between the tabulated values.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @param min            the value of x corresponding to the first element of values
-     * @param max            the value of x corresponding to the last element of values
+     * @param[out] values         the tabulated values of the function f(x) at uniformly spaced values of x between min
+     *                            and max.  A natural cubic spline is used to interpolate between the tabulated values.
+     *                            The function is assumed to be zero for x &lt; min or x &gt; max.
+     * @param[out] min            the value of x corresponding to the first element of values
+     * @param[out] max            the value of x corresponding to the last element of values
      */
     void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
     /**
@@ -113,7 +113,7 @@ class OPENMM_EXPORT Continuous2DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Continuous2DFunction f(x,y) based on a set of tabulated values.
-     * 
+     *
      * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
      *                   and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
      *                   The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
@@ -129,16 +129,16 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
-     *                   and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
-     *                   The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
-     *                   values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
-     * @param xsize      the number of table elements along the x direction
-     * @param ysize      the number of table elements along the y direction
-     * @param xmin       the value of x corresponding to the first element of values
-     * @param xmax       the value of x corresponding to the last element of values
-     * @param ymin       the value of y corresponding to the first element of values
-     * @param ymax       the value of y corresponding to the last element of values
+     * @param[out] values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
+     *                        and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
+     *                        The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
+     *                        values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] ymax       the value of y corresponding to the last element of values
      */
     void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
     /**
@@ -173,7 +173,7 @@ class OPENMM_EXPORT Continuous3DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
-     * 
+     *
      * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
      *                   and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
      *                   A natural cubic spline is used to interpolate between the tabulated values.  The function is
@@ -194,21 +194,21 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
-     *                   and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
-     *                   A natural cubic spline is used to interpolate between the tabulated values.  The function is
-     *                   assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
-     *                   that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
-     *                   This must be of length xsize*ysize*zsize.
-     * @param xsize      the number of table elements along the x direction
-     * @param ysize      the number of table elements along the y direction
-     * @param ysize      the number of table elements along the z direction
-     * @param xmin       the value of x corresponding to the first element of values
-     * @param xmax       the value of x corresponding to the last element of values
-     * @param ymin       the value of y corresponding to the first element of values
-     * @param ymax       the value of y corresponding to the last element of values
-     * @param zmin       the value of z corresponding to the first element of values
-     * @param zmax       the value of z corresponding to the last element of values
+     * @param[out] values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
+     *                        and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
+     *                        A natural cubic spline is used to interpolate between the tabulated values.  The function is
+     *                        assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
+     *                        that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
+     *                        This must be of length xsize*ysize*zsize.
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] zsize      the number of table elements along the z direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] ymax       the value of y corresponding to the last element of values
+     * @param[out] zmin       the value of z corresponding to the first element of values
+     * @param[out] zmax       the value of z corresponding to the last element of values
      */
     void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const;
     /**
@@ -222,7 +222,7 @@ public:
      *                   This must be of length xsize*ysize*zsize.
      * @param xsize      the number of table elements along the x direction
      * @param ysize      the number of table elements along the y direction
-     * @param ysize      the number of table elements along the z direction
+     * @param zsize      the number of table elements along the z direction
      * @param xmin       the value of x corresponding to the first element of values
      * @param xmax       the value of x corresponding to the last element of values
      * @param ymin       the value of y corresponding to the first element of values
@@ -250,14 +250,14 @@ class OPENMM_EXPORT Discrete1DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Discrete1DFunction f(x) based on a set of tabulated values.
-     * 
+     *
      * @param values         the tabulated values of the function f(x)
      */
     Discrete1DFunction(const std::vector<double>& values);
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values         the tabulated values of the function f(x)
+     * @param[out] values    the tabulated values of the function f(x)
      */
     void getFunctionParameters(std::vector<double>& values) const;
     /**
@@ -283,7 +283,7 @@ class OPENMM_EXPORT Discrete2DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Discrete2DFunction f(x,y) based on a set of tabulated values.
-     * 
+     *
      * @param xsize     the number of table elements along the x direction
      * @param ysize     the number of table elements along the y direction
      * @param values    the tabulated values of the function f(x,y), ordered so that
@@ -293,10 +293,10 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param xsize     the number of table elements along the x direction
-     * @param ysize     the number of table elements along the y direction
-     * @param values    the tabulated values of the function f(x,y), ordered so that
-     *                  values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] values    the tabulated values of the function f(x,y), ordered so that
+     *                       values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
      */
     void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const;
     /**
@@ -326,7 +326,7 @@ class OPENMM_EXPORT Discrete3DFunction : public TabulatedFunction {
 public:
     /**
      * Create a Discrete3DFunction f(x,y,z) based on a set of tabulated values.
-     * 
+     *
      * @param xsize     the number of table elements along the x direction
      * @param ysize     the number of table elements along the y direction
      * @param zsize     the number of table elements along the z direction
@@ -337,11 +337,11 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param xsize     the number of table elements along the x direction
-     * @param ysize     the number of table elements along the y direction
-     * @param zsize     the number of table elements along the z direction
-     * @param values    the tabulated values of the function f(x,y,z), ordered so that
-     *                  values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] zsize     the number of table elements along the z direction
+     * @param[out] values    the tabulated values of the function f(x,y,z), ordered so that
+     *                       values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
      */
     void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const;
     /**

openmmapi/include/openmm/internal/OSRngSeed.h

-#ifndef OPENMM_OSRNGSEED_H_
+#ifndef OPENMM_OSRNGSEED_H_
 #define OPENMM_OSRNGSEED_H_
 
 

openmmapi/include/openmm/internal/timer.h

+#ifndef OPENMM_TIMER_H_
+#define OPENMM_TIMER_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   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) 2016 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This header provides a static function for querying the current system time in seconds.
+ * It is useful when profiling.
+ */
+
+#ifdef _MSC_VER
+    #include <Windows.h>
+    static double getCurrentTime() {
+        FILETIME ft;
+        GetSystemTimeAsFileTime(&ft); // 100-nanoseconds since 1-1-1601
+        ULARGE_INTEGER result;
+        result.LowPart = ft.dwLowDateTime;
+        result.HighPart = ft.dwHighDateTime;
+        return 1e-7*result.QuadPart;
+    }
+#else
+    #include <sys/time.h> 
+    static double getCurrentTime() {
+        struct timeval tod;
+        gettimeofday(&tod, 0);
+        return tod.tv_sec+1e-6*tod.tv_usec;
+    }
+#endif
+
+#endif /*OPENMM_TIMER_H_*/

openmmapi/src/CMAPTorsionForce.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) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-CMAPTorsionForce::CMAPTorsionForce() {
+CMAPTorsionForce::CMAPTorsionForce() : usePeriodic(false) {
 }
 
 int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
 void CMAPTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CMAPTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CMAPTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/ContextImpl.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) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     // Validate the list of properties.
 
     const vector<string>& platformProperties = platform->getPropertyNames();
+    map<string, string> validatedProperties;
     for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
+        string property = iter->first;
+        if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
+            property = platform->deprecatedPropertyReplacements[property];
         bool valid = false;
         for (int i = 0; i < (int) platformProperties.size(); i++)
-            if (platformProperties[i] == iter->first) {
+            if (platformProperties[i] == property) {
                 valid = true;
                 break;
             }
         if (!valid)
             throw OpenMMException("Illegal property name: "+iter->first);
+        validatedProperties[property] = iter->second;
     }
     
     // Find the list of kernels required.
@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
         try {
             this->platform = platform = candidatePlatforms[i].second;
-            platform->contextCreated(*this, properties);
+            platform->contextCreated(*this, validatedProperties);
             break;
         }
         catch (...) {
@@ -449,4 +454,5 @@ void ContextImpl::loadCheckpoint(istream& stream) {
         parameters[name] = value;
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
+    hasSetPositions = true;
 }

openmmapi/src/CustomAngleForce.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:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy) {
+CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomAngleForce::getEnergyFunction() const {
@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const {
 void CustomAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomBondForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy) {
+CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomBondForce::getEnergyFunction() const {
@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const {
 void CustomBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) {
+CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy), usePeriodic(false) {
 }
 
 CustomCentroidBondForce::~CustomCentroidBondForce() {
@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const {
 void CustomCentroidBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCentroidBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCentroidBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomCompoundBondForce.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) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) {
+CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy), usePeriodic(false) {
 }
 
 
@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const {
 void CustomCompoundBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCompoundBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCompoundBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomIntegrator.cpp

@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() {
 int CustomIntegrator::beginIfBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginIfBlock, "", expression));
+    computations.push_back(ComputationInfo(IfBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::beginWhileBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginWhileBlock, "", expression));
+    computations.push_back(ComputationInfo(WhileBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::endBlock() {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(EndBlock, "", ""));
+    computations.push_back(ComputationInfo(BlockEnd, "", ""));
     return computations.size()-1;
 }
 

openmmapi/src/CustomIntegratorUtilities.cpp

@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     for (int step = 0; step < numSteps; step++) {
         string expression;
         integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) {
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart) {
             // This step involves a condition.
 
             string lhs, rhs;
@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     vector<int> blockStart;
     blockEnd.resize(numSteps, -1);
     for (int step = 0; step < numSteps; step++) {
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
             blockStart.push_back(step);
-        else if (stepType[step] == CustomIntegrator::EndBlock) {
+        else if (stepType[step] == CustomIntegrator::BlockEnd) {
             if (blockStart.size() == 0) {
                 stringstream error("CustomIntegrator: Unexpected end of block at computation ");
                 error << step;
@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
             jumps[step] = -1;
             step = nextStep;
         }
-        else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
+        else if (stepType[step] == CustomIntegrator::IfBlockStart) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
 
             step++;
         }
-        else if (stepType[step] == CustomIntegrator::BeginWhileBlock && jumps[step] != -2) {
+        else if (stepType[step] == CustomIntegrator::WhileBlockStart && jumps[step] != -2) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);

openmmapi/src/CustomNonbondedForce.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) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -195,6 +195,9 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
 void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
     if (bondCutoff < 1)
         return;
+    for (int i = 0; i < (int) bonds.size(); ++i)
+        if (bonds[i].first < 0 || bonds[i].second < 0 || bonds[i].first >= particles.size() || bonds[i].second >= particles.size())
+            throw OpenMMException("createExclusionsFromBonds: Illegal particle index in list of bonds");
     vector<set<int> > exclusions(particles.size());
     vector<set<int> > bonded12(exclusions.size());
     for (int i = 0; i < (int) bonds.size(); ++i) {

openmmapi/src/CustomTorsionForce.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:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy) {
+CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomTorsionForce::getEnergyFunction() const {
@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const {
 void CustomTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicAngleForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicAngleForce::HarmonicAngleForce() {
+HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
 }
 
 int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const {
 void HarmonicAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicBondForce.cpp

@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicBondForce::HarmonicBondForce() {
+HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
 }
 
 int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const {
 void HarmonicBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/LocalEnergyMinimizer.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) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,6 +36,7 @@
 #include <cmath>
 #include <sstream>
 #include <vector>
+#include <algorithm>
 
 using namespace OpenMM;
 using namespace std;
@@ -108,7 +109,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
     if (x == NULL)
         throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
     double constraintTol = context.getIntegrator().getConstraintTolerance();
-    double k = tolerance/constraintTol;
+    double workingConstraintTol = std::max(1e-4, constraintTol);
+    double k = tolerance/workingConstraintTol;
 
     // Initialize the minimizer.
 
@@ -121,7 +123,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
 
     // Make sure the initial configuration satisfies all constraints.
 
-    context.applyConstraints(constraintTol);
+    context.applyConstraints(workingConstraintTol);
 
     // Record the initial positions and determine a normalization constant for scaling the tolerance.
 
@@ -162,14 +164,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
             if (error > maxError)
                 maxError = error;
         }
-        if (maxError <= constraintTol)
+        if (maxError <= workingConstraintTol)
             break; // All constraints are satisfied.
         context.setPositions(initialPos);
         if (maxError >= prevMaxError)
             break; // Further tightening the springs doesn't seem to be helping, so just give up.
         prevMaxError = maxError;
         k *= 10;
-        if (maxError > 100*constraintTol) {
+        if (maxError > 100*workingConstraintTol) {
             // We've gotten far enough from a valid state that we might have trouble getting
             // back, so reset to the original positions.
             
@@ -181,5 +183,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
         }
     }
     lbfgs_free(x);
+    
+    // If necessary, do a final constraint projection to make sure they are satisfied
+    // to the full precision requested by the user.
+    
+    if (constraintTol < workingConstraintTol)
+        context.applyConstraints(workingConstraintTol);
 }
 

openmmapi/src/MonteCarloAnisotropicBarostat.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:                                                              *
  *                                                                            *
@@ -34,8 +34,8 @@
 
 using namespace OpenMM;
 
-MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
-        defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
+MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
+        defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
     setRandomNumberSeed(0);
 }