Added index bounds checking to lots of methods

openmmapi/include/openmm/System.h

@@ -97,9 +97,7 @@ class OPENMM_EXPORT System {
      * 
      * @param index the index of the particle for which to get the mass
      */
-    double getParticleMass(int index) const {
-        return masses[index];
-    }
+    double getParticleMass(int index) const;
     /**
      * Set the mass (in atomic mass units) of a particle.  If the mass is 0, Integrators will ignore
      * the particle and not modify its position or velocity.  This is most often
@@ -109,9 +107,7 @@ class OPENMM_EXPORT System {
      * @param index  the index of the particle for which to set the mass
      * @param mass   the mass of the particle
      */
-    void setParticleMass(int index, double mass) {
-        masses[index] = mass;
-    }
+    void setParticleMass(int index, double mass);
     /**
      * Set a particle to be a virtual site.  The VirtualSite object should have
      * been created on the heap with the "new" operator.  The System takes over
@@ -195,17 +191,13 @@ class OPENMM_EXPORT System {
      * 
      * @param index  the index of the Force to get
      */
-    const Force& getForce(int index) const {
-        return *forces[index];
-    }
+    const Force& getForce(int index) const;
     /**
      * Get a writable reference to one of the Forces in this System.
      *
      * @param index  the index of the Force to get
      */
-    Force& getForce(int index) {
-        return *forces[index];
-    }
+    Force& getForce(int index);
     /**
      * Get the default values of the vectors defining the axes of the periodic box (measured in nm).  Any newly
      * created Context will have its box vectors set to these.  They will affect

tests/AssertionUtilities.h → openmmapi/include/openmm/internal/AssertionUtilities.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,23 +36,15 @@
  * This file provides a variety of macros useful in test cases.
  */
 
-#include "openmm/OpenMMException.h"
 #include <cmath>
 #include <string>
 #include <sstream>
 
-void throwException(const char* file, int line, const std::string& details) {
-    std::string fn(file);
-    std::string::size_type pos = fn.find_last_of("/\\");
-    if (pos+1>=fn.size())
-        pos=0;
-    std::string filename(fn,(int)(pos+1),(int)(fn.size()-(pos+1)));
-    std::stringstream message;
-    message << "Assertion failure at "<<filename<<":"<<line;
-    if (details.size() > 0)
-        message << ".  "<<details;
-    throw OpenMM::OpenMMException(message.str());
-}
+namespace OpenMM {
+
+void throwException(const char* file, int line, const std::string& details);
+
+} // namespace OpenMM
 
 #define ASSERT(cond) {if (!(cond)) throwException(__FILE__, __LINE__, "");};
 
@@ -64,4 +56,6 @@ void throwException(const char* file, int line, const std::string& details) {
 
 #define ASSERT_USUALLY_EQUAL_TOL(expected, found, tol) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found)<<" (This test is stochastic and may occasionally fail)"; throwException(__FILE__, __LINE__, details.str());}};
 
+#define ASSERT_VALID_INDEX(index, vector) {if (index < 0 || index >= vector.size()) throwException(__FILE__, __LINE__, "Index out of range");};
+
 #endif /*OPENMM_ASSERTIONUTILITIES_H_*/

openmmapi/src/AssertionUtilities.cpp

@@ -0,0 +1,56 @@
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2012 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 file provides a variety of macros useful in test cases.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/OpenMMException.h"
+#include <string>
+#include <sstream>
+
+namespace OpenMM {
+
+void throwException(const char* file, int line, const std::string& details) {
+    std::string fn(file);
+    std::string::size_type pos = fn.find_last_of("/\\");
+    if (pos+1>=fn.size())
+        pos=0;
+    std::string filename(fn,(int)(pos+1),(int)(fn.size()-(pos+1)));
+    std::stringstream message;
+    message << "Assertion failure at "<<filename<<":"<<line;
+    if (details.size() > 0)
+        message << ".  "<<details;
+    throw OpenMMException(message.str());
+}
+
+} // namespace OpenMM

openmmapi/src/CMAPTorsionForce.cpp

@@ -32,6 +32,7 @@
 #include "openmm/Force.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/CMAPTorsionForce.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/CMAPTorsionForceImpl.h"
 
 using namespace OpenMM;
@@ -47,11 +48,13 @@ int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
 }
 
 void CMAPTorsionForce::getMapParameters(int index, int& size, std::vector<double>& energy) const {
+    ASSERT_VALID_INDEX(index, maps);
     size = maps[index].size;
     energy = maps[index].energy;
 }
 
 void CMAPTorsionForce::setMapParameters(int index, int size, const std::vector<double>& energy) {
+    ASSERT_VALID_INDEX(index, maps);
     if (energy.size() != size*size)
         throw OpenMMException("CMAPTorsionForce: incorrect number of energy values");
     maps[index].size = size;
@@ -64,6 +67,7 @@ int CMAPTorsionForce::addTorsion(int map, int a1, int a2, int a3, int a4, int b1
 }
 
 void CMAPTorsionForce::getTorsionParameters(int index, int& map, int& a1, int& a2, int& a3, int& a4, int& b1, int& b2, int& b3, int& b4) const {
+    ASSERT_VALID_INDEX(index, torsions);
     map = torsions[index].map;
     a1 = torsions[index].a1;
     a2 = torsions[index].a2;
@@ -76,6 +80,7 @@ void CMAPTorsionForce::getTorsionParameters(int index, int& map, int& a1, int& a
 }
 
 void CMAPTorsionForce::setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) {
+    ASSERT_VALID_INDEX(index, torsions);
     torsions[index].map = map;
     torsions[index].a1 = a1;
     torsions[index].a2 = a2;

openmmapi/src/CustomAngleForce.cpp

@@ -32,6 +32,7 @@
 #include "openmm/Force.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/CustomAngleForce.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/CustomAngleForceImpl.h"
 #include <cmath>
 #include <map>
@@ -60,10 +61,12 @@ int CustomAngleForce::addPerAngleParameter(const string& name) {
 }
 
 const string& CustomAngleForce::getPerAngleParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, parameters);
     return parameters[index].name;
 }
 
 void CustomAngleForce::setPerAngleParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, parameters);
     parameters[index].name = name;
 }
 
@@ -73,18 +76,22 @@ int CustomAngleForce::addGlobalParameter(const string& name, double defaultValue
 }
 
 const string& CustomAngleForce::getGlobalParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].name;
 }
 
 void CustomAngleForce::setGlobalParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].name = name;
 }
 
 double CustomAngleForce::getGlobalParameterDefaultValue(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].defaultValue;
 }
 
 void CustomAngleForce::setGlobalParameterDefaultValue(int index, double defaultValue) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].defaultValue = defaultValue;
 }
 
@@ -94,13 +101,15 @@ int CustomAngleForce::addAngle(int particle1, int particle2, int particle3, cons
 }
 
 void CustomAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, std::vector<double>& parameters) const {
+    ASSERT_VALID_INDEX(index, angles);
     particle1 = angles[index].particle1;
     particle2 = angles[index].particle2;
     particle3 = angles[index].particle3;
     parameters = angles[index].parameters;
 }
 
 void CustomAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, const vector<double>& parameters) {
+    ASSERT_VALID_INDEX(index, angles);
     angles[index].parameters = parameters;
     angles[index].particle1 = particle1;
     angles[index].particle2 = particle2;

openmmapi/src/CustomBondForce.cpp

@@ -32,6 +32,7 @@
 #include "openmm/Force.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/CustomBondForce.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/CustomBondForceImpl.h"
 #include <cmath>
 #include <map>
@@ -60,10 +61,12 @@ int CustomBondForce::addPerBondParameter(const string& name) {
 }
 
 const string& CustomBondForce::getPerBondParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, parameters);
     return parameters[index].name;
 }
 
 void CustomBondForce::setPerBondParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, parameters);
     parameters[index].name = name;
 }
 
@@ -73,18 +76,22 @@ int CustomBondForce::addGlobalParameter(const string& name, double defaultValue)
 }
 
 const string& CustomBondForce::getGlobalParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].name;
 }
 
 void CustomBondForce::setGlobalParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].name = name;
 }
 
 double CustomBondForce::getGlobalParameterDefaultValue(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].defaultValue;
 }
 
 void CustomBondForce::setGlobalParameterDefaultValue(int index, double defaultValue) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].defaultValue = defaultValue;
 }
 
@@ -94,12 +101,14 @@ int CustomBondForce::addBond(int particle1, int particle2, const vector<double>&
 }
 
 void CustomBondForce::getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const {
+    ASSERT_VALID_INDEX(index, bonds);
     particle1 = bonds[index].particle1;
     particle2 = bonds[index].particle2;
     parameters = bonds[index].parameters;
 }
 
 void CustomBondForce::setBondParameters(int index, int particle1, int particle2, const vector<double>& parameters) {
+    ASSERT_VALID_INDEX(index, bonds);
     bonds[index].parameters = parameters;
     bonds[index].particle1 = particle1;
     bonds[index].particle2 = particle2;

openmmapi/src/CustomExternalForce.cpp

@@ -32,6 +32,7 @@
 #include "openmm/Force.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/CustomExternalForce.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/CustomExternalForceImpl.h"
 #include <cmath>
 #include <map>
@@ -60,10 +61,12 @@ int CustomExternalForce::addPerParticleParameter(const string& name) {
 }
 
 const string& CustomExternalForce::getPerParticleParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, parameters);
     return parameters[index].name;
 }
 
 void CustomExternalForce::setPerParticleParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, parameters);
     parameters[index].name = name;
 }
 
@@ -73,18 +76,22 @@ int CustomExternalForce::addGlobalParameter(const string& name, double defaultVa
 }
 
 const string& CustomExternalForce::getGlobalParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].name;
 }
 
 void CustomExternalForce::setGlobalParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].name = name;
 }
 
 double CustomExternalForce::getGlobalParameterDefaultValue(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
     return globalParameters[index].defaultValue;
 }
 
 void CustomExternalForce::setGlobalParameterDefaultValue(int index, double defaultValue) {
+    ASSERT_VALID_INDEX(index, globalParameters);
     globalParameters[index].defaultValue = defaultValue;
 }
 
@@ -94,11 +101,13 @@ int CustomExternalForce::addParticle(int particle, const vector<double>& paramet
 }
 
 void CustomExternalForce::getParticleParameters(int index, int& particle, std::vector<double>& parameters) const {
+    ASSERT_VALID_INDEX(index, particles);
     particle = particles[index].particle;
     parameters = particles[index].parameters;
 }
 
 void CustomExternalForce::setParticleParameters(int index, int particle, const vector<double>& parameters) {
+    ASSERT_VALID_INDEX(index, particles);
     particles[index].parameters = parameters;
     particles[index].particle = particle;
 }