Added lots of checks for invalid parameter values (#3286)

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

openmmapi/include/openmm/BrownianIntegrator.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) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -65,9 +65,7 @@ public:
      *
      * @param temp    the temperature of the heat bath, measured in Kelvin.
      */
-    void setTemperature(double temp) {
-        temperature = temp;
-    }
+    void setTemperature(double temp);
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
@@ -83,9 +81,7 @@ public:
      *
      * @param coeff    the friction coefficient, measured in 1/ps
      */
-    void setFriction(double coeff) {
-        friction = coeff;
-    }
+    void setFriction(double coeff);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/CMMotionRemover.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) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -58,9 +58,7 @@ public:
     /**
      * Set the frequency (in time steps) at which center of mass motion should be removed
      */
-    void setFrequency(int freq) {
-        frequency = freq;
-    }
+    void setFrequency(int freq);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.

openmmapi/include/openmm/LangevinIntegrator.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) 2008-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -65,9 +65,7 @@ public:
      *
      * @param temp    the temperature of the heat bath, measured in Kelvin
      */
-    void setTemperature(double temp) {
-        temperature = temp;
-    }
+    void setTemperature(double temp);
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
@@ -83,9 +81,7 @@ public:
      *
      * @param coeff    the friction coefficient, measured in 1/ps
      */
-    void setFriction(double coeff) {
-        friction = coeff;
-    }
+    void setFriction(double coeff);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/LangevinMiddleIntegrator.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) 2008-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -74,9 +74,7 @@ public:
      *
      * @param temp    the temperature of the heat bath, measured in Kelvin
      */
-    void setTemperature(double temp) {
-        temperature = temp;
-    }
+    void setTemperature(double temp);
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
@@ -92,9 +90,7 @@ public:
      *
      * @param coeff    the friction coefficient, measured in 1/ps
      */
-    void setFriction(double coeff) {
-        friction = coeff;
-    }
+    void setFriction(double coeff);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/MonteCarloAnisotropicBarostat.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) 2010-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -114,9 +114,7 @@ public:
      *
      * @param pressure   the default pressure acting on the system, measured in bar.
      */
-    void setDefaultPressure(const Vec3& pressure) {
-        defaultPressure = pressure;
-    }
+    void setDefaultPressure(const Vec3& pressure);
     /**
      * Get whether to allow the X dimension of the periodic box to change size.
      */
@@ -146,9 +144,7 @@ public:
      * Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
      */
-    void setFrequency(int freq) {
-        frequency = freq;
-    }
+    void setFrequency(int freq);
     /**
      * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
@@ -161,9 +157,7 @@ public:
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setDefaultTemperature(double temp) {
-        defaultTemperature = temp;
-    }
+    void setDefaultTemperature(double temp);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/MonteCarloBarostat.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) 2010-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -88,9 +88,7 @@ public:
      *
      * @param pressure   the default pressure acting on the system, measured in bar.
      */
-    void setDefaultPressure(double pressure) {
-        defaultPressure = pressure;
-    }
+    void setDefaultPressure(double pressure);
     /**
      * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
@@ -102,9 +100,7 @@ public:
      * Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
      */
-    void setFrequency(int freq) {
-        frequency = freq;
-    }
+    void setFrequency(int freq);
     /**
      * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
@@ -117,9 +113,7 @@ public:
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setDefaultTemperature(double temp) {
-        defaultTemperature = temp;
-    }
+    void setDefaultTemperature(double temp);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/MonteCarloFlexibleBarostat.h

@@ -101,9 +101,7 @@ public:
      *
      * @param pressure   the default pressure acting on the system, measured in bar.
      */
-    void setDefaultPressure(double pressure) {
-        defaultPressure = pressure;
-    }
+    void setDefaultPressure(double pressure);
     /**
      * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
@@ -115,9 +113,7 @@ public:
      * Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
      */
-    void setFrequency(int freq) {
-        frequency = freq;
-    }
+    void setFrequency(int freq);
     /**
      * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
@@ -130,9 +126,7 @@ public:
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setDefaultTemperature(double temp) {
-        defaultTemperature = temp;
-    }
+    void setDefaultTemperature(double temp);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/MonteCarloMembraneBarostat.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) 2010-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -144,9 +144,7 @@ public:
      *
      * @param pressure   the default pressure acting on the system, measured in bar.
      */
-    void setDefaultPressure(double pressure) {
-        defaultPressure = pressure;
-    }
+    void setDefaultPressure(double pressure);
     /**
      * Get the default surface tension acting on the system (in bar*nm).
      *
@@ -161,9 +159,7 @@ public:
      *
      * @param surfaceTension   the default surface tension acting on the system, measured in bar.
      */
-    void setDefaultSurfaceTension(double surfaceTension) {
-        defaultSurfaceTension = surfaceTension;
-    }
+    void setDefaultSurfaceTension(double surfaceTension);
     /**
      * Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
@@ -175,9 +171,7 @@ public:
      * Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted.  If this is set to
      * 0, the barostat is disabled.
      */
-    void setFrequency(int freq) {
-        frequency = freq;
-    }
+    void setFrequency(int freq);
     /**
      * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
@@ -190,9 +184,7 @@ public:
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setDefaultTemperature(double temp) {
-        defaultTemperature = temp;
-    }
+    void setDefaultTemperature(double temp);
     /**
      * Get the mode specifying the behavior of the X and Y axes.
      */

openmmapi/include/openmm/VariableLangevinIntegrator.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) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -79,9 +79,7 @@ public:
      *
      * @param temp    the temperature of the heat bath, measured in Kelvin
      */
-    void setTemperature(double temp) {
-        temperature = temp;
-    }
+    void setTemperature(double temp);
     /**
      * Get the friction coefficient which determines how strongly the system is coupled to
      * the heat bath (in inverse ps).
@@ -97,9 +95,7 @@ public:
      *
      * @param coeff    the friction coefficient, measured in 1/ps
      */
-    void setFriction(double coeff) {
-        friction = coeff;
-    }
+    void setFriction(double coeff);
     /**
      * Get the error tolerance.
      */
@@ -109,9 +105,7 @@ public:
     /**
      * Set the error tolerance.
      */
-    void setErrorTolerance(double tol) {
-        errorTol = tol;
-    }
+    void setErrorTolerance(double tol);
     /**
      * Get the maximum step size the integrator will ever use, in ps.  If this
      * is 0 (the default), no limit will be applied to step sizes.
@@ -123,9 +117,7 @@ public:
      * Set the maximum step size the integrator will ever use, in ps.  If this
      * is 0 (the default), no limit will be applied to step sizes.
      */
-    void setMaximumStepSize(double size) {
-        maxStepSize = size;
-    }
+    void setMaximumStepSize(double size);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/VariableVerletIntegrator.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) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -79,9 +79,7 @@ public:
     /**
      * Set the error tolerance.
      */
-    void setErrorTolerance(double tol) {
-        errorTol = tol;
-    }
+    void setErrorTolerance(double tol);
     /**
      * Get the maximum step size the integrator will ever use, in ps.  If this
      * is 0 (the default), no limit will be applied to step sizes.
@@ -93,9 +91,7 @@ public:
      * Set the maximum step size the integrator will ever use, in ps.  If this
      * is 0 (the default), no limit will be applied to step sizes.
      */
-    void setMaximumStepSize(double size) {
-        maxStepSize = size;
-    }
+    void setMaximumStepSize(double size);
     /**
      * Advance a simulation through time by taking a series of time steps.
      *

openmmapi/src/AndersenThermostatImpl.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) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,6 +32,7 @@
 #include "openmm/internal/AndersenThermostatImpl.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/Integrator.h"
+#include "openmm/OpenMMException.h"
 #include "openmm/System.h"
 #include "openmm/kernels.h"
 #include <vector>
@@ -43,6 +44,10 @@ AndersenThermostatImpl::AndersenThermostatImpl(const AndersenThermostat& owner)
 }
 
 void AndersenThermostatImpl::initialize(ContextImpl& context) {
+    if (owner.getDefaultTemperature() < 0)
+        throw OpenMMException("AndersenThermostat: temperature cannot be negative");
+    if (owner.getDefaultCollisionFrequency() < 0)
+        throw OpenMMException("AndersenThermostat: collision frequency cannot be negative");
     kernel = context.getPlatform().createKernel(ApplyAndersenThermostatKernel::Name(), context);
     kernel.getAs<ApplyAndersenThermostatKernel>().initialize(context.getSystem(), owner);
 }

openmmapi/src/BrownianIntegrator.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) 2008-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -57,6 +57,18 @@ void BrownianIntegrator::initialize(ContextImpl& contextRef) {
     kernel.getAs<IntegrateBrownianStepKernel>().initialize(contextRef.getSystem(), *this);
 }
 
+void BrownianIntegrator::setTemperature(double temp) {
+    if (temp < 0)
+        throw OpenMMException("Temperature cannot be negative");
+    temperature = temp;
+}
+
+void BrownianIntegrator::setFriction(double coeff) {
+    if (coeff <= 0)
+        throw OpenMMException("Friction must be positive");
+    friction = coeff;
+}
+
 void BrownianIntegrator::cleanup() {
     kernel = Kernel();
 }

openmmapi/src/CMAPTorsionForceImpl.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) 2010-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,6 +37,7 @@
 #include "openmm/internal/SplineFitter.h"
 #include "openmm/kernels.h"
 #include <cmath>
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;
@@ -48,6 +49,25 @@ CMAPTorsionForceImpl::~CMAPTorsionForceImpl() {
 }
 
 void CMAPTorsionForceImpl::initialize(ContextImpl& context) {
+    const System& system = context.getSystem();
+    for (int i = 0; i < owner.getNumTorsions(); i++) {
+        int particle[8], map;
+        owner.getTorsionParameters(i, map, particle[0], particle[1], particle[2], particle[3], particle[4], particle[5], particle[6], particle[7]);
+        if (map < 0 || map >= owner.getNumMaps()) {
+            stringstream msg;
+            msg << "CMAPTorsionForce: Illegal map index for a torsion: ";
+            msg << map;
+            throw OpenMMException(msg.str());
+        }
+        for (int j = 0; j < 8; j++) {
+            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
+                stringstream msg;
+                msg << "CMAPTorsionForce: Illegal particle index for a torsion: ";
+                msg << particle[j];
+                throw OpenMMException(msg.str());
+            }
+        }
+    }
     kernel = context.getPlatform().createKernel(CalcCMAPTorsionForceKernel::Name(), context);
     kernel.getAs<CalcCMAPTorsionForceKernel>().initialize(context.getSystem(), owner);
 }

openmmapi/src/CMMotionRemover.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,11 +30,19 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/CMMotionRemover.h"
+#include "openmm/OpenMMException.h"
 #include "openmm/internal/CMMotionRemoverImpl.h"
 
 using namespace OpenMM;
 
-CMMotionRemover::CMMotionRemover(int frequency) : frequency(frequency) {
+CMMotionRemover::CMMotionRemover(int frequency) {
+    setFrequency(frequency);
+}
+
+void CMMotionRemover::setFrequency(int freq) {
+    if (freq <= 0)
+        throw OpenMMException("CMMotionRemover: frequency must be positive");
+    frequency = freq;
 }
 
 ForceImpl* CMMotionRemover::createImpl() const {

openmmapi/src/CustomAngleForceImpl.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) 2010-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -57,25 +57,15 @@ void CustomAngleForceImpl::initialize(ContextImpl& context) {
     vector<double> parameters;
     int numParameters = owner.getNumPerAngleParameters();
     for (int i = 0; i < owner.getNumAngles(); i++) {
-        int particle1, particle2, particle3;
-        owner.getAngleParameters(i, particle1, particle2, particle3, parameters);
-        if (particle1 < 0 || particle1 >= system.getNumParticles()) {
+        int particle[3];
+        owner.getAngleParameters(i, particle[0], particle[1], particle[2], parameters);
+        for (int j = 0; j < 3; j++) {
+            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomAngleForce: Illegal particle index for an angle: ";
-            msg << particle1;
+                msg << particle[j];
                 throw OpenMMException(msg.str());
             }
-        if (particle2 < 0 || particle2 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomAngleForce: Illegal particle index for an angle: ";
-            msg << particle2;
-            throw OpenMMException(msg.str());
-        }
-        if (particle3 < 0 || particle3 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomAngleForce: Illegal particle index for an angle: ";
-            msg << particle3;
-            throw OpenMMException(msg.str());
         }
         if (parameters.size() != numParameters) {
             stringstream msg;

openmmapi/src/CustomBondForceImpl.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -58,19 +58,15 @@ void CustomBondForceImpl::initialize(ContextImpl& context) {
     vector<double> parameters;
     int numParameters = owner.getNumPerBondParameters();
     for (int i = 0; i < owner.getNumBonds(); i++) {
-        int particle1, particle2;
-        owner.getBondParameters(i, particle1, particle2, parameters);
-        if (particle1 < 0 || particle1 >= system.getNumParticles()) {
+        int particle[2];
+        owner.getBondParameters(i, particle[0], particle[1], parameters);
+        for (int j = 0; j < 2; j++) {
+            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
                 stringstream msg;
                 msg << "CustomBondForce: Illegal particle index for a bond: ";
-            msg << particle1;
+                msg << particle[j];
                 throw OpenMMException(msg.str());
             }
-        if (particle2 < 0 || particle2 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomBondForce: Illegal particle index for a bond: ";
-            msg << particle2;
-            throw OpenMMException(msg.str());
         }
         if (parameters.size() != numParameters) {
             stringstream msg;

openmmapi/src/CustomTorsionForceImpl.cpp

@@ -58,31 +58,15 @@ void CustomTorsionForceImpl::initialize(ContextImpl& context) {
     vector<double> parameters;
     int numParameters = owner.getNumPerTorsionParameters();
     for (int i = 0; i < owner.getNumTorsions(); i++) {
-        int particle1, particle2, particle3, particle4;
-        owner.getTorsionParameters(i, particle1, particle2, particle3, particle4, parameters);
-        if (particle1 < 0 || particle1 >= system.getNumParticles()) {
+        int particle[4];
+        owner.getTorsionParameters(i, particle[0], particle[1], particle[2], particle[3], parameters);
+        for (int j = 0; j < 4; j++) {
+            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
                 stringstream msg;
-            msg << "CustomTorsionForce: Illegal particle index for an torsion: ";
-            msg << particle1;
+                msg << "CustomTorsionForce: Illegal particle index for a torsion: ";
+                msg << particle[j];
                 throw OpenMMException(msg.str());
             }
-        if (particle2 < 0 || particle2 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomTorsionForce: Illegal particle index for an torsion: ";
-            msg << particle2;
-            throw OpenMMException(msg.str());
-        }
-        if (particle3 < 0 || particle3 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomTorsionForce: Illegal particle index for an torsion: ";
-            msg << particle3;
-            throw OpenMMException(msg.str());
-        }
-        if (particle4 < 0 || particle4 >= system.getNumParticles()) {
-            stringstream msg;
-            msg << "CustomTorsionForce: Illegal particle index for an torsion: ";
-            msg << particle4;
-            throw OpenMMException(msg.str());
         }
         if (parameters.size() != numParameters) {
             stringstream msg;

openmmapi/src/GBSAOBCForceImpl.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -52,6 +52,14 @@ void GBSAOBCForceImpl::initialize(ContextImpl& context) {
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("GBSAOBCForce: The cutoff distance cannot be greater than half the periodic box size.");
     }
+    for (int i = 0; i < owner.getNumParticles(); i++) {
+        double charge, radius, scalingFactor;
+        owner.getParticleParameters(i, charge, radius, scalingFactor);
+        if (radius <= 0)
+            throw OpenMMException("GBSAOBCForce: particle radius must be positive");
+        if (scalingFactor <= 0)
+            throw OpenMMException("GBSAOBCForce: particle scaling factor must be positive");
+    }
     kernel.getAs<CalcGBSAOBCForceKernel>().initialize(context.getSystem(), owner);
 }
 

openmmapi/src/GayBerneForceImpl.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) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -73,34 +73,42 @@ void GayBerneForceImpl::initialize(ContextImpl& context) {
             msg << yparticle;
             throw OpenMMException(msg.str());
         }
+        if (sigma < 0)
+            throw OpenMMException("GayBerneForce: sigma for a particle cannot be negative");
+        if (epsilon < 0)
+            throw OpenMMException("GayBerneForce: epsilon for a particle cannot be negative");
+        if (rx <= 0 || ry <= 0 || rz <= 0)
+            throw OpenMMException("GayBerneForce: radii for a particle must be positive");
+        if (ex <= 0 || ey <= 0 || ez <= 0)
+            throw OpenMMException("GayBerneForce: scale factors for a particle must be positive");
     }
     vector<set<int> > exceptions(owner.getNumParticles());
     for (int i = 0; i < owner.getNumExceptions(); i++) {
-        int particle1, particle2;
+        int particle[2];
         double sigma, epsilon;
-        owner.getExceptionParameters(i, particle1, particle2, sigma, epsilon);
-        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
+        owner.getExceptionParameters(i, particle[0], particle[1], sigma, epsilon);
+        for (int j = 0; j < 2; j++) {
+            if (particle[j] < 0 || particle[j] >= owner.getNumParticles()) {
                 stringstream msg;
                 msg << "GayBerneForce: Illegal particle index for an exception: ";
-            msg << particle1;
+                msg << particle[j];
                 throw OpenMMException(msg.str());
             }
-        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
-            stringstream msg;
-            msg << "GayBerneForce: Illegal particle index for an exception: ";
-            msg << particle2;
-            throw OpenMMException(msg.str());
         }
-        if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
+        if (exceptions[particle[0]].count(particle[1]) > 0 || exceptions[particle[1]].count(particle[0]) > 0) {
             stringstream msg;
             msg << "GayBerneForce: Multiple exceptions are specified for particles ";
-            msg << particle1;
+            msg << particle[0];
             msg << " and ";
-            msg << particle2;
+            msg << particle[1];
             throw OpenMMException(msg.str());
         }
-        exceptions[particle1].insert(particle2);
-        exceptions[particle2].insert(particle1);
+        if (sigma < 0)
+            throw OpenMMException("GayBerneForce: sigma for an exception cannot be negative");
+        if (epsilon < 0)
+            throw OpenMMException("GayBerneForce: epsilon for an exception cannot be negative");
+        exceptions[particle[0]].insert(particle[1]);
+        exceptions[particle[1]].insert(particle[0]);
     }
     if (owner.getNonbondedMethod() == GayBerneForce::CutoffPeriodic) {
         Vec3 boxVectors[3];

openmmapi/src/HarmonicAngleForceImpl.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,14 +29,18 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
+#include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/HarmonicAngleForceImpl.h"
 #include "openmm/kernels.h"
+#include <cmath>
+#include <sstream>
 
 using namespace OpenMM;
-using std::pair;
-using std::vector;
-using std::set;
+using namespace std;
 
 HarmonicAngleForceImpl::HarmonicAngleForceImpl(const HarmonicAngleForce& owner) : owner(owner) {
 }
@@ -45,6 +49,24 @@ HarmonicAngleForceImpl::~HarmonicAngleForceImpl() {
 }
 
 void HarmonicAngleForceImpl::initialize(ContextImpl& context) {
+    const System& system = context.getSystem();
+    for (int i = 0; i < owner.getNumAngles(); i++) {
+        int particle[3];
+        double angle, k;
+        owner.getAngleParameters(i, particle[0], particle[1], particle[2], angle, k);
+        for (int j = 0; j < 3; j++) {
+            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
+                stringstream msg;
+                msg << "HarmonicAngleForce: Illegal particle index for an angle: ";
+                msg << particle[j];
+                throw OpenMMException(msg.str());
+            }
+        }
+        if (angle < 0 || angle > M_PI*1.000001)
+            throw OpenMMException("HarmonicAngleForce: angle must be between 0 and pi");
+        if (k < 0)
+            throw OpenMMException("HarmonicAngleForce: force constant cannot be negative");
+    }
     kernel = context.getPlatform().createKernel(CalcHarmonicAngleForceKernel::Name(), context);
     kernel.getAs<CalcHarmonicAngleForceKernel>().initialize(context.getSystem(), owner);
 }