Removed duplicate kernels, slightly modified API for Python compatibility.

olla/include/openmm/kernels.h

@@ -1107,46 +1107,7 @@ public:
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
      */
-    virtual void initialize(const System& system, const MonteCarloBarostat& barostat) = 0;
-    /**
-     * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
-     * This version scales the x, y, and z positions independently.
-     * This is called BEFORE the periodic box size is modified.  It should begin by translating each particle
-     * or cluster into the first periodic box, so that coordinates will still be correct after the box size
-     * is changed.
-     *
-     * @param context    the context in which to execute this kernel
-     * @param scaleX     the scale factor by which to multiply particle x-coordinate
-     * @param scaleY     the scale factor by which to multiply particle y-coordinate
-     * @param scaleZ     the scale factor by which to multiply particle z-coordinate
-     */
-    virtual void scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) = 0;
-    /**
-     * Reject the most recent Monte Carlo step, restoring the particle positions to where they were before
-     * scaleCoordinates() was last called.
-     *
-     * @param context    the context in which to execute this kernel
-     */
-    virtual void restoreCoordinates(ContextImpl& context) = 0;
-};
-
-/**
- * This kernel is invoked by MonteCarloAnisotropicBarostat to adjust the periodic box volume
- */
-class ApplyMonteCarloAnisotropicBarostatKernel : public KernelImpl {
-public:
-    static std::string Name() {
-        return "ApplyMonteCarloAnisotropicBarostat";
-    }
-    ApplyMonteCarloAnisotropicBarostatKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
-    }
-    /**
-     * Initialize the kernel.
-     *
-     * @param system     the System this kernel will be applied to
-     * @param barostat   the MonteCarloAnisotropicBarostat this kernel will be used for
-     */
-    virtual void initialize(const System& system, const MonteCarloAnisotropicBarostat& barostat) = 0;
+    virtual void initialize(const System& system, const Force& barostat) = 0;
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.

openmmapi/include/openmm/MonteCarloBarostat.h

@@ -35,7 +35,6 @@
 #include "Force.h"
 #include <string>
 #include "internal/windowsExport.h"
-#include "Vec3.h"
 
 namespace OpenMM {
 
@@ -176,21 +175,23 @@ public:
     /**
      * Create a MonteCarloAnisotropicBarostat.
      *
-     * @param defaultPressure   3-element vector specifying the default pressure acting on each axis (in bar)
+     * @param defaultPressureX  The default pressure acting on the X-axis (in bar)
+     * @param defaultPressureY  The default pressure acting on the Y-axis (in bar)
+     * @param defaultPressureZ  The default pressure acting on the Z-axis (in bar)
      * @param temperature       the temperature at which the system is being maintained (in Kelvin)
      * @param frequency         the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
      * @param scaleX            on/off switch for whether to scale the X axis
      * @param scaleY            on/off switch for whether to scale the Y axis
      * @param scaleZ            on/off switch for whether to scale the Z axis
      */
-    MonteCarloAnisotropicBarostat(Vec3 defaultPressure, double temperature, int frequency = 25, bool scaleX = 1, bool scaleY = 1, bool scaleZ = 1);
+    MonteCarloAnisotropicBarostat(double defaultPressureX, double defaultPressureY, double defaultPressureZ, double temperature, int frequency = 25, bool scaleX = 1, bool scaleY = 1, bool scaleZ = 1);
     /**
      * Get the default pressure acting on the X-axis (in bar).
      *
      * @return the default pressure acting on the system, measured in bar.
      */
     double getDefaultPressureX() const {
-        return defaultPressure[0];
+        return defaultPressureX;
     }
     /**
      * Get the default pressure acting on the Y-axis (in bar).
@@ -198,7 +199,7 @@ public:
      * @return the default pressure acting on the system, measured in bar.
      */
     double getDefaultPressureY() const {
-        return defaultPressure[1];
+        return defaultPressureY;
     }
     /**
      * Get the default pressure acting on the Z-axis (in bar).
@@ -206,7 +207,7 @@ public:
      * @return the default pressure acting on the system, measured in bar.
      */
     double getDefaultPressureZ() const {
-        return defaultPressure[2];
+        return defaultPressureZ;
     }
     /**
      * Get the true/false flag for scaling the X-axis.
@@ -279,7 +280,7 @@ public:
 protected:
     ForceImpl* createImpl() const;
 private:
-    Vec3 defaultPressure;
+    double defaultPressureX, defaultPressureY, defaultPressureZ;
     double temperature;
     bool scaleX, scaleY, scaleZ;
     int frequency, randomNumberSeed;

openmmapi/include/openmm/internal/MonteCarloBarostatImpl.h

@@ -35,7 +35,6 @@
 #include "ForceImpl.h"
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/Kernel.h"
-#include "openmm/Vec3.h"
 #include "sfmt/SFMT.h"
 #include <string>
 

openmmapi/src/MonteCarloBarostat.cpp

@@ -44,8 +44,8 @@ ForceImpl* MonteCarloBarostat::createImpl() const {
     return new MonteCarloBarostatImpl(*this);
 }
 
-MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(Vec3 defaultPressure, double temperature, int frequency, bool scaleX, bool scaleY, bool scaleZ) :
-  defaultPressure(defaultPressure), temperature(temperature), frequency(frequency), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ) {
+MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(double defaultPressureX, double defaultPressureY, double defaultPressureZ, double temperature, int frequency, bool scaleX, bool scaleY, bool scaleZ) :
+    defaultPressureX(defaultPressureX), defaultPressureY(defaultPressureY), defaultPressureZ(defaultPressureZ), temperature(temperature), frequency(frequency), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ) {
     setRandomNumberSeed((int) time(NULL));
 }
 

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -126,8 +126,8 @@ MonteCarloAnisotropicBarostatImpl::MonteCarloAnisotropicBarostatImpl(const Monte
 }
 
 void MonteCarloAnisotropicBarostatImpl::initialize(ContextImpl& context) {
-    kernel = context.getPlatform().createKernel(ApplyMonteCarloAnisotropicBarostatKernel::Name(), context);
-    kernel.getAs<ApplyMonteCarloAnisotropicBarostatKernel>().initialize(context.getSystem(), owner);
+    kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
+    kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner);
     Vec3 box[3];
     context.getPeriodicBoxVectors(box[0], box[1], box[2]);
     double volume = box[0][0]*box[1][1]*box[2][2];
@@ -181,7 +181,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     for (int i=0; i<3; i++)
         lengthScale[i] = 1.0;
     lengthScale[axis] = newVolume/volume;
-    kernel.getAs<ApplyMonteCarloAnisotropicBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
+    kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale[0], lengthScale[1], lengthScale[2]);
     context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale[0], box[1]*lengthScale[1], box[2]*lengthScale[2]);
     
     // Compute the energy of the modified system.
@@ -192,7 +192,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
         
-        kernel.getAs<ApplyMonteCarloAnisotropicBarostatKernel>().restoreCoordinates(context);
+        kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
         volume = newVolume;
     }
@@ -223,7 +223,7 @@ std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParam
 
 std::vector<std::string> MonteCarloAnisotropicBarostatImpl::getKernelNames() {
     std::vector<std::string> names;
-    names.push_back(ApplyMonteCarloAnisotropicBarostatKernel::Name());
+    names.push_back(ApplyMonteCarloBarostatKernel::Name());
     return names;
 }
 

platforms/cuda/src/CudaKernels.cpp

@@ -5310,7 +5310,7 @@ CudaApplyMonteCarloBarostatKernel::~CudaApplyMonteCarloBarostatKernel() {
         delete moleculeStartIndex;
 }
 
-void CudaApplyMonteCarloBarostatKernel::initialize(const System& system, const MonteCarloBarostat& thermostat) {
+void CudaApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat) {
     cu.setAsCurrent();
     savedPositions = new CudaArray(cu, cu.getPaddedNumAtoms(), cu.getUseDoublePrecision() ? sizeof(double4) : sizeof(float4), "savedPositions");
     CUmodule module = cu.createModule(CudaKernelSources::monteCarloBarostat);
@@ -5372,13 +5372,6 @@ void CudaApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context)
     }
 }
 
-void CudaApplyMonteCarloAnisotropicBarostatKernel::initialize(const System& system, const MonteCarloAnisotropicBarostat& thermostat) {
-    cu.setAsCurrent();
-    savedPositions = new CudaArray(cu, cu.getPaddedNumAtoms(), cu.getUseDoublePrecision() ? sizeof(double4) : sizeof(float4), "savedPositions");
-    CUmodule module = cu.createModule(CudaKernelSources::monteCarloBarostat);
-    kernel = cu.getKernel(module, "scalePositions");
-}
-
 CudaRemoveCMMotionKernel::~CudaRemoveCMMotionKernel() {
     cu.setAsCurrent();
     if (cmMomentum != NULL)

platforms/cuda/src/CudaKernels.h

@@ -1254,7 +1254,7 @@ public:
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
      */
-    void initialize(const System& system, const MonteCarloBarostat& barostat);
+    void initialize(const System& system, const Force& barostat);
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.
@@ -1286,29 +1286,6 @@ private:
     std::vector<int> lastAtomOrder;
 };
 
-/**
- * This kernel is invoked by MonteCarloAnisotropicBarostat to adjust the periodic box volume
- */
-class CudaApplyMonteCarloAnisotropicBarostatKernel : public CudaApplyMonteCarloBarostatKernel {
-public:
-    /**
-     * Initialize the kernel.
-     *
-     * @param system     the System this kernel will be applied to
-     * @param barostat   the MonteCarloAnisotropicBarostat this kernel will be used for
-     */
-    void initialize(const System& system, const MonteCarloAnisotropicBarostat& barostat);
-private:
-    CudaContext& cu;
-    bool hasInitializedKernels;
-    int numMolecules;
-    CudaArray* savedPositions;
-    CudaArray* moleculeAtoms;
-    CudaArray* moleculeStartIndex;
-    CUfunction kernel;
-    std::vector<int> lastAtomOrder;
-};
-
 /**
  * This kernel is invoked to remove center of mass motion from the system.
  */

platforms/cuda/tests/TestCudaMonteCarloBarostat.cpp

@@ -112,7 +112,7 @@ void testIdealGas(int aniso) {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     if (aniso)
-        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, pressure, pressure, temp[0], frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -256,7 +256,7 @@ void testWater(int aniso) {
     system.addForce(nonbonded);
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
     if (aniso)
-        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, pressure, pressure, temp, frequency);
     system.addForce(barostat);
     
     // Simulate it and see if the density matches the expected value (1 g/mL).

platforms/opencl/src/OpenCLKernels.cpp

@@ -5536,7 +5536,7 @@ OpenCLApplyMonteCarloBarostatKernel::~OpenCLApplyMonteCarloBarostatKernel() {
         delete moleculeStartIndex;
 }
 
-void OpenCLApplyMonteCarloBarostatKernel::initialize(const System& system, const MonteCarloBarostat& thermostat) {
+void OpenCLApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat) {
     savedPositions = OpenCLArray::create<mm_float4>(cl, cl.getPaddedNumAtoms(), "savedPositions");
     cl::Program program = cl.createProgram(OpenCLKernelSources::monteCarloBarostat);
     kernel = cl::Kernel(program, "scalePositions");

platforms/opencl/src/OpenCLKernels.h

@@ -1268,7 +1268,7 @@ public:
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
      */
-    void initialize(const System& system, const MonteCarloBarostat& barostat);
+    void initialize(const System& system, const Force& barostat);
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.
@@ -1300,29 +1300,6 @@ private:
     std::vector<int> lastAtomOrder;
 };
 
-/**
- * This kernel is invoked by MonteCarloAnisotropicBarostat to adjust the periodic box volume
- */
-class OpenCLApplyMonteCarloAnisotropicBarostatKernel : public OpenCLApplyMonteCarloBarostatKernel {
-public:
-    /**
-     * Initialize the kernel.
-     *
-     * @param system     the System this kernel will be applied to
-     * @param barostat   the MonteCarloAnisotropicBarostat this kernel will be used for
-     */
-    void initialize(const System& system, const MonteCarloAnisotropicBarostat& barostat);
-private:
-    OpenCLContext& cl;
-    bool hasInitializedKernels;
-    int numMolecules;
-    OpenCLArray* savedPositions;
-    OpenCLArray* moleculeAtoms;
-    OpenCLArray* moleculeStartIndex;
-    cl::Kernel kernel;
-    std::vector<int> lastAtomOrder;
-};
-
 /**
  * This kernel is invoked to remove center of mass motion from the system.
  */

platforms/opencl/tests/TestOpenCLMonteCarloBarostat.cpp

@@ -112,7 +112,7 @@ void testIdealGas(int aniso) {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     if (aniso)
-      MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, pressure, pressure, temp[0], frequency);
     system.addForce(barostat);
 
     // Test it for three different temperatures.
@@ -259,7 +259,7 @@ void testWater(int aniso) {
     system.addForce(nonbonded);
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, frequency);
     if (aniso)
-      MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, pressure, pressure, temp, frequency);
     system.addForce(barostat);
 
     // Simulate it and see if the density matches the expected value (1 g/mL).

platforms/reference/src/ReferenceKernels.cpp

@@ -2140,7 +2140,7 @@ ReferenceApplyMonteCarloBarostatKernel::~ReferenceApplyMonteCarloBarostatKernel(
         delete barostat;
 }
 
-void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, const MonteCarloBarostat& barostat) {
+void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& barostat) {
 }
 
 void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
@@ -2156,9 +2156,6 @@ void ReferenceApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& con
     barostat->restorePositions(posData);
 }
 
-void ReferenceApplyMonteCarloAnisotropicBarostatKernel::initialize(const System& system, const MonteCarloAnisotropicBarostat& barostat) {
-}
-
 void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMotionRemover& force) {
     frequency = force.getFrequency();
     masses.resize(system.getNumParticles());

platforms/reference/src/ReferenceKernels.h

@@ -1182,7 +1182,7 @@ public:
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
      */
-    void initialize(const System& system, const MonteCarloBarostat& barostat);
+    void initialize(const System& system, const Force& barostat);
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.
@@ -1207,22 +1207,6 @@ private:
     ReferenceMonteCarloBarostat* barostat;
 };
 
-/**
- * This kernel is invoked by MonteCarloAnisotropicBarostat to adjust the periodic box volume
- */
-class ReferenceApplyMonteCarloAnisotropicBarostatKernel : public ReferenceApplyMonteCarloBarostatKernel{
-public:
-    /**
-     * Initialize the kernel.
-     *
-     * @param system     the System this kernel will be applied to
-     * @param barostat   the MonteCarloAnisotropicBarostat this kernel will be used for
-     */
-    void initialize(const System& system, const MonteCarloAnisotropicBarostat& barostat);
-private:
-    ReferenceMonteCarloBarostat* barostat;
-};
-
 /**
  * This kernel is invoked to remove center of mass motion from the system.
  */

platforms/reference/tests/TestReferenceMonteCarloBarostat.cpp

@@ -112,7 +112,7 @@ void testIdealGas(int aniso) {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     if (aniso)
-        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+        MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(pressure, pressure, pressure, temp[0], frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -32,7 +32,6 @@ SKIP_METHODS = [('State',),
                 ('ApplyAndersenThermostatKernel',),
                 ('ApplyConstraintsKernel',),
                 ('ApplyMonteCarloBarostatKernel',),
-                ('ApplyMonteCarloAnisotropicBarostatKernel',),
                 ('BondInfo',),
                 ('BondParameterInfo',),
                 ('CalcAmoebaGeneralizedKirkwoodForceKernel',),