Merge github.com:leeping/openmm

CMakeLists.txt

@@ -396,6 +396,20 @@ IF(OPENMM_BUILD_DRUDE_PLUGIN)
    ADD_SUBDIRECTORY(plugins/drude)
 ENDIF(OPENMM_BUILD_DRUDE_PLUGIN)
 
+# CPU PME plugin
+
+FIND_PACKAGE(FFTW QUIET)
+IF(FFTW_FOUND)
+    SET(OPENMM_BUILD_PME_PLUGIN ON CACHE BOOL "Build CPU PME plugin")
+ELSE(FFTW_FOUND)
+    SET(OPENMM_BUILD_PME_PLUGIN OFF CACHE BOOL "Build CPU PME plugin")
+ENDIF(FFTW_FOUND)
+SET(OPENMM_BUILD_PME_PATH)
+IF(OPENMM_BUILD_PME_PLUGIN)
+   SET(OPENMM_BUILD_PME_PATH ${CMAKE_CURRENT_SOURCE_DIR}/plugins/cpupme)
+   ADD_SUBDIRECTORY(plugins/cpupme)
+ENDIF(OPENMM_BUILD_PME_PLUGIN)
+
 INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET})
 IF(OPENMM_BUILD_STATIC_LIB)
   INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET})
@@ -403,9 +417,11 @@ ENDIF(OPENMM_BUILD_STATIC_LIB)
 FILE(GLOB CORE_HEADERS     include/*.h          */include/*.h)
 FILE(GLOB TOP_HEADERS      include/openmm/*.h          */include/openmm/*.h)
 FILE(GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h )
+FILE(GLOB REFERENCE_HEADERS platforms/reference/include/*.h)
 INSTALL_FILES(/include                 FILES ${CORE_HEADERS})
 INSTALL_FILES(/include/openmm          FILES ${TOP_HEADERS})
 INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
+INSTALL_FILES(/include/openmm/reference FILES ${REFERENCE_HEADERS})
 
 # Serialization support
 

cmake_modules/FindFFTW.cmake

+# - Find FFTW
+# Find the native FFTW includes and library
+#
+#  FFTW_INCLUDES        - where to find fftw3.h
+#  FFTW_LIBRARY         - the main FFTW library.
+#  FFTW_THREADS_LIBRARY - the FFTW multithreading support library.
+#  FFTW_FOUND           - True if FFTW found.
+
+if (FFTW_INCLUDES)
+  # Already in cache, be silent
+  set (FFTW_FIND_QUIETLY TRUE)
+endif (FFTW_INCLUDES)
+
+find_path (FFTW_INCLUDES fftw3.h)
+
+find_library (FFTW_LIBRARY NAMES fftw3f)
+find_library (FFTW_THREADS_LIBRARY NAMES fftw3f_threads)
+
+# handle the QUIETLY and REQUIRED arguments and set FFTW_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (FFTW DEFAULT_MSG FFTW_LIBRARY FFTW_INCLUDES)
+find_package_handle_standard_args (FFTW_THREADS DEFAULT_MSG FFTW_THREADS_LIBRARY FFTW_INCLUDES)
+
+mark_as_advanced (FFTW_LIBRARY FFTW_THREADS_LIBRARY FFTW_INCLUDES)

libraries/lepton/src/Parser.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) 2009-2011 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -112,7 +112,7 @@ ParseToken Parser::getNextToken(const string& expression, int start) {
             }
             if ((c == 'e' || c == 'E') && !foundExp) {
                 foundExp = true;
-                if (pos < (int) expression.size()-1 && expression[pos+1] == '-')
+                if (pos < (int) expression.size()-1 && (expression[pos+1] == '-' || expression[pos+1] == '+'))
                     pos++;
                 continue;
             }

olla/include/openmm/kernels.h

@@ -1155,6 +1155,70 @@ public:
     virtual void execute(ContextImpl& context) = 0;
 };
 
+/**
+ * This kernel performs the reciprocal space calculation for PME.  In most cases, this
+ * calculation is done directly by CalcNonbondedForceKernel so this kernel is unneeded.
+ * In some cases it may want to outsource the work to a different kernel.  In particular,
+ * GPU based platforms sometimes use a CPU based implementation provided by a separate
+ * plugin.
+ */
+class CalcPmeReciprocalForceKernel : public KernelImpl {
+public:
+    class IO;
+    static std::string Name() {
+        return "CalcPmeReciprocalForce";
+    }
+    CalcPmeReciprocalForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param gridx        the x size of the PME grid
+     * @param gridy        the y size of the PME grid
+     * @param gridz        the z size of the PME grid
+     * @param numParticles the number of particles in the system
+     * @param alpha        the Ewald blending parameter
+     */
+    virtual void initialize(int gridx, int gridy, int gridz, int numParticles, double alpha) = 0;
+    /**
+     * Begin computing the force and energy.
+     * 
+     * @param io               an object that coordinates data transfer
+     * @param periodicBoxSize  the size of the periodic box (measured in nm)
+     * @param includeEnergy    true if potential energy should be computed
+     */
+    virtual void beginComputation(IO& io, Vec3 periodicBoxSize, bool includeEnergy) = 0;
+    /**
+     * Finish computing the force and energy.
+     * 
+     * @param io   an object that coordinates data transfer
+     * @return the potential energy due to the PME reciprocal space interactions
+     */
+    virtual double finishComputation(IO& io) = 0;
+};
+
+/**
+ * Any class that uses CalcPmeReciprocalForceKernel should create an implementation of this
+ * class, then pass it to the kernel to manage communication with it.
+ */
+class CalcPmeReciprocalForceKernel::IO {
+public:
+    /**
+     * Get a pointer to the atom charges and positions.  This array should contain four
+     * elements for each atom: x, y, z, and q in that order.
+     */
+    virtual float* getPosq() = 0;
+    /**
+     * Record the forces calculated by the kernel.
+     * 
+     * @param force    an array containing four elements for each atom.  The first three
+     *                 are the x, y, and z components of the force, while the fourth element
+     *                 should be ignored.
+     */
+    virtual void setForce(float* force) = 0;
+};
+
+
 } // namespace OpenMM
 
 #endif /*OPENMM_KERNELS_H_*/

openmmapi/include/OpenMM.h

@@ -53,6 +53,7 @@
 #include "openmm/Integrator.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/LocalEnergyMinimizer.h"
+#include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Context.h"

openmmapi/include/openmm/GBSAOBCForce.h

@@ -40,13 +40,19 @@ namespace OpenMM {
 
 /**
  * This class implements an implicit solvation force using the GBSA-OBC model.
- * <p>
+ * 
  * To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the
  * System to define its parameters.  The number of particles for which you define GBSA parameters must
  * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
  * try to create a Context.  After a particle has been added, you can modify its force field parameters
  * by calling setParticleParameters().  This will have no effect on Contexts that already exist unless you
  * call updateParametersInContext().
+ * 
+ * When using this Force, the System should also include a NonbondedForce, and both objects must specify
+ * identical charges for all particles.  Otherwise, the results will not be correct.  Furthermore, if the
+ * nonbonded method is set to CutoffNonPeriodic or CutoffPeriodic, you should call setReactionFieldDielectric(1.0)
+ * on the NonbondedForce to turn off the reaction field approximation, which does not produce correct results
+ * when combined with GBSA.
  */
 
 class OPENMM_EXPORT GBSAOBCForce : public Force {
@@ -70,7 +76,7 @@ public:
          */
         CutoffPeriodic = 2,
     };
-    /*
+    /**
      * Create a GBSAOBCForce.
      */
     GBSAOBCForce();

openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h

+#ifndef OPENMM_MONTECARLOANISOTROPICBAROSTAT_H_
+#define OPENMM_MONTECARLOANISOTROPICBAROSTAT_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) 2010-2013 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Lee-Ping Wang                                      *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "Force.h"
+#include "Vec3.h"
+#include <string>
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the
+ * effect of constant pressure.
+ *
+ * This class is similar to MonteCarloBarostat, but each Monte Carlo move is applied to only one axis
+ * of the periodic box (unlike MonteCarloBarostat, which scales the entire box isotropically).  This
+ * means that the box may change shape as well as size over the course of the simulation.  It also
+ * allows you to specify a different pressure for each axis of the box, or to keep the box size fixed
+ * along certain axes while still allowing it to change along others.
+ * 
+ * This class assumes the simulation is also being run at constant temperature, and requires you
+ * to specify the system temperature (since it affects the acceptance probability for Monte Carlo
+ * moves).  It does not actually perform temperature regulation, however.  You must use another
+ * mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.
+ */
+
+class OPENMM_EXPORT MonteCarloAnisotropicBarostat : public Force {
+public:
+    /**
+     * This is the name of the parameter which stores the current pressure acting on
+     * the X-axis (in bar).
+     */
+    static const std::string& PressureX() {
+        static const std::string key = "MonteCarloPressureX";
+        return key;
+    }
+    /**
+     * This is the name of the parameter which stores the current pressure acting on
+     * the Y-axis (in bar).
+     */
+    static const std::string& PressureY() {
+        static const std::string key = "MonteCarloPressureY";
+        return key;
+    }
+    /**
+     * This is the name of the parameter which stores the current pressure acting on
+     * the Z-axis (in bar).
+     */
+    static const std::string& PressureZ() {
+        static const std::string key = "MonteCarloPressureZ";
+        return key;
+    }
+    /**
+     * Create a MonteCarloAnisotropicBarostat.
+     *
+     * @param defaultPressure   The default pressure acting on each 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            whether to allow the X dimension of the periodic box to change size
+     * @param scaleY            whether to allow the Y dimension of the periodic box to change size
+     * @param scaleZ            whether to allow the Z dimension of the periodic box to change size
+     */
+    MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, int frequency = 25, bool scaleX = 1, bool scaleY = 1, bool scaleZ = 1);
+    /**
+     * Get the default pressure (in bar).
+     *
+     * @return the default pressure acting along each axis, measured in bar.
+     */
+    const Vec3& getDefaultPressure() const {
+        return defaultPressure;
+    }
+    /**
+     * Get whether to allow the X dimension of the periodic box to change size.
+     */
+    bool getScaleX() const {
+      return scaleX;
+    }
+    /**
+     * Get whether to allow the Y dimension of the periodic box to change size.
+     */
+    bool getScaleY() const {
+      return scaleY;
+    }
+    /**
+     * Get whether to allow the Z dimension of the periodic box to change size.
+     */
+    bool getScaleZ() const {
+      return scaleZ;
+    }
+    /**
+     * 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.
+     */
+    int getFrequency() const {
+        return frequency;
+    }
+    /**
+     * 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;
+    }
+    /**
+     * Get the temperature at which the system is being maintained, measured in Kelvin.
+     */
+    double getTemperature() const {
+        return temperature;
+    }
+    /**
+     * Set the temperature at which the system is being maintained.
+     *
+     * @param temp     the system temperature, measured in Kelvin.
+     */
+    void setTemperature(double temp) {
+        temperature = temp;
+    }
+    /**
+     * Get the random number seed.  See setRandomNumberSeed() for details.
+     */
+    int getRandomNumberSeed() const {
+        return randomNumberSeed;
+    }
+    /**
+     * Set the random number seed.  It is guaranteed that if two simulations are run
+     * with different random number seeds, the sequence of Monte Carlo steps will be different.  On
+     * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
+     * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
+     * results on successive runs, even if those runs were initialized identically.
+     */
+    void setRandomNumberSeed(int seed) {
+        randomNumberSeed = seed;
+    }
+protected:
+    ForceImpl* createImpl() const;
+private:
+    Vec3 defaultPressure;
+    double temperature;
+    bool scaleX, scaleY, scaleZ;
+    int frequency, randomNumberSeed;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_MONTECARLOANISOTROPICBAROSTAT_H_*/

openmmapi/include/openmm/MonteCarloBarostat.h

@@ -123,176 +123,7 @@ protected:
 private:
     double defaultPressure, temperature;
     int frequency, randomNumberSeed;
-
-        double GetTemperature() const {
-            return temperature;
-        }
-
-        void SetTemperature(double temperature) {
-            this->temperature = temperature;
-        }
-    };
-
-/**
- * This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the
- * effect of constant pressure.
- *
- * Compared to MonteCarloBarostat, this class scales the three axes of the simulation cell independently.
- * The user supplies three doubles to specify the pressure along each axis.
- *
- * This class assumes the simulation is also being run at constant temperature, and requires you
- * to specify the system temperature (since it affects the acceptance probability for Monte Carlo
- * moves).  It does not actually perform temperature regulation, however.  You must use another
- * mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.
- */
-
-class OPENMM_EXPORT MonteCarloAnisotropicBarostat : public Force {
-public:
-    /**
-     * This is the name of the parameter which stores the current pressure acting on
-     * the X-axis (in bar).
-     */
-    static const std::string& PressureX() {
-        static const std::string key = "MonteCarloPressureX";
-        return key;
-    }
-    /**
-     * This is the name of the parameter which stores the current pressure acting on
-     * the Y-axis (in bar).
-     */
-    static const std::string& PressureY() {
-        static const std::string key = "MonteCarloPressureY";
-        return key;
-    }
-    /**
-     * This is the name of the parameter which stores the current pressure acting on
-     * the Z-axis (in bar).
-     */
-    static const std::string& PressureZ() {
-        static const std::string key = "MonteCarloPressureZ";
-        return key;
-    }
-    /**
-     * Create a MonteCarloAnisotropicBarostat.
-     *
-     * @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(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 defaultPressureX;
-    }
-    /**
-     * Get the default pressure acting on the Y-axis (in bar).
-     *
-     * @return the default pressure acting on the system, measured in bar.
-     */
-    double getDefaultPressureY() const {
-        return defaultPressureY;
-    }
-    /**
-     * Get the default pressure acting on the Z-axis (in bar).
-     *
-     * @return the default pressure acting on the system, measured in bar.
-     */
-    double getDefaultPressureZ() const {
-        return defaultPressureZ;
-    }
-    /**
-     * Get the true/false flag for scaling the X-axis.
-     *
-     * @return the true/false flag for scaling the X-axis.
-     */
-    bool getScaleX() const {
-      return scaleX;
-    }
-    /**
-     * Get the true/false flag for scaling the Y-axis.
-     *
-     * @return the true/false flag for scaling the Y-axis.
-     */
-    bool getScaleY() const {
-      return scaleY;
-    }
-    /**
-     * Get the true/false flag for scaling the Z-axis.
-     *
-     * @return the true/false flag for scaling the Z-axis.
-     */
-    bool getScaleZ() const {
-      return scaleZ;
-    }
-    /**
-     * 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.
-     */
-    int getFrequency() const {
-        return frequency;
-    }
-    /**
-     * 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;
-    }
-    /**
-     * Get the temperature at which the system is being maintained, measured in Kelvin.
-     */
-    double getTemperature() const {
-        return temperature;
-    }
-    /**
-     * Set the temperature at which the system is being maintained.
-     *
-     * @param temp     the system temperature, measured in Kelvin.
-     */
-    void setTemperature(double temp) {
-        temperature = temp;
-    }
-    /**
-     * Get the random number seed.  See setRandomNumberSeed() for details.
-     */
-    int getRandomNumberSeed() const {
-        return randomNumberSeed;
-    }
-    /**
-     * Set the random number seed.  It is guaranteed that if two simulations are run
-     * with different random number seeds, the sequence of Monte Carlo steps will be different.  On
-     * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
-     * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
-     * results on successive runs, even if those runs were initialized identically.
-     */
-    void setRandomNumberSeed(int seed) {
-        randomNumberSeed = seed;
-    }
-protected:
-    ForceImpl* createImpl() const;
-private:
-    double defaultPressureX, defaultPressureY, defaultPressureZ;
-    double temperature;
-    bool scaleX, scaleY, scaleZ;
-    int frequency, randomNumberSeed;
-
-        double GetTemperature() const {
-            return temperature;
-        }
-
-        void SetTemperature(double temperature) {
-            this->temperature = temperature;
-        }
-    };
+};
 
 } // namespace OpenMM
 

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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -54,6 +54,8 @@ void OPENMM_EXPORT throwException(const char* file, int line, const std::string&
 
 #define ASSERT_EQUAL_VEC(expected, found, tol) {double _norm_ = std::sqrt((expected).dot(expected)); double _scale_ = _norm_ > 1.0 ? _norm_ : 1.0; if ((std::abs(((expected)[0])-((found)[0]))/_scale_ > (tol)) || (std::abs(((expected)[1])-((found)[1]))/_scale_ > (tol)) || (std::abs(((expected)[2])-((found)[2]))/_scale_ > (tol))) {std::stringstream details; details << " Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
 
+#define ASSERT_USUALLY_TRUE(cond) {if (!(cond)) throwException(__FILE__, __LINE__, "(This test is stochastic and may occasionally fail)");};
+
 #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 >= (int) vector.size()) throwException(__FILE__, __LINE__, "Index out of range");};

openmmapi/include/openmm/internal/MonteCarloAnisotropicBarostatImpl.h

+#ifndef OPENMM_MONTECARLOANISOTROPICBAROSTATIMPL_H_
+#define OPENMM_MONTECARLOANISOTROPICBAROSTATIMPL_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) 2010 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ForceImpl.h"
+#include "openmm/MonteCarloAnisotropicBarostat.h"
+#include "openmm/Kernel.h"
+#include "sfmt/SFMT.h"
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of MonteCarloAnisotropicBarostat.
+ */
+
+class MonteCarloAnisotropicBarostatImpl : public ForceImpl {
+public:
+    MonteCarloAnisotropicBarostatImpl(const MonteCarloAnisotropicBarostat& owner);
+    void initialize(ContextImpl& context);
+    const MonteCarloAnisotropicBarostat& getOwner() const {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+        // This force doesn't apply forces to particles.
+        return 0.0;
+    }
+    std::map<std::string, double> getDefaultParameters();
+    std::vector<std::string> getKernelNames();
+private:
+    const MonteCarloAnisotropicBarostat& owner;
+    int step, numAttempted[3], numAccepted[3];
+    double volumeScale[3];
+    OpenMM_SFMT::SFMT random;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_MONTECARLOANISOTROPICBAROSTATIMPL_H_*/

openmmapi/include/openmm/internal/MonteCarloBarostatImpl.h

@@ -66,28 +66,6 @@ private:
     Kernel kernel;
 };
 
-class MonteCarloAnisotropicBarostatImpl : public ForceImpl {
-public:
-    MonteCarloAnisotropicBarostatImpl(const MonteCarloAnisotropicBarostat& owner);
-    void initialize(ContextImpl& context);
-    const MonteCarloAnisotropicBarostat& getOwner() const {
-        return owner;
-    }
-    void updateContextState(ContextImpl& context);
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
-        // This force doesn't apply forces to particles.
-        return 0.0;
-    }
-    std::map<std::string, double> getDefaultParameters();
-    std::vector<std::string> getKernelNames();
-private:
-    const MonteCarloAnisotropicBarostat& owner;
-    int step, numAttempted[3], numAccepted[3];
-    double volumeScale[3];
-    OpenMM_SFMT::SFMT random;
-    Kernel kernel;
-};
-
 } // namespace OpenMM
 
 #endif /*OPENMM_MONTECARLOBAROSTATIMPL_H_*/

openmmapi/src/Context.cpp

@@ -33,7 +33,7 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ForceImpl.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <cmath>
 

openmmapi/src/MonteCarloAnisotropicBarostat.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2010 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/MonteCarloAnisotropicBarostat.h"
+#include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
+#include <ctime>
+
+using namespace OpenMM;
+
+MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, int frequency, bool scaleX, bool scaleY, bool scaleZ) :
+        defaultPressure(defaultPressure), temperature(temperature), frequency(frequency), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ) {
+    setRandomNumberSeed((int) time(NULL));
+}
+
+ForceImpl* MonteCarloAnisotropicBarostat::createImpl() const {
+    return new MonteCarloAnisotropicBarostatImpl(*this);
+}

openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2010-2013 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Lee-Ping Wang                                      *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/Context.h"
+#include "openmm/kernels.h"
+#include <cmath>
+#include <vector>
+
+using namespace OpenMM;
+using namespace OpenMM_SFMT;
+using std::vector;
+
+const float BOLTZMANN = 1.380658e-23f; // (J/K)
+const float AVOGADRO = 6.0221367e23f;
+const float RGAS = BOLTZMANN*AVOGADRO; // (J/(mol K))
+const float BOLTZ = RGAS/1000;         // (kJ/(mol K))
+
+MonteCarloAnisotropicBarostatImpl::MonteCarloAnisotropicBarostatImpl(const MonteCarloAnisotropicBarostat& owner) : owner(owner), step(0) {
+}
+
+void MonteCarloAnisotropicBarostatImpl::initialize(ContextImpl& context) {
+    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];
+    for (int i=0; i<3; i++) {
+        volumeScale[i] = 0.01*volume;
+        numAttempted[i] = 0;
+        numAccepted[i] = 0;
+    }
+    init_gen_rand(owner.getRandomNumberSeed(), random);
+}
+
+void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context) {
+    if (++step < owner.getFrequency() || owner.getFrequency() == 0)
+        return;
+    if (!owner.getScaleX() && !owner.getScaleY() && !owner.getScaleZ())
+        return;
+    step = 0;
+    
+    // Compute the current potential energy.
+    
+    double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    double pressure;
+    
+    // Choose which axis to modify at random.
+    int axis;
+    while (true) {
+        double rnd = genrand_real2(random)*3.0;
+        if (rnd < 1.0) {
+            if (owner.getScaleX()) {
+                axis = 0;
+                pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureX())*(AVOGADRO*1e-25);
+                break;
+            }
+        } else if (rnd < 2.0) {
+            if (owner.getScaleY()) {
+                axis = 1;
+                pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureY())*(AVOGADRO*1e-25);
+                break;
+            }
+        } else if (owner.getScaleZ()) {
+            axis = 2;
+            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
+            break;
+        }
+    }
+    
+    // Modify the periodic box size.
+    
+    Vec3 box[3];
+    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
+    double volume = box[0][0]*box[1][1]*box[2][2];
+    double deltaVolume = volumeScale[axis]*2*(genrand_real2(random)-0.5);
+    double newVolume = volume+deltaVolume;
+    Vec3 lengthScale(1.0, 1.0, 1.0);
+    lengthScale[axis] = newVolume/volume;
+    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.
+    
+    double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    double kT = BOLTZ*owner.getTemperature();
+    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
+    if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
+        // Reject the step.
+        
+        kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
+        context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
+        volume = newVolume;
+    }
+    else
+        numAccepted[axis]++;
+    numAttempted[axis]++;
+    if (numAttempted[axis] >= 10) {
+        if (numAccepted[axis] < 0.25*numAttempted[axis]) {
+            volumeScale[axis] /= 1.1;
+            numAttempted[axis] = 0;
+            numAccepted[axis] = 0;
+        }
+        else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
+            volumeScale[axis] = std::min(volumeScale[axis]*1.1, volume*0.3);
+            numAttempted[axis] = 0;
+            numAccepted[axis] = 0;
+        }
+    }
+}
+
+std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParameters() {
+    std::map<std::string, double> parameters;
+    parameters[MonteCarloAnisotropicBarostat::PressureX()] = getOwner().getDefaultPressure()[0];
+    parameters[MonteCarloAnisotropicBarostat::PressureY()] = getOwner().getDefaultPressure()[1];
+    parameters[MonteCarloAnisotropicBarostat::PressureZ()] = getOwner().getDefaultPressure()[2];
+    return parameters;
+}
+
+std::vector<std::string> MonteCarloAnisotropicBarostatImpl::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(ApplyMonteCarloBarostatKernel::Name());
+    return names;
+}
+

openmmapi/src/MonteCarloBarostat.cpp

@@ -43,12 +43,3 @@ MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperatur
 ForceImpl* MonteCarloBarostat::createImpl() const {
     return new MonteCarloBarostatImpl(*this);
 }
-
-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));
-}
-
-ForceImpl* MonteCarloAnisotropicBarostat::createImpl() const {
-    return new MonteCarloAnisotropicBarostatImpl(*this);
-}

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -64,13 +64,13 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     if (++step < owner.getFrequency() || owner.getFrequency() == 0)
         return;
     step = 0;
-    
+
     // Compute the current potential energy.
-    
+
     double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-    
+
     // Modify the periodic box size.
-    
+
     Vec3 box[3];
     context.getPeriodicBoxVectors(box[0], box[1], box[2]);
     double volume = box[0][0]*box[1][1]*box[2][2];
@@ -79,7 +79,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     double lengthScale = std::pow(newVolume/volume, 1.0/3.0);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
     context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
-    
+
     // Compute the energy of the modified system.
     
     double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
@@ -88,7 +88,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context) {
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
         // Reject the step.
-        
+
         kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
         volume = newVolume;
@@ -122,108 +122,3 @@ std::vector<std::string> MonteCarloBarostatImpl::getKernelNames() {
     return names;
 }
 
-MonteCarloAnisotropicBarostatImpl::MonteCarloAnisotropicBarostatImpl(const MonteCarloAnisotropicBarostat& owner) : owner(owner), step(0) {
-}
-
-void MonteCarloAnisotropicBarostatImpl::initialize(ContextImpl& context) {
-    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];
-    for (int i=0; i<3; i++) {
-        volumeScale[i] = 0.01*volume;
-        numAttempted[i] = 0;
-        numAccepted[i] = 0;
-    }
-    init_gen_rand(owner.getRandomNumberSeed(), random);
-}
-
-void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context) {
-    if (++step < owner.getFrequency() || owner.getFrequency() == 0)
-        return;
-    if (owner.getScaleX() == 0 && owner.getScaleY() == 0 && owner.getScaleZ() == 0)
-        return;
-    step = 0;
-    
-    // Compute the current potential energy.
-    
-    double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-    double pressure;
-    
-    // Choose which axis to modify at random.
-    double rnd = genrand_real2(random)*3.0;
-    int axis;
-    while (1) {
-        if (rnd < 1.0 && owner.getScaleX()) {
-            axis = 0;
-            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureX())*(AVOGADRO*1e-25);
-            break;
-        } else if (rnd < 2.0 && owner.getScaleY()) {
-            axis = 1;
-            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureY())*(AVOGADRO*1e-25);
-            break;
-        } else if (owner.getScaleZ()) {
-            axis = 2;
-            pressure = context.getParameter(MonteCarloAnisotropicBarostat::PressureZ())*(AVOGADRO*1e-25);
-            break;
-        }
-    }
-    
-    // Modify the periodic box size.
-    
-    Vec3 box[3];
-    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
-    double volume = box[0][0]*box[1][1]*box[2][2];
-    double deltaVolume = volumeScale[axis]*2*(genrand_real2(random)-0.5);
-    double newVolume = volume+deltaVolume;
-    Vec3 lengthScale;
-    for (int i=0; i<3; i++)
-        lengthScale[i] = 1.0;
-    lengthScale[axis] = newVolume/volume;
-    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.
-    
-    double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
-    double kT = BOLTZ*owner.getTemperature();
-    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
-    if (w > 0 && genrand_real2(random) > std::exp(-w/kT)) {
-        // Reject the step.
-        
-        kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
-        context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
-        volume = newVolume;
-    }
-    else
-        numAccepted[axis]++;
-    numAttempted[axis]++;
-    if (numAttempted[axis] >= 10) {
-        if (numAccepted[axis] < 0.25*numAttempted[axis]) {
-            volumeScale[axis] /= 1.1;
-            numAttempted[axis] = 0;
-            numAccepted[axis] = 0;
-        }
-        else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
-            volumeScale[axis] = std::min(volumeScale[axis]*1.1, volume*0.3);
-            numAttempted[axis] = 0;
-            numAccepted[axis] = 0;
-        }
-    }
-}
-
-std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParameters() {
-    std::map<std::string, double> parameters;
-    parameters[MonteCarloAnisotropicBarostat::PressureX()] = getOwner().getDefaultPressureX();
-    parameters[MonteCarloAnisotropicBarostat::PressureY()] = getOwner().getDefaultPressureY();
-    parameters[MonteCarloAnisotropicBarostat::PressureZ()] = getOwner().getDefaultPressureZ();
-    return parameters;
-}
-
-std::vector<std::string> MonteCarloAnisotropicBarostatImpl::getKernelNames() {
-    std::vector<std::string> names;
-    names.push_back(ApplyMonteCarloBarostatKernel::Name());
-    return names;
-}
-

platforms/cuda/CMakeLists.txt

@@ -16,7 +16,6 @@
 
 IF (APPLE)
     SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.6")
-    SET (CMAKE_OSX_SYSROOT "/Developer/SDKs/MacOSX10.6.sdk")
 ENDIF (APPLE)
 
 set(OPENMM_BUILD_CUDA_TESTS TRUE CACHE BOOL "Whether to build CUDA test cases")
@@ -103,4 +102,9 @@ SET(CUDA_KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${CUDA_SOURCE_CLASS}.h)
 SET(SOURCE_FILES ${SOURCE_FILES} ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H})
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
 
+# Install headers
+
+FILE(GLOB CORE_HEADERS include/*.h)
+INSTALL_FILES(/include/openmm/cuda FILES ${CORE_HEADERS})
+
 SUBDIRS (sharedTarget)

platforms/cuda/src/CudaContext.h → platforms/cuda/include/CudaContext.h

@@ -70,6 +70,8 @@ public:
     class WorkTask;
     class WorkThread;
     class ReorderListener;
+    class ForcePreComputation;
+    class ForcePostComputation;
     static const int ThreadBlockSize;
     static const int TileSize;
     CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const std::string& precision,
@@ -454,6 +456,28 @@ public:
     std::vector<ReorderListener*>& getReorderListeners() {
         return reorderListeners;
     }
+    /**
+     * Add a pre-computation that should be called at the very start of force and energy evaluations.
+     * The CudaContext assumes ownership of the object, and deletes it when the context itself is deleted.
+     */
+    void addPreComputation(ForcePreComputation* computation);
+    /**
+     * Get the list of ForcePreComputations.
+     */
+    std::vector<ForcePreComputation*>& getPreComputations() {
+        return preComputations;
+    }
+    /**
+     * Add a post-computation that should be called at the very end of force and energy evaluations.
+     * The CudaContext assumes ownership of the object, and deletes it when the context itself is deleted.
+     */
+    void addPostComputation(ForcePostComputation* computation);
+    /**
+     * Get the list of ForcePostComputations.
+     */
+    std::vector<ForcePostComputation*>& getPostComputations() {
+        return postComputations;
+    }
     /**
      * Mark that the current molecule definitions (and hence the atom order) may be invalid.
      * This should be called whenever force field parameters change.  It will cause the definitions
@@ -519,6 +543,8 @@ private:
     std::vector<CUdeviceptr> autoclearBuffers;
     std::vector<int> autoclearBufferSizes;
     std::vector<ReorderListener*> reorderListeners;
+    std::vector<ForcePreComputation*> preComputations;
+    std::vector<ForcePostComputation*> postComputations;
     CudaIntegrationUtilities* integration;
     CudaExpressionUtilities* expression;
     CudaBondedUtilities* bonded;
@@ -580,7 +606,7 @@ private:
 
 /**
  * This abstract class defines a function to be executed whenever atoms get reordered.
- * Objects that need to know when reordering happens should create a reorderListener
+ * Objects that need to know when reordering happens should create a ReorderListener
  * and register it by calling addReorderListener().
  */
 class CudaContext::ReorderListener {
@@ -590,6 +616,39 @@ public:
     }
 };
 
+/**
+ * This abstract class defines a function to be executed at the very beginning of force and
+ * energy evaluation, before any other calculation has been done.  It is useful for operations
+ * that need to be performed at a nonstandard point in the process.  After creating a
+ * ForcePreComputation, register it by calling addForcePreComputation().
+ */
+class CudaContext::ForcePreComputation {
+public:
+    /**
+     * @param includeForce  true if forces should be computed
+     * @param includeEnergy true if potential energy should be computed
+     * @param groups        a set of bit flags for which force groups to include
+     */
+    virtual void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) = 0;
+};
+
+/**
+ * This abstract class defines a function to be executed at the very end of force and
+ * energy evaluation, after all other calculations have been done.  It is useful for operations
+ * that need to be performed at a nonstandard point in the process.  After creating a
+ * ForcePostComputation, register it by calling addForcePostComputation().
+ */
+class CudaContext::ForcePostComputation {
+public:
+    /**
+     * @param includeForce  true if forces should be computed
+     * @param includeEnergy true if potential energy should be computed
+     * @param groups        a set of bit flags for which force groups to include
+     * @return an optional contribution to add to the potential energy.
+     */
+    virtual double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) = 0;
+};
+
 } // namespace OpenMM
 
 #endif /*OPENMM_CUDACONTEXT_H_*/