Merge branch 'master' of github.com:SimTk/openmm

CMakeLists.txt

@@ -273,7 +273,8 @@ ENDIF(WIN32)
 SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
     ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
+    SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)

openmmapi/include/openmm/Context.h

@@ -35,12 +35,12 @@
 #include "Integrator.h"
 #include "State.h"
 #include "System.h"
-#include <ctime>
 #include <iosfwd>
 #include <map>
 #include <string>
 #include <vector>
 #include "internal/windowsExport.h"
+#include "internal/OSRngSeed.h"
 
 namespace OpenMM {
 
@@ -164,7 +164,7 @@ public:
      * @param temperature    the temperature for which to select the velocities (measured in Kelvin)
      * @param randomSeed     the random number seed to use when selecting velocities
      */
-    void setVelocitiesToTemperature(double temperature, int randomSeed=time(NULL));
+    void setVelocitiesToTemperature(double temperature, int randomSeed=osrngseed());
     /**
      * Get the value of an adjustable parameter defined by a Force object in the System.
      * 

openmmapi/include/openmm/internal/OSRngSeed.h

+#ifndef OPENMM_OSRNGSEED_H_
+#define OPENMM_OSRNGSEED_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) 2013 Stanford University and the Authors.           *
+ * Authors: Robert T. McGibbon                                                *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+
+
+/**
+ * Return an integer int for use as a seed for a random number generator.
+ * 
+ * The behavior of this function is platform dependent. On Windows machines,
+ * this uses CryptGenRandom from the CryptoAPI to get a single int. On other
+ * platforms (*nix, apple), we read from /dev/urandom
+ */
+int osrngseed(void);
+
+#endif /* OPENMM_OSRNGSEED_H_ */
\ No newline at end of file

openmmapi/src/AndersenThermostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/AndersenThermostat.h"
 #include "openmm/internal/AndersenThermostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 AndersenThermostat::AndersenThermostat(double defaultTemperature, double defaultCollisionFrequency) :
         defaultTemp(defaultTemperature), defaultFreq(defaultCollisionFrequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* AndersenThermostat::createImpl() const {

openmmapi/src/BrownianIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -46,7 +46,7 @@ BrownianIntegrator::BrownianIntegrator(double temperature, double frictionCoeff,
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void BrownianIntegrator::initialize(ContextImpl& contextRef) {

openmmapi/src/CustomIntegrator.cpp

@@ -34,8 +34,8 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/AssertionUtilities.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -45,7 +45,7 @@ using std::vector;
 CustomIntegrator::CustomIntegrator(double stepSize) : globalsAreCurrent(true), forcesAreValid(false) {
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
     kineticEnergy = "m*v*v/2";
 }
 

openmmapi/src/LangevinIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -46,7 +46,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void LangevinIntegrator::initialize(ContextImpl& contextRef) {

openmmapi/src/MonteCarloAnisotropicBarostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/internal/MonteCarloAnisotropicBarostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
         defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* MonteCarloAnisotropicBarostat::createImpl() const {

openmmapi/src/MonteCarloBarostat.cpp

@@ -31,13 +31,13 @@
 
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/internal/MonteCarloBarostatImpl.h"
-#include <ctime>
+#include "openmm/internal/OSRngSeed.h"
 
 using namespace OpenMM;
 
 MonteCarloBarostat::MonteCarloBarostat(double defaultPressure, double temperature, int frequency) :
         defaultPressure(defaultPressure), temperature(temperature), frequency(frequency) {
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 ForceImpl* MonteCarloBarostat::createImpl() const {

openmmapi/src/OSRngSeed.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) 2013 Stanford University and the Authors.           *
+ * Authors: Robert T. McGibbon                                                *
+ * 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 <stdexcept>
+#if defined(_WIN32) || defined(__CYGWIN__)
+#include <windows.h>
+static HCRYPTPROV hCryptProv = 0;
+#pragma comment(lib, "advapi32.lib")
+#else
+#include <fcntl.h>
+#include <unistd.h>
+#endif
+#include "openmm/internal/OSRngSeed.h"
+
+int osrngseed(void) {
+    int value;
+#if defined(_WIN32) || defined(__CYGWIN__)
+    if (!::CryptAcquireContextW(&hCryptProv, 0, 0, PROV_RSA_FULL, CRYPT_VERIFYCONTEXT | CRYPT_SILENT)) {
+        throw std::runtime_error("Failed to initialize Windows random API (CryptoGen)");
+    }
+    if (!CryptGenRandom(hCryptProv, sizeof(int), (BYTE*) &value)) {
+        ::CryptReleaseContext(hCryptProv, 0);
+        throw std::runtime_error("Failed to get random numbers");
+    }
+    if (!::CryptReleaseContext(hCryptProv, 0)) {
+        throw std::runtime_error("Failed to release Windows random API context");
+    }
+#else
+    int m_fd = open("/dev/urandom", O_RDONLY);
+    if (m_fd == -1) {
+        throw std::runtime_error("Failed to open /dev/urandom");
+    }
+    if (read(m_fd, &value, sizeof(int)) != sizeof(int)) {
+        throw std::runtime_error("Failed to read bytes from /dev/urandom");
+    }
+    close(m_fd);
+#endif
+    return value;
+}
\ No newline at end of file

openmmapi/src/VariableLangevinIntegrator.cpp

@@ -33,10 +33,11 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/kernels.h"
 #include <limits>
 #include <string>
-#include <ctime>
+
 
 using namespace OpenMM;
 using std::string;
@@ -47,7 +48,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
     setFriction(frictionCoeff);
     setErrorTolerance(errorTol);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void VariableLangevinIntegrator::initialize(ContextImpl& contextRef) {

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/DrudeKernels.h"
-#include <cmath>
 #include <ctime>
 #include <string>
 
@@ -49,7 +49,7 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
     setDrudeFriction(drudeFrictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -33,10 +33,10 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/RpmdKernels.h"
 #include "SimTKOpenMMRealType.h"
 #include <cmath>
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -48,7 +48,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
@@ -57,7 +57,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void RPMDIntegrator::initialize(ContextImpl& contextRef) {