Merge pull request #3 from openmm/master

Update from upstream

platforms/reference/tests/TestReferenceNoseHooverIntegrator.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) 2015 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 "ReferenceTests.h"
+#include "TestNoseHooverIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/reference/tests/TestReferenceNoseHooverThermostat.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) 2019 Stanford University and the Authors.           *
+ * Authors: Andreas Krämer and Andrew C. Simmonett                            *
+ * 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 "ReferenceTests.h"
+#include "TestNoseHooverThermostat.h"
+
+void runPlatformTests() {
+}

plugins/drude/openmmapi/include/OpenMMDrude.h

@@ -35,5 +35,6 @@
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
 #include "openmm/DrudeSCFIntegrator.h"
+#include "openmm/DrudeNoseHooverIntegrator.h"
 
 #endif /*OPENMM_DRUDE_H_*/

plugins/drude/openmmapi/include/openmm/DrudeNoseHooverIntegrator.h

+#ifndef OPENMM_DRUDENOSEHOOVERINTEGRATOR_H_
+#define OPENMM_DRUDENOSEHOOVERINTEGRATOR_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) 2019 Stanford University and the Authors.           *
+ * Authors: Andreas Krämer and Andrew C. Simmonett                            *
+ * 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/NoseHooverIntegrator.h"
+#include "openmm/Kernel.h"
+#include "openmm/internal/windowsExportDrude.h"
+
+namespace OpenMM {
+
+/**
+ * This Integrator simulates systems that include Drude particles.  It applies two different Nose-Hoover
+ * chain thermostats to the different parts of the system.  The first is applied to ordinary particles (ones
+ * that are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair.
+ * A second thermostat, typically with a much lower temperature, is applied to the relative internal
+ * displacement of each pair.
+ *
+ * This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude
+ * particles.
+ */
+
+class OPENMM_EXPORT_DRUDE DrudeNoseHooverIntegrator : public NoseHooverIntegrator {
+public:
+    /**
+     * Create a DrudeNoseHooverIntegrator.
+     *
+     * @param temperature the target temperature for the system (in Kelvin).
+     * @param collisionFrequency the frequency of the system's interaction with the heat bath (in inverse picoseconds).
+     * @param drudeTemperature the target temperature for the Drude particles, relative to their parent atom (in Kelvin).
+     * @param drudeCollisionFrequency the frequency of the drude particles' interaction with the heat bath (in inverse picoseconds).
+     * @param stepSize       the step size with which to integrator the system (in picoseconds)
+     * @param chainLength the number of beads in the Nose-Hoover chain.
+     * @param numMTS the number of step in the  multiple time step chain propagation algorithm.
+     * @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
+     *        used in the chain propagation algorithm (must be 1, 3, or 5).
+     */
+    DrudeNoseHooverIntegrator(double temperature, double collisionFrequency, 
+                              double drudeTemperature, double drudeCollisionFrequency, double stepSize, 
+                              int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
+
+    virtual ~DrudeNoseHooverIntegrator();
+    /**
+     * This will be called by the Context when it is created.  It informs the Integrator
+     * of what context it will be integrating, and gives it a chance to do any necessary initialization.
+     * It will also get called again if the application calls reinitialize() on the Context.
+     */
+    void initialize(ContextImpl& context);
+    /**
+     * Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
+     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
+     */
+    double getMaxDrudeDistance() const;
+    /**
+     * Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
+     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
+     */
+    void setMaxDrudeDistance(double distance);
+    /**
+     * Compute the kinetic energy of the drude particles at the current time.
+     */
+    double computeDrudeKineticEnergy();
+    /**
+     * Compute the kinetic energy of all (real and drude) particles at the current time.
+     */
+    double computeTotalKineticEnergy();
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_DRUDENOSEHOOVERINTEGRATOR_H_*/

plugins/drude/platforms/cuda/tests/CMakeLists.txt

@@ -5,6 +5,7 @@
 ENABLE_TESTING()
 
 INCLUDE_DIRECTORIES(${CUDA_INCLUDE_DIR})
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
 
 # Automatically create tests using files named "Test*.cpp"
 FILE(GLOB TEST_PROGS "*Test*.cpp")

plugins/drude/platforms/opencl/tests/CMakeLists.txt

@@ -5,6 +5,7 @@
 ENABLE_TESTING()
 
 INCLUDE_DIRECTORIES(${OPENCL_INCLUDE_DIR})
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
 
 # Automatically create tests using files named "Test*.cpp"
 FILE(GLOB TEST_PROGS "*Test*.cpp")

plugins/drude/platforms/reference/tests/CMakeLists.txt

@@ -5,6 +5,7 @@ ENABLE_TESTING()
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/include)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/openmmapi/include/openmm)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
 
 SET(SHARED_OPENMM_DRUDE_TARGET OpenMMDrude)
 

plugins/drude/serialization/include/openmm/serialization/DrudeNoseHooverIntegratorProxy.h

+#ifndef OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_
+#define OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/SerializationProxy.h"
+#include "openmm/internal/windowsExportDrude.h"
+
+namespace OpenMM {
+
+class OPENMM_EXPORT_DRUDE DrudeNoseHooverIntegratorProxy : public SerializationProxy {
+public:
+    DrudeNoseHooverIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_DRUDE_NOSE_HOOVER_INTEGRATOR_PROXY_H_*/

plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp

@@ -42,11 +42,13 @@
 
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
+#include "openmm/DrudeNoseHooverIntegrator.h"
 
 #include "openmm/serialization/SerializationProxy.h"
 
 #include "openmm/serialization/DrudeForceProxy.h"
 #include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
+#include "openmm/serialization/DrudeNoseHooverIntegratorProxy.h"
 
 #if defined(WIN32)
     #include <windows.h>
@@ -65,4 +67,5 @@ using namespace OpenMM;
 extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies() {
     SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
     SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
+    SerializationProxy::registerProxy(typeid(DrudeNoseHooverIntegrator), new DrudeNoseHooverIntegratorProxy());
 }