Merge github.com:SimTk/openmm

examples/CMakeLists.txt

@@ -33,7 +33,9 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
         ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.cpp)
         SET_TARGET_PROPERTIES(${EX_ROOT}
             PROPERTIES
-	      PROJECT_LABEL "Example - ${EX_ROOT}")
+            PROJECT_LABEL "Example - ${EX_ROOT}"
+            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
         TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
     ENDIF (BUILD_TESTING_SHARED)
 
@@ -43,8 +45,9 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
         ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.cpp)
         SET_TARGET_PROPERTIES(${EX_STATIC}
             PROPERTIES
-		COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
-		PROJECT_LABEL "Example - ${EX_STATIC}")
+            PROJECT_LABEL "Example - ${EX_STATIC}"
+            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
         TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
     ENDIF (BUILD_TESTING_STATIC)
 
@@ -64,7 +67,9 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
             ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.c Empty.cpp)
             SET_TARGET_PROPERTIES(${EX_ROOT}
                 PROPERTIES
-              PROJECT_LABEL "Example C - ${EX_ROOT}")
+                PROJECT_LABEL "Example C - ${EX_ROOT}"
+                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
             TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
             ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
         ENDIF (BUILD_TESTING_SHARED)
@@ -77,8 +82,9 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
             ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.c Empty.cpp)
             SET_TARGET_PROPERTIES(${EX_STATIC}
                 PROPERTIES
-            COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
-            PROJECT_LABEL "Example C - ${EX_STATIC}")
+                PROJECT_LABEL "Example C - ${EX_STATIC}"
+                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
             TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
             ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)
         ENDIF (BUILD_TESTING_STATIC)

examples/HelloArgonInFortran.f90

@@ -11,6 +11,8 @@
 ! other visualization tool to produce an animation of the resulting trajectory.
 ! -----------------------------------------------------------------------------
 
+INCLUDE 'OpenMMFortranModule.f90'
+
 PROGRAM HelloArgon
     use OpenMM; implicit none
     type(OpenMM_System)           system

examples/HelloSodiumChlorideInFortran.f90

@@ -17,6 +17,8 @@
 ! interface module.
 ! ------------------------------------------------------------------------------
 
+INCLUDE 'OpenMMFortranModule.f90'
+
 !-------------------------------------------------------------------------------
 !                ATOM, FORCE FIELD, AND SIMULATION PARAMETERS
 !-------------------------------------------------------------------------------

examples/Makefile

@@ -56,11 +56,11 @@ HelloSodiumChlorideInC: HelloSodiumChlorideInC.c
 
 HelloArgonInFortran: HelloArgonInFortran.f90 openmm.mod 
 	gfortran $(FFLAGS) HelloArgonInFortran.f90 \
-	    -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloArgonInFortran
+	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloArgonInFortran
 
 HelloSodiumChlorideInFortran: HelloSodiumChlorideInFortran.f90 openmm.mod 
 	gfortran $(FFLAGS) HelloSodiumChlorideInFortran.f90 \
-	    -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloSodiumChlorideInFortran
+	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloSodiumChlorideInFortran
 
 
 # Build Fortran 95 Module file

examples/benchmark.py

+from __future__ import print_function
+import simtk.openmm.app as app
+import simtk.openmm as mm
+import simtk.unit as unit
+import sys
+from datetime import datetime
+from optparse import OptionParser
+
+def timeIntegration(context, steps):
+    """Integrate a Context for a specified number of steps, then return how many seconds it took."""
+    context.getIntegrator().step(5) # Make sure everything is fully initialized
+    context.getState(getEnergy=True)
+    start = datetime.now()
+    context.getIntegrator().step(steps)
+    context.getState(getEnergy=True)
+    end = datetime.now()
+    elapsed = end -start
+    return elapsed.seconds + elapsed.microseconds*1e-6
+
+def runOneTest(testName, options):
+    """Perform a single benchmarking simulation."""
+    explicit = (testName in ('rf', 'pme', 'amoebapme'))
+    amoeba = (testName in ('amoebagk', 'amoebapme'))
+    hydrogenMass = None
+    print()
+    if amoeba:
+        print('Test: %s (epsilon=%g)' % (testName, options.epsilon))
+    elif testName == 'pme':
+        print('Test: pme (cutoff=%g)' % options.cutoff)
+    else:
+        print('Test: %s' % testName)
+    platform = mm.Platform.getPlatformByName(options.platform)
+    
+    # Create the System.
+    
+    if amoeba:
+        constraints = None
+        epsilon = float(options.epsilon)
+        if epsilon == 0:
+            polarization = 'direct'
+        else:
+            polarization = 'mutual'
+        if explicit:
+            ff = app.ForceField('amoeba2009.xml')
+            pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
+            cutoff = 0.7*unit.nanometers
+            vdwCutoff = 0.9*unit.nanometers
+            system = ff.createSystem(pdb.topology, nonbondedMethod=app.PME, nonbondedCutoff=cutoff, vdwCutoff=vdwCutoff, constraints=constraints, ewaldErrorTolerance=0.00075, mutualInducedTargetEpsilon=epsilon, polarization=polarization)
+        else:
+            ff = app.ForceField('amoeba2009.xml', 'amoeba2009_gk.xml')
+            pdb = app.PDBFile('5dfr_minimized.pdb')
+            cutoff = 2.0*unit.nanometers
+            vdwCutoff = 1.2*unit.nanometers
+            system = ff.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=constraints, mutualInducedTargetEpsilon=epsilon, polarization=polarization)
+        dt = 0.001*unit.picoseconds
+    else:
+        if explicit:
+            ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
+            pdb = app.PDBFile('5dfr_solv-cube_equil.pdb')
+            if testName == 'pme':
+                method = app.PME
+                cutoff = options.cutoff
+            else:
+                method = app.CutoffPeriodic
+                cutoff = 1*unit.nanometers
+        else:
+            ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
+            pdb = app.PDBFile('5dfr_minimized.pdb')
+            method = app.CutoffNonPeriodic
+            cutoff = 2*unit.nanometers
+        if options.heavy:
+            dt = 0.005*unit.picoseconds
+            constraints = app.AllBonds
+            hydrogenMass = 4*unit.amu
+        else:
+            dt = 0.002*unit.picoseconds
+            constraints = app.HBonds
+            hydrogenMass = None
+        system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
+    print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
+    properties = {}
+    if options.device is not None:
+        if platform.getName() == 'CUDA':
+            properties['CudaDeviceIndex'] = options.device
+        elif platform.getName() == 'OpenCL':
+            properties['OpenCLDeviceIndex'] = options.device
+    if options.precision is not None:
+        if platform.getName() == 'CUDA':
+            properties['CudaPrecision'] = options.precision
+        elif platform.getName() == 'OpenCL':
+            properties['OpenCLPrecision'] = options.precision
+    
+    # Run the simulation.
+    
+    integ = mm.LangevinIntegrator(300*unit.kelvin, 91*(1/unit.picoseconds), dt)
+    integ.setConstraintTolerance(1e-5)
+    if len(properties) > 0:
+        context = mm.Context(system, integ, platform, properties)
+    else:
+        context = mm.Context(system, integ, platform)
+    context.setPositions(pdb.positions)
+    context.setVelocitiesToTemperature(300*unit.kelvin)
+    steps = 20
+    while True:
+        time = timeIntegration(context, steps)
+        if time >= 0.5*options.seconds:
+            break
+        if time < 0.5:
+            steps = int(steps*1.0/time) # Integrate enough steps to get a reasonable estimate for how many we'll need.
+        else:
+            steps = int(steps*options.seconds/time)
+    print('Integrated %d steps in %g seconds' % (steps, time))
+    print('%g ns/day' % (dt*steps*86400/time).value_in_unit(unit.nanoseconds))
+
+# Parse the command line options.
+
+parser = OptionParser()
+platformNames = [mm.Platform.getPlatform(i).getName() for i in range(mm.Platform.getNumPlatforms())]
+parser.add_option('--platform', dest='platform', choices=platformNames, help='name of the platform to benchmark')
+parser.add_option('--test', dest='test', choices=('gbsa', 'rf', 'pme', 'amoebagk', 'amoebapme'), help='the test to perform: gbsa, rf, pme, amoebagk, or amoebapme [default: all]')
+parser.add_option('--pme-cutoff', default='0.9', dest='cutoff', type='float', help='direct space cutoff for PME in nm [default: 0.9]')
+parser.add_option('--seconds', default='60', dest='seconds', type='float', help='target simulation length in seconds [default: 60]')
+parser.add_option('--mutual-epsilon', default='1e-4', dest='epsilon', type='float', help='mutual induced epsilon for AMOEBA [default: 1e-4]')
+parser.add_option('--heavy-hydrogens', action='store_true', default=False, dest='heavy', help='repartition mass to allow a larger time step')
+parser.add_option('--device', default=None, dest='device', help='device index for CUDA or OpenCL')
+parser.add_option('--precision', default='single', dest='precision', choices=('single', 'mixed', 'double'), help='precision mode for CUDA or OpenCL: single, mixed, or double [default: single]')
+(options, args) = parser.parse_args()
+if len(args) > 0:
+    parser.error('Unknown argument: '+args[0])
+if options.platform is None:
+    parser.error('No platform specified')
+print('Platform:', options.platform)
+if options.platform in ('CUDA', 'OpenCL'):
+    print('Precision:', options.precision)
+    if options.device is not None:
+        print('Device:', options.device)
+
+# Run the simulations.
+
+if options.test is None:
+    for test in ('gbsa', 'rf', 'pme', 'amoebagk', 'amoebapme'):
+        try:
+            runOneTest(test, options)
+        except Exception as ex:
+            print('Test failed: %s' % ex.message)
+else:
+    runOneTest(options.test, options)

libraries/lepton/include/lepton/Operation.h

@@ -40,6 +40,7 @@
 #include <string>
 #include <vector>
 #include <sstream>
+#include <algorithm>
 
 namespace Lepton {
 

libraries/lepton/src/MSVC_erfc.h

@@ -2,16 +2,16 @@
 #define LEPTON_MSVC_ERFC_H_
 
 /*
- * At least up to version 8 (VC++ 2005), Microsoft does not support the
- * standard C99 erf() and erfc() functions. For now we're including these
- * definitions for an MSVC compilation; if these are added later then
- * the #ifdef below should change to compare _MSC_VER with a particular
- * version level.
+ * Up to version 11 (VC++ 2012), Microsoft does not support the
+ * standard C99 erf() and erfc() functions so we have to fake them here. 
+ * These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
+ * (VC11 has _MSC_VER=1700).
  */
 
-#ifdef _MSC_VER
-
+#if defined(_MSC_VER) 
+#define M_PI 3.14159265358979323846264338327950288
 
+#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 
 /***************************
 *   erf.cpp
 *   author:  Steve Strand
@@ -20,8 +20,6 @@
 
 #include <cmath>
 
-#define M_PI 3.14159265358979323846264338327950288
-
 static const double rel_error= 1E-12;        //calculate 12 significant figures
 //you can adjust rel_error to trade off between accuracy and speed
 //but don't ask for > 15 figures (assuming usual 52 bit mantissa in a double)
@@ -83,6 +81,7 @@ static double erfc(double x)
     return one_sqrtpi*exp(-x*x)*q2;
 }
 
+#endif // _MSC_VER <= 1700
 #endif // _MSC_VER
 
 #endif // LEPTON_MSVC_ERFC_H_

libraries/sfmt/src/SFMT.cpp

@@ -90,8 +90,10 @@ namespace OpenMM_SFMT {
 
 class SFMTData {
 public:
+    /** Possibly incorrectly aligned memory for internal state array */
+    char baseData[(N+1)*sizeof(w128_t)];
 	/** the 128-bit internal state array */
-	w128_t sfmt[N];
+	w128_t* sfmt;
 	/** the 32bit integer pointer to the 128-bit internal state array */
 	uint32_t *psfmt32;
 	#if !defined(BIG_ENDIAN64) || defined(ONLY64)
@@ -106,6 +108,9 @@ public:
 	/** a parity check vector which certificate the period of 2^{MEXP} */
 	uint32_t parity[4];
 	SFMTData() {
+        char* offsetData = baseData+15;
+        offsetData -= (long long)offsetData&0xF;
+        sfmt = (w128_t*) offsetData;
 		psfmt32 = &sfmt[0].u[0];
 #if !defined(BIG_ENDIAN64) || defined(ONLY64)
 		psfmt64 = (uint64_t *)&sfmt[0].u[0];

olla/src/Platform.cpp

@@ -88,7 +88,12 @@ const string& Platform::getPropertyDefaultValue(const string& property) const {
 }
 
 void Platform::setPropertyDefaultValue(const string& property, const string& value) {
+    for (int i = 0; i < (int) platformProperties.size(); i++)
+        if (platformProperties[i] == property) {
             defaultProperties[property] = value;
+            return;
+        }
+    throw OpenMMException("setPropertyDefaultValue: Illegal property name");
 }
 
 void Platform::contextCreated(ContextImpl& context, const map<string, string>& properties) const {

openmmapi/include/OpenMM.h

@@ -69,5 +69,6 @@
 #include "openmm/VerletIntegrator.h"
 #include "openmm/VirtualSite.h"
 #include "openmm/Platform.h"
+#include "openmm/serialization/XmlSerializer.h"
 
 #endif /*OPENMM_H_*/

openmmapi/include/openmm/AndersenThermostat.h

@@ -74,6 +74,15 @@ public:
     double getDefaultTemperature() const {
         return defaultTemp;
     }
+    /**
+     * Set the default temperature of the heat bath.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param temperature         the default temperature of the heat bath (in Kelvin)
+     */
+    void setDefaultTemperature(double temperature) {
+        defaultTemp = temperature;
+    }
     /**
      * Get the default collision frequency (in 1/ps).
      *
@@ -82,6 +91,15 @@ public:
     double getDefaultCollisionFrequency() const {
         return defaultFreq;
     }
+    /**
+     * Set the default collision frequency.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param frequency         the default collision frequency (in 1/ps)
+     */
+    void setDefaultCollisionFrequency(double frequency) {
+        defaultFreq = frequency;
+    }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h

@@ -100,6 +100,15 @@ public:
     const Vec3& getDefaultPressure() const {
         return defaultPressure;
     }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(const Vec3& pressure) {
+        defaultPressure = pressure;
+    }
     /**
      * Get whether to allow the X dimension of the periodic box to change size.
      */

openmmapi/include/openmm/MonteCarloBarostat.h

@@ -74,6 +74,15 @@ public:
     double getDefaultPressure() const {
         return defaultPressure;
     }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(double pressure) {
+        defaultPressure = pressure;
+    }
     /**
      * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.

openmmapi/include/openmm/State.h

@@ -34,6 +34,7 @@
 
 #include "Vec3.h"
 #include <map>
+#include <string>
 #include <vector>
 #include "internal/windowsExport.h"
 

openmmapi/include/openmm/internal/MSVC_erfc.h

@@ -2,16 +2,16 @@
 #define OPENMM_MSVC_ERFC_H_
 
 /*
- * At least up to version 8 (VC++ 2005), Microsoft does not support the
- * standard C99 erf() and erfc() functions. For now we're including these
- * definitions for an MSVC compilation; if these are added later then
- * the #ifdef below should change to compare _MSC_VER with a particular
- * version level.
+ * Up to version 11 (VC++ 2012), Microsoft does not support the
+ * standard C99 erf() and erfc() functions so we have to fake them here. 
+ * These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
+ * (VC11 has _MSC_VER=1700).
  */
 
-#ifdef _MSC_VER
-
+#if defined(_MSC_VER) 
+#define M_PI 3.14159265358979323846264338327950288
 
+#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 
 /***************************
 *   erf.cpp
 *   author:  Steve Strand
@@ -81,6 +81,7 @@ static double erfc(double x)
     return one_sqrtpi*exp(-x*x)*q2;
 }
 
+#endif // _MSC_VER <= 1700
 #endif // _MSC_VER
 
 #endif // OPENMM_MSVC_ERFC_H_