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Commit 9936ec46 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods

parent 40610876
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platforms/brook/tests/CMakeLists.txt
View file @ 9936ec46
# # Testing
#
# Testing
#
ENABLE_TESTING()
......@@ -19,7 +20,6 @@ ENDIF(LOG)
INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/../brook-cmake/FindBrook.cmake)
# SET(BROOK_SRC ../src )
SET(BROOK_LIB brook)
SET(OpenMM_BROOK_LIBRARY_NAME OpenMM_Brook)
......@@ -27,46 +27,30 @@ SET(OpenMM_BROOK_LIBRARY_NAME OpenMM_Brook)
SET(SHARED_BROOK_TARGET ${OpenMM_BROOK_LIBRARY_NAME})
SET(STATIC_BROOK_TARGET ${OpenMM_BROOK_LIBRARY_NAME}_static)
# problem w/ brook.lib
IF( UNIX AND CMAKE_BUILD_TYPE MATCHES Debug )
SET(SHARED_BROOK_TARGET ${SHARED_BROOK_TARGET}_d )
SET(STATIC_BROOK_TARGET ${STATIC_BROOK_TARGET}_d )
SET(BROOK_LIB ${BROOK_LIB}_d )
# ELSE(UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# SET(BROOK_LIB ${BROOK_LIB}_d )
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# Link with shared library
# ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
# LINK_DIRECTORIES( ${TEST_ROOT} ${BROOK_SDK} )
# TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${BROOK_LIB} )
# ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
# Link with static library
SET(TEST_STATIC ${TEST_ROOT}Static)
LINK_DIRECTORIES(${TEST_STATIC} ${BROOK_LIB_PATH})
#ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
#TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
# ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
# STRING_APPEND( CMAKE_EXE_LINKER_FLAGS_DEBUG "/NODEFAULTLIB:\"LIBCMT.lib\"")
SET( CMAKE_EXE_LINKER_FLAGS_DEBUG "/NODEFAULTLIB:\"LIBCMT.lib\"")
# SET( CMAKE_EXE_LINKER_FLAGS "/NODEFAULTLIB:\"LIBCMTD.lib\"")
SET( CMAKE_EXE_LINKER_FLAGS_DEBUG "/NODEFAULTLIB:\"LIBCMTD.lib\"")
# SET( CMAKE_EXE_LINKER_FLAGS "/NODEFAULTLIB:\"LIBCMT.lib\"")
ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
ADD_DEFINITIONS(-D_WIN32 )
SET_TARGET_PROPERTIES(${TEST_STATIC}
PROPERTIES
COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
)
TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET} ${BROOK_LIB} )
# Link with static library
SET(TEST_STATIC ${TEST_ROOT}Static)
ADD_EXECUTABLE(${TEST_STATIC} ${TEST_PROG})
# SET_TARGET_PROPERTIES(${TEST_STATIC}
# PROPERTIES
# COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES"
# )
TARGET_LINK_LIBRARIES(${TEST_STATIC} ${STATIC_TARGET} ${STATIC_BROOK_TARGET} ${BROOK_LIB})
# ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
# ----------------------------------------------------------------------------
IF(LOG)
......@@ -74,7 +58,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
ENDIF(LOG)
# ----------------------------------------------------------------------------
ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
# ADD_TEST(${TEST_STATIC} ${EXECUTABLE_OUTPUT_PATH}/${TEST_STATIC})
ENDFOREACH(TEST_PROG ${TEST_PROGS})
......@@ -84,5 +68,3 @@ IF(LOG)
FILE( APPEND ${LOG_FILE} "Leaving Brook Test Cmake\n")
ENDIF(LOG)
# ----------------------------------------------------------------------------
platforms/brook/tests/TestBrookStream.cpp
View file @ 9936ec46
......@@ -48,13 +48,19 @@
#include "OpenMMContext.h"
#include "CMMotionRemover.h"
#include "NonbondedForce.h"
#include "HarmonicBondForce.h"
#include "HarmonicAngleForce.h"
#include "RBTorsionForce.h"
#include "PeriodicTorsionForce.h"
#include "GBSAOBCForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "BrownianIntegrator.h"
#include "VerletIntegrator.h"
#include "BrookRandomNumberGenerator.h"
#include "BrookShakeAlgorithm.h"
#include "BrookStochasticDynamics.h"
#include "BrookLangevinDynamics.h"
#include "BrookBrownianDynamics.h"
#include "BrookVerletDynamics.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
......@@ -89,7 +95,7 @@ void testWriteRead( void ){
// get factory & create stream
const BrookStreamFactory& brookStreamFactory = dynamic_cast<const BrookStreamFactory&> (platform.getDefaultStreamFactory());
StreamImpl* testStream = brookStreamFactory.createStreamImpl( OpenMM::BrookStreamFactory::BondedAtomIndicesStream, ArraySz, Stream::Float, platform );
StreamImpl* testStream = brookStreamFactory.createStreamImpl( OpenMM::BrookStreamFactory::BondedParticleIndicesStream, ArraySz, Stream::Float, platform );
// load & retreive data
......@@ -513,7 +519,7 @@ int SimTKOpenMMUtilities::tokenizeString( const std::string& line, StringVector&
--------------------------------------------------------------------------------------- */
int readParameterFile( int numberOfAtomIndices, int numberOfParameters,
int readParameterFile( int numberOfParticleIndices, int numberOfParameters,
vector<vector<int> >& atomIndices,
vector<vector<double> >& parameters,
const std::string& parameterFileName ){
......@@ -573,14 +579,14 @@ int readParameterFile( int numberOfAtomIndices, int numberOfParameters,
vector<int> entry;
atomIndices.push_back( entry );
for( int ii = 0; ii < numberOfAtomIndices; ii++ ){
for( int ii = 0; ii < numberOfParticleIndices; ii++ ){
int atomIndex = (int) atoi( tokens[startColumnIndex+ii].c_str() );
entry.push_back( atomIndex );
}
vector<double> entryP;
parameters.push_back( entryP );
int startParameterIndex = startColumnIndex + numberOfAtomIndices;
int startParameterIndex = startColumnIndex + numberOfParticleIndices;
for( int ii = 0; ii < numberOfParameters; ii++ ){
double parameter = (double) atof( tokens[startParameterIndex+ii].c_str() );
entryP.push_back( parameter );
......@@ -790,7 +796,7 @@ class ParameterInfo {
private:
int _numberOfAtomIndices;
int _numberOfParticleIndices;
int _numberOfParameterIndices;
std::string _fileName;
std::string _directoryName;
......@@ -799,18 +805,18 @@ class ParameterInfo {
public:
ParameterInfo( int numberOfAtomIndices, int numberOfParameterIndices, std::string fileName, std::string directoryName ){
_numberOfAtomIndices = numberOfAtomIndices;
ParameterInfo( int numberOfParticleIndices, int numberOfParameterIndices, std::string fileName, std::string directoryName ){
_numberOfParticleIndices = numberOfParticleIndices;
_numberOfParameterIndices = numberOfParameterIndices;
_fileName = fileName;
_directoryName = directoryName;
}
~ParameterInfo( void ){};
std::string getFullFileName( void ){ std::string name; name = _directoryName; name.append( _fileName ); return name; }
int getNumberOfAtomIndices( void ){ return _numberOfAtomIndices; };
int getNumberOfParticleIndices( void ){ return _numberOfParticleIndices; };
int getNumberOfParameters( void ){ return _numberOfParameterIndices; };
vector<vector<int> >& getAtomIndices( void ){ return _atomIndices; };
vector<vector<int> >& getParticleIndices( void ){ return _atomIndices; };
vector<vector<double> >& getParameters( void ){ return _parameters; };
};
*/
......@@ -846,8 +852,8 @@ void testBrookBonded( void ){
for( unsigned int ii = 0; ii < parameterInfoVector.size(); ii++ ){
ParameterInfo parameterInfo = parameterInfoVector[ii];
readParameterFile( parameterInfo.getNumberOfAtomIndices(), parameterInfo.getNumberOfParameters(),
parameterInfo.getAtomIndices(), parameterInfo.getParameters(), parameterInfo.getFullFileName() );
readParameterFile( parameterInfo.getNumberOfParticleIndices(), parameterInfo.getNumberOfParameters(),
parameterInfo.getParticleIndices(), parameterInfo.getParameters(), parameterInfo.getFullFileName() );
if( debug ){
(void) fprintf( log, "%s %d\n", parameterInfo.getFullFileName().c_str(), parameterInfo.getParameters().size() );
}
......@@ -868,11 +874,11 @@ void testBrookBonded( void ){
double lj14Scale = 8.33300e-001;
double coulombScale = 1.0;
brookBonded.setup( atomTypes.size(),
parameterInfoVector[0].getAtomIndices(), parameterInfoVector[0].getParameters(),
parameterInfoVector[1].getAtomIndices(), parameterInfoVector[1].getParameters(),
parameterInfoVector[2].getAtomIndices(), parameterInfoVector[2].getParameters(),
parameterInfoVector[3].getAtomIndices(), parameterInfoVector[3].getParameters(),
parameterInfoVector[4].getAtomIndices(), ljCoulombParameterInfo.getParameters(),
parameterInfoVector[0].getParticleIndices(), parameterInfoVector[0].getParameters(),
parameterInfoVector[1].getParticleIndices(), parameterInfoVector[1].getParameters(),
parameterInfoVector[2].getParticleIndices(), parameterInfoVector[2].getParameters(),
parameterInfoVector[3].getParticleIndices(), parameterInfoVector[3].getParameters(),
parameterInfoVector[4].getParticleIndices(), ljCoulombParameterInfo.getParameters(),
lj14Scale, coulombScale, brookPlatform, log );
// read in coordinates and forces
......@@ -901,7 +907,7 @@ exit(0);
// get factory & create stream
const BrookStreamFactory& brookStreamFactory = dynamic_cast<const BrookStreamFactory&> (platform.getDefaultStreamFactory());
StreamImpl* testStream = brookStreamFactory.createStreamImpl( OpenMM::BrookStreamFactory::BondedAtomIndicesStream, ArraySz, Stream::Float, platform );
StreamImpl* testStream = brookStreamFactory.createStreamImpl( OpenMM::BrookStreamFactory::BondedParticleIndicesStream, ArraySz, Stream::Float, platform );
// load & retreive data
......@@ -925,12 +931,12 @@ void testBrookBondedHarmonicBond( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
System system( numberOfAtoms, 0);
for( int ii = 0; ii < numberOfAtoms; ii++ ){
system.setAtomMass( ii, mass );
System system( numberOfParticles, 0);
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.setParticleMass( ii, mass );
}
LangevinIntegrator integrator(0, 0.1, 0.01);
......@@ -967,7 +973,7 @@ void testBrookBondedHarmonicBond( void ){
std::vector<std::vector<double> > lj14Parameters;
(void) fprintf( log, "testBrookBondedHarmonicBond: Calling brookBonded.setup\n" );
brookBonded.setup( numberOfAtoms,
brookBonded.setup( numberOfParticles,
harmonicBondsIndices, harmonicBondsParameters,
angleBondsIndices, angleBondsParameters,
rbTorsionBondsIndices, rbTorsionBondsParameters,
......@@ -979,12 +985,12 @@ void testBrookBondedHarmonicBond( void ){
(void) fprintf( log, "testBrookBondedHarmonicBond: brookBonded::contents\n%s", contents.c_str() );
(void) fflush( log );
BrookStochasticDynamics brookStochasticDynamics;
BrookLangevinDynamics brookLangevinDynamics;
BrookShakeAlgorithm brookShakeAlgorithm;
BrookRandomNumberGenerator brookRandomNumberGenerator;
contents = brookStochasticDynamics.getContentsString( );
(void) fprintf( log, "testBrookBondedHarmonicBond: brookStochasticDynamics::contents\n%s", contents.c_str() );
contents = brookLangevinDynamics.getContentsString( );
(void) fprintf( log, "testBrookBondedHarmonicBond: brookLangevinDynamics::contents\n%s", contents.c_str() );
contents = brookShakeAlgorithm.getContentsString( );
(void) fprintf( log, "testBrookBondedHarmonicBond: brookShakeAlgorithm::contents\n%s", contents.c_str() );
......@@ -1002,14 +1008,14 @@ void testBrookNonBonded( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
System system( numberOfAtoms, 0);
for( int ii = 0; ii < numberOfAtoms; ii++ ){
system.setAtomMass( ii, mass );
System system( numberOfParticles, 0);
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.setParticleMass( ii, mass );
}
LangevinIntegrator integrator(0, 0.1, 0.01);
......@@ -1021,7 +1027,7 @@ void testBrookNonBonded( void ){
// load nonbonded parameters
std::vector<std::vector<double> > nonbondedParameters;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
std::vector<double> parameters;
parameters.push_back( 1.0 );
parameters.push_back( 1.0 );
......@@ -1032,14 +1038,14 @@ void testBrookNonBonded( void ){
// exclusions
std::vector<std::set<int> > exclusions;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
std::set<int> exclusion;
exclusions.push_back( exclusion );
}
(void) fprintf( log, "testBrookBondedHarmonicBond: Calling brookNonBonded::setup\n" );
(void) fflush( log );
brookNonBonded.setup( numberOfAtoms, nonbondedParameters, exclusions, brookPlatform );
brookNonBonded.setup( numberOfParticles, nonbondedParameters, exclusions, brookPlatform );
std::string contents = brookNonBonded.getContentsString( );
(void) fprintf( log, "testBrookBondedHarmonicBond: Called brookNonBonded.getContentsString \n" );
(void) fflush( log );
......@@ -1056,7 +1062,7 @@ void testBrookBonds( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 3;
int numberOfParticles = 3;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1065,12 +1071,12 @@ void testBrookBonds( void ){
(void) fflush( log );
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator(0, 0.1, 0.01);
// int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
NonbondedForce* forceField = new NonbondedForce( 3, 2, 0, 0, 0 );
HarmonicBondForce* forceField = new HarmonicBondForce( 2 );
// ( index, atom1, atom2, length, k )
forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
......@@ -1096,7 +1102,7 @@ void testBrookBonds( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "Harmonic bond forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1119,7 +1125,7 @@ void testBrookAngles( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 4;
int numberOfParticles = 4;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1128,12 +1134,12 @@ void testBrookAngles( void ){
(void) fflush( log );
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, 0, 2, 0, 0 );
HarmonicAngleForce* forceField = new HarmonicAngleForce(2);
// int index, int atom1, int atom2, int atom3, double angle, double k
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
......@@ -1144,7 +1150,7 @@ void testBrookAngles( void ){
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......@@ -1160,7 +1166,7 @@ void testBrookAngles( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "Angle bond forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1188,7 +1194,7 @@ void testBrookPeriodicTorsions( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 4;
int numberOfParticles = 4;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1197,22 +1203,22 @@ void testBrookPeriodicTorsions( void ){
(void) fflush( log );
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, 0, 0, 1, 0 );
PeriodicTorsionForce* forceField = new PeriodicTorsionForce( 1 );
// int index, int atom1, int atom2, int atom3, double angle, double k
forceField->setPeriodicTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
//(void) fprintf( log, "%s: Calling context\n", methodName.c_str() );
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......@@ -1228,7 +1234,7 @@ void testBrookPeriodicTorsions( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "Periodic torsion bond forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1260,7 +1266,7 @@ void testBrookRBTorsions( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 4;
int numberOfParticles = 4;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1269,25 +1275,20 @@ void testBrookRBTorsions( void ){
(void) fflush( log );
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, 0, 0, 0, 1 );
for( int ii = 0; ii < numberOfAtoms; ii++ ){
forceField->setAtomParameters( ii, 0.0, 1, 0);
}
forceField->setRBTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
RBTorsionForce* forceField = new RBTorsionForce( 1 );
forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
//(void) fprintf( log, "%s: Calling context\n", methodName.c_str() );
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......@@ -1304,7 +1305,7 @@ void testBrookRBTorsions( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "RB torsion bond forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1342,7 +1343,7 @@ void testBrookCoulomb( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1351,21 +1352,21 @@ void testBrookCoulomb( void ){
(void) fflush( log );
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, 0, 0, 0, 0 );
forceField->setAtomParameters(0, 0.5, 1, 0);
forceField->setAtomParameters(1, -1.5, 1, 0);
NonbondedForce* forceField = new NonbondedForce( numberOfParticles, 0 );
forceField->setParticleParameters(0, 0.5, 1, 0);
forceField->setParticleParameters(1, -1.5, 1, 0);
system.addForce(forceField);
//(void) fprintf( log, "%s: Calling context\n", methodName.c_str() );
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
......@@ -1379,7 +1380,7 @@ void testBrookCoulomb( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "Coulomb forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1403,7 +1404,7 @@ void testBrookLJ( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1413,21 +1414,21 @@ void testBrookLJ( void ){
BrookPlatform platform( 32, "cal", log );
// ReferencePlatform platform;
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, 0, 0, 0, 0 );
forceField->setAtomParameters(0, 0, 1.2, 1);
forceField->setAtomParameters(1, 0, 1.4, 2);
NonbondedForce* forceField = new NonbondedForce( numberOfParticles, 0 );
forceField->setParticleParameters(0, 0, 1.2, 1);
forceField->setParticleParameters(1, 0, 1.4, 2);
system.addForce(forceField);
//(void) fprintf( log, "%s: Calling context\n", methodName.c_str() );
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
......@@ -1441,7 +1442,7 @@ void testBrookLJ( void ){
const vector<Vec3>& forces = state.getForces();
(void) fprintf( log, "LJ forces\n");
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
......@@ -1465,7 +1466,7 @@ void testBrookExclusionsAnd14( void ){
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 5;
int numberOfParticles = 5;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -1476,37 +1477,47 @@ void testBrookExclusionsAnd14( void ){
BrookPlatform platform( 32, "cpu", log );
//BrookPlatform platform( 32, "cal", log );
//ReferencePlatform platform;
System system( numberOfAtoms, 0 );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int index, double charge, double radius, double depth
NonbondedForce* forceField = new NonbondedForce( numberOfAtoms, numberOfAtoms-1, 0, 0, 0 );
for( int ii = 1; ii < numberOfAtoms; ii++ ){
forceField->setBondParameters(ii-1, ii-1, ii, 1, 0);
}
system.addForce(forceField);
HarmonicBondForce* bonds = new HarmonicBondForce(4);
bonds->setBondParameters(0, 0, 1, 1, 0);
bonds->setBondParameters(1, 1, 2, 1, 0);
bonds->setBondParameters(2, 2, 3, 1, 0);
bonds->setBondParameters(3, 3, 4, 1, 0);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce( numberOfParticles, 2);
system.addForce(nonbonded);
//(void) fprintf( log, "%s: Calling context\n", methodName.c_str() );
//(void) fflush( log );
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
const double r = 1.0;
positions[0] = Vec3(0, 0, 0);
for( int ii = 1; ii < numberOfAtoms; ii++ ){
for( int ii = 1; ii < numberOfParticles; ii++ ){
positions[ii] = Vec3(r, 0, 0);
}
for( int ii = 1; ii < numberOfAtoms; ii++ ){
for( int ii = 1; ii < numberOfParticles; ii++ ){
// Test LJ forces
forceField->setAtomParameters(0, 0, 1.5, 1);
for (int jj = 1; jj < numberOfAtoms; ++jj){
forceField->setAtomParameters(jj, 0, 1.5, 0);
}
forceField->setAtomParameters(ii, 0, 1.5, 1);
vector<Vec3> positions(5);
const double r = 1.0;
for (int j = 0; j < 5; ++j) {
nonbonded->setParticleParameters(j, 0, 1.5, 0);
positions[j] = Vec3(0, j, 0);
}
nonbonded->setParticleParameters(0, 0, 1.5, 1);
nonbonded->setParticleParameters(ii, 0, 1.5, 1);
nonbonded->setNonbonded14Parameters(0, 0, 3, 0, 1.5, ii == 3 ? 0.5 : 0.0);
nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
positions[ii] = Vec3(r, 0, 0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState( State::Forces | State::Energy );
......@@ -1524,7 +1535,7 @@ void testBrookExclusionsAnd14( void ){
energy = 0;
}
(void) fprintf( log, "14 LJ forces ii=%d F=%.6e\n", ii, force );
for( int jj = 0; jj < numberOfAtoms; jj++ ){
for( int jj = 0; jj < numberOfParticles; jj++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", jj, forces[jj][0], forces[jj][1], forces[jj][2] );
}
(void) fflush( log );
......@@ -1536,8 +1547,11 @@ void testBrookExclusionsAnd14( void ){
// Test Coulomb forces
forceField->setAtomParameters(0, 2, 1.5, 0);
forceField->setAtomParameters(ii, 2, 1.5, 0);
nonbonded->setParticleParameters( 0, 2, 1.5, 0 );
nonbonded->setParticleParameters( ii, 2, 1.5, 0 );
nonbonded->setNonbonded14Parameters( 0, 0, 3, ii == 3 ? 4/1.2 : 0, 1.5, 0 );
nonbonded->setNonbonded14Parameters( 1, 1, 4, 0, 1.5, 0 );
context.reinitialize();
context.setPositions(positions);
state = context.getState( State::Forces | State::Energy );
......@@ -1553,7 +1567,7 @@ void testBrookExclusionsAnd14( void ){
energy = 0;
}
(void) fprintf( log, "14 Coulomb forces ii=%d F=%.6e\n", ii, force );
for( int jj = 0; jj < numberOfAtoms; jj++ ){
for( int jj = 0; jj < numberOfParticles; jj++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", jj, forces[jj][0], forces[jj][1], forces[jj][2] );
}
(void) fflush( log );
......@@ -1567,7 +1581,7 @@ void testBrookExclusionsAnd14( void ){
}
static OpenMMContext* testObcForceSetup( int numAtoms, int brookContext ){
static OpenMMContext* testObcForceSetup( int numParticles, int brookContext ){
// ---------------------------------------------------------------------------------------
......@@ -1587,23 +1601,23 @@ static OpenMMContext* testObcForceSetup( int numAtoms, int brookContext ){
platform = new ReferencePlatform();
}
System* system = new System( numAtoms, 0 );
System* system = new System( numParticles, 0 );
LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(numAtoms);
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
for (int i = 0; i < numAtoms; ++i){
for (int i = 0; i < numParticles; ++i){
// charge radius scalingFactor
forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
//forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
//forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
}
system->addForce(forceField);
OpenMMContext* context = new OpenMMContext( *system, *integrator, *platform );
// Set random positions for all the atoms.
vector<Vec3> positions(numAtoms);
vector<Vec3> positions(numParticles);
init_gen_rand(0);
for (int i = 0; i < numAtoms; ++i){
for (int i = 0; i < numParticles; ++i){
positions[i] = Vec3(1.0*genrand_real2(), 1.0*genrand_real2(), 1.0*genrand_real2());
}
context->setPositions(positions);
......@@ -1661,7 +1675,7 @@ static char* localStrsep( char** lineBuffer, const char* delimiter ){
}
static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookContext, int* numAtoms ){
static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookContext, int* numParticles ){
// ---------------------------------------------------------------------------------------
......@@ -1709,17 +1723,17 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
return NULL;
}
StringVectorI ii = tokens.begin();
int numberOfAtoms = atoi( (*ii).c_str() );
(void) fprintf( log, "\n%s %d\n", methodName.c_str(), numberOfAtoms );
*numAtoms = numberOfAtoms;
int numberOfParticles = atoi( (*ii).c_str() );
(void) fprintf( log, "\n%s %d\n", methodName.c_str(), numberOfParticles );
*numParticles = numberOfParticles;
lineCount++;
System* system = new System( *numAtoms, 0 );
GBSAOBCForce* forceField = new GBSAOBCForce(numberOfAtoms);
System* system = new System( *numParticles, 0 );
GBSAOBCForce* forceField = new GBSAOBCForce(numberOfParticles);
vector<Vec3> positions(numberOfAtoms);
vector<Vec3> positions(numberOfParticles);
int index = 0;
for (int i = 0; i < numberOfAtoms; ++i){
for (int i = 0; i < numberOfParticles; ++i){
(void) fgets( buffer, bufferSize, readFile );
StringVector tokens;
......@@ -1743,7 +1757,7 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
positions[index++] = Vec3( coordX, coordY, coordZ );
// charge radius scalingFactor
forceField->setAtomParameters( i, charge, radius, scalingFactor );
forceField->setParticleParameters( i, charge, radius, scalingFactor );
(void) fprintf( log, "%d [%.6f %.6f %.6f] q=%.6f rad=%.6f scl=%.6f bR=%.6f\n", i,
coordX, coordY, coordZ, charge, radius, scalingFactor, bornRadi );
......@@ -1774,13 +1788,13 @@ void testObcForce() {
// ---------------------------------------------------------------------------------------
int numAtoms = 10;
//OpenMMContext* context = testObcForceSetup( numAtoms, 0 );
//OpenMMContext* brookContext = testObcForceSetup( numAtoms, 1 );
int numParticles = 10;
//OpenMMContext* context = testObcForceSetup( numParticles, 0 );
//OpenMMContext* brookContext = testObcForceSetup( numParticles, 1 );
OpenMMContext* context = testObcForceFileSetup( std::string( "ObcInfo.txt" ), 0, &numAtoms );
OpenMMContext* context = testObcForceFileSetup( std::string( "ObcInfo.txt" ), 0, &numParticles );
//OpenMMContext* context = NULL;
OpenMMContext* brookContext = testObcForceFileSetup( std::string( "ObcInfo.txt" ), 1, &numAtoms );
OpenMMContext* brookContext = testObcForceFileSetup( std::string( "ObcInfo.txt" ), 1, &numParticles );
//OpenMMContext* brookContext = NULL;
vector<Vec3> forces;
......@@ -1796,7 +1810,7 @@ void testObcForce() {
}
(void) fprintf( log, "%s OBC forces [%s %s]\n", methodName.c_str(), (context?"Ref":""), (brookContext?"Brook":"") );
for( int ii = 0; ii < numAtoms; ii++ ){
for( int ii = 0; ii < numParticles; ii++ ){
(void) fprintf( log, "%4d ", ii );
if( context && brookContext ){
double diff[3];
......@@ -1830,7 +1844,7 @@ void testObcForce() {
double tolerance = 1.0e-03;
if( context && brookContext ){
for (int i = 0; i < numAtoms; ++i) {
for (int i = 0; i < numParticles; ++i) {
Vec3 f = forces[i];
Vec3 fBrook = brookForces[i];
ASSERT_EQUAL_VEC( f, fBrook, tolerance );
......@@ -1841,11 +1855,11 @@ void testObcForce() {
}
void testObcSingleAtom() {
void testObcSingleParticle() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testObcSingleAtom";
static const std::string methodName = "testObcSingleParticle";
FILE* log = stdout;
// ---------------------------------------------------------------------------------------
......@@ -1853,10 +1867,10 @@ void testObcSingleAtom() {
BrookPlatform platform;
//ReferencePlatform platform;
System system(1, 0);
system.setAtomMass(0, 2.0);
system.setParticleMass(0, 2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(1);
forceField->setAtomParameters(0, 0.5, 0.15, 1);
forceField->setParticleParameters(0, 0.5, 0.15, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(1);
......@@ -1883,22 +1897,22 @@ void testObcEConsistentForce() {
// ---------------------------------------------------------------------------------------
BrookPlatform platform;
//ReferencePlatform platform;
const int numAtoms = 10;
System system(numAtoms, 0);
//BrookPlatform platform;
ReferencePlatform platform;
const int numParticles = 10;
System system(numParticles, 0);
LangevinIntegrator integrator(0, 0.1, 0.01);
GBSAOBCForce* forceField = new GBSAOBCForce(numAtoms);
for (int i = 0; i < numAtoms; ++i)
forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
for (int i = 0; i < numParticles; ++i)
forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
// Set random positions for all the atoms.
vector<Vec3> positions(numAtoms);
vector<Vec3> positions(numParticles);
init_gen_rand(0);
for (int i = 0; i < numAtoms; ++i)
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......@@ -1906,14 +1920,14 @@ void testObcEConsistentForce() {
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
for (int i = 0; i < numAtoms; ++i) {
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-3;
double step = delta/norm;
for (int i = 0; i < numAtoms; ++i) {
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
......@@ -1925,7 +1939,8 @@ void testObcEConsistentForce() {
State state2 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
(void) fprintf( log, "%s ok\n", methodName.c_str() ); (void) fflush( log );
(void) fprintf( log, "%s ok %.8e %.8e %.8e %.8e\n", methodName.c_str(),
state2.getPotentialEnergy(), state.getPotentialEnergy(), norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta ); (void) fflush( log );
}
int testBrookStreams( int streamSize ){
......@@ -2063,7 +2078,7 @@ static OpenMMContext* testLangevinSingleBondSetup( int brookContext, LangevinInt
static const int debug = 1;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -2078,15 +2093,15 @@ static OpenMMContext* testLangevinSingleBondSetup( int brookContext, LangevinInt
platform = new ReferencePlatform();
}
System* system = new System( numberOfAtoms, 0);
system->setAtomMass(0, 2.0);
system->setAtomMass(1, 2.0);
System* system = new System( numberOfParticles, 0);
system->setParticleMass(0, 2.0);
system->setParticleMass(1, 2.0);
// double temperature, double frictionCoeff, double stepSize
LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.01);
*outIntegrator = integrator;
NonbondedForce* forceField = new NonbondedForce(2, 1, 0, 0, 0);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system->addForce(forceField);
OpenMMContext* context = new OpenMMContext( *system, *integrator, *platform );
......@@ -2165,7 +2180,7 @@ void testLangevinTemperature() {
static const int debug = 1;
FILE* log = stdout;
const int numberOfAtoms = 8;
const int numberOfParticles = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -2176,20 +2191,20 @@ void testLangevinTemperature() {
BrookPlatform platform( 32, "cal", log );
// ReferencePlatform platform;
const double temp = 100.0;
System system(numberOfAtoms, 0);
LangevinIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce(numberOfAtoms, 0, 0, 0, 0);
for (int i = 0; i < numberOfAtoms; ++i){
system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
const double temp = 300.0;
System system(numberOfParticles, 0);
LangevinIntegrator integrator(temp, 1.0, 0.002);
NonbondedForce* forceField = new NonbondedForce(numberOfParticles, 0);
for (int i = 0; i < numberOfParticles; ++i){
system.setParticleMass(i, 2.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; ++i)
vector<Vec3> positions(numberOfParticles);
for (int i = 0; i < numberOfParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
context.setPositions(positions);
......@@ -2209,7 +2224,7 @@ void testLangevinTemperature() {
/*
vector<Vec3> positions = state.getPositions();
vector<Vec3> velocities = state.getVelocities();
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, " %d q[%12.5e %12.5e %12.5e] v[%12.5e %12.5e %12.5e]\n", ii,
positions[ii][0], positions[ii][1], positions[ii][2],
velocities[ii][0], velocities[ii][1], velocities[ii][2] );
......@@ -2220,7 +2235,7 @@ void testLangevinTemperature() {
integrator.step(1);
}
ke /= 1000;
double expected = 0.5*numberOfAtoms*3*BOLTZ*temp;
double expected = 0.5*numberOfParticles*3*BOLTZ*temp;
double tol = 3*expected/std::sqrt(1000.0);
(void) fprintf( log, "%s expected=%12.5e found=%12.5e tol=%12.5e ok\n", methodName.c_str(), expected, ke, tol ); fflush( log );
......@@ -2243,7 +2258,7 @@ void testLangevinConstraints() {
static const int debug = 0;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 1.0;
// ---------------------------------------------------------------------------------------
......@@ -2253,17 +2268,17 @@ void testLangevinConstraints() {
BrookPlatform platform( 32, "cal", log );
const int numAtoms = 8;
const int numParticles = 8;
const double temp = 100.0;
//ReferencePlatform platform;
System system(numAtoms, numAtoms-1);
System system(numParticles, numParticles-1);
LangevinIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, mass);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, mass);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numAtoms-1; ++i)
for (int i = 0; i < numParticles-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addForce(forceField);
......@@ -2271,10 +2286,10 @@ void testLangevinConstraints() {
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
vector<Vec3> velocities(numAtoms);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
for (int i = 0; i < numAtoms; ++i) {
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
}
......@@ -2285,7 +2300,7 @@ void testLangevinConstraints() {
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numAtoms-1; ++j) {
for (int j = 0; j < numParticles-1; ++j) {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
......@@ -2308,20 +2323,20 @@ void testVerletSingleBond( void ){
static const int debug = 0;
FILE* log = stdout;
int numberOfAtoms = 2;
int numberOfParticles = 2;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
BrookPlatform platform( 32, "cal", log );
System system( numberOfAtoms, 0 );
system.setAtomMass(0, 2.0);
system.setAtomMass(1, 2.0);
System system( numberOfParticles, 0 );
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce(2, 1, 0, 0, 0);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField);
......@@ -2406,7 +2421,7 @@ void testVerletConstraints() {
static const int debug = 1;
FILE* log = stdout;
const int numAtoms = 8;
const int numParticles = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
......@@ -2414,16 +2429,16 @@ void testVerletConstraints() {
//BrookPlatform platform( 32, "cal", log );
ReferencePlatform platform;
System system(numAtoms, numAtoms/2);
System system(numParticles, numParticles/2);
VerletIntegrator integrator(0.0005);
NonbondedForce* forceField = new NonbondedForce(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 1.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 1.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
int index = 0;
for (int i = 0; i < numAtoms-1; i += 2){
for (int i = 0; i < numParticles-1; i += 2){
//(void) fprintf( log, "%s %d %d %d\n", methodName.c_str(), index, i, i+1 ); fflush( log );
//system.setConstraintParameters(i, i, i+1, 1.0);
system.setConstraintParameters( index++, i, i+1, 1.0);
......@@ -2433,11 +2448,11 @@ void testVerletConstraints() {
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
vector<Vec3> velocities(numAtoms);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
double scale = 0.01;
for (int i = 0; i < numAtoms; ++i) {
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3( scale*(genrand_real2()-0.5), scale*(genrand_real2()-0.5), scale*(genrand_real2()-0.5) );
}
......@@ -2449,7 +2464,7 @@ void testVerletConstraints() {
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy);
for (int j = 0; j < numAtoms; j += 2) {
for (int j = 0; j < numParticles; j += 2) {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
......@@ -2475,6 +2490,245 @@ void testVerletConstraints() {
(void) fflush( log );
}
void testBrownianSingleBond() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrownianSingleBond";
static const int debug = 0;
FILE* log = stdout;
const int numParticles = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
BrookPlatform platform( 32, "cal", log );
//ReferencePlatform platform;
System system(2, 0);
system.setParticleMass(0, 2.0);
system.setParticleMass(1, 2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce(1);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
double rate = 2*1.0/0.1;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::exp(-rate*time);
Vec3 position0 = state.getPositions()[0];
Vec3 position1 = state.getPositions()[1];
if( debug ){
(void) fprintf( log, "%s %d Pos expected=[%12.5e 0 0] actual=[%12.5e %12.5e %12.5e] [%12.5e %12.5e %12.5e]\n",
methodName.c_str(), i, -0.5*expectedDist,
position0[0], position0[1], position0[2],
position1[0], position1[1], position1[2] );
(void) fflush( log );
}
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
Vec3 velocity0 = state.getVelocities()[0];
Vec3 velocity1 = state.getVelocities()[1];
double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
if( debug ){
(void) fprintf( log, "%s %d Vel expected=[%12.5e 0 0] actual=[%12.5e %12.5e %12.5e] [%12.5e %12.5e %12.5e]\n",
methodName.c_str(), i, -0.5*expectedSpeed,
velocity0[0], velocity0[1], velocity0[2],
velocity1[0], velocity1[1], velocity1[2] );
(void) fflush( log );
}
if (i > 0) {
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
}
integrator.step(1);
}
(void) fprintf( log, "%s ok\n", methodName.c_str() );
(void) fflush( log );
}
void testBrownianTemperature() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrownianTemperature";
static const int debug = 1;
FILE* log = stdout;
const int numParticles = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
//BrookPlatform platform( 32, "cal", log );
ReferencePlatform platform;
const int numBonds = numParticles-1;
const double temp = 100.0;
const double deltaT = 0.001;
const double friction = 2.0;
System system(numParticles, 0);
BrownianIntegrator integrator(temp, friction, deltaT);
HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
/*
ReferencePlatform platform;
System system(numParticles, numParticles/2);
VerletIntegrator integrator(0.0005);
NonbondedForce* forceField = new NonbondedForce(numParticles, 0, 0, 0, 0);
*/
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 2.0);
// forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
for (int i = 0; i < numBonds; ++i){
// ( index, atom1, atom2, length, k )
forceField->setBondParameters(i, i, i+1, 1.0, 0.8);
}
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
context.setPositions(positions);
// Let it equilibrate.
int equilibrateSteps = 1000;
int runSteps = 1000;
(void) fprintf( log, "Begin equilibration: %d\n", equilibrateSteps );
integrator.step(equilibrateSteps);
(void) fprintf( log, "End equilibration: %d\n", equilibrateSteps );
// Now run it for a while and see if the temperature is correct.
State state = context.getState(State::Parameters);
const map<std::string, double> params = state.getParameters();
(void) fprintf( log, "Parameters:\n" );
for( map<std::string, double>::const_iterator iter = params.begin(); iter != params.end(); iter++){
std::string label = iter->first;
(void) fprintf( log, " %s %12.5e\n", label.c_str(), iter->second );
}
(void) fprintf( log, "End of Parameters:\n" );
(void) fprintf( log, "Begin run: %d\n", runSteps );
double pe = 0.0;
for (int i = 0; i < runSteps; ++i) {
State state = context.getState(State::Energy | State::Positions | State::Velocities );
pe += state.getPotentialEnergy();
if( debug ){
(void) fprintf( log, "%s %d PE=%12.5e ttl=%12.5e\n",
methodName.c_str(), i, state.getPotentialEnergy(), pe );
vector<Vec3> positions = state.getPositions();
vector<Vec3> velocities = state.getVelocities();
for( int ii = 0; ii < numParticles; ii++ ){
double dist;
if( ii < (numParticles - 1) ){
dist = (positions[ii][0] - positions[ii+1][0] )*(positions[ii][0] - positions[ii+1][0] ) +
(positions[ii][1] - positions[ii+1][1] )*(positions[ii][1] - positions[ii+1][1] ) +
(positions[ii][2] - positions[ii+1][2] )*(positions[ii][2] - positions[ii+1][2] );
dist = sqrt( dist );
} else {
dist = 0.0;
}
(void) fprintf( log, " %d %.8f q[%12.5e %12.5e %12.5e] v[%12.5e %12.5e %12.5e]\n", ii,
dist, positions[ii][0], positions[ii][1], positions[ii][2],
velocities[ii][0], velocities[ii][1], velocities[ii][2] );
}
(void)fflush( log );
}
integrator.step(1);
}
(void) fprintf( log, "End run: %d\n", runSteps );
pe /= (double) runSteps;
double expected = 0.5*numBonds*BOLTZ*temp;
double tol = 3*expected/std::sqrt( (double) runSteps );
(void) fprintf( log, "%s expected=%12.5e found=%12.5e tol=%12.5e ok\n", methodName.c_str(), expected, pe, tol ); fflush( log );
ASSERT_EQUAL_TOL(expected, pe, tol );
(void) fprintf( log, "%s ok\n", methodName.c_str() );
(void) fflush( log );
}
void testBrownianConstraints() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrownianConstraints";
static const int debug = 1;
FILE* log = stdout;
const int numParticles = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
//ReferencePlatform platform;
BrookPlatform platform( 32, "cal", log );
const double temp = 100.0;
System system(numParticles, numParticles-1);
BrownianIntegrator integrator(temp, 2.0, 0.001);
NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
for (int i = 0; i < numParticles; ++i) {
system.setParticleMass(i, 10.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numParticles-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions);
for (int j = 0; j < numParticles-1; ++j) {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
}
integrator.step(1);
}
(void) fprintf( log, "%s ok\n", methodName.c_str() );
(void) fflush( log );
}
int main( ){
(void) fflush( stdout );
......@@ -2483,14 +2737,15 @@ int main( ){
// testBrookBondedHarmonicBond( );
// testBrookNonBonded( );
/*
testBrookStreams( 50 );
testBrookStreams( 63 );
testBrookStreams( 64 );
testBrookStreams( 65 );
*/
testBrookBonds();
/*
testBrookAngles();
testBrookRBTorsions();
testBrookPeriodicTorsions();
......@@ -2502,15 +2757,21 @@ int main( ){
testLangevinConstraints();
testObcForce();
testObcSingleAtom();
testObcSingleParticle();
testObcEConsistentForce();
testVerletSingleBond();
testLangevinConstraints();
testBrownianSingleBond();
*/
//testVerletSingleBond();
testVerletConstraints();
// not working
// testVerletConstraints();
//testObcForce();
//testObcSingleParticle();
// testObcEConsistentForce();
// testLangevinTemperature();
//testBrownianTemperature();
} catch( const exception& e ){
cout << "exception: " << e.what() << endl;
......
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