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Commit 0cae89d3 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods for wrapper code; added yAxis parameter to multipole force-field

parent 077a93c8
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Showing with 300 additions and 251 deletions
plugins/amoeba/CMakeLists.txt
View file @ 0cae89d3
...@@ -16,24 +16,6 @@ ...@@ -16,24 +16,6 @@
#INCLUDE(Dart) #INCLUDE(Dart)
SET(LOG FALSE)
# ----------------------------------------------------------------------------
IF(LOG)
SET(LOG_FILE "CMakeLog.txt" )
FILE( WRITE ${LOG_FILE} "In OpenMM Cmake\n")
ENDIF(LOG)
IF(LOG)
MACRO(LOG_DIR LOG_FILE DIR_LIST )
FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
FOREACH(currentFile ${ARGN})
FILE( APPEND ${LOG_FILE} " ${currentFile}\n" )
ENDFOREACH(currentFile)
ENDMACRO(LOG_DIR)
ENDIF(LOG)
# ---------------------------------------------------------------------------- # ----------------------------------------------------------------------------
# The source is organized into subdirectories, but we handle them all from # The source is organized into subdirectories, but we handle them all from
...@@ -107,23 +89,15 @@ INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference) ...@@ -107,23 +89,15 @@ INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
# ----------------------------------------------------------------------------
IF(LOG)
FILE( APPEND ${LOG_FILE} "SOURCE_AMOEBA_FILES=" ${SOURCE_AMOEBA_FILES} "\n" )
FILE( APPEND ${LOG_FILE} "SOURCE_AMOEBA_INCLUDE_FILES=" ${SOURCE_AMOEBA_INCLUDE_FILES} "\n" )
FILE( APPEND ${LOG_FILE} "OPENMM_PATH=" ${OPENMM_PATH} "\n" )
FILE( APPEND ${LOG_FILE} "CUDA_PATH=" ${CUDA_PATH} "\n" )
ENDIF(LOG)
# ---------------------------------------------------------------------------- # ----------------------------------------------------------------------------
# If API_AMOEBA wrappers are being generated, and add them to the build. # If API_AMOEBA wrappers are being generated, and add them to the build.
#SET(OPENMM_BUILD_API_AMOEBA_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran") #SET(OPENMM_BUILD_API_AMOEBA_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran")
#IF(OPENMM_BUILD_API_AMOEBA_WRAPPERS) IF(OPENMM_BUILD_API_WRAPPERS)
# ADD_SUBDIRECTORY(wrappers) ADD_SUBDIRECTORY(wrappers)
# SET(SOURCE_AMOEBA_FILES ${SOURCE_AMOEBA_FILES} wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp) SET(SOURCE_AMOEBA_FILES ${SOURCE_AMOEBA_FILES} wrappers/AmoebaOpenMMCWrapper.cpp wrappers/AmoebaOpenMMFortranWrapper.cpp)
# SET_SOURCE_AMOEBA_FILES_PROPERTIES(wrappers/OpenMMCWrapper.cpp wrappers/OpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE) SET_SOURCE_FILES_PROPERTIES(wrappers/AmoebaOpenMMCWrapper.cpp wrappers/AmoebaOpenMMFortranWrapper.cpp PROPERTIES GENERATED TRUE)
#ENDIF(OPENMM_BUILD_API_AMOEBA_WRAPPERS) ENDIF(OPENMM_BUILD_API_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
...@@ -135,10 +109,14 @@ IF(OPENMM_BUILD_STATIC_LIB) ...@@ -135,10 +109,14 @@ IF(OPENMM_BUILD_STATIC_LIB)
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY") SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
#IF(OPENMM_BUILD_API_AMOEBA_WRAPPERS) IF(OPENMM_BUILD_API_WRAPPERS)
# ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} ApiWrappers) ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} AmoebaApiWrappers)
# ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} ApiWrappers) IF(OPENMM_BUILD_STATIC_LIB)
#ENDIF(OPENMM_BUILD_API_AMOEBA_WRAPPERS) ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} AmoebaApiWrappers)
ENDIF(OPENMM_BUILD_STATIC_LIB)
ENDIF(OPENMM_BUILD_API_WRAPPERS)
# ----------------------------------------------------------------------------
# On Linux need to link to libdl # On Linux need to link to libdl
FIND_LIBRARY(DL_LIBRARY dl) FIND_LIBRARY(DL_LIBRARY dl)
...@@ -177,11 +155,6 @@ IF(OPENMM_BUILD_AMOEBA_CUDA_LIB) ...@@ -177,11 +155,6 @@ IF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda) SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB) ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
#SET(OPENMM_BUILD_BROOK_LIB OFF CACHE BOOL "Build OpenMMBrook library for ATI GPUs")
#IF(OPENMM_BUILD_BROOK_LIB)
# ADD_SUBDIRECTORY(platforms/brook)
#ENDIF(OPENMM_BUILD_BROOK_LIB)
#
#SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs") #SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs")
#IF(OPENMM_BUILD_OPENCL_LIB) #IF(OPENMM_BUILD_OPENCL_LIB)
# ADD_SUBDIRECTORY(platforms/opencl) # ADD_SUBDIRECTORY(platforms/opencl)
...@@ -210,7 +183,6 @@ INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS}) ...@@ -210,7 +183,6 @@ INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
# ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug) # ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
#ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE) #ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE)
# #
# Testing # Testing
# #
......
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ 0cae89d3
...@@ -162,8 +162,9 @@ public: ...@@ -162,8 +162,9 @@ public:
* @param molecularDipole the particle's molecular dipole (vector of size 3) * @param molecularDipole the particle's molecular dipole (vector of size 3)
* @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9) * @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9)
* @param axisType the particle's axis type ( ZThenX, Bisector ) * @param axisType the particle's axis type ( ZThenX, Bisector )
* @param multipoleAtomId1 index of first atom used in constructing lab<->molecular frames * @param multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param multipoleAtomId2 index of second atom used in constructing lab<->molecular frames * @param multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param thole Thole parameter * @param thole Thole parameter
* @param dampingFactor dampingFactor parameter * @param dampingFactor dampingFactor parameter
* @param polarity polarity parameter * @param polarity polarity parameter
...@@ -171,7 +172,7 @@ public: ...@@ -171,7 +172,7 @@ public:
* @return the index of the particle that was added * @return the index of the particle that was added
*/ */
int addParticle( double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, int axisType, int addParticle( double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity ); int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity );
/** /**
* Get the multipole parameters for a particle. * Get the multipole parameters for a particle.
...@@ -181,14 +182,15 @@ public: ...@@ -181,14 +182,15 @@ public:
* @param molecularDipole the particle's molecular dipole (vector of size 3) * @param molecularDipole the particle's molecular dipole (vector of size 3)
* @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9) * @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9)
* @param axisType the particle's axis type ( ZThenX, Bisector ) * @param axisType the particle's axis type ( ZThenX, Bisector )
* @param multipoleAtomId1 index of first atom used in constructing lab<->molecular frames * @param multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param multipoleAtomId2 index of second atom used in constructing lab<->molecular frames * @param multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param thole Thole parameter * @param thole Thole parameter
* @param dampingFactor dampingFactor parameter * @param dampingFactor dampingFactor parameter
* @param polarity polarity parameter * @param polarity polarity parameter
*/ */
void getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, void getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int& axisType, int& multipoleAtomId1, int& multipoleAtomId2, double& thole, double& dampingFactor, double& polarity ) const; int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity ) const;
/** /**
* Set the multipole parameters for a particle. * Set the multipole parameters for a particle.
...@@ -198,12 +200,13 @@ public: ...@@ -198,12 +200,13 @@ public:
* @param molecularDipole the particle's molecular dipole (vector of size 3) * @param molecularDipole the particle's molecular dipole (vector of size 3)
* @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9) * @param molecularQuadrupole the particle's molecular quadrupole (vector of size 9)
* @param axisType the particle's axis type ( ZThenX, Bisector ) * @param axisType the particle's axis type ( ZThenX, Bisector )
* @param multipoleAtomId1 index of first atom used in constructing lab<->molecular frames * @param multipoleAtomZ index of first atom used in constructing lab<->molecular frames
* @param multipoleAtomId2 index of second atom used in constructing lab<->molecular frames * @param multipoleAtomX index of second atom used in constructing lab<->molecular frames
* @param multipoleAtomY index of second atom used in constructing lab<->molecular frames
* @param polarity polarity parameter * @param polarity polarity parameter
*/ */
void setMultipoleParameters(int index, double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, void setMultipoleParameters(int index, double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int axisType, int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity); int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity);
/** /**
* Set the CovalentMap for an atom * Set the CovalentMap for an atom
...@@ -338,7 +341,7 @@ private: ...@@ -338,7 +341,7 @@ private:
class AmoebaMultipoleForce::MultipoleInfo { class AmoebaMultipoleForce::MultipoleInfo {
public: public:
int axisType, multipoleAtomId1, multipoleAtomId2; int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity; double charge, thole, dampingFactor, polarity;
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
...@@ -346,7 +349,7 @@ public: ...@@ -346,7 +349,7 @@ public:
std::vector< std::vector<int> > covalentInfo; std::vector< std::vector<int> > covalentInfo;
MultipoleInfo() { MultipoleInfo() {
axisType = multipoleAtomId1 = multipoleAtomId2 = -1; axisType = multipoleAtomZ = multipoleAtomX = multipoleAtomY = -1;
charge = thole = dampingFactor = 0.0; charge = thole = dampingFactor = 0.0;
molecularDipole.resize( 3 ); molecularDipole.resize( 3 );
...@@ -355,8 +358,8 @@ public: ...@@ -355,8 +358,8 @@ public:
} }
MultipoleInfo( double charge, std::vector<double>& inputMolecularDipole, std::vector<double>& inputMolecularQuadrupole, MultipoleInfo( double charge, std::vector<double>& inputMolecularDipole, std::vector<double>& inputMolecularQuadrupole,
int axisType, int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity) : int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) :
charge(charge), axisType(axisType), multipoleAtomId1(multipoleAtomId1), multipoleAtomId2(multipoleAtomId2), charge(charge), axisType(axisType), multipoleAtomZ(multipoleAtomZ), multipoleAtomX(multipoleAtomX), multipoleAtomY(multipoleAtomY),
thole(thole), dampingFactor(dampingFactor), polarity(polarity) { thole(thole), dampingFactor(dampingFactor), polarity(polarity) {
covalentInfo.resize( CovalentEnd ); covalentInfo.resize( CovalentEnd );
......
plugins/amoeba/openmmapi/include/AmoebaTorsionForce.h
View file @ 0cae89d3
...@@ -75,7 +75,7 @@ public: ...@@ -75,7 +75,7 @@ public:
* @return the index of the torsion that was added * @return the index of the torsion that was added
*/ */
int addTorsion(int particle1, int particle2, int particle3, int particle4, int addTorsion(int particle1, int particle2, int particle3, int particle4,
std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3 ); std::vector<double>& torsion1, std::vector<double>& torsion2, std::vector<double>& torsion3 );
/** /**
* Get the force field parameters for a torsion term. * Get the force field parameters for a torsion term.
...@@ -105,7 +105,7 @@ public: ...@@ -105,7 +105,7 @@ public:
* @param torsion3 the vector of torsion params for third index (amplitude, phase, fold) * @param torsion3 the vector of torsion params for third index (amplitude, phase, fold)
*/ */
void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4,
std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3 ); std::vector<double>& torsion1, std::vector<double>& torsion2, std::vector<double>& torsion3 );
protected: protected:
ForceImpl* createImpl(); ForceImpl* createImpl();
......
plugins/amoeba/openmmapi/include/AmoebaTorsionTorsionForce.h
View file @ 0cae89d3
...@@ -117,7 +117,8 @@ public: ...@@ -117,7 +117,8 @@ public:
* @param gridIndex the grid index * @param gridIndex the grid index
* @return grid return grid reference * @return grid return grid reference
*/ */
const TorsionTorsionGrid& getTorsionTorsionGrid( int index ) const; //const TorsionTorsionGrid& getTorsionTorsionGrid( int index ) const;
const std::vector< std::vector< std::vector<double> > >& getTorsionTorsionGrid( int index ) const;
/** /**
* Set the torsion-torsion grid at the specified index * Set the torsion-torsion grid at the specified index
...@@ -131,7 +132,8 @@ public: ...@@ -131,7 +132,8 @@ public:
* grid[x][y][4] = dfdy value * grid[x][y][4] = dfdy value
* grid[x][y][5] = dfd(xy) value * grid[x][y][5] = dfd(xy) value
*/ */
void setTorsionTorsionGrid(int index, TorsionTorsionGrid& grid ); //void setTorsionTorsionGrid(int index, TorsionTorsionGrid& grid );
void setTorsionTorsionGrid(int index, std::vector< std::vector< std::vector<double> > >& grid );
protected: protected:
ForceImpl* createImpl(); ForceImpl* createImpl();
......
plugins/amoeba/openmmapi/include/AmoebaVdwForce.h
View file @ 0cae89d3
...@@ -104,28 +104,28 @@ public: ...@@ -104,28 +104,28 @@ public:
* *
* @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' * @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/ */
void setSigmaCombiningRule( std::string& sigmaCombiningRule ); void setSigmaCombiningRule( const std::string& sigmaCombiningRule );
/** /**
* Get sigma combining rule * Get sigma combining rule
* *
* @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' * @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/ */
std::string getSigmaCombiningRule( void ) const; const std::string& getSigmaCombiningRule( void ) const;
/** /**
* Set epsilon combining rule * Set epsilon combining rule
* *
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN' * @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/ */
void setEpsilonCombiningRule( std::string& epsilonCombiningRule ); void setEpsilonCombiningRule( const std::string& epsilonCombiningRule );
/** /**
* Get epsilon combining rule * Get epsilon combining rule
* *
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG' * @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/ */
std::string getEpsilonCombiningRule( void ) const; const std::string& getEpsilonCombiningRule( void ) const;
/** /**
* Set exclusions for specified particle * Set exclusions for specified particle
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 0cae89d3
...@@ -35,6 +35,8 @@ ...@@ -35,6 +35,8 @@
#include "internal/AmoebaMultipoleForceImpl.h" #include "internal/AmoebaMultipoleForceImpl.h"
using namespace OpenMM; using namespace OpenMM;
using std::string;
using std::vector;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60), AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), pmeBSplineOrder(5), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) { mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) {
...@@ -143,13 +145,13 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) { ...@@ -143,13 +145,13 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
} }
int AmoebaMultipoleForce::addParticle( double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, int axisType, int AmoebaMultipoleForce::addParticle( double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity) { int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomId1, multipoleAtomId2, thole, dampingFactor, polarity)); multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
return multipoles.size()-1; return multipoles.size()-1;
} }
void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int& axisType, int& multipoleAtomId1, int& multipoleAtomId2, double& thole, double& dampingFactor, double& polarity ) const { int& axisType, int& multipoleAtomZ, int& multipoleAtomX, int& multipoleAtomY, double& thole, double& dampingFactor, double& polarity ) const {
charge = multipoles[index].charge; charge = multipoles[index].charge;
molecularDipole.resize( 3 ); molecularDipole.resize( 3 );
...@@ -169,8 +171,9 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std ...@@ -169,8 +171,9 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
molecularQuadrupole[8] = multipoles[index].molecularQuadrupole[8]; molecularQuadrupole[8] = multipoles[index].molecularQuadrupole[8];
axisType = multipoles[index].axisType; axisType = multipoles[index].axisType;
multipoleAtomId1 = multipoles[index].multipoleAtomId1; multipoleAtomZ = multipoles[index].multipoleAtomZ;
multipoleAtomId2 = multipoles[index].multipoleAtomId2; multipoleAtomX = multipoles[index].multipoleAtomX;
multipoleAtomY = multipoles[index].multipoleAtomY;
thole = multipoles[index].thole; thole = multipoles[index].thole;
dampingFactor = multipoles[index].dampingFactor; dampingFactor = multipoles[index].dampingFactor;
...@@ -178,7 +181,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std ...@@ -178,7 +181,7 @@ void AmoebaMultipoleForce::getMultipoleParameters(int index, double& charge, std
} }
void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole,
int axisType, int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity ) { int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity ) {
multipoles[index].charge = charge; multipoles[index].charge = charge;
...@@ -197,8 +200,9 @@ void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, std: ...@@ -197,8 +200,9 @@ void AmoebaMultipoleForce::setMultipoleParameters(int index, double charge, std:
multipoles[index].molecularQuadrupole[8] = molecularQuadrupole[8]; multipoles[index].molecularQuadrupole[8] = molecularQuadrupole[8];
multipoles[index].axisType = axisType; multipoles[index].axisType = axisType;
multipoles[index].multipoleAtomId1 = multipoleAtomId1; multipoles[index].multipoleAtomZ = multipoleAtomZ;
multipoles[index].multipoleAtomId2 = multipoleAtomId2; multipoles[index].multipoleAtomX = multipoleAtomX;
multipoles[index].multipoleAtomY = multipoleAtomY;
multipoles[index].thole = thole; multipoles[index].thole = thole;
multipoles[index].dampingFactor = dampingFactor; multipoles[index].dampingFactor = dampingFactor;
multipoles[index].polarity = polarity; multipoles[index].polarity = polarity;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 0cae89d3
...@@ -54,12 +54,12 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) { ...@@ -54,12 +54,12 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
for( int ii = 0; ii < system.getNumParticles(); ii++ ){ for( int ii = 0; ii < system.getNumParticles(); ii++ ){
int index, axisType, multipoleAtomId1, multipoleAtomId2; int index, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity ; double charge, thole, dampingFactor, polarity ;
std::vector<double> molecularDipole; std::vector<double> molecularDipole;
std::vector<double> molecularQuadrupole; std::vector<double> molecularQuadrupole;
owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomId1, multipoleAtomId2, owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity ); thole, dampingFactor, polarity );
// only 'Z-then-X' or 'Bisector' currently handled // only 'Z-then-X' or 'Bisector' currently handled
......
plugins/amoeba/openmmapi/src/AmoebaTorsionForce.cpp
View file @ 0cae89d3
...@@ -40,7 +40,7 @@ AmoebaTorsionForce::AmoebaTorsionForce() { ...@@ -40,7 +40,7 @@ AmoebaTorsionForce::AmoebaTorsionForce() {
} }
int AmoebaTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, int AmoebaTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4,
std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3 ) { std::vector<double>& torsion1, std::vector<double>& torsion2, std::vector<double>& torsion3 ) {
torsions.push_back(TorsionInfo(particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3)); torsions.push_back(TorsionInfo(particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3));
return torsions.size()-1; return torsions.size()-1;
} }
...@@ -64,7 +64,7 @@ void AmoebaTorsionForce::getTorsionParameters(int index, int& particle1, int& pa ...@@ -64,7 +64,7 @@ void AmoebaTorsionForce::getTorsionParameters(int index, int& particle1, int& pa
} }
void AmoebaTorsionForce::setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, void AmoebaTorsionForce::setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4,
std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3 ) { std::vector<double>& torsion1, std::vector<double>& torsion2, std::vector<double>& torsion3 ) {
torsions[index].particle1 = particle1; torsions[index].particle1 = particle1;
torsions[index].particle2 = particle2; torsions[index].particle2 = particle2;
......
plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp
View file @ 0cae89d3
...@@ -35,6 +35,8 @@ ...@@ -35,6 +35,8 @@
#include "internal/AmoebaVdwForceImpl.h" #include "internal/AmoebaVdwForceImpl.h"
using namespace OpenMM; using namespace OpenMM;
using std::string;
using std::vector;
AmoebaVdwForce::AmoebaVdwForce() : usePBC(0), cutoff(1.0e+10) { AmoebaVdwForce::AmoebaVdwForce() : usePBC(0), cutoff(1.0e+10) {
} }
...@@ -62,19 +64,19 @@ void AmoebaVdwForce::setParticleParameters(int particleIndex, int ivIndex, int c ...@@ -62,19 +64,19 @@ void AmoebaVdwForce::setParticleParameters(int particleIndex, int ivIndex, int c
parameters[particleIndex].reductionFactor = reductionFactor; parameters[particleIndex].reductionFactor = reductionFactor;
} }
void AmoebaVdwForce::setSigmaCombiningRule(std::string& inputSigmaCombiningRule ) { void AmoebaVdwForce::setSigmaCombiningRule( const std::string& inputSigmaCombiningRule ) {
sigmaCombiningRule = inputSigmaCombiningRule; sigmaCombiningRule = inputSigmaCombiningRule;
} }
std::string AmoebaVdwForce::getSigmaCombiningRule( void ) const { const std::string& AmoebaVdwForce::getSigmaCombiningRule( void ) const {
return sigmaCombiningRule; return sigmaCombiningRule;
} }
void AmoebaVdwForce::setEpsilonCombiningRule(std::string& inputEpsilonCombiningRule ) { void AmoebaVdwForce::setEpsilonCombiningRule( const std::string& inputEpsilonCombiningRule ) {
epsilonCombiningRule = inputEpsilonCombiningRule; epsilonCombiningRule = inputEpsilonCombiningRule;
} }
std::string AmoebaVdwForce::getEpsilonCombiningRule( void ) const { const std::string& AmoebaVdwForce::getEpsilonCombiningRule( void ) const {
return epsilonCombiningRule; return epsilonCombiningRule;
} }
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
View file @ 0cae89d3
...@@ -38,7 +38,9 @@ extern "C" void OPENMMCUDA_EXPORT registerKernelFactories() { ...@@ -38,7 +38,9 @@ extern "C" void OPENMMCUDA_EXPORT registerKernelFactories() {
for( int ii = 0; ii < Platform::getNumPlatforms(); ii++ ){ for( int ii = 0; ii < Platform::getNumPlatforms(); ii++ ){
Platform& platform = Platform::getPlatform(ii); Platform& platform = Platform::getPlatform(ii);
if( platform.getName() == "Cuda" ){ if( platform.getName() == "Cuda" ){
AmoebaCudaKernelFactory* factory = new AmoebaCudaKernelFactory(); AmoebaCudaKernelFactory* factory = new AmoebaCudaKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory); platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 0cae89d3
...@@ -44,7 +44,9 @@ extern "C" int gpuSetConstants( gpuContext gpu ); ...@@ -44,7 +44,9 @@ extern "C" int gpuSetConstants( gpuContext gpu );
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
// *************************************************************************** /* -------------------------------------------------------------------------- *
* Calculates bonded forces *
* -------------------------------------------------------------------------- */
static void computeAmoebaLocalForces( AmoebaCudaData& data ) { static void computeAmoebaLocalForces( AmoebaCudaData& data ) {
amoebaGpuContext gpu = data.getAmoebaGpu(); amoebaGpuContext gpu = data.getAmoebaGpu();
...@@ -58,6 +60,10 @@ static void computeAmoebaLocalForces( AmoebaCudaData& data ) { ...@@ -58,6 +60,10 @@ static void computeAmoebaLocalForces( AmoebaCudaData& data ) {
} }
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicBond *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicBondForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaHarmonicBondForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaHarmonicBondForce& force) : force(force) { ForceInfo(const AmoebaHarmonicBondForce& force) : force(force) {
...@@ -127,6 +133,10 @@ double CudaCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool ...@@ -127,6 +133,10 @@ double CudaCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicAngle *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicAngleForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaHarmonicAngleForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaHarmonicAngleForce& force) : force(force) { ForceInfo(const AmoebaHarmonicAngleForce& force) : force(force) {
...@@ -195,6 +205,10 @@ double CudaCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, boo ...@@ -195,6 +205,10 @@ double CudaCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, boo
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicInPlaneAngle *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaHarmonicInPlaneAngleForce& force) : force(force) { ForceInfo(const AmoebaHarmonicInPlaneAngleForce& force) : force(force) {
...@@ -267,6 +281,10 @@ double CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& conte ...@@ -267,6 +281,10 @@ double CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& conte
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicTorsion *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaTorsionForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaTorsionForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaTorsionForce& force) : force(force) { ForceInfo(const AmoebaTorsionForce& force) : force(force) {
...@@ -358,6 +376,10 @@ double CudaCalcAmoebaTorsionForceKernel::execute(ContextImpl& context, bool incl ...@@ -358,6 +376,10 @@ double CudaCalcAmoebaTorsionForceKernel::execute(ContextImpl& context, bool incl
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicPiTorsion *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaPiTorsionForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaPiTorsionForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaPiTorsionForce& force) : force(force) { ForceInfo(const AmoebaPiTorsionForce& force) : force(force) {
...@@ -429,6 +451,10 @@ double CudaCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool in ...@@ -429,6 +451,10 @@ double CudaCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool in
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaStretchBend *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaStretchBendForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaStretchBendForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaStretchBendForce& force) : force(force) { ForceInfo(const AmoebaStretchBendForce& force) : force(force) {
...@@ -499,6 +525,10 @@ double CudaCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool ...@@ -499,6 +525,10 @@ double CudaCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaOutOfPlaneBend *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaOutOfPlaneBendForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaOutOfPlaneBendForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaOutOfPlaneBendForce& force) : force(force) { ForceInfo(const AmoebaOutOfPlaneBendForce& force) : force(force) {
...@@ -569,6 +599,10 @@ double CudaCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bo ...@@ -569,6 +599,10 @@ double CudaCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bo
return 0.0; return 0.0;
} }
/* -------------------------------------------------------------------------- *
* AmoebaTorsionTorsion *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaTorsionTorsionForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaTorsionTorsionForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaTorsionTorsionForce& force) : force(force) { ForceInfo(const AmoebaTorsionTorsionForce& force) : force(force) {
...@@ -716,10 +750,10 @@ public: ...@@ -716,10 +750,10 @@ public:
} }
bool areParticlesIdentical(int particle1, int particle2) { bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, thole1, thole2, damping1, damping2, polarity1, polarity2; double charge1, charge2, thole1, thole2, damping1, damping2, polarity1, polarity2;
int axis1, axis2, multipole11, multipole12, multipole21, multipole22; int axis1, axis2, multipole11, multipole12, multipole21, multipole22, multipole31, multipole32;
vector<double> dipole1, dipole2, quadrupole1, quadrupole2; vector<double> dipole1, dipole2, quadrupole1, quadrupole2;
force.getMultipoleParameters(particle1, charge1, dipole1, quadrupole1, axis1, multipole11, multipole21, thole1, damping1, polarity1); force.getMultipoleParameters(particle1, charge1, dipole1, quadrupole1, axis1, multipole11, multipole21, multipole31, thole1, damping1, polarity1);
force.getMultipoleParameters(particle2, charge2, dipole2, quadrupole2, axis2, multipole12, multipole22, thole2, damping2, polarity2); force.getMultipoleParameters(particle2, charge2, dipole2, quadrupole2, axis2, multipole12, multipole22, multipole32, thole2, damping2, polarity2);
if (charge1 != charge2 || thole1 != thole2 || damping1 != damping2 || polarity1 != polarity2 || axis1 != axis2) if (charge1 != charge2 || thole1 != thole2 || damping1 != damping2 || polarity1 != polarity2 || axis1 != axis2)
return false; return false;
for (int i = 0; i < (int) dipole1.size(); ++i) for (int i = 0; i < (int) dipole1.size(); ++i)
...@@ -756,8 +790,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -756,8 +790,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
std::vector<float> dampingFactors(numMultipoles); std::vector<float> dampingFactors(numMultipoles);
std::vector<float> polarity(numMultipoles); std::vector<float> polarity(numMultipoles);
std::vector<int> axisTypes(numMultipoles); std::vector<int> axisTypes(numMultipoles);
std::vector<int> multipoleAtomId1s(numMultipoles); std::vector<int> multipoleAtomZs(numMultipoles);
std::vector<int> multipoleAtomId2s(numMultipoles); std::vector<int> multipoleAtomXs(numMultipoles);
std::vector<int> multipoleAtomYs(numMultipoles);
std::vector< std::vector< std::vector<int> > > multipoleAtomCovalentInfo(numMultipoles); std::vector< std::vector< std::vector<int> > > multipoleAtomCovalentInfo(numMultipoles);
std::vector<int> minCovalentIndices(numMultipoles); std::vector<int> minCovalentIndices(numMultipoles);
std::vector<int> minCovalentPolarizationIndices(numMultipoles); std::vector<int> minCovalentPolarizationIndices(numMultipoles);
...@@ -786,17 +821,18 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -786,17 +821,18 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
// multipoles // multipoles
int axisType, multipoleAtomId1, multipoleAtomId2; int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, tholeD, dampingFactorD, polarityD; double charge, tholeD, dampingFactorD, polarityD;
std::vector<double> dipolesD; std::vector<double> dipolesD;
std::vector<double> quadrupolesD; std::vector<double> quadrupolesD;
force.getMultipoleParameters(i, charge, dipolesD, quadrupolesD, axisType, multipoleAtomId1, multipoleAtomId2, force.getMultipoleParameters(i, charge, dipolesD, quadrupolesD, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
tholeD, dampingFactorD, polarityD ); tholeD, dampingFactorD, polarityD );
totalCharge += charge; totalCharge += charge;
axisTypes[i] = axisType; axisTypes[i] = axisType;
multipoleAtomId1s[i] = multipoleAtomId1; multipoleAtomZs[i] = multipoleAtomZ;
multipoleAtomId2s[i] = multipoleAtomId2; multipoleAtomXs[i] = multipoleAtomX;
multipoleAtomYs[i] = multipoleAtomY;
charges[i] = static_cast<float>(charge); charges[i] = static_cast<float>(charge);
tholes[i] = static_cast<float>(tholeD); tholes[i] = static_cast<float>(tholeD);
...@@ -847,7 +883,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -847,7 +883,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n"); throw OpenMMException("AmoebaMultipoleForce nonbonded method not recognized.\n");
} }
gpuSetAmoebaMultipoleParameters(data.getAmoebaGpu(), charges, dipoles, quadrupoles, axisTypes, multipoleAtomId1s, multipoleAtomId2s, gpuSetAmoebaMultipoleParameters(data.getAmoebaGpu(), charges, dipoles, quadrupoles, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
tholes, scalingDistanceCutoff, dampingFactors, polarity, tholes, scalingDistanceCutoff, dampingFactors, polarity,
multipoleAtomCovalentInfo, covalentDegree, minCovalentIndices, minCovalentPolarizationIndices, (maxCovalentRange+2), multipoleAtomCovalentInfo, covalentDegree, minCovalentIndices, minCovalentPolarizationIndices, (maxCovalentRange+2),
static_cast<int>(force.getMutualInducedIterationMethod()), static_cast<int>(force.getMutualInducedIterationMethod()),
...@@ -957,6 +993,10 @@ static void computeAmoebaVdwForce( AmoebaCudaData& data ) { ...@@ -957,6 +993,10 @@ static void computeAmoebaVdwForce( AmoebaCudaData& data ) {
kCalculateAmoebaVdw14_7Forces(gpu, data.getApplyCutoff()); kCalculateAmoebaVdw14_7Forces(gpu, data.getApplyCutoff());
} }
/* -------------------------------------------------------------------------- *
* AmoebaVdw *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaVdwForceKernel::ForceInfo : public CudaForceInfo { class CudaCalcAmoebaVdwForceKernel::ForceInfo : public CudaForceInfo {
public: public:
ForceInfo(const AmoebaVdwForce& force) : force(force) { ForceInfo(const AmoebaVdwForce& force) : force(force) {
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp
View file @ 0cae89d3
...@@ -1446,7 +1446,7 @@ void gpuKirkwoodAllocate( amoebaGpuContext amoebaGpu ) ...@@ -1446,7 +1446,7 @@ void gpuKirkwoodAllocate( amoebaGpuContext amoebaGpu )
extern "C" extern "C"
void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vector<float>& charges, const std::vector<float>& dipoles, const std::vector<float>& quadrupoles, void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vector<float>& charges, const std::vector<float>& dipoles, const std::vector<float>& quadrupoles,
const std::vector<int>& axisType, const std::vector<int>& multipoleParticleId1, const std::vector<int>& multipoleParticleId2, const std::vector<int>& axisType, const std::vector<int>& multipoleParticleZ, const std::vector<int>& multipoleParticleX, const std::vector<int>& multipoleParticleY,
const std::vector<float>& tholes, float scalingDistanceCutoff,const std::vector<float>& dampingFactors, const std::vector<float>& polarity, const std::vector<float>& tholes, float scalingDistanceCutoff,const std::vector<float>& dampingFactors, const std::vector<float>& polarity,
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree, const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
...@@ -1562,10 +1562,10 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect ...@@ -1562,10 +1562,10 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
// axis type & multipole particles ids // axis type & multipole particles ids
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].x = multipoleParticleId1[ii]; amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].x = multipoleParticleZ[ii];
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].y = multipoleParticleId2[ii]; amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].y = multipoleParticleX[ii];
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].w = axisType[ii]; amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][ii].w = axisType[ii];
int axisParticleIndex = multipoleParticleId1[ii]; int axisParticleIndex = multipoleParticleZ[ii];
if( maxIndices[axisParticleIndex] < ii ){ if( maxIndices[axisParticleIndex] < ii ){
maxIndices[axisParticleIndex] = ii; maxIndices[axisParticleIndex] = ii;
} }
...@@ -1573,7 +1573,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect ...@@ -1573,7 +1573,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][axisParticleIndex].z = ii; amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][axisParticleIndex].z = ii;
} }
axisParticleIndex = multipoleParticleId2[ii]; axisParticleIndex = multipoleParticleX[ii];
if( maxIndices[axisParticleIndex] < ii ){ if( maxIndices[axisParticleIndex] < ii ){
maxIndices[axisParticleIndex] = ii; maxIndices[axisParticleIndex] = ii;
} }
...@@ -1583,11 +1583,11 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect ...@@ -1583,11 +1583,11 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
if( 0 && amoebaGpu->log ) if( 0 && amoebaGpu->log )
fprintf( amoebaGpu->log, "Z1 %4d [%4d %4d] %4d %4d %4d %4d %d %d\n", ii, fprintf( amoebaGpu->log, "Z1 %4d [%4d %4d] %4d %4d %4d %4d %d %d\n", ii,
multipoleParticleId1[ii], multipoleParticleId2[ii], multipoleParticleZ[ii], multipoleParticleX[ii],
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][multipoleParticleId1[ii]].z, amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][multipoleParticleZ[ii]].z,
maxIndices[multipoleParticleId1[ii]], maxIndices[multipoleParticleZ[ii]],
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][multipoleParticleId2[ii]].z, amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][multipoleParticleX[ii]].z,
maxIndices[multipoleParticleId2[ii]], maxIndices[multipoleParticleX[ii]],
amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][0].z, maxIndices[0] ); amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysStream[0][0].z, maxIndices[0] );
// charges // charges
...@@ -1991,7 +1991,6 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, ...@@ -1991,7 +1991,6 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
gpuContext gpu = amoebaGpu->gpuContext; gpuContext gpu = amoebaGpu->gpuContext;
amoebaGpu->paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms; amoebaGpu->paddedNumberOfAtoms = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;
unsigned int particles = sigmas.size(); unsigned int particles = sigmas.size();
...@@ -2162,7 +2161,11 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, ...@@ -2162,7 +2161,11 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
amoebaGpu->vdwSigmaCombiningRule, amoebaGpu->vdwEpsilonCombiningRule); amoebaGpu->vdwSigmaCombiningRule, amoebaGpu->vdwEpsilonCombiningRule);
for (unsigned int ii = 0; ii < gpu->natoms; ii++) for (unsigned int ii = 0; ii < gpu->natoms; ii++)
{ {
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, sigmas[ii], epsilons[ii] ); (void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e Ex[", ii, sigmas[ii], epsilons[ii] );
for (unsigned int jj = 0; jj < allExclusions[ii].size(); jj++){
(void) fprintf( amoebaGpu->log, "%d ", allExclusions[ii][jj] );
}
(void) fprintf( amoebaGpu->log, "]\n", ii, sigmas[ii], epsilons[ii] );
if( ii == maxPrint && ii < (amoebaGpu->paddedNumberOfAtoms - maxPrint) ) if( ii == maxPrint && ii < (amoebaGpu->paddedNumberOfAtoms - maxPrint) )
{ {
ii = (amoebaGpu->paddedNumberOfAtoms - maxPrint); ii = (amoebaGpu->paddedNumberOfAtoms - maxPrint);
...@@ -2172,6 +2175,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, ...@@ -2172,6 +2175,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
} }
#endif #endif
#undef AMOEBA_DEBUG
} }
extern "C" extern "C"
...@@ -2534,7 +2538,7 @@ extern "C" ...@@ -2534,7 +2538,7 @@ extern "C"
void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu, void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
const std::vector<float>& radii, const std::vector<float>& radii,
const std::vector<float>& epsilons, const std::vector<float>& epsilons,
const float totalMaxWcaDisperionEnergy, const float totalMaxWcaDispersionEnergy,
const float epso, const float epsh, const float rmino, const float rminh, const float epso, const float epsh, const float rmino, const float rminh,
const float awater, const float shctd, const float dispoff ) const float awater, const float shctd, const float dispoff )
{ {
...@@ -2563,7 +2567,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu, ...@@ -2563,7 +2567,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysStream[0][ii].y = 0.0f; amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysStream[0][ii].y = 0.0f;
} }
amoebaGpu->psWcaDispersionRadiusEpsilon->Upload(); amoebaGpu->psWcaDispersionRadiusEpsilon->Upload();
amoebaGpu->amoebaSim.totalMaxWcaDispersionEnergy = totalMaxWcaDisperionEnergy; amoebaGpu->amoebaSim.totalMaxWcaDispersionEnergy = totalMaxWcaDispersionEnergy;
amoebaGpu->amoebaSim.epso = epso; amoebaGpu->amoebaSim.epso = epso;
amoebaGpu->amoebaSim.epsh = epsh; amoebaGpu->amoebaSim.epsh = epsh;
amoebaGpu->amoebaSim.rmino = rmino; amoebaGpu->amoebaSim.rmino = rmino;
...@@ -2589,6 +2593,9 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu, ...@@ -2589,6 +2593,9 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
} }
#endif #endif
amoebaGpuBuildOutputBuffers( amoebaGpu );
amoebaGpuBuildThreadBlockWorkList( amoebaGpu );
} }
extern "C" extern "C"
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ 0cae89d3
...@@ -294,7 +294,7 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext gpu, const std::vector< st ...@@ -294,7 +294,7 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext gpu, const std::vector< st
extern "C" extern "C"
void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vector<float>& charges, const std::vector<float>& dipoles, const std::vector<float>& quadrupoles, void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vector<float>& charges, const std::vector<float>& dipoles, const std::vector<float>& quadrupoles,
const std::vector<int>& axisType, const std::vector<int>& multipoleAtomId1, const std::vector<int>& multipoleAtomId2, const std::vector<int>& axisType, const std::vector<int>& multipoleAtomZ, const std::vector<int>& multipoleAtomX, const std::vector<int>& multipoleAtomY,
const std::vector<float>& tholes, float scalingDistanceCutoff,const std::vector<float>& dampingFactors, const std::vector<float>& polarity, const std::vector<float>& tholes, float scalingDistanceCutoff,const std::vector<float>& dampingFactors, const std::vector<float>& polarity,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree, const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu
View file @ 0cae89d3
...@@ -177,8 +177,6 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -177,8 +177,6 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// set the permanent multipole and induced dipole values; // set the permanent multipole and induced dipole values;
float pdi = atomI.damp;
float pti = atomI.thole;
float ci = atomI.q; float ci = atomI.q;
float di1 = atomI.labFrameDipole[0]; float di1 = atomI.labFrameDipole[0];
...@@ -261,11 +259,9 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -261,11 +259,9 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
float ddsc72 = 0.0f; float ddsc72 = 0.0f;
float ddsc73 = 0.0f; float ddsc73 = 0.0f;
float pdk = atomJ.damp; float damp = atomI.damp*atomJ.damp;
float ptk = atomJ.thole;
float damp = pdi*pdk;
if( damp != 0.0f ){ if( damp != 0.0f ){
float pgamma = pti < ptk ? pti : ptk; float pgamma = atomI.thole < atomJ.thole ? atomI.thole : atomJ.thole;
float ratio = r/damp; float ratio = r/damp;
damp = -pgamma * ratio*ratio*ratio; damp = -pgamma * ratio*ratio*ratio;
if( damp > -50.0f ){ if( damp > -50.0f ){
...@@ -314,114 +310,130 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -314,114 +310,130 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
float dkxui1 = dk2*atomI.inducedDipole[2] - dk3*atomI.inducedDipole[1]; float dkxui1 = dk2*atomI.inducedDipole[2] - dk3*atomI.inducedDipole[1];
float dkxui2 = dk3*atomI.inducedDipole[0] - dk1*atomI.inducedDipole[2]; float dkxui2 = dk3*atomI.inducedDipole[0] - dk1*atomI.inducedDipole[2];
float dkxui3 = dk1*atomI.inducedDipole[1] - dk2*atomI.inducedDipole[0]; float dkxui3 = dk1*atomI.inducedDipole[1] - dk2*atomI.inducedDipole[0];
float dixukp1 = di2*atomJ.inducedDipoleP[2] - di3*atomJ.inducedDipoleP[1]; float dixukp1 = di2*atomJ.inducedDipoleP[2] - di3*atomJ.inducedDipoleP[1];
float dixukp2 = di3*atomJ.inducedDipoleP[0] - di1*atomJ.inducedDipoleP[2]; float dixukp2 = di3*atomJ.inducedDipoleP[0] - di1*atomJ.inducedDipoleP[2];
float dixukp3 = di1*atomJ.inducedDipoleP[1] - di2*atomJ.inducedDipoleP[0]; float dixukp3 = di1*atomJ.inducedDipoleP[1] - di2*atomJ.inducedDipoleP[0];
float dkxuip1 = dk2*atomI.inducedDipoleP[2] - dk3*atomI.inducedDipoleP[1]; float dkxuip1 = dk2*atomI.inducedDipoleP[2] - dk3*atomI.inducedDipoleP[1];
float dkxuip2 = dk3*atomI.inducedDipoleP[0] - dk1*atomI.inducedDipoleP[2]; float dkxuip2 = dk3*atomI.inducedDipoleP[0] - dk1*atomI.inducedDipoleP[2];
float dkxuip3 = dk1*atomI.inducedDipoleP[1] - dk2*atomI.inducedDipoleP[0]; float dkxuip3 = dk1*atomI.inducedDipoleP[1] - dk2*atomI.inducedDipoleP[0];
float dixr1 = di2*zr - di3*yr; float dixr1 = di2*zr - di3*yr;
float dixr2 = di3*xr - di1*zr; float dixr2 = di3*xr - di1*zr;
float dixr3 = di1*yr - di2*xr; float dixr3 = di1*yr - di2*xr;
float dkxr1 = dk2*zr - dk3*yr; float dkxr1 = dk2*zr - dk3*yr;
float dkxr2 = dk3*xr - dk1*zr; float dkxr2 = dk3*xr - dk1*zr;
float dkxr3 = dk1*yr - dk2*xr; float dkxr3 = dk1*yr - dk2*xr;
float qir1 = qi1*xr + qi4*yr + qi7*zr; float qir1 = qi1*xr + qi4*yr + qi7*zr;
float qir2 = qi2*xr + qi5*yr + qi8*zr; float qir2 = qi2*xr + qi5*yr + qi8*zr;
float qir3 = qi3*xr + qi6*yr + qi9*zr; float qir3 = qi3*xr + qi6*yr + qi9*zr;
float qkr1 = qk1*xr + qk4*yr + qk7*zr; float qkr1 = qk1*xr + qk4*yr + qk7*zr;
float qkr2 = qk2*xr + qk5*yr + qk8*zr; float qkr2 = qk2*xr + qk5*yr + qk8*zr;
float qkr3 = qk3*xr + qk6*yr + qk9*zr; float qkr3 = qk3*xr + qk6*yr + qk9*zr;
float qiqkr1 = qi1*qkr1 + qi4*qkr2 + qi7*qkr3; float qiqkr1 = qi1*qkr1 + qi4*qkr2 + qi7*qkr3;
float qiqkr2 = qi2*qkr1 + qi5*qkr2 + qi8*qkr3; float qiqkr2 = qi2*qkr1 + qi5*qkr2 + qi8*qkr3;
float qiqkr3 = qi3*qkr1 + qi6*qkr2 + qi9*qkr3; float qiqkr3 = qi3*qkr1 + qi6*qkr2 + qi9*qkr3;
float qkqir1 = qk1*qir1 + qk4*qir2 + qk7*qir3; float qkqir1 = qk1*qir1 + qk4*qir2 + qk7*qir3;
float qkqir2 = qk2*qir1 + qk5*qir2 + qk8*qir3; float qkqir2 = qk2*qir1 + qk5*qir2 + qk8*qir3;
float qkqir3 = qk3*qir1 + qk6*qir2 + qk9*qir3; float qkqir3 = qk3*qir1 + qk6*qir2 + qk9*qir3;
float qixqk1 = qi2*qk3 + qi5*qk6 + qi8*qk9
- qi3*qk2 - qi6*qk5 - qi9*qk8; float qixqk1 = qi2*qk3 + qi5*qk6 + qi8*qk9 - qi3*qk2 - qi6*qk5 - qi9*qk8;
float qixqk2 = qi3*qk1 + qi6*qk4 + qi9*qk7 float qixqk2 = qi3*qk1 + qi6*qk4 + qi9*qk7 - qi1*qk3 - qi4*qk6 - qi7*qk9;
- qi1*qk3 - qi4*qk6 - qi7*qk9; float qixqk3 = qi1*qk2 + qi4*qk5 + qi7*qk8 - qi2*qk1 - qi5*qk4 - qi8*qk7;
float qixqk3 = qi1*qk2 + qi4*qk5 + qi7*qk8
- qi2*qk1 - qi5*qk4 - qi8*qk7;
float rxqir1 = yr*qir3 - zr*qir2; float rxqir1 = yr*qir3 - zr*qir2;
float rxqir2 = zr*qir1 - xr*qir3; float rxqir2 = zr*qir1 - xr*qir3;
float rxqir3 = xr*qir2 - yr*qir1; float rxqir3 = xr*qir2 - yr*qir1;
float rxqkr1 = yr*qkr3 - zr*qkr2; float rxqkr1 = yr*qkr3 - zr*qkr2;
float rxqkr2 = zr*qkr1 - xr*qkr3; float rxqkr2 = zr*qkr1 - xr*qkr3;
float rxqkr3 = xr*qkr2 - yr*qkr1; float rxqkr3 = xr*qkr2 - yr*qkr1;
float rxqikr1 = yr*qiqkr3 - zr*qiqkr2; float rxqikr1 = yr*qiqkr3 - zr*qiqkr2;
float rxqikr2 = zr*qiqkr1 - xr*qiqkr3; float rxqikr2 = zr*qiqkr1 - xr*qiqkr3;
float rxqikr3 = xr*qiqkr2 - yr*qiqkr1; float rxqikr3 = xr*qiqkr2 - yr*qiqkr1;
float rxqkir1 = yr*qkqir3 - zr*qkqir2; float rxqkir1 = yr*qkqir3 - zr*qkqir2;
float rxqkir2 = zr*qkqir1 - xr*qkqir3; float rxqkir2 = zr*qkqir1 - xr*qkqir3;
float rxqkir3 = xr*qkqir2 - yr*qkqir1; float rxqkir3 = xr*qkqir2 - yr*qkqir1;
float qkrxqir1 = qkr2*qir3 - qkr3*qir2; float qkrxqir1 = qkr2*qir3 - qkr3*qir2;
float qkrxqir2 = qkr3*qir1 - qkr1*qir3; float qkrxqir2 = qkr3*qir1 - qkr1*qir3;
float qkrxqir3 = qkr1*qir2 - qkr2*qir1; float qkrxqir3 = qkr1*qir2 - qkr2*qir1;
float qidk1 = qi1*dk1 + qi4*dk2 + qi7*dk3; float qidk1 = qi1*dk1 + qi4*dk2 + qi7*dk3;
float qidk2 = qi2*dk1 + qi5*dk2 + qi8*dk3; float qidk2 = qi2*dk1 + qi5*dk2 + qi8*dk3;
float qidk3 = qi3*dk1 + qi6*dk2 + qi9*dk3; float qidk3 = qi3*dk1 + qi6*dk2 + qi9*dk3;
float qkdi1 = qk1*di1 + qk4*di2 + qk7*di3; float qkdi1 = qk1*di1 + qk4*di2 + qk7*di3;
float qkdi2 = qk2*di1 + qk5*di2 + qk8*di3; float qkdi2 = qk2*di1 + qk5*di2 + qk8*di3;
float qkdi3 = qk3*di1 + qk6*di2 + qk9*di3; float qkdi3 = qk3*di1 + qk6*di2 + qk9*di3;
float qiuk1 = qi1*atomJ.inducedDipole[0] + qi4*atomJ.inducedDipole[1]
+ qi7*atomJ.inducedDipole[2]; float qiuk1 = qi1*atomJ.inducedDipole[0] + qi4*atomJ.inducedDipole[1] + qi7*atomJ.inducedDipole[2];
float qiuk2 = qi2*atomJ.inducedDipole[0] + qi5*atomJ.inducedDipole[1] float qiuk2 = qi2*atomJ.inducedDipole[0] + qi5*atomJ.inducedDipole[1] + qi8*atomJ.inducedDipole[2];
+ qi8*atomJ.inducedDipole[2]; float qiuk3 = qi3*atomJ.inducedDipole[0] + qi6*atomJ.inducedDipole[1] + qi9*atomJ.inducedDipole[2];
float qiuk3 = qi3*atomJ.inducedDipole[0] + qi6*atomJ.inducedDipole[1]
+ qi9*atomJ.inducedDipole[2]; float qkui1 = qk1*atomI.inducedDipole[0] + qk4*atomI.inducedDipole[1] + qk7*atomI.inducedDipole[2];
float qkui1 = qk1*atomI.inducedDipole[0] + qk4*atomI.inducedDipole[1] float qkui2 = qk2*atomI.inducedDipole[0] + qk5*atomI.inducedDipole[1] + qk8*atomI.inducedDipole[2];
+ qk7*atomI.inducedDipole[2]; float qkui3 = qk3*atomI.inducedDipole[0] + qk6*atomI.inducedDipole[1] + qk9*atomI.inducedDipole[2];
float qkui2 = qk2*atomI.inducedDipole[0] + qk5*atomI.inducedDipole[1]
+ qk8*atomI.inducedDipole[2]; float qiukp1 = qi1*atomJ.inducedDipoleP[0] + qi4*atomJ.inducedDipoleP[1] + qi7*atomJ.inducedDipoleP[2];
float qkui3 = qk3*atomI.inducedDipole[0] + qk6*atomI.inducedDipole[1] float qiukp2 = qi2*atomJ.inducedDipoleP[0] + qi5*atomJ.inducedDipoleP[1] + qi8*atomJ.inducedDipoleP[2];
+ qk9*atomI.inducedDipole[2]; float qiukp3 = qi3*atomJ.inducedDipoleP[0] + qi6*atomJ.inducedDipoleP[1] + qi9*atomJ.inducedDipoleP[2];
float qiukp1 = qi1*atomJ.inducedDipoleP[0] + qi4*atomJ.inducedDipoleP[1]
+ qi7*atomJ.inducedDipoleP[2]; float qkuip1 = qk1*atomI.inducedDipoleP[0] + qk4*atomI.inducedDipoleP[1] + qk7*atomI.inducedDipoleP[2];
float qiukp2 = qi2*atomJ.inducedDipoleP[0] + qi5*atomJ.inducedDipoleP[1] float qkuip2 = qk2*atomI.inducedDipoleP[0] + qk5*atomI.inducedDipoleP[1] + qk8*atomI.inducedDipoleP[2];
+ qi8*atomJ.inducedDipoleP[2]; float qkuip3 = qk3*atomI.inducedDipoleP[0] + qk6*atomI.inducedDipoleP[1] + qk9*atomI.inducedDipoleP[2];
float qiukp3 = qi3*atomJ.inducedDipoleP[0] + qi6*atomJ.inducedDipoleP[1]
+ qi9*atomJ.inducedDipoleP[2];
float qkuip1 = qk1*atomI.inducedDipoleP[0] + qk4*atomI.inducedDipoleP[1]
+ qk7*atomI.inducedDipoleP[2];
float qkuip2 = qk2*atomI.inducedDipoleP[0] + qk5*atomI.inducedDipoleP[1]
+ qk8*atomI.inducedDipoleP[2];
float qkuip3 = qk3*atomI.inducedDipoleP[0] + qk6*atomI.inducedDipoleP[1]
+ qk9*atomI.inducedDipoleP[2];
float dixqkr1 = di2*qkr3 - di3*qkr2; float dixqkr1 = di2*qkr3 - di3*qkr2;
float dixqkr2 = di3*qkr1 - di1*qkr3; float dixqkr2 = di3*qkr1 - di1*qkr3;
float dixqkr3 = di1*qkr2 - di2*qkr1; float dixqkr3 = di1*qkr2 - di2*qkr1;
float dkxqir1 = dk2*qir3 - dk3*qir2; float dkxqir1 = dk2*qir3 - dk3*qir2;
float dkxqir2 = dk3*qir1 - dk1*qir3; float dkxqir2 = dk3*qir1 - dk1*qir3;
float dkxqir3 = dk1*qir2 - dk2*qir1; float dkxqir3 = dk1*qir2 - dk2*qir1;
float uixqkr1 = atomI.inducedDipole[1]*qkr3 - atomI.inducedDipole[2]*qkr2; float uixqkr1 = atomI.inducedDipole[1]*qkr3 - atomI.inducedDipole[2]*qkr2;
float uixqkr2 = atomI.inducedDipole[2]*qkr1 - atomI.inducedDipole[0]*qkr3; float uixqkr2 = atomI.inducedDipole[2]*qkr1 - atomI.inducedDipole[0]*qkr3;
float uixqkr3 = atomI.inducedDipole[0]*qkr2 - atomI.inducedDipole[1]*qkr1; float uixqkr3 = atomI.inducedDipole[0]*qkr2 - atomI.inducedDipole[1]*qkr1;
float ukxqir1 = atomJ.inducedDipole[1]*qir3 - atomJ.inducedDipole[2]*qir2; float ukxqir1 = atomJ.inducedDipole[1]*qir3 - atomJ.inducedDipole[2]*qir2;
float ukxqir2 = atomJ.inducedDipole[2]*qir1 - atomJ.inducedDipole[0]*qir3; float ukxqir2 = atomJ.inducedDipole[2]*qir1 - atomJ.inducedDipole[0]*qir3;
float ukxqir3 = atomJ.inducedDipole[0]*qir2 - atomJ.inducedDipole[1]*qir1; float ukxqir3 = atomJ.inducedDipole[0]*qir2 - atomJ.inducedDipole[1]*qir1;
float uixqkrp1 = atomI.inducedDipoleP[1]*qkr3 - atomI.inducedDipoleP[2]*qkr2; float uixqkrp1 = atomI.inducedDipoleP[1]*qkr3 - atomI.inducedDipoleP[2]*qkr2;
float uixqkrp2 = atomI.inducedDipoleP[2]*qkr1 - atomI.inducedDipoleP[0]*qkr3; float uixqkrp2 = atomI.inducedDipoleP[2]*qkr1 - atomI.inducedDipoleP[0]*qkr3;
float uixqkrp3 = atomI.inducedDipoleP[0]*qkr2 - atomI.inducedDipoleP[1]*qkr1; float uixqkrp3 = atomI.inducedDipoleP[0]*qkr2 - atomI.inducedDipoleP[1]*qkr1;
float ukxqirp1 = atomJ.inducedDipoleP[1]*qir3 - atomJ.inducedDipoleP[2]*qir2; float ukxqirp1 = atomJ.inducedDipoleP[1]*qir3 - atomJ.inducedDipoleP[2]*qir2;
float ukxqirp2 = atomJ.inducedDipoleP[2]*qir1 - atomJ.inducedDipoleP[0]*qir3; float ukxqirp2 = atomJ.inducedDipoleP[2]*qir1 - atomJ.inducedDipoleP[0]*qir3;
float ukxqirp3 = atomJ.inducedDipoleP[0]*qir2 - atomJ.inducedDipoleP[1]*qir1; float ukxqirp3 = atomJ.inducedDipoleP[0]*qir2 - atomJ.inducedDipoleP[1]*qir1;
float rxqidk1 = yr*qidk3 - zr*qidk2; float rxqidk1 = yr*qidk3 - zr*qidk2;
float rxqidk2 = zr*qidk1 - xr*qidk3; float rxqidk2 = zr*qidk1 - xr*qidk3;
float rxqidk3 = xr*qidk2 - yr*qidk1; float rxqidk3 = xr*qidk2 - yr*qidk1;
float rxqkdi1 = yr*qkdi3 - zr*qkdi2; float rxqkdi1 = yr*qkdi3 - zr*qkdi2;
float rxqkdi2 = zr*qkdi1 - xr*qkdi3; float rxqkdi2 = zr*qkdi1 - xr*qkdi3;
float rxqkdi3 = xr*qkdi2 - yr*qkdi1; float rxqkdi3 = xr*qkdi2 - yr*qkdi1;
float rxqiuk1 = yr*qiuk3 - zr*qiuk2; float rxqiuk1 = yr*qiuk3 - zr*qiuk2;
float rxqiuk2 = zr*qiuk1 - xr*qiuk3; float rxqiuk2 = zr*qiuk1 - xr*qiuk3;
float rxqiuk3 = xr*qiuk2 - yr*qiuk1; float rxqiuk3 = xr*qiuk2 - yr*qiuk1;
float rxqkui1 = yr*qkui3 - zr*qkui2; float rxqkui1 = yr*qkui3 - zr*qkui2;
float rxqkui2 = zr*qkui1 - xr*qkui3; float rxqkui2 = zr*qkui1 - xr*qkui3;
float rxqkui3 = xr*qkui2 - yr*qkui1; float rxqkui3 = xr*qkui2 - yr*qkui1;
float rxqiukp1 = yr*qiukp3 - zr*qiukp2; float rxqiukp1 = yr*qiukp3 - zr*qiukp2;
float rxqiukp2 = zr*qiukp1 - xr*qiukp3; float rxqiukp2 = zr*qiukp1 - xr*qiukp3;
float rxqiukp3 = xr*qiukp2 - yr*qiukp1; float rxqiukp3 = xr*qiukp2 - yr*qiukp1;
float rxqkuip1 = yr*qkuip3 - zr*qkuip2; float rxqkuip1 = yr*qkuip3 - zr*qkuip2;
float rxqkuip2 = zr*qkuip1 - xr*qkuip3; float rxqkuip2 = zr*qkuip1 - xr*qkuip3;
float rxqkuip3 = xr*qkuip2 - yr*qkuip1; float rxqkuip3 = xr*qkuip2 - yr*qkuip1;
...@@ -448,22 +460,18 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -448,22 +460,18 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
float sci3 = atomI.inducedDipole[0]*xr + atomI.inducedDipole[1]*yr + atomI.inducedDipole[2]*zr; float sci3 = atomI.inducedDipole[0]*xr + atomI.inducedDipole[1]*yr + atomI.inducedDipole[2]*zr;
float sci4 = atomJ.inducedDipole[0]*xr + atomJ.inducedDipole[1]*yr + atomJ.inducedDipole[2]*zr; float sci4 = atomJ.inducedDipole[0]*xr + atomJ.inducedDipole[1]*yr + atomJ.inducedDipole[2]*zr;
float sci7 = qir1*atomJ.inducedDipole[0] + qir2*atomJ.inducedDipole[1] float sci7 = qir1*atomJ.inducedDipole[0] + qir2*atomJ.inducedDipole[1] + qir3*atomJ.inducedDipole[2];
+ qir3*atomJ.inducedDipole[2]; float sci8 = qkr1*atomI.inducedDipole[0] + qkr2*atomI.inducedDipole[1] + qkr3*atomI.inducedDipole[2];
float sci8 = qkr1*atomI.inducedDipole[0] + qkr2*atomI.inducedDipole[1] float scip1 = atomI.inducedDipoleP[0]*dk1 + atomI.inducedDipoleP[1]*dk2 + atomI.inducedDipoleP[2]*dk3 + di1*atomJ.inducedDipoleP[0] + di2*atomJ.inducedDipoleP[1] + di3*atomJ.inducedDipoleP[2];
+ qkr3*atomI.inducedDipole[2];
float scip1 = atomI.inducedDipoleP[0]*dk1 + atomI.inducedDipoleP[1]*dk2
+ atomI.inducedDipoleP[2]*dk3 + di1*atomJ.inducedDipoleP[0]
+ di2*atomJ.inducedDipoleP[1] + di3*atomJ.inducedDipoleP[2];
float scip2 = atomI.inducedDipole[0]*atomJ.inducedDipoleP[0]+atomI.inducedDipole[1]*atomJ.inducedDipoleP[1] float scip2 = atomI.inducedDipole[0]*atomJ.inducedDipoleP[0]+atomI.inducedDipole[1]*atomJ.inducedDipoleP[1]
+ atomI.inducedDipole[2]*atomJ.inducedDipoleP[2]+atomI.inducedDipoleP[0]*atomJ.inducedDipole[0] + atomI.inducedDipole[2]*atomJ.inducedDipoleP[2]+atomI.inducedDipoleP[0]*atomJ.inducedDipole[0]
+ atomI.inducedDipoleP[1]*atomJ.inducedDipole[1]+atomI.inducedDipoleP[2]*atomJ.inducedDipole[2]; + atomI.inducedDipoleP[1]*atomJ.inducedDipole[1]+atomI.inducedDipoleP[2]*atomJ.inducedDipole[2];
float scip3 = atomI.inducedDipoleP[0]*xr + atomI.inducedDipoleP[1]*yr + atomI.inducedDipoleP[2]*zr; float scip3 = atomI.inducedDipoleP[0]*xr + atomI.inducedDipoleP[1]*yr + atomI.inducedDipoleP[2]*zr;
float scip4 = atomJ.inducedDipoleP[0]*xr + atomJ.inducedDipoleP[1]*yr + atomJ.inducedDipoleP[2]*zr; float scip4 = atomJ.inducedDipoleP[0]*xr + atomJ.inducedDipoleP[1]*yr + atomJ.inducedDipoleP[2]*zr;
float scip7 = qir1*atomJ.inducedDipoleP[0] + qir2*atomJ.inducedDipoleP[1]
+ qir3*atomJ.inducedDipoleP[2]; float scip7 = qir1*atomJ.inducedDipoleP[0] + qir2*atomJ.inducedDipoleP[1] + qir3*atomJ.inducedDipoleP[2];
float scip8 = qkr1*atomI.inducedDipoleP[0] + qkr2*atomI.inducedDipoleP[1] float scip8 = qkr1*atomI.inducedDipoleP[0] + qkr2*atomI.inducedDipoleP[1] + qkr3*atomI.inducedDipoleP[2];
+ qkr3*atomI.inducedDipoleP[2];
// calculate the gl functions for permanent components // calculate the gl functions for permanent components
...@@ -492,20 +500,13 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -492,20 +500,13 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
// compute the energy contributions for this interaction // compute the energy contributions for this interaction
float e = bn0*gl0 + bn1*(gl1+gl6) float e = bn0*gl0 + bn1*(gl1+gl6) + bn2*(gl2+gl7+gl8) + bn3*(gl3+gl5) + bn4*gl4;
+ bn2*(gl2+gl7+gl8) float ei = 0.5f * (bn1*(gli1+gli6) + bn2*(gli2+gli7) + bn3*gli3);
+ bn3*(gl3+gl5) + bn4*gl4;
float ei = 0.5f * (bn1*(gli1+gli6)
+ bn2*(gli2+gli7) + bn3*gli3);
// get the real energy without any screening function // get the real energy without any screening function
float erl = rr1*gl0 + rr3*(gl1+gl6) float erl = rr1*gl0 + rr3*(gl1+gl6) + rr5*(gl2+gl7+gl8) + rr7*(gl3+gl5) + rr9*gl4;
+ rr5*(gl2+gl7+gl8) float erli = 0.5f*(rr3*(gli1+gli6)*psc3 + rr5*(gli2+gli7)*psc5 + rr7*gli3*psc7);
+ rr7*(gl3+gl5) + rr9*gl4;
float erli = 0.5f*(rr3*(gli1+gli6)*psc3
+ rr5*(gli2+gli7)*psc5
+ rr7*gli3*psc7);
e = e - (1.0f-scalingFactors[MScaleIndex])*erl; e = e - (1.0f-scalingFactors[MScaleIndex])*erl;
ei = ei - erli; ei = ei - erli;
...@@ -638,6 +639,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -638,6 +639,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
+ 0.5f*gfri4*((qkui1-qiuk1)*psc5 + 0.5f*gfri4*((qkui1-qiuk1)*psc5
+ (qkuip1-qiukp1)*dsc5) + (qkuip1-qiukp1)*dsc5)
+ gfri5*qir1 + gfri6*qkr1; + gfri5*qir1 + gfri6*qkr1;
float ftm2ri2 = gfri1*yr + 0.5f* float ftm2ri2 = gfri1*yr + 0.5f*
(- rr3*ck*(atomI.inducedDipole[1]*psc3+atomI.inducedDipoleP[1]*dsc3) (- rr3*ck*(atomI.inducedDipole[1]*psc3+atomI.inducedDipoleP[1]*dsc3)
+ rr5*sc4*(atomI.inducedDipole[1]*psc5+atomI.inducedDipoleP[1]*dsc5) + rr5*sc4*(atomI.inducedDipole[1]*psc5+atomI.inducedDipoleP[1]*dsc5)
...@@ -652,6 +654,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros ...@@ -652,6 +654,7 @@ __device__ void calculatePmeDirectElectrostaticPairIxn_kernel( PmeDirectElectros
+ 0.5f*gfri4*((qkui2-qiuk2)*psc5 + 0.5f*gfri4*((qkui2-qiuk2)*psc5
+ (qkuip2-qiukp2)*dsc5) + (qkuip2-qiukp2)*dsc5)
+ gfri5*qir2 + gfri6*qkr2; + gfri5*qir2 + gfri6*qkr2;
float ftm2ri3 = gfri1*zr + 0.5f* float ftm2ri3 = gfri1*zr + 0.5f*
(- rr3*ck*(atomI.inducedDipole[2]*psc3+atomI.inducedDipoleP[2]*dsc3) (- rr3*ck*(atomI.inducedDipole[2]*psc3+atomI.inducedDipoleP[2]*dsc3)
+ rr5*sc4*(atomI.inducedDipole[2]*psc5+atomI.inducedDipoleP[2]*dsc5) + rr5*sc4*(atomI.inducedDipole[2]*psc5+atomI.inducedDipoleP[2]*dsc5)
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 0cae89d3
...@@ -1600,7 +1600,6 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc ...@@ -1600,7 +1600,6 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
int particle1, particle2, particle3, particle4; int particle1, particle2, particle3, particle4;
double k; double k;
outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k ); outOfPlaneBendForce->getOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
//k *= CalToJoule/(AngstromToNm*AngstromToNm);
k *= CalToJoule; k *= CalToJoule;
outOfPlaneBendForce->setOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k ); outOfPlaneBendForce->setOutOfPlaneBendParameters( ii, particle1, particle2, particle3, particle4, k );
} }
...@@ -2053,6 +2052,12 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2053,6 +2052,12 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
int axisType = atoi( lineTokens[tokenIndex++].c_str() ); int axisType = atoi( lineTokens[tokenIndex++].c_str() );
int zAxis = atoi( lineTokens[tokenIndex++].c_str() ); int zAxis = atoi( lineTokens[tokenIndex++].c_str() );
int xAxis = atoi( lineTokens[tokenIndex++].c_str() ); int xAxis = atoi( lineTokens[tokenIndex++].c_str() );
int yAxis;
if( version > 2 ){
yAxis = atoi( lineTokens[tokenIndex++].c_str() );
} else {
yAxis = -1;
}
double pdamp = atof( lineTokens[tokenIndex++].c_str() ); double pdamp = atof( lineTokens[tokenIndex++].c_str() );
double tholeDamp = atof( lineTokens[tokenIndex++].c_str() ); double tholeDamp = atof( lineTokens[tokenIndex++].c_str() );
double polarity = atof( lineTokens[tokenIndex++].c_str() ); double polarity = atof( lineTokens[tokenIndex++].c_str() );
...@@ -2069,7 +2074,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2069,7 +2074,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
quadrupole[6] = atof( lineTokens[tokenIndex++].c_str() ); quadrupole[6] = atof( lineTokens[tokenIndex++].c_str() );
quadrupole[7] = atof( lineTokens[tokenIndex++].c_str() ); quadrupole[7] = atof( lineTokens[tokenIndex++].c_str() );
quadrupole[8] = atof( lineTokens[tokenIndex++].c_str() ); quadrupole[8] = atof( lineTokens[tokenIndex++].c_str() );
multipoleForce->addParticle( charge, dipole, quadrupole, axisType, zAxis, xAxis, tholeDamp, pdamp, polarity ); multipoleForce->addParticle( charge, dipole, quadrupole, axisType, zAxis, xAxis, yAxis, tholeDamp, pdamp, polarity );
} else { } else {
(void) fprintf( log, "%s AmoebaMultipoleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount ); (void) fprintf( log, "%s AmoebaMultipoleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) fflush( log ); (void) fflush( log );
...@@ -2160,11 +2165,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2160,11 +2165,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
for( int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){ for( int ii = 0; ii < multipoleForce->getNumMultipoles(); ii++ ){
int axisType, zAxis, xAxis; int axisType, zAxis, xAxis, yAxis;
std::vector<double> dipole; std::vector<double> dipole;
std::vector<double> quadrupole; std::vector<double> quadrupole;
double charge, thole, dampingFactor, polarity; double charge, thole, dampingFactor, polarity;
multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity ); multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, yAxis, thole, dampingFactor, polarity );
for( unsigned int jj = 0; jj < dipole.size(); jj++ ){ for( unsigned int jj = 0; jj < dipole.size(); jj++ ){
dipole[jj] *= dipoleConversion; dipole[jj] *= dipoleConversion;
...@@ -2175,7 +2180,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2175,7 +2180,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
polarity *= polarityConversion; polarity *= polarityConversion;
dampingFactor *= dampingFactorConversion; dampingFactor *= dampingFactorConversion;
multipoleForce->setMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity ); multipoleForce->setMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, yAxis, thole, dampingFactor, polarity );
} }
} else { } else {
...@@ -2227,11 +2232,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2227,11 +2232,11 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
(void) fflush( log ); (void) fflush( log );
for( unsigned int ii = 0; ii < arraySize; ii++ ){ for( unsigned int ii = 0; ii < arraySize; ii++ ){
int axisType, zAxis, xAxis; int axisType, zAxis, xAxis, yAxis;
std::vector<double> dipole; std::vector<double> dipole;
std::vector<double> quadrupole; std::vector<double> quadrupole;
double charge, thole, dampingFactor, polarity; double charge, thole, dampingFactor, polarity;
multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, thole, dampingFactor, polarity ); multipoleForce->getMultipoleParameters( ii, charge, dipole, quadrupole, axisType, zAxis, xAxis, yAxis, thole, dampingFactor, polarity );
(void) fprintf( log, "%8d %8d %8d %8d q %10.4f thl %10.4f pgm %10.4f pol %10.4f d[%10.4f %10.4f %10.4f]\n", (void) fprintf( log, "%8d %8d %8d %8d q %10.4f thl %10.4f pgm %10.4f pol %10.4f d[%10.4f %10.4f %10.4f]\n",
ii, axisType, zAxis, xAxis, charge, thole, dampingFactor, polarity, dipole[0], dipole[1], dipole[2] ); ii, axisType, zAxis, xAxis, charge, thole, dampingFactor, polarity, dipole[0], dipole[1], dipole[2] );
(void) fprintf( log, " q[%10.4f %10.4f %10.4f] [%10.4f %10.4f %10.4f] [%10.4f %10.4f %10.4f]\n", (void) fprintf( log, " q[%10.4f %10.4f %10.4f] [%10.4f %10.4f %10.4f] [%10.4f %10.4f %10.4f]\n",
...@@ -2361,7 +2366,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2361,7 +2366,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
} }
} }
// get supplementart fields // get supplementary fields
isNotEof = 1; isNotEof = 1;
int totalFields = 2; int totalFields = 2;
...@@ -2850,7 +2855,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2850,7 +2855,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
//static const unsigned int maxPrint = MAX_PRINT; //static const unsigned int maxPrint = MAX_PRINT;
static const unsigned int maxPrint = 15; static const unsigned int maxPrint = 15;
unsigned int arraySize = static_cast<unsigned int>(wcaDispersionForce->getNumParticles()); unsigned int arraySize = static_cast<unsigned int>(wcaDispersionForce->getNumParticles());
(void) fprintf( log, "%s: %u sample of AmoebaVdwForce parameters in %s units.\n", (void) fprintf( log, "%s: %u sample of AmoebaWcaForce parameters in %s units.\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") ); methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba") );
(void) fprintf( log, "Eps[%14.7f %14.7f] Rmin[%14.7f %14.7f]\nAwater %14.7f Shctd %14.7f Dispoff %14.7f Slevy %14.7f\n", (void) fprintf( log, "Eps[%14.7f %14.7f] Rmin[%14.7f %14.7f]\nAwater %14.7f Shctd %14.7f Dispoff %14.7f Slevy %14.7f\n",
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPME.cpp
View file @ 0cae89d3
...@@ -65,7 +65,7 @@ void testPMEWater() { ...@@ -65,7 +65,7 @@ void testPMEWater() {
quadrupole[8] = 3.622635596e-3; quadrupole[8] = 3.622635596e-3;
double damp = 9.707801995e-01*sqrt(0.1); double damp = 9.707801995e-01*sqrt(0.1);
double polarity = 0.837*0.001; double polarity = 0.837*0.001;
mp->addParticle(-0.51966, dipole, quadrupole, 1, 1, 2, 0.39, damp, polarity); mp->addParticle(-0.51966, dipole, quadrupole, 1, 1, 2, -1, 0.39, damp, polarity);
dipole[0] = -2.042094848e-2; dipole[0] = -2.042094848e-2;
dipole[2] = -3.078753000e-2; dipole[2] = -3.078753000e-2;
quadrupole[0] = -3.428482490e-3; quadrupole[0] = -3.428482490e-3;
...@@ -75,8 +75,8 @@ void testPMEWater() { ...@@ -75,8 +75,8 @@ void testPMEWater() {
quadrupole[8] = 1.345257001e-2; quadrupole[8] = 1.345257001e-2;
damp = 8.897068742e-01*sqrt(0.1); damp = 8.897068742e-01*sqrt(0.1);
polarity = 0.496*0.001; polarity = 0.496*0.001;
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 2, 0.39, damp, polarity); mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 2, -1, 0.39, damp, polarity);
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 1, 0.39, damp, polarity); mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 1, -1, 0.39, damp, polarity);
mp->setCutoffDistance(1.0); mp->setCutoffDistance(1.0);
std::vector<int> intVector; std::vector<int> intVector;
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 0cae89d3
...@@ -423,8 +423,9 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c ...@@ -423,8 +423,9 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
dampingFactors.resize(numMultipoles); dampingFactors.resize(numMultipoles);
polarity.resize(numMultipoles); polarity.resize(numMultipoles);
axisTypes.resize(numMultipoles); axisTypes.resize(numMultipoles);
multipoleAtomId1s.resize(numMultipoles); multipoleAtomZs.resize(numMultipoles);
multipoleAtomId2s.resize(numMultipoles); multipoleAtomXs.resize(numMultipoles);
multipoleAtomYs.resize(numMultipoles);
multipoleAtomCovalentInfo.resize(numMultipoles); multipoleAtomCovalentInfo.resize(numMultipoles);
int dipoleIndex = 0; int dipoleIndex = 0;
...@@ -435,17 +436,18 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c ...@@ -435,17 +436,18 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
// multipoles // multipoles
int axisType, multipoleAtomId1, multipoleAtomId2; int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, tholeD, dampingFactorD, polarityD; double charge, tholeD, dampingFactorD, polarityD;
std::vector<double> dipolesD; std::vector<double> dipolesD;
std::vector<double> quadrupolesD; std::vector<double> quadrupolesD;
force.getMultipoleParameters(ii, charge, dipolesD, quadrupolesD, axisType, multipoleAtomId1, multipoleAtomId2, force.getMultipoleParameters(ii, charge, dipolesD, quadrupolesD, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
tholeD, dampingFactorD, polarityD ); tholeD, dampingFactorD, polarityD );
totalCharge += charge; totalCharge += charge;
axisTypes[ii] = axisType; axisTypes[ii] = axisType;
multipoleAtomId1s[ii] = multipoleAtomId1; multipoleAtomZs[ii] = multipoleAtomZ;
multipoleAtomId2s[ii] = multipoleAtomId2; multipoleAtomXs[ii] = multipoleAtomX;
multipoleAtomYs[ii] = multipoleAtomY;
charges[ii] = static_cast<RealOpenMM>(charge); charges[ii] = static_cast<RealOpenMM>(charge);
tholes[ii] = static_cast<RealOpenMM>(tholeD); tholes[ii] = static_cast<RealOpenMM>(tholeD);
...@@ -494,7 +496,7 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo ...@@ -494,7 +496,7 @@ double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bo
RealOpenMM energy = amoebaReferenceMultipoleForce.calculateForceAndEnergy( numMultipoles, posData, RealOpenMM energy = amoebaReferenceMultipoleForce.calculateForceAndEnergy( numMultipoles, posData,
charges, dipoles, quadrupoles, tholes, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, dampingFactors, polarity, axisTypes,
multipoleAtomId1s, multipoleAtomId2s, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, forceData); multipoleAtomCovalentInfo, forceData);
return static_cast<double>(energy); return static_cast<double>(energy);
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 0cae89d3
...@@ -357,8 +357,9 @@ private: ...@@ -357,8 +357,9 @@ private:
std::vector<RealOpenMM> dampingFactors; std::vector<RealOpenMM> dampingFactors;
std::vector<RealOpenMM> polarity; std::vector<RealOpenMM> polarity;
std::vector<int> axisTypes; std::vector<int> axisTypes;
std::vector<int> multipoleAtomId1s; std::vector<int> multipoleAtomZs;
std::vector<int> multipoleAtomId2s; std::vector<int> multipoleAtomXs;
std::vector<int> multipoleAtomYs;
std::vector< std::vector< std::vector<int> > > multipoleAtomCovalentInfo; std::vector< std::vector< std::vector<int> > > multipoleAtomCovalentInfo;
//int iterativeMethod; //int iterativeMethod;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ 0cae89d3
...@@ -1443,8 +1443,9 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat ...@@ -1443,8 +1443,9 @@ void AmoebaReferenceMultipoleForce::mapTorqueToForce( const MultipoleParticleDat
RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData, RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ) const { RealOpenMM** forces ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -1523,7 +1524,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v ...@@ -1523,7 +1524,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
// map torques to forces // map torques to forces
for( unsigned int ii = 0; ii < particleData.size(); ii++ ){ for( unsigned int ii = 0; ii < particleData.size(); ii++ ){
mapTorqueToForce( particleData[ii], particleData[multipoleAtomId1s[ii]], particleData[multipoleAtomId2s[ii]], axisTypes[ii], torques[ii], forces ); mapTorqueToForce( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]], axisTypes[ii], torques[ii], forces );
} }
// diagnostics // diagnostics
...@@ -1555,8 +1556,9 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -1555,8 +1556,9 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
const std::vector<RealOpenMM>& dampingFactors, const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity, const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ){ RealOpenMM** forces ){
...@@ -1579,8 +1581,8 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -1579,8 +1581,8 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
tholes, dampingFactors, polarity, particleData ); tholes, dampingFactors, polarity, particleData );
for( unsigned int ii = 0; ii < numParticles; ii++ ){ for( unsigned int ii = 0; ii < numParticles; ii++ ){
if( multipoleAtomId1s[ii] >= 0 && multipoleAtomId2s[ii] >= 0 ){ if( multipoleAtomZs[ii] >= 0 && multipoleAtomXs[ii] >= 0 ){
applyRotationMatrix( particleData[ii], particleData[multipoleAtomId1s[ii]], particleData[multipoleAtomId2s[ii]], axisTypes[ii] ); applyRotationMatrix( particleData[ii], particleData[multipoleAtomZs[ii]], particleData[multipoleAtomXs[ii]], axisTypes[ii] );
} }
} }
...@@ -1637,7 +1639,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig ...@@ -1637,7 +1639,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsig
throw OpenMMException(message.str()); throw OpenMMException(message.str());
} }
RealOpenMM energy = calculateNoCutoffElectrostatic( particleData, axisTypes, multipoleAtomId1s, multipoleAtomId2s, forces ); RealOpenMM energy = calculateNoCutoffElectrostatic( particleData, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, forces );
return energy; return energy;
...@@ -1652,8 +1654,9 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic ...@@ -1652,8 +1654,9 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic
const std::vector<RealOpenMM>& dampingFactors, const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity, const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo,
RealOpenMM** forces ){ RealOpenMM** forces ){
...@@ -1662,7 +1665,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic ...@@ -1662,7 +1665,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic
if( getNonbondedMethod() == NoCutoff || 1 ){ if( getNonbondedMethod() == NoCutoff || 1 ){
return calculateNoCutoffForceAndEnergy( static_cast<unsigned int>(numParticles), particlePositions, charges, dipoles, quadrupoles, tholes, dampingFactors, return calculateNoCutoffForceAndEnergy( static_cast<unsigned int>(numParticles), particlePositions, charges, dipoles, quadrupoles, tholes, dampingFactors,
polarity, axisTypes, multipoleAtomId1s, multipoleAtomId2s, forces ); polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, forces );
} }
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ 0cae89d3
...@@ -211,8 +211,9 @@ public: ...@@ -211,8 +211,9 @@ public:
const std::vector<RealOpenMM>& dampingFactors, const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity, const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
RealOpenMM** forces ); RealOpenMM** forces );
...@@ -461,8 +462,9 @@ private: ...@@ -461,8 +462,9 @@ private:
RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData, RealOpenMM calculateNoCutoffElectrostatic( std::vector<MultipoleParticleData>& particleData,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ) const; RealOpenMM** forces ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -491,8 +493,9 @@ private: ...@@ -491,8 +493,9 @@ private:
const std::vector<RealOpenMM>& dampingFactors, const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity, const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes, const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomId1s, const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomId2s, const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
RealOpenMM** forces ); RealOpenMM** forces );
}; };
......
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