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Commit c6ebf6e2 authored by Peter Eastman's avatar Peter Eastman
Browse files

Removed the word "harmonic" from lots of places it didn't belong, including class and method names

parent 58b094ce
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Showing with 408 additions and 408 deletions
plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaHarmonicAngleForce.cpp → plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaAngleForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the Cuda implementation of CudaAmoebaHarmonicAngleForce.
* This tests the Cuda implementation of CudaAmoebaAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -119,22 +119,22 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
return;
}
static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3;
double idealAngle;
double quadraticK;
amoebaHarmonicAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
amoebaAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
double cubicK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleCubic();
double quarticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleQuartic();
double penticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAnglePentic();
double sexticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleSextic();
double cubicK = amoebaAngleForce.getAmoebaGlobalAngleCubic();
double quarticK = amoebaAngleForce.getAmoebaGlobalAngleQuartic();
double penticK = amoebaAngleForce.getAmoebaGlobalAnglePentic();
double sexticK = amoebaAngleForce.getAmoebaGlobalAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
(void) fprintf( log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
}
......@@ -201,7 +201,7 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& p
*energy += energyTerm;
}
static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -217,13 +217,13 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicAngleForce(ii, positions, amoebaHarmonicAngleForce, expectedForces, expectedEnergy, log );
for( int ii = 0; ii < amoebaAngleForce.getNumAngles(); ii++ ){
computeAmoebaAngleForce(ii, positions, amoebaAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -235,19 +235,19 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
void compareWithExpectedForceAndEnergy( Context& context, AmoebaAngleForce& amoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicAngleForces( context, amoebaHarmonicAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaAngleForces( context, amoebaAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -272,7 +272,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicAngleForce* amoebaHarmonicAngleForce = new AmoebaHarmonicAngleForce();
AmoebaAngleForce* amoebaAngleForce = new AmoebaAngleForce();
double angle = 100.0;
double quadraticK = 1.0;
......@@ -280,14 +280,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 1.0e-02;
double penticK = 1.0e-03;
double sexticK = 1.0e-04;
amoebaHarmonicAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleCubic(cubicK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleQuartic(quarticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAnglePentic(penticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleSextic(sexticK);
amoebaAngleForce->setAmoebaGlobalAngleCubic(cubicK);
amoebaAngleForce->setAmoebaGlobalAngleQuartic(quarticK);
amoebaAngleForce->setAmoebaGlobalAnglePentic(penticK);
amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
system.addForce(amoebaHarmonicAngleForce);
system.addForce(amoebaAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "Cuda"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -297,14 +297,14 @@ void testOneAngle( FILE* log ) {
positions[2] = Vec3(0, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicAngleForce running test..." << std::endl;
std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testOneAngle( log );
......
plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaHarmonicBondForce.cpp → plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaBondForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the Cuda implementation of HarmonicBondForce.
* This tests the Cuda implementation of AmoebaBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -46,15 +46,15 @@
using namespace OpenMM;
const double TOL = 1e-5;
static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaBondForce& amoebaBondForce,
std::vector<Vec3>& forces, double* energy ) {
int particle1, particle2;
double bondLength;
double quadraticK;
double cubicK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondCubic();
double quarticK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondQuartic();
amoebaHarmonicBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
double cubicK = amoebaBondForce.getAmoebaGlobalBondCubic();
double quarticK = amoebaBondForce.getAmoebaGlobalBondQuartic();
amoebaBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
double deltaR[3];
double r2 = 0.0;
......@@ -82,7 +82,7 @@ static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& po
}
static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
static void computeAmoebaBondForces( Context& context, AmoebaBondForce& amoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -98,13 +98,13 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicBondForce.getNumBonds(); ii++ ){
computeAmoebaHarmonicBondForce(ii, positions, amoebaHarmonicBondForce, expectedForces, expectedEnergy );
for( int ii = 0; ii < amoebaBondForce.getNumBonds(); ii++ ){
computeAmoebaBondForce(ii, positions, amoebaBondForce, expectedForces, expectedEnergy );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -115,18 +115,18 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce, double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& amoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicBondForces( context, amoebaHarmonicBondForce, expectedForces, &expectedEnergy, NULL );
computeAmoebaBondForces( context, amoebaBondForce, expectedForces, &expectedEnergy, NULL );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -150,17 +150,17 @@ void testOneBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5;
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce);
system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "Cuda"));
std::vector<Vec3> positions(2);
......@@ -168,7 +168,7 @@ void testOneBond( FILE* log ) {
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testOneBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond", log );
}
void testTwoBond( FILE* log ) {
......@@ -182,18 +182,18 @@ void testTwoBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5;
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaHarmonicBondForce->addBond(1, 2, bondLength, quadraticK);
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce);
system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "Cuda"));
//Context context(system, integrator, platform );
std::vector<Vec3> positions(3);
......@@ -203,13 +203,13 @@ void testTwoBond( FILE* log ) {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicBondForce running test..." << std::endl;
std::cout << "TestCudaAmoebaBondForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testTwoBond( log );
......
plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp
View file @ c6ebf6e2
......@@ -277,20 +277,20 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Polar
 
// 1-2 bonds needed
/*
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* AmoebaBondForce = new AmoebaBondForce();
 
// addBond: particle1, particle2, length, quadraticK
 
amoebaHarmonicBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
 
amoebaHarmonicBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
AmoebaBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
AmoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(AmoebaBondForce);
*/
std::vector<Vec3> positions(numberOfParticles);
 
......
plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp → plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaInPlaneAngleForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the Cuda implementation of CudaAmoebaHarmonicInPlaneAngleForce.
* This tests the Cuda implementation of AmoebaInPlaneAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -120,22 +120,22 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
return;
}
static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3, particle4;
double idealInPlaneAngle;
double quadraticK;
amoebaHarmonicInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
amoebaInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
double cubicK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleCubic();
double quarticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleQuartic();
double penticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAnglePentic();
double sexticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleSextic();
double cubicK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleCubic();
double quarticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic();
double penticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic();
double sexticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
}
......@@ -182,7 +182,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log );
}
#endif
......@@ -278,7 +278,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
}
static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -294,13 +294,13 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicInPlaneAngleForce(ii, positions, amoebaHarmonicInPlaneAngleForce, expectedForces, expectedEnergy, log );
for( int ii = 0; ii < amoebaInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaInPlaneAngleForce(ii, positions, amoebaInPlaneAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -311,19 +311,19 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
void compareWithExpectedForceAndEnergy( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicInPlaneAngleForces( context, amoebaHarmonicInPlaneAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaInPlaneAngleForces( context, amoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -348,7 +348,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicInPlaneAngleForce* amoebaHarmonicInPlaneAngleForce = new AmoebaHarmonicInPlaneAngleForce();
AmoebaInPlaneAngleForce* amoebaInPlaneAngleForce = new AmoebaInPlaneAngleForce();
double angle = 65.0;
double quadraticK = 1.0;
......@@ -356,14 +356,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 0.0e-02;
double penticK = 0.0e-03;
double sexticK = 0.0e-04;
amoebaHarmonicInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleCubic(cubicK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleQuartic(quarticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAnglePentic(penticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleSextic(sexticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleCubic(cubicK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleQuartic(quarticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAnglePentic(penticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
system.addForce(amoebaHarmonicInPlaneAngleForce);
system.addForce(amoebaInPlaneAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "Cuda"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -374,14 +374,14 @@ void testOneAngle( FILE* log ) {
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicInPlaneAngleForce running test..." << std::endl;
std::cout << "TestCudaAmoebaInPlaneAngleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testOneAngle( NULL );
......
plugins/amoeba/platforms/cuda-old/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ c6ebf6e2
......@@ -274,20 +274,20 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Nonbo
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
amoebaHarmonicBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -611,18 +611,18 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -836,18 +836,18 @@ static void testQuadrupoleValidation( FILE* log ){
}
*/
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -1089,18 +1089,18 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 2; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -1321,18 +1321,18 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( 0.0 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 0.0 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( 0.0 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 0.0 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......
plugins/amoeba/platforms/cuda/CMakeLists.txt
View file @ c6ebf6e2
......@@ -75,9 +75,9 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda2/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda2/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_BINARY_DIR}/platforms/cuda2/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/include)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/cuda/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_BINARY_DIR}/platforms/cuda/src)
# Set variables needed for encoding kernel sources into a C++ class
......@@ -95,7 +95,7 @@ INCLUDE_DIRECTORIES(${CUDA_TOOLKIT_INCLUDE})
FILE(GLOB CUDA_KERNELS ${CUDA_SOURCE_DIR}/kernels/*.cu)
ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
COMMAND ${CMAKE_COMMAND}
ARGS -D CUDA_SOURCE_DIR=${CUDA_SOURCE_DIR} -D CUDA_KERNELS_CPP=${CUDA_KERNELS_CPP} -D CUDA_KERNELS_H=${CUDA_KERNELS_H} -D CUDA_SOURCE_CLASS=${CUDA_SOURCE_CLASS} -P ${CMAKE_SOURCE_DIR}/platforms/cuda2/EncodeCUDAFiles.cmake
ARGS -D CUDA_SOURCE_DIR=${CUDA_SOURCE_DIR} -D CUDA_KERNELS_CPP=${CUDA_KERNELS_CPP} -D CUDA_KERNELS_H=${CUDA_KERNELS_H} -D CUDA_SOURCE_CLASS=${CUDA_SOURCE_CLASS} -P ${CMAKE_SOURCE_DIR}/platforms/cuda/EncodeCUDAFiles.cmake
DEPENDS ${CUDA_KERNELS}
)
SET_SOURCE_FILES_PROPERTIES(${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H} PROPERTIES GENERATED TRUE)
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
View file @ c6ebf6e2
......@@ -40,9 +40,9 @@ extern "C" OPENMM_EXPORT void registerKernelFactories() {
try {
Platform& platform = Platform::getPlatformByName("CUDA");
AmoebaCudaKernelFactory* factory = new AmoebaCudaKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
......@@ -71,14 +71,14 @@ KernelImpl* AmoebaCudaKernelFactory::createKernelImpl(std::string name, const Pl
CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
CudaContext& cu = *data.contexts[0];
if (name == CalcAmoebaHarmonicBondForceKernel::Name())
return new CudaCalcAmoebaHarmonicBondForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaBondForceKernel::Name())
return new CudaCalcAmoebaBondForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
return new CudaCalcAmoebaHarmonicAngleForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaAngleForceKernel::Name())
return new CudaCalcAmoebaAngleForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
return new CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaInPlaneAngleForceKernel::Name())
return new CudaCalcAmoebaInPlaneAngleForceKernel(name, platform, cu, context.getSystem());
if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new CudaCalcAmoebaPiTorsionForceKernel(name, platform, cu, context.getSystem());
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ c6ebf6e2
......@@ -54,12 +54,12 @@ using namespace std;
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicBond *
* AmoebaBondForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicBondForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaBondForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicBondForce& force) : force(force) {
ForceInfo(const AmoebaBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -80,20 +80,20 @@ public:
return (length1 == length2 && k1 == k2);
}
private:
const AmoebaHarmonicBondForce& force;
const AmoebaBondForce& force;
};
CudaCalcAmoebaHarmonicBondForceKernel::CudaCalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaHarmonicBondForceKernel(name, platform), cu(cu), system(system), params(NULL) {
CudaCalcAmoebaBondForceKernel::CudaCalcAmoebaBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaBondForceKernel(name, platform), cu(cu), system(system), params(NULL) {
}
CudaCalcAmoebaHarmonicBondForceKernel::~CudaCalcAmoebaHarmonicBondForceKernel() {
CudaCalcAmoebaBondForceKernel::~CudaCalcAmoebaBondForceKernel() {
cu.setAsCurrent();
if (params != NULL)
delete params;
}
void CudaCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, const AmoebaHarmonicBondForce& force) {
void CudaCalcAmoebaBondForceKernel::initialize(const System& system, const AmoebaBondForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*force.getNumBonds()/numContexts;
......@@ -113,23 +113,23 @@ void CudaCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, con
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaBondForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicBondCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicBondQuartic());
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalBondCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalBondQuartic());
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::bondForce, replacements), force.getForceGroup());
cu.addForce(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicAngle *
* AmoebaAngleForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicAngleForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicAngleForce& force) : force(force) {
ForceInfo(const AmoebaAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -151,20 +151,20 @@ public:
return (angle1 == angle2 && k1 == k2);
}
private:
const AmoebaHarmonicAngleForce& force;
const AmoebaAngleForce& force;
};
CudaCalcAmoebaHarmonicAngleForceKernel::CudaCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaHarmonicAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
CudaCalcAmoebaAngleForceKernel::CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
}
CudaCalcAmoebaHarmonicAngleForceKernel::~CudaCalcAmoebaHarmonicAngleForceKernel() {
CudaCalcAmoebaAngleForceKernel::~CudaCalcAmoebaAngleForceKernel() {
cu.setAsCurrent();
if (params != NULL)
delete params;
}
void CudaCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, const AmoebaHarmonicAngleForce& force) {
void CudaCalcAmoebaAngleForceKernel::initialize(const System& system, const AmoebaAngleForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*force.getNumAngles()/numContexts;
......@@ -184,26 +184,26 @@ void CudaCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, co
map<string, string> replacements;
replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaAngleForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicAngleCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicAngleQuartic());
replacements["PENTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicAnglePentic());
replacements["SEXTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicAngleSextic());
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalAngleCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalAngleQuartic());
replacements["PENTIC_K"] = cu.doubleToString(force.getAmoebaGlobalAnglePentic());
replacements["SEXTIC_K"] = cu.doubleToString(force.getAmoebaGlobalAngleSextic());
replacements["RAD_TO_DEG"] = cu.doubleToString(180/M_PI);
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::angleForce, replacements), force.getForceGroup());
cu.addForce(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicInPlaneAngle *
* AmoebaInPlaneAngleForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicInPlaneAngleForce& force) : force(force) {
ForceInfo(const AmoebaInPlaneAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -226,20 +226,20 @@ public:
return (angle1 == angle2 && k1 == k2);
}
private:
const AmoebaHarmonicInPlaneAngleForce& force;
const AmoebaInPlaneAngleForce& force;
};
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
CudaCalcAmoebaInPlaneAngleForceKernel::CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system) :
CalcAmoebaInPlaneAngleForceKernel(name, platform), cu(cu), system(system), params(NULL) {
}
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::~CudaCalcAmoebaHarmonicInPlaneAngleForceKernel() {
CudaCalcAmoebaInPlaneAngleForceKernel::~CudaCalcAmoebaInPlaneAngleForceKernel() {
cu.setAsCurrent();
if (params != NULL)
delete params;
}
void CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) {
void CudaCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, const AmoebaInPlaneAngleForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*force.getNumAngles()/numContexts;
......@@ -258,16 +258,16 @@ void CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& sys
params->upload(paramVector);
map<string, string> replacements;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicInPlaneAngleCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicInPlaneAngleQuartic());
replacements["PENTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicInPlaneAnglePentic());
replacements["SEXTIC_K"] = cu.doubleToString(force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleQuartic());
replacements["PENTIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAnglePentic());
replacements["SEXTIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleSextic());
replacements["RAD_TO_DEG"] = cu.doubleToString(180/M_PI);
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaAmoebaKernelSources::amoebaInPlaneForce, replacements), force.getForceGroup());
cu.addForce(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
return 0.0;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ c6ebf6e2
......@@ -40,22 +40,22 @@ namespace OpenMM {
class CudaCalcAmoebaGeneralizedKirkwoodForceKernel;
/**
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaBondForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicBondForceKernel : public CalcAmoebaHarmonicBondForceKernel {
class CudaCalcAmoebaBondForceKernel : public CalcAmoebaBondForceKernel {
public:
CudaCalcAmoebaHarmonicBondForceKernel(std::string name,
CudaCalcAmoebaBondForceKernel(std::string name,
const Platform& platform,
CudaContext& cu,
System& system);
~CudaCalcAmoebaHarmonicBondForceKernel();
~CudaCalcAmoebaBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicBondForce this kernel will be used for
* @param force the AmoebaBondForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicBondForce& force);
void initialize(const System& system, const AmoebaBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -74,19 +74,19 @@ private:
};
/**
* This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicAngleForceKernel : public CalcAmoebaHarmonicAngleForceKernel {
class CudaCalcAmoebaAngleForceKernel : public CalcAmoebaAngleForceKernel {
public:
CudaCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
~CudaCalcAmoebaHarmonicAngleForceKernel();
CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
~CudaCalcAmoebaAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicAngleForce this kernel will be used for
* @param force the AmoebaAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicAngleForce& force);
void initialize(const System& system, const AmoebaAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -105,19 +105,19 @@ private:
};
/**
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
class CudaCalcAmoebaInPlaneAngleForceKernel : public CalcAmoebaInPlaneAngleForceKernel {
public:
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
~CudaCalcAmoebaHarmonicInPlaneAngleForceKernel();
CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, System& system);
~CudaCalcAmoebaInPlaneAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
* @param force the AmoebaInPlaneAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force);
void initialize(const System& system, const AmoebaInPlaneAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicAngleForce.cpp → plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaAngleForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CudaAmoebaHarmonicAngleForce.
* This tests the CUDA implementation of CudaAmoebaAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -120,22 +120,22 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
return;
}
static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3;
double idealAngle;
double quadraticK;
amoebaHarmonicAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
amoebaAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
double cubicK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleCubic();
double quarticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleQuartic();
double penticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAnglePentic();
double sexticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleSextic();
double cubicK = amoebaAngleForce.getAmoebaGlobalAngleCubic();
double quarticK = amoebaAngleForce.getAmoebaGlobalAngleQuartic();
double penticK = amoebaAngleForce.getAmoebaGlobalAnglePentic();
double sexticK = amoebaAngleForce.getAmoebaGlobalAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
(void) fprintf( log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
}
......@@ -202,7 +202,7 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& p
*energy += energyTerm;
}
static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -218,13 +218,13 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicAngleForce(ii, positions, amoebaHarmonicAngleForce, expectedForces, expectedEnergy, log );
for( int ii = 0; ii < amoebaAngleForce.getNumAngles(); ii++ ){
computeAmoebaAngleForce(ii, positions, amoebaAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -236,19 +236,19 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce,
void compareWithExpectedForceAndEnergy( Context& context, AmoebaAngleForce& amoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicAngleForces( context, amoebaHarmonicAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaAngleForces( context, amoebaAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -273,7 +273,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicAngleForce* amoebaHarmonicAngleForce = new AmoebaHarmonicAngleForce();
AmoebaAngleForce* amoebaAngleForce = new AmoebaAngleForce();
double angle = 100.0;
double quadraticK = 1.0;
......@@ -281,14 +281,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 1.0e-02;
double penticK = 1.0e-03;
double sexticK = 1.0e-04;
amoebaHarmonicAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleCubic(cubicK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleQuartic(quarticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAnglePentic(penticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleSextic(sexticK);
amoebaAngleForce->setAmoebaGlobalAngleCubic(cubicK);
amoebaAngleForce->setAmoebaGlobalAngleQuartic(quarticK);
amoebaAngleForce->setAmoebaGlobalAnglePentic(penticK);
amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
system.addForce(amoebaHarmonicAngleForce);
system.addForce(amoebaAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "CUDA"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -298,14 +298,14 @@ void testOneAngle( FILE* log ) {
positions[2] = Vec3(0, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicAngleForce running test..." << std::endl;
std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testOneAngle( log );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicBondForce.cpp → plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaBondForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the Cuda implementation of HarmonicBondForce.
* This tests the Cuda implementation of AmoebaBondForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -47,15 +47,15 @@ using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaBondForce& amoebaBondForce,
std::vector<Vec3>& forces, double* energy ) {
int particle1, particle2;
double bondLength;
double quadraticK;
double cubicK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondCubic();
double quarticK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondQuartic();
amoebaHarmonicBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
double cubicK = amoebaBondForce.getAmoebaGlobalBondCubic();
double quarticK = amoebaBondForce.getAmoebaGlobalBondQuartic();
amoebaBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
double deltaR[3];
double r2 = 0.0;
......@@ -83,7 +83,7 @@ static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& po
}
static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
static void computeAmoebaBondForces( Context& context, AmoebaBondForce& amoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -99,13 +99,13 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicBondForce.getNumBonds(); ii++ ){
computeAmoebaHarmonicBondForce(ii, positions, amoebaHarmonicBondForce, expectedForces, expectedEnergy );
for( int ii = 0; ii < amoebaBondForce.getNumBonds(); ii++ ){
computeAmoebaBondForce(ii, positions, amoebaBondForce, expectedForces, expectedEnergy );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -116,18 +116,18 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce, double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& amoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicBondForces( context, amoebaHarmonicBondForce, expectedForces, &expectedEnergy, NULL );
computeAmoebaBondForces( context, amoebaBondForce, expectedForces, &expectedEnergy, NULL );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -151,17 +151,17 @@ void testOneBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5;
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce);
system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "CUDA"));
std::vector<Vec3> positions(2);
......@@ -169,7 +169,7 @@ void testOneBond( FILE* log ) {
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testOneBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond", log );
}
void testTwoBond( FILE* log ) {
......@@ -182,18 +182,18 @@ void testTwoBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5;
double quadraticK = 1.0;
double cubicK = 2.0;
double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaHarmonicBondForce->addBond(1, 2, bondLength, quadraticK);
amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce);
system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "CUDA"));
//Context context(system, integrator, platform );
std::vector<Vec3> positions(3);
......@@ -203,13 +203,13 @@ void testTwoBond( FILE* log ) {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicBondForce running test..." << std::endl;
std::cout << "TestCudaAmoebaBondForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testTwoBond( log );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp
View file @ c6ebf6e2
......@@ -278,20 +278,20 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Polar
 
// 1-2 bonds needed
/*
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* AmoebaBondForce = new AmoebaBondForce();
 
// addBond: particle1, particle2, length, quadraticK
 
amoebaHarmonicBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
 
amoebaHarmonicBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
AmoebaBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
AmoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
AmoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(AmoebaBondForce);
*/
std::vector<Vec3> positions(numberOfParticles);
 
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp → plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaInPlaneAngleForce.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CudaAmoebaHarmonicInPlaneAngleForce.
* This tests the CUDA implementation of AmoebaInPlaneAngleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
......@@ -121,22 +121,22 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
return;
}
static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3, particle4;
double idealInPlaneAngle;
double quadraticK;
amoebaHarmonicInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
amoebaInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
double cubicK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleCubic();
double quarticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleQuartic();
double penticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAnglePentic();
double sexticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleSextic();
double cubicK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleCubic();
double quarticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic();
double penticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic();
double sexticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
}
......@@ -183,7 +183,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log );
}
#endif
......@@ -279,7 +279,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
}
static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
......@@ -295,13 +295,13 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicInPlaneAngleForce(ii, positions, amoebaHarmonicInPlaneAngleForce, expectedForces, expectedEnergy, log );
for( int ii = 0; ii < amoebaInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaInPlaneAngleForce(ii, positions, amoebaInPlaneAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
......@@ -312,19 +312,19 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
void compareWithExpectedForceAndEnergy( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicInPlaneAngleForces( context, amoebaHarmonicInPlaneAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaInPlaneAngleForces( context, amoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
(void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
......@@ -349,7 +349,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicInPlaneAngleForce* amoebaHarmonicInPlaneAngleForce = new AmoebaHarmonicInPlaneAngleForce();
AmoebaInPlaneAngleForce* amoebaInPlaneAngleForce = new AmoebaInPlaneAngleForce();
double angle = 65.0;
double quadraticK = 1.0;
......@@ -357,14 +357,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 0.0e-02;
double penticK = 0.0e-03;
double sexticK = 0.0e-04;
amoebaHarmonicInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleCubic(cubicK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleQuartic(quarticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAnglePentic(penticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleSextic(sexticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleCubic(cubicK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleQuartic(quarticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAnglePentic(penticK);
amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
system.addForce(amoebaHarmonicInPlaneAngleForce);
system.addForce(amoebaInPlaneAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "CUDA"));
std::vector<Vec3> positions(numberOfParticles);
......@@ -375,14 +375,14 @@ void testOneAngle( FILE* log ) {
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaHarmonicInPlaneAngleForce running test..." << std::endl;
std::cout << "TestCudaAmoebaInPlaneAngleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testOneAngle( NULL );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ c6ebf6e2
......@@ -275,20 +275,20 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Nonbo
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
amoebaHarmonicBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -612,18 +612,18 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -837,18 +837,18 @@ static void testQuadrupoleValidation( FILE* log ){
}
*/
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -1090,18 +1090,18 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 2; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( -2.5500000e+01 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 3.7931250e+02 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......@@ -1322,18 +1322,18 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
// 1-2 bonds needed
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
// addBond: particle1, particle2, length, quadraticK
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaHarmonicBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+1, 0.0000000e+00, 0.0000000e+00 );
amoebaBondForce->addBond( jj, jj+2, 0.0000000e+00, 0.0000000e+00 );
}
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( 0.0 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 0.0 );
system.addForce(amoebaHarmonicBondForce);
amoebaBondForce->setAmoebaGlobalBondCubic( 0.0 );
amoebaBondForce->setAmoebaGlobalBondQuartic( 0.0 );
system.addForce(amoebaBondForce);
std::vector<Vec3> positions(numberOfParticles);
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp
View file @ c6ebf6e2
......@@ -52,9 +52,9 @@ extern "C" void initAmoebaReferenceKernels() {
AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
......@@ -74,14 +74,14 @@ KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, con
// create AmoebaReferenceData object if contextToAmoebaDataMap does not contain
// key equal to current context
if (name == CalcAmoebaHarmonicBondForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicBondForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaBondForceKernel::Name())
return new ReferenceCalcAmoebaBondForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaAngleForceKernel::Name())
return new ReferenceCalcAmoebaAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaInPlaneAngleForceKernel::Name())
return new ReferenceCalcAmoebaInPlaneAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new ReferenceCalcAmoebaPiTorsionForceKernel(name, platform, context.getSystem());
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ c6ebf6e2
......@@ -25,9 +25,9 @@
* -------------------------------------------------------------------------- */
#include "AmoebaReferenceKernels.h"
#include "AmoebaReferenceHarmonicBondForce.h"
#include "AmoebaReferenceHarmonicAngleForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
#include "AmoebaReferenceBondForce.h"
#include "AmoebaReferenceAngleForce.h"
#include "AmoebaReferenceInPlaneAngleForce.h"
#include "AmoebaReferencePiTorsionForce.h"
#include "AmoebaReferenceStretchBendForce.h"
#include "AmoebaReferenceOutOfPlaneBendForce.h"
......@@ -72,14 +72,14 @@ static RealVec& extractBoxSize(ContextImpl& context) {
// ***************************************************************************
ReferenceCalcAmoebaHarmonicBondForceKernel::ReferenceCalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaHarmonicBondForceKernel(name, platform), system(system) {
ReferenceCalcAmoebaBondForceKernel::ReferenceCalcAmoebaBondForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaBondForceKernel(name, platform), system(system) {
}
ReferenceCalcAmoebaHarmonicBondForceKernel::~ReferenceCalcAmoebaHarmonicBondForceKernel() {
ReferenceCalcAmoebaBondForceKernel::~ReferenceCalcAmoebaBondForceKernel() {
}
void ReferenceCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, const AmoebaHarmonicBondForce& force) {
void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const AmoebaBondForce& force) {
numBonds = force.getNumBonds();
for( int ii = 0; ii < numBonds; ii++) {
......@@ -93,30 +93,30 @@ void ReferenceCalcAmoebaHarmonicBondForceKernel::initialize(const System& system
length.push_back( static_cast<RealOpenMM>( lengthValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( kValue ) );
}
globalHarmonicBondCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicBondCubic());
globalHarmonicBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicBondQuartic());
globalBondCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
globalBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondQuartic());
}
double ReferenceCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double ReferenceCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicBondForce amoebaReferenceHarmonicBondForce;
RealOpenMM energy = amoebaReferenceHarmonicBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic,
globalHarmonicBondCubic, globalHarmonicBondQuartic,
AmoebaReferenceBondForce amoebaReferenceBondForce;
RealOpenMM energy = amoebaReferenceBondForce.calculateForceAndEnergy( numBonds, posData, particle1, particle2, length, kQuadratic,
globalBondCubic, globalBondQuartic,
forceData );
return static_cast<double>(energy);
}
// ***************************************************************************
ReferenceCalcAmoebaHarmonicAngleForceKernel::ReferenceCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaHarmonicAngleForceKernel(name, platform), system(system) {
ReferenceCalcAmoebaAngleForceKernel::ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaAngleForceKernel(name, platform), system(system) {
}
ReferenceCalcAmoebaHarmonicAngleForceKernel::~ReferenceCalcAmoebaHarmonicAngleForceKernel() {
ReferenceCalcAmoebaAngleForceKernel::~ReferenceCalcAmoebaAngleForceKernel() {
}
void ReferenceCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, const AmoebaHarmonicAngleForce& force) {
void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const AmoebaAngleForce& force) {
numAngles = force.getNumAngles();
......@@ -130,29 +130,29 @@ void ReferenceCalcAmoebaHarmonicAngleForceKernel::initialize(const System& syste
angle.push_back( static_cast<RealOpenMM>( angleValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( k) );
}
globalHarmonicAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicAngleCubic());
globalHarmonicAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicAngleQuartic());
globalHarmonicAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicAnglePentic());
globalHarmonicAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicAngleSextic());
globalAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleCubic());
globalAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleQuartic());
globalAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalAnglePentic());
globalAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleSextic());
}
double ReferenceCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double ReferenceCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicAngleForce amoebaReferenceHarmonicAngleForce;
RealOpenMM energy = amoebaReferenceHarmonicAngleForce.calculateForceAndEnergy( numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalHarmonicAngleCubic, globalHarmonicAngleQuartic, globalHarmonicAnglePentic, globalHarmonicAngleSextic, forceData );
AmoebaReferenceAngleForce amoebaReferenceAngleForce;
RealOpenMM energy = amoebaReferenceAngleForce.calculateForceAndEnergy( numAngles,
posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData );
return static_cast<double>(energy);
}
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform), system(system) {
ReferenceCalcAmoebaInPlaneAngleForceKernel::ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaInPlaneAngleForceKernel(name, platform), system(system) {
}
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel() {
ReferenceCalcAmoebaInPlaneAngleForceKernel::~ReferenceCalcAmoebaInPlaneAngleForceKernel() {
}
void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) {
void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, const AmoebaInPlaneAngleForce& force) {
numAngles = force.getNumAngles();
for (int ii = 0; ii < numAngles; ii++) {
......@@ -166,20 +166,20 @@ void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System
angle.push_back( static_cast<RealOpenMM>( angleValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( k ) );
}
globalHarmonicInPlaneAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleCubic());
globalHarmonicInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleQuartic());
globalHarmonicInPlaneAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAnglePentic());
globalHarmonicInPlaneAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
globalInPlaneAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleCubic());
globalInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
globalInPlaneAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAnglePentic());
globalInPlaneAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleSextic());
}
double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
AmoebaReferenceHarmonicInPlaneAngleForce amoebaReferenceHarmonicInPlaneAngleForce;
RealOpenMM energy = amoebaReferenceHarmonicInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4,
angle, kQuadratic, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic,
globalHarmonicInPlaneAnglePentic, globalHarmonicInPlaneAngleSextic, forceData );
AmoebaReferenceInPlaneAngleForce amoebaReferenceInPlaneAngleForce;
RealOpenMM energy = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy( numAngles, posData, particle1, particle2, particle3, particle4,
angle, kQuadratic, globalInPlaneAngleCubic, globalInPlaneAngleQuartic,
globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData );
return static_cast<double>(energy);
}
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ c6ebf6e2
......@@ -35,21 +35,21 @@
namespace OpenMM {
/**
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaBondForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcAmoebaHarmonicBondForceKernel : public CalcAmoebaHarmonicBondForceKernel {
class ReferenceCalcAmoebaBondForceKernel : public CalcAmoebaBondForceKernel {
public:
ReferenceCalcAmoebaHarmonicBondForceKernel(std::string name,
ReferenceCalcAmoebaBondForceKernel(std::string name,
const Platform& platform,
System& system);
~ReferenceCalcAmoebaHarmonicBondForceKernel();
~ReferenceCalcAmoebaBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicBondForce this kernel will be used for
* @param force the AmoebaBondForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicBondForce& force);
void initialize(const System& system, const AmoebaBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -65,25 +65,25 @@ private:
std::vector<int> particle2;
std::vector<RealOpenMM> length;
std::vector<RealOpenMM> kQuadratic;
RealOpenMM globalHarmonicBondCubic;
RealOpenMM globalHarmonicBondQuartic;
RealOpenMM globalBondCubic;
RealOpenMM globalBondQuartic;
System& system;
};
/**
* This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcAmoebaHarmonicAngleForceKernel : public CalcAmoebaHarmonicAngleForceKernel {
class ReferenceCalcAmoebaAngleForceKernel : public CalcAmoebaAngleForceKernel {
public:
ReferenceCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, System& system);
~ReferenceCalcAmoebaHarmonicAngleForceKernel();
ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, System& system);
~ReferenceCalcAmoebaAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicAngleForce this kernel will be used for
* @param force the AmoebaAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicAngleForce& force);
void initialize(const System& system, const AmoebaAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -100,27 +100,27 @@ private:
std::vector<int> particle3;
std::vector<RealOpenMM> angle;
std::vector<RealOpenMM> kQuadratic;
RealOpenMM globalHarmonicAngleCubic;
RealOpenMM globalHarmonicAngleQuartic;
RealOpenMM globalHarmonicAnglePentic;
RealOpenMM globalHarmonicAngleSextic;
RealOpenMM globalAngleCubic;
RealOpenMM globalAngleQuartic;
RealOpenMM globalAnglePentic;
RealOpenMM globalAngleSextic;
System& system;
};
/**
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
class ReferenceCalcAmoebaInPlaneAngleForceKernel : public CalcAmoebaInPlaneAngleForceKernel {
public:
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system);
~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel();
ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system);
~ReferenceCalcAmoebaInPlaneAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
* @param force the AmoebaInPlaneAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force);
void initialize(const System& system, const AmoebaInPlaneAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -138,10 +138,10 @@ private:
std::vector<int> particle4;
std::vector<RealOpenMM> angle;
std::vector<RealOpenMM> kQuadratic;
RealOpenMM globalHarmonicInPlaneAngleCubic;
RealOpenMM globalHarmonicInPlaneAngleQuartic;
RealOpenMM globalHarmonicInPlaneAnglePentic;
RealOpenMM globalHarmonicInPlaneAngleSextic;
RealOpenMM globalInPlaneAngleCubic;
RealOpenMM globalInPlaneAngleQuartic;
RealOpenMM globalInPlaneAnglePentic;
RealOpenMM globalInPlaneAngleSextic;
System& system;
};
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.cpp → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.cpp
View file @ c6ebf6e2
......@@ -23,7 +23,7 @@
*/
#include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicAngleForce.h"
#include "AmoebaReferenceAngleForce.h"
using std::vector;
using OpenMM::RealVec;
......@@ -46,7 +46,7 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine,
RealOpenMM AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine,
RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
......@@ -62,7 +62,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
static const RealOpenMM five = 5.0;
static const RealOpenMM six = 6.0;
// static const std::string methodName = "AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine";
// static const std::string methodName = "AmoebaReferenceAngleForce::getPrefactorsGivenAngleCosine";
// ---------------------------------------------------------------------------------------
......@@ -96,7 +96,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy)
Calculate Amoeba angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
......@@ -113,7 +113,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::getPrefactorsGivenAngleCosine( Rea
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM AmoebaReferenceAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealVec& positionAtomC,
RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
......@@ -122,7 +122,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealVec&
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceHarmonicAngleForce::calculateHarmonicForce";
//static const std::string methodName = "AmoebaReferenceAngleForce::calculateAngleIxn";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
......@@ -183,7 +183,7 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealVec&
return energy;
}
RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
RealOpenMM AmoebaReferenceAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<int>& particle3,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.h → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.h
View file @ c6ebf6e2
......@@ -22,15 +22,15 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __AmoebaReferenceHarmonicAngleForce_H__
#define __AmoebaReferenceHarmonicAngleForce_H__
#ifndef __AmoebaReferenceAngleForce_H__
#define __AmoebaReferenceAngleForce_H__
#include "SimTKUtilities/RealVec.h"
#include <vector>
// ---------------------------------------------------------------------------------------
class AmoebaReferenceHarmonicAngleForce {
class AmoebaReferenceAngleForce {
public:
......@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicAngleForce( ){};
AmoebaReferenceAngleForce( ){};
/**---------------------------------------------------------------------------------------
......@@ -48,11 +48,11 @@ public:
--------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicAngleForce( ){};
~AmoebaReferenceAngleForce( ){};
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixns (force and energy)
Calculate Amoeba angle ixns (force and energy)
@param numBonds number of angles
@param posData particle positions
......@@ -78,10 +78,10 @@ public:
const std::vector<int>& particle3,
const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicAngleCubic,
RealOpenMM globalHarmonicAngleQuartic,
RealOpenMM globalHarmonicAnglePentic,
RealOpenMM globalHarmonicAngleSextic,
RealOpenMM globalAngleCubic,
RealOpenMM globalAngleQuartic,
RealOpenMM globalAnglePentic,
RealOpenMM globalAngleSextic,
std::vector<OpenMM::RealVec>& forceData ) const;
private:
......@@ -111,7 +111,7 @@ private:
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy)
Calculate Amoeba angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
......@@ -139,4 +139,4 @@ private:
// ---------------------------------------------------------------------------------------
#endif // _AmoebaReferenceHarmonicAngleForce___
#endif // _AmoebaReferenceAngleForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.cpp → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.cpp
View file @ c6ebf6e2
......@@ -22,7 +22,7 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "AmoebaReferenceHarmonicBondForce.h"
#include "AmoebaReferenceBondForce.h"
#include "AmoebaReferenceForce.h"
using std::vector;
......@@ -30,7 +30,7 @@ using OpenMM::RealVec;
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixn (force and energy)
Calculate Amoeba bond ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
......@@ -44,14 +44,14 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM AmoebaReferenceBondForce::calculateBondIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
RealOpenMM bondLength, RealOpenMM bondK,
RealOpenMM bondCubic, RealOpenMM bondQuartic,
RealVec* forces ) const {
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceHarmonicBondForce::calculateHarmonicForce";
//static const std::string methodName = "AmoebaReferenceBondForce::calculateBondIxn";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
......@@ -88,14 +88,14 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealVec& po
return energy;
}
RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBonds,
RealOpenMM AmoebaReferenceBondForce::calculateForceAndEnergy( int numBonds,
vector<RealVec>& particlePositions,
const std::vector<int>& particle1,
const std::vector<int>& particle2,
const std::vector<RealOpenMM>& length,
const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicBondCubic,
RealOpenMM globalHarmonicBondQuartic,
RealOpenMM globalBondCubic,
RealOpenMM globalBondQuartic,
vector<RealVec>& forceData ) const {
RealOpenMM energy = 0.0;
for( int ii = 0; ii < numBonds; ii++ ){
......@@ -106,7 +106,7 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBon
RealVec forces[2];
energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index],
bondLength, bondK, globalHarmonicBondCubic, globalHarmonicBondQuartic,
bondLength, bondK, globalBondCubic, globalBondQuartic,
forces );
for( int jj = 0; jj < 3; jj++ ){
......
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