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Commit a568bb12 authored by peastman's avatar peastman
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Deleted more debugging code

parent 162d69a2
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plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaAngleForce.cpp
View file @ a568bb12
......@@ -77,7 +77,7 @@ static void crossProductVector3( double* vectorX, double* vectorY, double* vecto
static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log ) {
double* dEdR, double* energyTerm ) {
double angle;
if( cosine >= 1.0 ){
......@@ -88,13 +88,6 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
angle = RADIAN*acos(cosine);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "getPrefactorsGivenAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealAngle );
(void) fflush( log );
}
#endif
double deltaIdeal = angle - idealAngle;
double deltaIdeal2 = deltaIdeal*deltaIdeal;
double deltaIdeal3 = deltaIdeal*deltaIdeal2;
......@@ -121,7 +114,7 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
}
static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy ) {
int particle1, particle2, particle3;
double idealAngle;
......@@ -133,14 +126,6 @@ static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions
double penticK = amoebaAngleForce.getAmoebaGlobalAnglePentic();
double sexticK = amoebaAngleForce.getAmoebaGlobalAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(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 );
}
#endif
double deltaR[2][3];
double r2_0 = 0.0;
double r2_1 = 0.0;
......@@ -163,17 +148,10 @@ static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions
double dot = deltaR[0][0]*deltaR[1][0] + deltaR[0][1]*deltaR[1][1] + deltaR[0][2]*deltaR[1][2];
double cosine = dot/sqrt(r2_0*r2_1);
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "dot=%10.3e r2_0=%10.3e r2_1=%10.3e\n", dot, r2_0, r2_1 );
(void) fflush( log );
}
#endif
double dEdR;
double energyTerm;
getPrefactorsGivenAngleCosine( cosine, idealAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log );
quarticK, penticK, sexticK, &dEdR, &energyTerm );
double termA = -dEdR/(r2_0*rp);
double termC = dEdR/(r2_1*rp);
......@@ -203,7 +181,7 @@ static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions
}
static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& amoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy ) {
// get positions and zero forces
......@@ -219,51 +197,30 @@ static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& amoeba
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaAngleForce.getNumAngles(); ii++ ){
computeAmoebaAngleForce(ii, positions, amoebaAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
computeAmoebaAngleForce(ii, positions, amoebaAngleForce, expectedForces, expectedEnergy );
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaAngleForce& amoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) {
double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaAngleForces( context, amoebaAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaAngleForces( context, amoebaAngleForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneAngle( FILE* log ) {
void testOneAngle() {
System system;
int numberOfParticles = 3;
......@@ -298,7 +255,7 @@ void testOneAngle( FILE* log ) {
positions[2] = Vec3(0, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle" );
// Try changing the angle parameters and make sure it's still correct.
......@@ -306,14 +263,14 @@ void testOneAngle( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle" );
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaAngleForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle" );
}
int main(int argc, char* argv[]) {
......@@ -322,8 +279,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testOneAngle( log );
testOneAngle();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaBondForce.cpp
View file @ a568bb12
......@@ -84,7 +84,7 @@ static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions,
}
static void computeAmoebaBondForces( Context& context, AmoebaBondForce& amoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy ) {
// get positions and zero forces
......@@ -102,47 +102,24 @@ static void computeAmoebaBondForces( Context& context, AmoebaBondForce& amoebaBo
for( int ii = 0; ii < amoebaBondForce.getNumBonds(); ii++ ){
computeAmoebaBondForce(ii, positions, amoebaBondForce, expectedForces, expectedEnergy );
}
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& amoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& amoebaBondForce, double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaBondForces( context, amoebaBondForce, expectedForces, &expectedEnergy, NULL );
computeAmoebaBondForces( context, amoebaBondForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneBond( FILE* log ) {
void testOneBond() {
System system;
......@@ -169,10 +146,10 @@ void testOneBond( FILE* log ) {
positions[1] = Vec3(0, 0, 0);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond" );
}
void testTwoBond( FILE* log ) {
void testTwoBond( ) {
System system;
......@@ -203,7 +180,7 @@ void testTwoBond( FILE* log ) {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond" );
// Try changing the bond parameters and make sure it's still correct.
......@@ -212,14 +189,14 @@ void testTwoBond( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond" );
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaBondForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond" );
}
int main(int argc, char* argv[]) {
......@@ -228,8 +205,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testTwoBond( log );
testTwoBond();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp
View file @ a568bb12
......@@ -273,7 +273,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
system.addForce(amoebaGeneralizedKirkwoodForce);
}
 
static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>& forces, double& energy, FILE* log) {
static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>& forces, double& energy) {
std::vector<Vec3> positions(context.getSystem().getNumParticles());
 
positions[0] = Vec3( 1.5927280e-01, 1.7000000e-06, 1.6491000e-03 );
......@@ -294,7 +294,7 @@ static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>&
// setup for villin
 
static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::PolarizationType polarizationType,
int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
int includeCavityTerm, std::vector<Vec3>& forces, double& energy ){
 
// beginning of Multipole setup
 
......@@ -6978,45 +6978,7 @@ static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Polari
 
static void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
const std::vector<Vec3>& expectedForces,
const std::vector<Vec3>& forces, double tolerance, FILE* log ) {
//#define AMOEBA_DEBUG
#ifdef AMOEBA_DEBUG
if( log ){
double conversion = 1.0/4.184;
double energyAbsDiff = fabs( expectedEnergy - energy );
double energyRelDiff = 2.0*energyAbsDiff/( fabs( expectedEnergy ) + fabs( energy ) + 1.0e-08 );
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e absDiff=%15.7e relDiff=%15.7e\n", testName.c_str(), conversion*expectedEnergy, conversion*energy,
conversion*energyAbsDiff, conversion*energyRelDiff );
if( conversion != 1.0 )conversion *= -0.1;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
double expectedNorm = sqrt( expectedForces[ii][0]*expectedForces[ii][0] +
expectedForces[ii][1]*expectedForces[ii][1] +
expectedForces[ii][2]*expectedForces[ii][2] );
double norm = sqrt( forces[ii][0]*forces[ii][0] + forces[ii][1]*forces[ii][1] + forces[ii][2]*forces[ii][2] );
double absDiff = fabs( norm - expectedNorm );
double relDiff = 2.0*absDiff/(fabs( norm ) + fabs( expectedNorm ) + 1.0e-08);
(void) fprintf( log, "%6u %15.7e %15.7e [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
conversion*absDiff, conversion*relDiff,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2], conversion*expectedNorm, conversion*norm );
}
(void) fflush( log );
conversion = 1.0;
(void) fprintf( log, "\n%s: expected energy=%14.7e %14.7e no conversion\n", testName.c_str(), conversion*expectedEnergy, conversion*energy );
if( conversion != 1.0 )conversion = -1.0;
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,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2] );
}
(void) fflush( log );
}
#endif
const std::vector<Vec3>& forces, double tolerance ) {
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
......@@ -7027,47 +6989,7 @@ static void compareForcesEnergy( std::string& testName, double expectedEnergy, d
 
static void compareForceNormsEnergy( std::string& testName, double expectedEnergy, double energy,
std::vector<Vec3>& expectedForces,
const std::vector<Vec3>& forces, double tolerance, FILE* log ) {
//#define AMOEBA_DEBUG
#ifdef AMOEBA_DEBUG
if( log ){
double conversion = 1.0/4.184;
double energyAbsDiff = fabs( expectedEnergy - energy );
double energyRelDiff = 2.0*energyAbsDiff/( fabs( expectedEnergy ) + fabs( energy ) + 1.0e-08 );
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e absDiff=%15.7e relDiff=%15.7e\n", testName.c_str(), conversion*expectedEnergy, conversion*energy,
conversion*energyAbsDiff, conversion*energyRelDiff );
if( conversion != 1.0 )conversion *= -0.1;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
double expectedNorm = sqrt( expectedForces[ii][0]*expectedForces[ii][0] +
expectedForces[ii][1]*expectedForces[ii][1] +
expectedForces[ii][2]*expectedForces[ii][2] );
double norm = sqrt( forces[ii][0]*forces[ii][0] + forces[ii][1]*forces[ii][1] + forces[ii][2]*forces[ii][2] );
double absDiff = fabs( (norm - expectedNorm) );
double relDiff = 2.0*absDiff/(fabs( norm ) + fabs( expectedNorm ) + 1.0e-08);
(void) fprintf( log, "%6u %15.7e %15.7e [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e] %15.7e %15.7e\n", ii,
fabs(conversion)*absDiff, relDiff,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2],
fabs(conversion)*expectedNorm, fabs(conversion)*norm );
}
(void) fflush( log );
conversion = 1.0;
(void) fprintf( log, "\n%s: expected energy=%14.7e %14.7e no conversion\n", testName.c_str(), conversion*expectedEnergy, conversion*energy );
if( conversion != 1.0 )conversion = -1.0;
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,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2] );
}
(void) fflush( log );
}
#endif
const std::vector<Vec3>& forces, double tolerance ) {
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
double expectedNorm = sqrt( expectedForces[ii][0]*expectedForces[ii][0] +
expectedForces[ii][1]*expectedForces[ii][1] +
......@@ -7096,7 +7018,7 @@ static void compareForceNormsEnergy( std::string& testName, double expectedEnerg
 
// test GK direct polarization for system comprised of two ammonia molecules
 
static void testGeneralizedKirkwoodAmmoniaDirectPolarization( FILE* log ) {
static void testGeneralizedKirkwoodAmmoniaDirectPolarization() {
 
std::string testName = "testGeneralizedKirkwoodAmmoniaDirectPolarization";
 
......@@ -7109,7 +7031,7 @@ static void testGeneralizedKirkwoodAmmoniaDirectPolarization( FILE* log ) {
setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Direct, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log );
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -7.6636680e+01;
......@@ -7124,12 +7046,12 @@ static void testGeneralizedKirkwoodAmmoniaDirectPolarization( FILE* log ) {
expectedForces[7] = Vec3( 9.7274235e+00, -6.3130458e+01, 1.4949024e+02 );
 
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
 
// test GK mutual polarization for system comprised of two ammonia molecules
 
static void testGeneralizedKirkwoodAmmoniaMutualPolarization( FILE* log ) {
static void testGeneralizedKirkwoodAmmoniaMutualPolarization() {
 
std::string testName = "testGeneralizedKirkwoodAmmoniaMutualPolarization";
 
......@@ -7142,7 +7064,7 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarization( FILE* log ) {
setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Mutual, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log );
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -7.8018875e+01;
......@@ -7157,13 +7079,13 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarization( FILE* log ) {
expectedForces[7] = Vec3( 5.3895456e+00, -7.7131137e+01, 1.5826273e+02 );
 
double tolerance = 2.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
 
// test GK mutual polarization for system comprised of two ammonia molecules
// including cavity term
 
static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE* log ) {
static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( ) {
 
std::string testName = "testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm";
 
......@@ -7176,7 +7098,7 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Mutual, 1);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log );
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -6.0434582e+01;
......@@ -7191,7 +7113,7 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
expectedForces[7] = Vec3( 7.9205382e+00, -7.3716473e+01, 1.5960993e+02 );
 
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance);
// Try changing the particle parameters and make sure it's still correct.
......@@ -7208,7 +7130,7 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
bool exceptionThrown = false;
try {
// This should throw an exception.
compareForcesEnergy(testName, state2.getPotentialEnergy(), state1.getPotentialEnergy(), state2.getForces(), state1.getForces(), tolerance, log);
compareForcesEnergy(testName, state2.getPotentialEnergy(), state1.getPotentialEnergy(), state2.getForces(), state1.getForces(), tolerance);
}
catch (std::exception ex) {
exceptionThrown = true;
......@@ -7216,12 +7138,12 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
ASSERT(exceptionThrown);
amoebaGeneralizedKirkwoodForce->updateParametersInContext(context);
state1 = context.getState(State::Forces | State::Energy);
compareForcesEnergy(testName, state2.getPotentialEnergy(), state1.getPotentialEnergy(), state2.getForces(), state1.getForces(), tolerance, log);
compareForcesEnergy(testName, state2.getPotentialEnergy(), state1.getPotentialEnergy(), state2.getForces(), state1.getForces(), tolerance);
}
 
// test GK direct polarization for villin system
 
static void testGeneralizedKirkwoodVillinDirectPolarization( FILE* log ) {
static void testGeneralizedKirkwoodVillinDirectPolarization( ) {
 
std::string testName = "testGeneralizedKirkwoodVillinDirectPolarization";
 
......@@ -7229,7 +7151,7 @@ static void testGeneralizedKirkwoodVillinDirectPolarization( FILE* log ) {
std::vector<Vec3> forces;
double energy;
 
setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Direct, 0, forces, energy, log );
setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Direct, 0, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -8.4281157e+03;
......@@ -7840,12 +7762,12 @@ static void testGeneralizedKirkwoodVillinDirectPolarization( FILE* log ) {
}
 
double tolerance = 1.0e-05;
compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance);
}
 
// test GK mutual polarization for villin system
 
static void testGeneralizedKirkwoodVillinMutualPolarization( FILE* log ) {
static void testGeneralizedKirkwoodVillinMutualPolarization( ) {
 
std::string testName = "testGeneralizedKirkwoodVillinMutualPolarization";
 
......@@ -7853,7 +7775,7 @@ static void testGeneralizedKirkwoodVillinMutualPolarization( FILE* log ) {
std::vector<Vec3> forces;
double energy;
 
setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Mutual, 0, forces, energy, log );
setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Mutual, 0, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -8.6477811e+03;
......@@ -8464,7 +8386,7 @@ static void testGeneralizedKirkwoodVillinMutualPolarization( FILE* log ) {
}
 
double tolerance = 1.0e-05;
compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForceNormsEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
 
int main(int argc, char* argv[]) {
......@@ -8474,17 +8396,15 @@ int main(int argc, char* argv[]) {
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
 
FILE* log = NULL;
// test direct and mutual polarization cases and
// mutual polarization w/ the cavity term
 
testGeneralizedKirkwoodAmmoniaDirectPolarization( log );
testGeneralizedKirkwoodAmmoniaMutualPolarization( log );
testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( log );
testGeneralizedKirkwoodAmmoniaDirectPolarization();
testGeneralizedKirkwoodAmmoniaMutualPolarization();
testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm();
 
testGeneralizedKirkwoodVillinDirectPolarization( log );
testGeneralizedKirkwoodVillinMutualPolarization( log );
testGeneralizedKirkwoodVillinDirectPolarization();
testGeneralizedKirkwoodVillinMutualPolarization();
 
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaInPlaneAngleForce.cpp
View file @ a568bb12
......@@ -78,7 +78,7 @@ static double dotVector3( double* vectorX, double* vectorY ){
static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInPlaneAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log ) {
double* dEdR, double* energyTerm ) {
double angle;
if( cosine >= 1.0 ){
......@@ -89,13 +89,6 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
angle = RADIAN*acos(cosine);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "getPrefactorsGivenInPlaneAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealInPlaneAngle );
(void) fflush( log );
}
#endif
double deltaIdeal = angle - idealInPlaneAngle;
double deltaIdeal2 = deltaIdeal*deltaIdeal;
double deltaIdeal3 = deltaIdeal*deltaIdeal2;
......@@ -122,7 +115,7 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
}
static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy ) {
int particle1, particle2, particle3, particle4;
double idealInPlaneAngle;
......@@ -134,14 +127,6 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
double penticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic();
double sexticK = amoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic();
#ifdef AMOEBA_DEBUG
if( log ){
(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 );
}
#endif
// T = AD x CD
// P = B + T*delta
// AP = A - P
......@@ -181,14 +166,6 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
double rAp2 = dotVector3( deltaR[AP], deltaR[AP] );
double rCp2 = dotVector3( deltaR[CP], deltaR[CP] );
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log );
}
#endif
return;
}
crossProductVector3( deltaR[CP], deltaR[AP], deltaR[M] );
......@@ -205,7 +182,7 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
double dEdR;
double energyTerm;
getPrefactorsGivenInPlaneAngleCosine( cosine, idealInPlaneAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log );
quarticK, penticK, sexticK, &dEdR, &energyTerm );
double termA = -dEdR/(rAp2*rm);
double termC = dEdR/(rCp2*rm);
......@@ -280,7 +257,7 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
}
static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy ) {
// get positions and zero forces
......@@ -296,50 +273,26 @@ static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngl
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaInPlaneAngleForce(ii, positions, amoebaInPlaneAngleForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
computeAmoebaInPlaneAngleForce(ii, positions, amoebaInPlaneAngleForce, expectedForces, expectedEnergy);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaInPlaneAngleForce& amoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaInPlaneAngleForces( context, amoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log );
computeAmoebaInPlaneAngleForces( context, amoebaInPlaneAngleForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneAngle( FILE* log ) {
void testOneAngle() {
System system;
int numberOfParticles = 4;
......@@ -375,7 +328,7 @@ void testOneAngle( FILE* log ) {
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle" );
// Try changing the angle parameters and make sure it's still correct.
......@@ -383,14 +336,14 @@ void testOneAngle( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle" );
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaInPlaneAngleForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle" );
}
int main(int argc, char* argv[]) {
......@@ -399,8 +352,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testOneAngle( NULL );
testOneAngle();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaOutOfPlaneBendForce.cpp
View file @ a568bb12
......@@ -78,7 +78,7 @@ static double dotVector3( double* vectorX, double* vectorY ){
static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>& positions, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy ) {
double kAngleCubic = amoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendCubic();
......@@ -90,14 +90,6 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>&
double kAngleQuadratic;
amoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters(bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic );
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bond %d [%d %d %d %d] k=[%10.3e %10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic, kAngleCubic, kAngleQuartic, kAnglePentic, kAngleSextic );
(void) fflush( log );
}
#endif
enum { A, B, C, D, LastAtomIndex };
enum { AB, CB, DB, AD, CD, LastDeltaIndex };
......@@ -138,14 +130,6 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>&
} else {
angle = RADIAN*acos(cosine);
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bkk2=%14.7e rDB2=%14.7e cos=%14.7e dt=%14.7e]\n",
bkk2, rDB2, cosine, angle );
(void) fflush( log );
}
#endif
// chain rule
......@@ -242,7 +226,7 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>&
}
static void computeAmoebaOutOfPlaneBendForces( Context& context, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy ) {
// get positions and zero forces
......@@ -258,51 +242,26 @@ static void computeAmoebaOutOfPlaneBendForces( Context& context, AmoebaOutOfPlan
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaOutOfPlaneBendForce.getNumOutOfPlaneBends(); ii++ ){
computeAmoebaOutOfPlaneBendForce(ii, positions, amoebaOutOfPlaneBendForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: 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] );
}
(void) fflush( log );
computeAmoebaOutOfPlaneBendForce(ii, positions, amoebaOutOfPlaneBendForce, expectedForces, expectedEnergy);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
double tolerance, const std::string& idString, FILE* log) {
double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaOutOfPlaneBendForces( context, amoebaOutOfPlaneBendForce, expectedForces, &expectedEnergy, log );
computeAmoebaOutOfPlaneBendForces( context, amoebaOutOfPlaneBendForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: 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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneOutOfPlaneBend( FILE* log ) {
void testOneOutOfPlaneBend( ) {
System system;
int numberOfParticles = 4;
......@@ -334,7 +293,7 @@ void testOneOutOfPlaneBend( FILE* log ) {
positions[3] = Vec3( 0.245568230E+02, 0.250215290E+02, 0.796852800E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend");
// Try changing the bend parameters and make sure it's still correct.
......@@ -342,17 +301,17 @@ void testOneOutOfPlaneBend( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend");
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaOutOfPlaneBendForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend");
}
void testOneOutOfPlaneBend2( FILE* log, int setId ) {
void testOneOutOfPlaneBend2(int setId ) {
System system;
int numberOfParticles = 4;
......@@ -436,21 +395,10 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
particleIndices.push_back( 442 );
kOutOfPlaneBend = 0.214755281E-01;
} else {
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "Set id %d not recognized.\n", setId );
}
#endif
std::stringstream buffer;
buffer << "Set id " << setId << " not recognized.";
throw OpenMMException( buffer.str() );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "Set id %d.\n", setId );
}
#endif
amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
system.addForce(amoebaOutOfPlaneBendForce);
......@@ -459,12 +407,6 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
if( coordinates.find( particleIndices[ii] ) == coordinates.end() ){
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "Coordinates %d not loaded.", particleIndices[ii] );
}
#endif
std::stringstream buffer;
buffer << "Coordinates " << particleIndices[ii] << " not loaded.";
throw OpenMMException( buffer.str() );
......@@ -473,7 +415,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
}
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend");
static int iter = 0;
static std::map<int,Vec3> totalForces;
......@@ -496,7 +438,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
std::vector<Vec3> forces;
forces.resize( numberOfParticles );
double energy;
computeAmoebaOutOfPlaneBendForce( 0, positions, *amoebaOutOfPlaneBendForce, forces, &energy, log );
computeAmoebaOutOfPlaneBendForce( 0, positions, *amoebaOutOfPlaneBendForce, forces, &energy);
totalEnergy += energy;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
......@@ -504,22 +446,6 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
totalForces[particleIndices[ii]][jj] += forces[ii][jj];
}
}
if( iter == 6 ){
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: energy=%14.7e\n", totalEnergy);
for( std::map<int,Vec3>::iterator ii = totalForces.begin(); ii != totalForces.end(); ii++ ){
int particleIndex = ii->first;
Vec3 forces = ii->second;
(void) fprintf( log, "%6d [%14.7e %14.7e %14.7e] \n", particleIndex,
forces[0], forces[1], forces[2] );
}
(void) fflush( log );
}
#endif
}
}
int main(int argc, char* argv[]) {
......@@ -528,9 +454,8 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testOneOutOfPlaneBend( log );
testOneOutOfPlaneBend();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPiTorsionForce.cpp
View file @ a568bb12
......@@ -78,21 +78,13 @@ static double dotVector3( double* vectorX, double* vectorY ){
static void computeAmoebaPiTorsionForce(int bondIndex, std::vector<Vec3>& positions, AmoebaPiTorsionForce& amoebaPiTorsionForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy) {
int particle1, particle2, particle3, particle4, particle5, particle6;
double kTorsion;
amoebaPiTorsionForce.getPiTorsionParameters(bondIndex, particle1, particle2, particle3, particle4, particle5, particle6, kTorsion);
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaPiTorsionForce: bond %d [%d %d %d %d %d %d] k=%10.3e\n",
bondIndex, particle1, particle2, particle3, particle4, particle5, particle6, kTorsion );
(void) fflush( log );
}
#endif
enum { AD, BD, EC, FC, P, Q, CP, DC, QD, T, U, TU, DP, QC, dT, dU, dP, dQ, dC1, dC2, dD1, dD2, LastDeltaIndex };
double deltaR[LastDeltaIndex][3];
......@@ -213,7 +205,7 @@ static void computeAmoebaPiTorsionForce(int bondIndex, std::vector<Vec3>& posit
}
static void computeAmoebaPiTorsionForces( Context& context, AmoebaPiTorsionForce& amoebaPiTorsionForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy ) {
// get positions and zero forces
......@@ -229,50 +221,27 @@ static void computeAmoebaPiTorsionForces( Context& context, AmoebaPiTorsionForce
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaPiTorsionForce.getNumPiTorsions(); ii++ ){
computeAmoebaPiTorsionForce(ii, positions, amoebaPiTorsionForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaPiTorsionForces: 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] );
}
(void) fflush( log );
computeAmoebaPiTorsionForce(ii, positions, amoebaPiTorsionForce, expectedForces, expectedEnergy);
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaPiTorsionForce& amoebaPiTorsionForce,
double tolerance, const std::string& idString, FILE* log) {
double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaPiTorsionForces( context, amoebaPiTorsionForce, expectedForces, &expectedEnergy, log );
computeAmoebaPiTorsionForces( context, amoebaPiTorsionForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaPiTorsionForces: 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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOnePiTorsion( FILE* log ) {
void testOnePiTorsion() {
System system;
int numberOfParticles = 6;
......@@ -301,7 +270,7 @@ void testOnePiTorsion( FILE* log ) {
positions[5] = Vec3( 0.254124630E+02, 0.234691880E+02, 0.773335400E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion", log );
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion");
// Try changing the torsion parameters and make sure it's still correct.
......@@ -309,14 +278,14 @@ void testOnePiTorsion( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion", log );
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion");
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaPiTorsionForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion", log );
compareWithExpectedForceAndEnergy( context, *amoebaPiTorsionForce, TOL, "testOnePiTorsion" );
}
int main(int argc, char* argv[]) {
......@@ -325,8 +294,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testOnePiTorsion( log );
testOnePiTorsion();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaStretchBendForce.cpp
View file @ a568bb12
......@@ -79,21 +79,13 @@ static double dotVector3( double* vectorX, double* vectorY ){
static void computeAmoebaStretchBendForce(int bondIndex, std::vector<Vec3>& positions, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
std::vector<Vec3>& forces, double* energy) {
int particle1, particle2, particle3;
double abBondLength, cbBondLength, angleStretchBend, kStretchBend, k2StretchBend;
amoebaStretchBendForce.getStretchBendParameters(bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend, k2StretchBend);
angleStretchBend *= RADIAN;
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: bond %d [%d %d %d] ab=%10.3e cb=%10.3e angle=%10.3e k1=%10.3e k2=%10.3e\n",
bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend, k2StretchBend );
(void) fflush( log );
}
#endif
enum { A, B, C, LastAtomIndex };
enum { AB, CB, CBxAB, ABxP, CBxP, LastDeltaIndex };
......@@ -188,18 +180,10 @@ static void computeAmoebaStretchBendForce(int bondIndex, std::vector<Vec3>& pos
forces[particle3][2] -= subForce[2][2];
*energy += dt*drkk;
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: angle=%10.3e dt=%10.3e dr=%10.3e\n", angle, dt, dr );
(void) fflush( log );
}
#endif
return;
}
static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
std::vector<Vec3>& expectedForces, double* expectedEnergy) {
// get positions and zero forces
......@@ -215,50 +199,26 @@ static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendF
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaStretchBendForce.getNumStretchBends(); ii++ ){
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: 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] );
}
(void) fflush( log );
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy );
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
double tolerance, const std::string& idString, FILE* log) {
double tolerance, const std::string& idString) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaStretchBendForces( context, amoebaStretchBendForce, expectedForces, &expectedEnergy, log );
computeAmoebaStretchBendForces( context, amoebaStretchBendForce, expectedForces, &expectedEnergy );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: 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] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneStretchBend( FILE* log ) {
void testOneStretchBend() {
System system;
int numberOfParticles = 3;
......@@ -288,7 +248,7 @@ void testOneStretchBend( FILE* log ) {
positions[2] = Vec3( 0.269573220E+02, 0.236108860E+02, 0.216376800E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend" );
// Try changing the stretch-bend parameters and make sure it's still correct.
......@@ -296,14 +256,14 @@ void testOneStretchBend( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend" );
}
catch (std::exception ex) {
exceptionThrown = true;
}
ASSERT(exceptionThrown);
amoebaStretchBendForce->updateParametersInContext(context);
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend", log );
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend" );
}
int main(int argc, char* argv[]) {
......@@ -312,8 +272,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testOneStretchBend( log );
testOneStretchBend();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp
View file @ a568bb12
......@@ -2584,7 +2584,7 @@ TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
return grids[gridIndex];
}
void testTorsionTorsion( FILE* log, int systemId ) {
void testTorsionTorsion(int systemId) {
System system;
int numberOfParticles = 6;
......@@ -2660,19 +2660,6 @@ void testTorsionTorsion( FILE* log, int systemId ) {
forces[ii][1] *= conversion;
forces[ii][2] *= conversion;
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaTorsionTorsionForces: 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] );
}
(void) fflush( log );
}
#endif
double tolerance = 1.0e-03;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
......@@ -2687,8 +2674,7 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testTorsionTorsion( log, 1 );
testTorsionTorsion(1);
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaVdwForce.cpp
View file @ a568bb12
......@@ -57,7 +57,7 @@ extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-4;
void testVdw( FILE* log ) {
void testVdw() {
System system;
int numberOfParticles = 6;
......@@ -159,18 +159,6 @@ void testVdw( FILE* log ) {
forces[ii][2] *= conversion;
}
expectedEnergy *= CalToJoule;
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaVdwForces: 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] );
}
(void) fflush( log );
}
#endif
double tolerance = 1.0e-03;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
......@@ -208,7 +196,7 @@ void testVdw( FILE* log ) {
}
void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, const std::string& epsilonCombiningRule, double cutoff,
double boxDimension, std::vector<Vec3>& forces, double& energy, FILE* log ){
double boxDimension, std::vector<Vec3>& forces, double& energy){
// beginning of Vdw setup
......@@ -343,24 +331,7 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
std::vector<Vec3>& expectedForces,
std::vector<Vec3>& forces, double tolerance, FILE* log ) {
#define AMOEBA_DEBUG
#ifdef AMOEBA_DEBUG
if( log ){
double conversion = 1.0/4.184;
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e\n", testName.c_str(), conversion*expectedEnergy, conversion*energy );
conversion *= -0.1;
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,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2] );
}
(void) fflush( log );
}
#endif
std::vector<Vec3>& forces, double tolerance) {
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
......@@ -369,7 +340,7 @@ void compareForcesEnergy( std::string& testName, double expectedEnergy, double e
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
void testVdwAmmoniaCubicMeanHhg( FILE* log ) {
void testVdwAmmoniaCubicMeanHhg() {
std::string testName = "testVdwAmmoniaCubicMeanHhg";
......@@ -379,7 +350,7 @@ void testVdwAmmoniaCubicMeanHhg( FILE* log ) {
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.8012258e+00;
......@@ -394,12 +365,12 @@ void testVdwAmmoniaCubicMeanHhg( FILE* log ) {
expectedForces[7] = Vec3( 1.6756544e+00, 3.2497316e-01, -1.7906832e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
void testVdwAmmoniaArithmeticArithmetic( FILE* log ) {
void testVdwAmmoniaArithmeticArithmetic() {
std::string testName = "testVdwAmmoniaArithmeticArithmetic";
......@@ -409,7 +380,7 @@ void testVdwAmmoniaArithmeticArithmetic( FILE* log ) {
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "ARITHMETIC", "ARITHMETIC", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "ARITHMETIC", "ARITHMETIC", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.2252403e+00;
......@@ -424,12 +395,12 @@ void testVdwAmmoniaArithmeticArithmetic( FILE* log ) {
expectedForces[7] = Vec3( 2.3761408e+00, 4.6871961e-01, -2.4731607e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
// test VDW w/ sigmaRule=Geometric and epsilonRule=Geometric
void testVdwAmmoniaGeometricGeometric( FILE* log ) {
void testVdwAmmoniaGeometricGeometric( ) {
std::string testName = "testVdwAmmoniaGeometricGeometric";
......@@ -438,7 +409,7 @@ void testVdwAmmoniaGeometricGeometric( FILE* log ) {
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "GEOMETRIC", "GEOMETRIC", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "GEOMETRIC", "GEOMETRIC", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 2.5249914e+00;
......@@ -453,10 +424,10 @@ void testVdwAmmoniaGeometricGeometric( FILE* log ) {
expectedForces[7] = Vec3( 1.8109211e+00, 3.5273117e-01, -1.9224723e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
void testVdwAmmoniaCubicMeanHarmonic( FILE* log ) {
void testVdwAmmoniaCubicMeanHarmonic( ) {
std::string testName = "testVdwAmmoniaCubicMeanHarmonic";
......@@ -465,7 +436,7 @@ void testVdwAmmoniaCubicMeanHarmonic( FILE* log ) {
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HARMONIC", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HARMONIC", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 4.1369069e+00;
......@@ -480,14 +451,14 @@ void testVdwAmmoniaCubicMeanHarmonic( FILE* log ) {
expectedForces[7] = Vec3( 1.5080748e+00, 2.9058422e-01, -1.6274118e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
// test w/ cutoff=0.25 nm; single ixn between two particles (0 and 6); force nonzero on
// particle 4 due to reduction applied to NH
// the distance between 0 and 6 is ~ 0.235 so the ixn is in the tapered region
void testVdwTaper( FILE* log ) {
void testVdwTaper( ) {
std::string testName = "testVdwTaper";
......@@ -497,7 +468,7 @@ void testVdwTaper( FILE* log ) {
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 3.5478444e+00;
......@@ -512,12 +483,12 @@ void testVdwTaper( FILE* log ) {
expectedForces[7] = Vec3( -0.0000000e+00, -0.0000000e+00, -0.0000000e+00 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
// test PBC
void testVdwPBC( FILE* log ) {
void testVdwPBC( ) {
std::string testName = "testVdwPBC";
......@@ -527,7 +498,7 @@ void testVdwPBC( FILE* log ) {
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy, log );
setupAndGetForcesEnergyVdwAmmonia( "CUBIC-MEAN", "HHG", cutoff, boxDimension, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = 1.4949141e+01;
......@@ -545,14 +516,14 @@ void testVdwPBC( FILE* log ) {
// if tapering turned off, then absolute difference < 2.0e-05
double tolerance = 5.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
}
// create box of 216 water molecules
void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, const std::string& epsilonCombiningRule, double cutoff,
double boxDimension, int includeVdwDispersionCorrection,
std::vector<Vec3>& forces, double& energy, FILE* log ){
std::vector<Vec3>& forces, double& energy ){
// beginning of Vdw setup
......@@ -1271,7 +1242,7 @@ void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, con
// test employing box of 216 water molecules w/ and w/o dispersion correction
void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
void testVdwWater( int includeVdwDispersionCorrection ) {
std::string testName;
......@@ -1287,7 +1258,7 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyVdwWater( "CUBIC-MEAN", "HHG", cutoff, boxDimension, includeVdwDispersionCorrection, forces, energy, log );
setupAndGetForcesEnergyVdwWater( "CUBIC-MEAN", "HHG", cutoff, boxDimension, includeVdwDispersionCorrection, forces, energy );
std::vector<Vec3> expectedForces(numberOfParticles);
// initialize expected energy and forces
......@@ -1952,7 +1923,7 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
// if tapering turned off, then absolute difference < 2.0e-05
double tolerance = 5.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
// test sigma/epsilon rules for dispersion correction
......@@ -1975,7 +1946,7 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
expectedEnergies.push_back( 3.2774624e+03 );
for( unsigned int ii = 0; ii < sigmaRules.size(); ii++ ){
setupAndGetForcesEnergyVdwWater( sigmaRules[ii], epsilonRules[ii], cutoff, boxDimension, includeVdwDispersionCorrection, forces, energy, log );
setupAndGetForcesEnergyVdwWater( sigmaRules[ii], epsilonRules[ii], cutoff, boxDimension, includeVdwDispersionCorrection, forces, energy );
testName = "testVdwWaterWithDispersionCorrection_" + sigmaRules[ii] + '_' + epsilonRules[ii];
ASSERT_EQUAL_TOL_MOD( expectedEnergies[ii], energy, tolerance, testName );
}
......@@ -2045,48 +2016,47 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
testVdw( log );
testVdw();
// tests using two ammonia molecules
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
testVdwAmmoniaCubicMeanHhg( log );
testVdwAmmoniaCubicMeanHhg();
// test VDW w/ sigmaRule=Arithmetic and epsilonRule=Arithmetic
testVdwAmmoniaArithmeticArithmetic( log );
testVdwAmmoniaArithmeticArithmetic();
// test VDW w/ sigmaRule=Geometric and epsilonRule=Geometric
testVdwAmmoniaGeometricGeometric( log );
testVdwAmmoniaGeometricGeometric();
// test VDW w/ sigmaRule=CubicMean and epsilonRule=Harmonic
testVdwAmmoniaCubicMeanHarmonic( log );
testVdwAmmoniaCubicMeanHarmonic();
// test w/ cutoff=0.25 nm; single ixn between two particles (0 and 6); force nonzero on
// particle 4 due to reduction applied to NH
// the distance between 0 and 6 is ~ 0.235 so the ixn is in the tapered region
testVdwTaper( log );
testVdwTaper();
// test PBC
testVdwPBC( log );
testVdwPBC();
// tests based on box of water
int includeVdwDispersionCorrection = 0;
testVdwWater( includeVdwDispersionCorrection, log );
testVdwWater( includeVdwDispersionCorrection);
// includes tests for various combinations of sigma/epsilon rules
// when computing vdw dispersion correction
includeVdwDispersionCorrection = 1;
testVdwWater( includeVdwDispersionCorrection, log );
testVdwWater( includeVdwDispersionCorrection);
// test triclinic boxes
......
plugins/amoeba/platforms/cuda/tests/TestCudaWcaDispersionForce.cpp
View file @ a568bb12
......@@ -56,19 +56,7 @@ extern "C" void registerAmoebaCudaKernelFactories();
void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
const std::vector<Vec3>& expectedForces,
const std::vector<Vec3>& forces, double tolerance, FILE* log ) {
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e\n", testName.c_str(), expectedEnergy, energy );
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] );
}
(void) fflush( log );
}
#endif
const std::vector<Vec3>& forces, double tolerance) {
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
......@@ -77,7 +65,7 @@ void compareForcesEnergy( std::string& testName, double expectedEnergy, double e
// test Wca dispersion
void testWcaDispersionAmmonia( FILE* log ) {
void testWcaDispersionAmmonia() {
std::string testName = "testWcaDispersionAmmonia";
......@@ -151,7 +139,7 @@ void testWcaDispersionAmmonia( FILE* log ) {
expectedForces[7] = Vec3( -1.1888087e+00, 1.2889802e+00, -3.8615387e-01 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance );
// Try changing the particle parameters and make sure it's still correct.
......@@ -168,7 +156,7 @@ void testWcaDispersionAmmonia( FILE* log ) {
bool exceptionThrown = false;
try {
// This should throw an exception.
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance, log);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance);
}
catch (std::exception ex) {
exceptionThrown = true;
......@@ -176,7 +164,7 @@ void testWcaDispersionAmmonia( FILE* log ) {
ASSERT(exceptionThrown);
amoebaWcaDispersionForce->updateParametersInContext(context);
state1 = context.getState(State::Forces | State::Energy);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance, log);
compareForcesEnergy(testName, state1.getPotentialEnergy(), state2.getPotentialEnergy(), state1.getForces(), state2.getForces(), tolerance);
}
int main(int argc, char* argv[]) {
......@@ -185,11 +173,10 @@ int main(int argc, char* argv[]) {
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
FILE* log = NULL;
// test Wca dispersion force using two ammonia molecules
testWcaDispersionAmmonia( log );
testWcaDispersionAmmonia();
} catch(const std::exception& e) {
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp
View file @ a568bb12
......@@ -60,14 +60,6 @@ void testSerialization() {
stringstream buffer;
XmlSerializer::serialize<AmoebaGeneralizedKirkwoodForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("GeneralizedKirkwood.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaGeneralizedKirkwoodForce* copy = XmlSerializer::deserialize<AmoebaGeneralizedKirkwoodForce>(buffer);
// Compare the two forces to see if they are identical.
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ a568bb12
......@@ -99,13 +99,6 @@ void testSerialization() {
stringstream buffer;
XmlSerializer::serialize<AmoebaMultipoleForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("Multipole.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaMultipoleForce* copy = XmlSerializer::deserialize<AmoebaMultipoleForce>(buffer);
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp
View file @ a568bb12
......@@ -94,14 +94,6 @@ void testSerialization() {
stringstream buffer;
XmlSerializer::serialize<AmoebaTorsionTorsionForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("TorsionTorsion.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaTorsionTorsionForce* copy = XmlSerializer::deserialize<AmoebaTorsionTorsionForce>(buffer);
// Compare the two force1s to see if they are identical.
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp
View file @ a568bb12
......@@ -65,14 +65,6 @@ void testSerialization() {
stringstream buffer;
XmlSerializer::serialize<AmoebaVdwForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("Vdw.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
// Compare the two forces to see if they are identical.
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp
View file @ a568bb12
......@@ -62,14 +62,6 @@ void testSerialization() {
stringstream buffer;
XmlSerializer::serialize<AmoebaWcaDispersionForce>(&force1, "Force", buffer);
#ifdef AMOEBA_DEBUG
if( 0 ){
FILE* filePtr = fopen("WcaDispersion.xml", "w" );
(void) fprintf( filePtr, "%s", buffer.str().c_str() );
(void) fclose( filePtr );
}
#endif
AmoebaWcaDispersionForce* copy = XmlSerializer::deserialize<AmoebaWcaDispersionForce>(buffer);
// Compare the two forces to see if they are identical.
......
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