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Commit c44c956d authored by peastman's avatar peastman
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Deleted lots of debugging code

parent 41cd79a5
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plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp
View file @ c44c956d
......@@ -275,7 +275,7 @@ 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);
......@@ -296,7 +296,7 @@ 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
 
......@@ -6980,44 +6980,7 @@ static void setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Polariz
 
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);
......@@ -7029,47 +6992,7 @@ static void compareForcesEnergy(std::string& testName, double expectedEnergy, do
 
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] +
......@@ -7098,7 +7021,7 @@ static void compareForceNormsEnergy(std::string& testName, double expectedEnergy
 
// test GK direct polarization for system comprised of two ammonia molecules
 
static void testGeneralizedKirkwoodAmmoniaDirectPolarization(FILE* log) {
static void testGeneralizedKirkwoodAmmoniaDirectPolarization() {
 
std::string testName = "testGeneralizedKirkwoodAmmoniaDirectPolarization";
 
......@@ -7111,7 +7034,7 @@ 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("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log);
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -7.6636680e+01;
......@@ -7126,12 +7049,12 @@ 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";
 
......@@ -7144,7 +7067,7 @@ 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("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log);
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -7.8018875e+01;
......@@ -7159,13 +7082,13 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarization(FILE* log) {
expectedForces[7] = Vec3( 5.3895456e+00, -7.7131137e+01, 1.5826273e+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
// including cavity term
 
static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm(FILE* log) {
static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm() {
 
std::string testName = "testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm";
 
......@@ -7180,7 +7103,7 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm(FILE*
ASSERT(!system.usesPeriodicBoundaryConditions());
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy, log);
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> expectedForces(numberOfParticles);
 
double expectedEnergy = -6.0434582e+01;
......@@ -7195,7 +7118,7 @@ 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.
......@@ -7212,7 +7135,7 @@ 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;
......@@ -7220,12 +7143,12 @@ 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";
 
......@@ -7233,7 +7156,7 @@ 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;
......@@ -7844,12 +7767,12 @@ 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";
 
......@@ -7857,7 +7780,7 @@ 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;
......@@ -8468,7 +8391,7 @@ 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 numberOfArguments, char* argv[]) {
......@@ -8477,16 +8400,14 @@ int main(int numberOfArguments, char* argv[]) {
std::cout << "TestReferenceAmoebaGeneralizedKirkwoodForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
 
FILE* log = NULL;
// test direct and mutual polarization cases and
// mutual polarization w/ the cavity term
 
testGeneralizedKirkwoodAmmoniaMutualPolarization(log);
testGeneralizedKirkwoodAmmoniaDirectPolarization(log);
testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm(log);
testGeneralizedKirkwoodVillinDirectPolarization(log);
testGeneralizedKirkwoodVillinMutualPolarization(log);
testGeneralizedKirkwoodAmmoniaMutualPolarization();
testGeneralizedKirkwoodAmmoniaDirectPolarization();
testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm();
testGeneralizedKirkwoodVillinDirectPolarization();
testGeneralizedKirkwoodVillinMutualPolarization();
 
}
catch(const std::exception& e) {
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp
View file @ c44c956d
......@@ -79,7 +79,7 @@ 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) {
......@@ -91,12 +91,6 @@ static void getPrefactorsGivenInPlaneAngleCosine(double cosine, double idealInPl
else {
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;
......@@ -124,7 +118,7 @@ static void getPrefactorsGivenInPlaneAngleCosine(double cosine, double idealInPl
}
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;
......@@ -135,13 +129,6 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& po
double quarticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic();
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
......@@ -182,12 +169,6 @@ 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;
}
......@@ -205,7 +186,7 @@ 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);
......@@ -281,7 +262,7 @@ 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
......@@ -297,40 +278,19 @@ static void computeAmoebaInPlaneAngleForces(Context& context, AmoebaInPlaneAngle
*expectedEnergy = 0.0;
for (int ii = 0; ii < AmoebaInPlaneAngleForce.getNumAngles(); ii++) {
computeAmoebaInPlaneAngleForce(ii, positions, AmoebaInPlaneAngleForce, expectedForces, expectedEnergy, log);
computeAmoebaInPlaneAngleForce(ii, positions, AmoebaInPlaneAngleForce, expectedForces, expectedEnergy);
}
#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);
}
#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);
......@@ -338,7 +298,7 @@ void compareWithExpectedForceAndEnergy(Context& context, AmoebaInPlaneAngleForce
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOneAngle(FILE* log) {
void testOneAngle() {
System system;
int numberOfParticles = 4;
......@@ -376,7 +336,7 @@ 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.
......@@ -384,14 +344,14 @@ 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 numberOfArguments, char* argv[]) {
......@@ -399,16 +359,7 @@ int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
//FILE* log = stderr;
//FILE* log = fopen("AmoebaInPlaneAngleForce.log", "w");;
testOneAngle(NULL);
#ifdef AMOEBA_DEBUG
if (log && log != stderr)
(void) fclose(log);
#endif
testOneAngle();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp
View file @ c44c956d
......@@ -79,7 +79,7 @@ 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>&
int particle1, particle2, particle3, particle4;
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 };
......@@ -141,13 +133,6 @@ 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
......@@ -244,7 +229,7 @@ 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
......@@ -260,41 +245,19 @@ static void computeAmoebaOutOfPlaneBendForces(Context& context, AmoebaOutOfPlane
*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);
......@@ -302,7 +265,7 @@ void compareWithExpectedForceAndEnergy(Context& context, AmoebaOutOfPlaneBendFor
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOneOutOfPlaneBend(FILE* log) {
void testOneOutOfPlaneBend() {
System system;
int numberOfParticles = 4;
......@@ -336,7 +299,7 @@ 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.
......@@ -344,17 +307,17 @@ 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;
......@@ -444,20 +407,10 @@ void testOneOutOfPlaneBend2(FILE* log, int setId) {
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);
......@@ -467,11 +420,6 @@ void testOneOutOfPlaneBend2(FILE* log, int setId) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(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());
......@@ -480,7 +428,7 @@ 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;
......@@ -503,7 +451,7 @@ 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 < static_cast<unsigned int>(numberOfParticles); ii++) {
......@@ -511,22 +459,6 @@ 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 numberOfArguments, char* argv[]) {
......@@ -534,21 +466,11 @@ int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
//FILE* log = stderr;
FILE* log = NULL;
//FILE* log = fopen("AmoebaOutOfPlaneBendForce.log", "w");;
testOneOutOfPlaneBend(log);
//testOneOutOfPlaneBend2(log, atoi(argv[1]));
testOneOutOfPlaneBend();
//testOneOutOfPlaneBend2(atoi(argv[1]));
//for (int ii = 1; ii <= 6; ii++) {
// testOneOutOfPlaneBend2(log, ii);
// testOneOutOfPlaneBend2(ii);
//}
#ifdef AMOEBA_DEBUG
if (log && log != stderr)
(void) fclose(log);
#endif
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.cpp
View file @ c44c956d
......@@ -78,19 +78,12 @@ 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];
......@@ -212,7 +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
......@@ -228,40 +221,19 @@ 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);
......@@ -269,7 +241,7 @@ void compareWithExpectedForceAndEnergy(Context& context, AmoebaPiTorsionForce& a
ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), tolerance);
}
void testOnePiTorsion(FILE* log) {
void testOnePiTorsion() {
System system;
int numberOfParticles = 6;
......@@ -300,7 +272,7 @@ 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.
......@@ -308,14 +280,14 @@ 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 numberOfArguments, char* argv[]) {
......@@ -323,16 +295,7 @@ int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaPiTorsionForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
//FILE* log = stderr;
//FILE* log = fopen("AmoebaPiTorsionForce1.log", "w");;
testOnePiTorsion(log);
#ifdef AMOEBA_DEBUG
if (log && log != stderr)
(void) fclose(log);
#endif
testOnePiTorsion();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.cpp
View file @ c44c956d
......@@ -80,20 +80,13 @@ 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 };
......@@ -189,18 +182,10 @@ 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
......@@ -216,48 +201,26 @@ static void computeAmoebaStretchBendForces(Context& context, AmoebaStretchBendFo
*expectedEnergy = 0.0;
for (int ii = 0; ii < amoebaStretchBendForce.getNumStretchBends(); ii++) {
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy, log);
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy);
}
#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);
}
#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;
......@@ -289,7 +252,7 @@ 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.
......@@ -297,14 +260,14 @@ 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 numberOfArguments, char* argv[]) {
......@@ -312,16 +275,7 @@ int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
FILE* log = NULL;
//FILE* log = stderr;
//FILE* log = fopen("AmoebaStretchBendForce1.log", "w");;
testOneStretchBend(log);
#ifdef AMOEBA_DEBUG
if (log && log != stderr)
(void) fclose(log);
#endif
testOneStretchBend();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp
View file @ c44c956d
......@@ -57,7 +57,7 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
const double TOL = 1e-4;
void testVdw(FILE* log) {
void testVdw() {
System system;
int numberOfParticles = 6;
......@@ -162,17 +162,6 @@ void testVdw(FILE* log) {
}
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);
......@@ -210,7 +199,7 @@ 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
......@@ -353,24 +342,7 @@ void setupAndGetForcesEnergyVdwAmmonia(const std::string& sigmaCombiningRule, co
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);
}
......@@ -379,7 +351,7 @@ void compareForcesEnergy(std::string& testName, double expectedEnergy, double en
// test VDW w/ sigmaRule=CubicMean and epsilonRule=HHG
void testVdwAmmoniaCubicMeanHhg(FILE* log) {
void testVdwAmmoniaCubicMeanHhg() {
std::string testName = "testVdwAmmoniaCubicMeanHhg";
......@@ -389,7 +361,7 @@ 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;
......@@ -404,12 +376,12 @@ 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";
......@@ -419,7 +391,7 @@ 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;
......@@ -434,12 +406,12 @@ 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";
......@@ -448,7 +420,7 @@ 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;
......@@ -463,10 +435,10 @@ 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";
......@@ -475,7 +447,7 @@ 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;
......@@ -490,14 +462,14 @@ 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";
......@@ -507,7 +479,7 @@ 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;
......@@ -522,12 +494,12 @@ 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";
......@@ -537,7 +509,7 @@ 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;
......@@ -555,14 +527,14 @@ 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
......@@ -1282,7 +1254,7 @@ void setupAndGetForcesEnergyVdwWater(const std::string& sigmaCombiningRule, cons
// 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;
......@@ -1299,7 +1271,7 @@ 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
......@@ -1965,7 +1937,7 @@ 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
......@@ -1988,7 +1960,7 @@ 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);
}
......@@ -2057,49 +2029,46 @@ int main(int numberOfArguments, char* argv[]) {
try {
std::cout << "TestReferenceAmoebaVdwForce running test..." << std::endl;
registerAmoebaReferenceKernelFactories();
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
......
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