Skip to content

GitLab

Commit e763e1cd authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Mods

parent 003ef5cc
Hide whitespace changes
Inline Side-by-side
Showing with 123 additions and 15 deletions
platforms/brook/tests/TestBrookStream.cpp
View file @ e763e1cd
......@@ -46,6 +46,7 @@
#include "BrookNonBonded.h"
#include "OpenMMContext.h"
#include "CMMotionRemover.h"
#include "StandardMMForceField.h"
#include "GBSAOBCForceField.h"
#include "System.h"
......@@ -2176,15 +2177,16 @@ void testLangevinTemperature() {
// ReferencePlatform platform;
const double temp = 100.0;
//ReferencePlatform platform;
System system(numberOfAtoms, 0);
LangevinIntegrator integrator(temp, 2.0, 0.01);
LangevinIntegrator integrator(temp, 2.0, 0.001);
StandardMMForceField* forceField = new StandardMMForceField(numberOfAtoms, 0, 0, 0, 0);
for (int i = 0; i < numberOfAtoms; ++i){
system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; ++i)
......@@ -2193,26 +2195,43 @@ void testLangevinTemperature() {
// Let it equilibrate.
integrator.step(10);
exit(0);
//integrator.step(10000);
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double ke = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
State state = context.getState(State::Positions | State::Velocities | State::Energy);
ke += state.getKineticEnergy();
if( debug ){
(void) fprintf( log, "%s %d KE=%12.5e ttl=%12.5e\n", methodName.c_str(), i, state.getKineticEnergy(), ke ); fflush( log );
(void) fprintf( log, "%s %d KE=%12.5e ttl=%12.5e\n",
methodName.c_str(), i, state.getKineticEnergy(), ke );
/*
vector<Vec3> positions = state.getPositions();
vector<Vec3> velocities = state.getVelocities();
for( int ii = 0; ii < numberOfAtoms; ii++ ){
(void) fprintf( log, " %d q[%12.5e %12.5e %12.5e] v[%12.5e %12.5e %12.5e]\n", ii,
positions[ii][0], positions[ii][1], positions[ii][2],
velocities[ii][0], velocities[ii][1], velocities[ii][2] );
}
*/
(void)fflush( log );
}
integrator.step(1);
}
ke /= 1000;
double expected = 0.5*numberOfAtoms*3*BOLTZ*temp;
ASSERT_EQUAL_TOL(expected, ke, 3*expected/std::sqrt(1000.0));
double tol = 3*expected/std::sqrt(1000.0);
(void) fprintf( log, "%s ok\n", methodName.c_str() ); fflush( log );
(void) fprintf( log, "%s expected=%12.5e found=%12.5e tol=%12.5e ok\n", methodName.c_str(), expected, ke, tol ); fflush( log );
/*
/tests/AssertionUtilities.h
#define ASSERT_EQUAL_TOL(expected, found, tol){
double _scale_ = std::fabs(expected) > 1.0 ? std::fabs(expected) : 1.0;
if (std::fabs((expected)-(found))/_scale_ > (t ol)) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
ASSERT_EQUAL_TOL(expected, ke, tol );
*/
}
......@@ -2221,11 +2240,11 @@ void testLangevinConstraints() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "LangevinConstraints";
static const int debug = 1;
static const int debug = 0;
FILE* log = stdout;
int numberOfAtoms = 2;
RealOpenMM mass = 2.0;
RealOpenMM mass = 1.0;
// ---------------------------------------------------------------------------------------
......@@ -2238,15 +2257,19 @@ void testLangevinConstraints() {
const double temp = 100.0;
//ReferencePlatform platform;
System system(numAtoms, numAtoms-1);
LangevinIntegrator integrator(temp, 2.0, 0.01);
LangevinIntegrator integrator(temp, 2.0, 0.001);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0);
system.setAtomMass(i, mass);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numAtoms-1; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
vector<Vec3> velocities(numAtoms);
......@@ -2266,6 +2289,9 @@ void testLangevinConstraints() {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
if( debug ){
(void) fprintf( log, "%s %d %d dist=%12.5e %12.5e ok\n", methodName.c_str(), i, j, dist, fabs(dist-1.0) ); fflush( log );
}
ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
}
integrator.step(1);
......@@ -2299,6 +2325,9 @@ void testVerletSingleBond( void ){
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
......@@ -2369,6 +2398,82 @@ void testVerletSingleBond( void ){
(void) fflush( log );
}
void testVerletConstraints() {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testVerletConstraints";
static const int debug = 1;
FILE* log = stdout;
const int numAtoms = 8;
RealOpenMM mass = 2.0;
// ---------------------------------------------------------------------------------------
//BrookPlatform platform( 32, "cal", log );
ReferencePlatform platform;
System system(numAtoms, numAtoms/2);
VerletIntegrator integrator(0.0005);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 1.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
int index = 0;
for (int i = 0; i < numAtoms-1; i += 2){
//(void) fprintf( log, "%s %d %d %d\n", methodName.c_str(), index, i, i+1 ); fflush( log );
//system.setConstraintParameters(i, i, i+1, 1.0);
system.setConstraintParameters( index++, i, i+1, 1.0);
}
system.addForce(forceField);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numAtoms);
vector<Vec3> velocities(numAtoms);
init_gen_rand(0);
double scale = 0.01;
for (int i = 0; i < numAtoms; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3( scale*(genrand_real2()-0.5), scale*(genrand_real2()-0.5), scale*(genrand_real2()-0.5) );
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy);
for (int j = 0; j < numAtoms; j += 2) {
Vec3 p1 = state.getPositions()[j];
Vec3 p2 = state.getPositions()[j+1];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
if( debug ){
(void) fprintf( log, "%s %d %d dist=%12.5e diff=%12.5e\n", methodName.c_str(), i, j, dist, fabs( dist - 1.0) );
(void) fflush( log );
}
ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
}
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1){
initialEnergy = energy;
} else if (i > 0){
if( debug ){
(void) fprintf( log, "%s %d E=%12.5e Ecalc=%12.5e\n", methodName.c_str(), i, initialEnergy, energy );
}
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
}
integrator.step(1);
}
(void) fprintf( log, "%s ok\n", methodName.c_str() );
(void) fflush( log );
}
int main( ){
......@@ -2393,15 +2498,18 @@ int main( ){
testBrookLJ();
testBrookExclusionsAnd14();
testLangevinSingleBond();
*/
testLangevinTemperature();
testLangevinConstraints();
/*
testObcForce();
testObcSingleAtom();
testObcEConsistentForce();
testVerletSingleBond();
testLangevinConstraints();
*/
//testVerletSingleBond();
testVerletConstraints();
} catch( const exception& e ){
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment