void System::removeTotalMomentum()
{
StatisticsSampler sampler;
vector<double> momentum = sampler.calculateTotalMomentum(shared_from_this());
if(numberOfAtoms() > 0) {
momentum[0] /= numberOfAtoms();
momentum[1] /= numberOfAtoms();
momentum[2] /= numberOfAtoms();
}
atomManager().atoms().iterate([&](Atom &atom) {
atom.velocity[0] -= momentum[0]*atom.type()->massInverse();
atom.velocity[1] -= momentum[1]*atom.type()->massInverse();
atom.velocity[2] -= momentum[2]*atom.type()->massInverse();
});
}
std::ostream& operator<<(std::ostream &stream, System &system) {
StatisticsSampler sampler;
stream << "System information:" << endl;
stream << "Length [Å]: " << UnitConverter::lengthToAngstroms(system.systemLength()) << endl;
stream << "Number of atoms: " << system.numberOfAtoms() << endl;
stream << "Number of ghost atoms: " << system.numberOfGhostAtoms() << endl;
stream << "Potentials (" << system.potentials().size() << "): " << endl;
for(Potential *potential : system.potentials()) {
stream << " " << potential->name() << endl;
}
std::shared_ptr<System> system_ptr(&system);
vector<double> momentum = sampler.calculateTotalMomentum(system_ptr);
stream << "Total momentum: (" << momentum.at(0) << "," << momentum.at(1) << "," << momentum.at(2) << ")";
return stream;
}
int main() {
double dt = UnitConverter::timeFromSI(1e-14);
System system;
VelocityVerlet *integrator = new VelocityVerlet();
//EulerCromer *integrator = new EulerCromer();
system.setIntegrator(integrator);
system.createFCCLattice(5, UnitConverter::lengthFromAngstroms(5.26), 700.0);
system.removeMomentum();
LennardJones *potential = new LennardJones(3.405, 1.);
system.setPotential(potential);
StatisticsSampler statisticsSampler;
Thermostat thermostat(&statisticsSampler, &system);
thermostat.setThermostat(false);
Neighbourlists neighbourlist(&system);
IO *output = new IO();
output->open((char *)"output.dat");
IO *movie = new IO();
movie->open((char *)"movie.xyz");
movie->saveState(system);
for(int timestep=0; timestep<1000; timestep++) {
system.step(dt, thermostat, neighbourlist);
statisticsSampler.sample(system);
movie->saveState(system);
//if(timestep % 10 == 0) {
output->saveOutput(system, statisticsSampler);
//}
if(timestep % 100 == 0) {
cout << timestep << endl;
}
}
statisticsSampler.getEnergyVariance();
cout << "The standard deviation of the energy is:" << statisticsSampler.energyTotalVariance << endl;
movie->close();
output->close();
return 0;
}
int main(int numberOfArguments, char **argumentList)
{
omp_set_num_threads(8); // initialize OpenMP
//DEFAULT PARAMETERS:
int numberOfUnitCells = 5;
double initialTemperature = UnitConverter::temperatureFromSI(1500.0); // measured in Kelvin
double latticeConstant = UnitConverter::lengthFromAngstroms(5.26); // measured in angstroms
double dt = UnitConverter::timeFromSI(1e-15); // measured in seconds
// USER DEFINED PARAMETERS:
if(numberOfArguments > 1) numberOfUnitCells = atoi(argumentList[1]);
if(numberOfArguments > 2) initialTemperature = UnitConverter::temperatureFromSI(atof(argumentList[2]));
if(numberOfArguments > 3) latticeConstant = UnitConverter::lengthFromAngstroms(atof(argumentList[3]));
if(numberOfArguments > 4) dt = UnitConverter::timeFromSI(atof(argumentList[4]));
// PRINT DIMENSION SCALING FACTORS:
cout << "One unit of length is " << UnitConverter::lengthToSI(1.0) << " meters" << endl;
cout << "One unit of velocity is " << UnitConverter::velocityToSI(1.0) << " meters/second" << endl;
cout << "One unit of time is " << UnitConverter::timeToSI(1.0) << " seconds" << endl;
cout << "One unit of mass is " << UnitConverter::massToSI(1.0) << " kg" << endl;
cout << "One unit of temperature is " << UnitConverter::temperatureToSI(1.0) << " K" << endl;
for(double T = UnitConverter::temperatureFromSI(100.0); T < UnitConverter::temperatureFromSI(3000.0); T += UnitConverter::temperatureFromSI(100.0)){
// CREATE AND INITIALIZE THE LATTICE:
System system;
bool NoBoundaries = 0; // flag to tigger boundary conditions
system.createFCCLattice(numberOfUnitCells, latticeConstant, T);
system.setPotential(new LennardJones(UnitConverter::lengthFromAngstroms(3.405),
UnitConverter::temperatureFromSI(119.8)));
system.setIntegrator(new VelocityVerlet());
system.removeTotalMomentum();
StatisticsSampler statisticsSampler;
/*
IO movie, data;
movie.open("movie.xyz", 1);
data.open("data.txt", 0);
movie.saveState(&system);
cout << "Timestep Time Temperature KineticEnergy PotentialEnergy TotalEnergy" << endl;
for(int timestep=0; timestep<20000; timestep++) {
if(NoBoundaries) system.stepNoBoundaries(dt);
else system.step(dt);
statisticsSampler.sample(system);
data.saveStatistcalData(&system, &statisticsSampler);
if( !(timestep % 100) ) {
cout << system.steps() << " "
<< UnitConverter::timeToSI(system.time()) << " "
<< UnitConverter::temperatureToSI(statisticsSampler.temperature()) << " "
<< statisticsSampler.kineticEnergy() << " "
<< statisticsSampler.potentialEnergy() << " "
<< statisticsSampler.totalEnergy()<< " "
<< statisticsSampler.diffusionConstant()<< " "
<< statisticsSampler.pressure()<< " "
<< statisticsSampler.momentum()
<< endl;
movie.saveState(&system);
}
}
movie.close(1);
data.close(0);
*/
double N = 3000;
for(int timestep=0; timestep<N; timestep++) {
system.step(dt);
}
double D = 0.0;
double D2 = 0.0;
for(int timestep=0; timestep<N; timestep++) {
system.step(dt);
statisticsSampler.sample(system);
D+=statisticsSampler.diffusionConstant();
D2+=statisticsSampler.diffusionConstant()*statisticsSampler.diffusionConstant();
}
D2 = sqrt(D2/N - D/N*D/N);
printf("%.f, %.15f, %.15f\n", UnitConverter::temperatureToSI(statisticsSampler.temperature()),
UnitConverter::diffusionToSI(D/N),
UnitConverter::diffusionToSI(D2));
}
return 0;
}
int main(int numberOfArguments, char **argumentList)
{
//omp_set_num_threads(8); // initialize OpenMP
//DEFAULT PARAMETERS:
int numberOfUnitCells = 10;
double initialTemperature = UnitConverter::temperatureFromSI(300.0); // measured in Kelvin
double latticeConstant = UnitConverter::lengthFromAngstroms(5.26); // measured in angstroms
double dt = UnitConverter::timeFromSI(1e-15); // measured in seconds
// USER DEFINED PARAMETERS:
if(numberOfArguments > 1) numberOfUnitCells = atoi(argumentList[1]);
if(numberOfArguments > 2) initialTemperature = UnitConverter::temperatureFromSI(atof(argumentList[2]));
if(numberOfArguments > 3) latticeConstant = UnitConverter::lengthFromAngstroms(atof(argumentList[3]));
if(numberOfArguments > 4) dt = UnitConverter::timeFromSI(atof(argumentList[4]));
// PRINT DIMENSION SCALING FACTORS:
cout << "One unit of length is " << UnitConverter::lengthToSI(1.0) << " meters" << endl;
cout << "One unit of velocity is " << UnitConverter::velocityToSI(1.0) << " meters/second" << endl;
cout << "One unit of time is " << UnitConverter::timeToSI(1.0) << " seconds" << endl;
cout << "One unit of mass is " << UnitConverter::massToSI(1.0) << " kg" << endl;
cout << "One unit of temperature is " << UnitConverter::temperatureToSI(1.0) << " K" << endl;
// CREATE AND INITIALIZE THE LATTICE:
System system;
system.createFCCLattice(numberOfUnitCells, latticeConstant, initialTemperature);
double sigma = UnitConverter::lengthFromAngstroms(3.405);
double epsilon = UnitConverter::temperatureFromSI(119.8);
system.setPotential(new LennardJones(sigma, epsilon));
system.potential()->rCut = 2.5*sigma;
system.potential()->rShell = 0.3*sigma;
system.setIntegrator(new VelocityVerlet());
system.setThermostat(new Thermostat(UnitConverter::timeFromSI(1e-13),
UnitConverter::temperatureFromSI(300.0)));
system.removeTotalMomentum();
system.thermostat()->setOff();
int numberOfTimesteps = 2000;
StatisticsSampler statisticsSampler;
IO movie, data;
movie.open("movie.xyz", 1);
data.open("data.txt", 0);
movie.saveState(&system);
cout << "Timestep Time Temperature KineticEnergy PotentialEnergy"
<< "TotalEnergy DiffusionK Pressure Momentum" << endl;
for(int timestep=0; timestep<numberOfTimesteps; timestep++) {
system.step(dt);
statisticsSampler.sample(system);
data.saveStatistcalData(&system, &statisticsSampler);
if( !(timestep % 100) ) {
cout << system.steps() << " "
<< UnitConverter::timeToSI(system.time()) << " "
<< UnitConverter::temperatureToSI(statisticsSampler.temperature()) << " "
<< statisticsSampler.kineticEnergy() << " "
<< statisticsSampler.potentialEnergy() << " "
<< statisticsSampler.totalEnergy()<< " "
<< statisticsSampler.diffusionConstant()<< " "
<< UnitConverter::pressureToSI(statisticsSampler.pressure())<< " "
<< statisticsSampler.momentum()
<< endl;
movie.saveState(&system);
}
}
movie.close(1);
data.close(0);
return 0;
}
int main(int numberOfArguments, char **argumentList)
{
clock_t executionTimeStart, executionTimeFinish;
executionTimeStart = clock();
int numberOfUnitCells = 5;
double initialTemperature = UnitConverter::temperatureFromSI(2000.0); // measured in Kelvin
double latticeConstant = UnitConverter::lengthFromAngstroms(5.26); // measured in angstroms
double dt = UnitConverter::timeFromSI(5e-15); // Measured in seconds
int integratorNumber = 2; //initially set to Velocity Verlet, 1 is Euler-Cromer
int numberOfTimesteps = 1000;
// If a first argument is provided, it is the number of unit cells
if(numberOfArguments > 1) numberOfUnitCells = atoi(argumentList[1]);
// If a second argument is provided, it is the initial temperature (measured in MD units)
if(numberOfArguments > 2) initialTemperature = atof(argumentList[2]);
// If a third argument is provided, it is the lattice constant determining the density (measured in MD units)
if(numberOfArguments > 3) latticeConstant = atof(argumentList[3]);
// If a fourth argument is provided, it is the time step length dt (measured in MD units)
if(numberOfArguments > 4) dt = atof(argumentList[4]);
// If a fifth argument is provided, it is the integrator number
if(numberOfArguments > 5) integratorNumber = atoi(argumentList[5]);
// If a sixth argument is provided, it is the number of timesteps
if(numberOfArguments > 6) numberOfTimesteps = atoi(argumentList[6]);
/* // Possible to print the MD units used in the simulation
cout << "One unit of length is " << UnitConverter::lengthToSI(1.0) << " meters" << endl;
cout << "One unit of velocity is " << UnitConverter::velocityToSI(1.0) << " meters/second" << endl;
cout << "One unit of time is " << UnitConverter::timeToSI(1.0) << " seconds" << endl;
cout << "One unit of mass is " << UnitConverter::massToSI(1.0) << " kg" << endl;
cout << "One unit of temperature is " << UnitConverter::temperatureToSI(1.0) << " K" << endl;
*/
System system;
system.createFCCLattice(numberOfUnitCells, latticeConstant, initialTemperature);
system.setPotential(new LennardJones(3.405, 1.0));
if(integratorNumber == 1) system.setIntegrator(new EulerCromer());
else if(integratorNumber == 2) system.setIntegrator(new VelocityVerlet());
system.removeTotalMomentum();
StatisticsSampler statisticsSampler;
IO statisticsFile; // To write statistics to file for plotting
IO movie; // To write the state to file to look at in Ovito
if(numberOfArguments > 5){ // making unique filenames for plotting with python
string filenameStatistics = "run_plot_python_output/statistics_file_NrOfCells" + to_string(numberOfUnitCells) + "_T" + to_string(int(initialTemperature*1000)) + "_b" + to_string(int(latticeConstant*1000)) + "_dt" + to_string(int(dt*10000)) + "_int" + to_string(integratorNumber) + ".txt";
statisticsFile.open(filenameStatistics.c_str());
string filenameMovie = "run_plot_python_output/movie_NrOfCells" + to_string(numberOfUnitCells) + "_T" + to_string(int(initialTemperature*1000)) + "_b" + to_string(int(latticeConstant*1000)) + "_dt" + to_string(int(dt*10000)) + "_int" + to_string(integratorNumber) + ".xyz";
movie.open(filenameMovie.c_str());
}
else{
statisticsFile.open("statistics_file.txt");
movie.open("movie.xyz");
}
cout << "Timestep Time Temperature KineticEnergy PotentialEnergy TotalEnergy DiffusionConstant MeanSquareDisplacement" << endl;
for(int timestep=0; timestep<numberOfTimesteps; timestep++) {
//movie.saveState(&system); //including also the starting position in the movie, uncomment to write to movie file
system.step(dt); //moving the particle one step
statisticsSampler.sample(system);
statisticsFile.saveStatistics(&system, &statisticsSampler, 0); //output done here
if( !(timestep % 100) ) {
// Print the timestep every 100 timesteps
cout << system.steps() << " " << system.time() << " " << statisticsSampler.temperature() << " " << statisticsSampler.kineticEnergy() << " " << statisticsSampler.potentialEnergy() << " " << statisticsSampler.totalEnergy() << " " << statisticsSampler.diffusionConstant() << " " << statisticsSampler.meanSquareDisplacement() << endl;
}
}
movie.close();
executionTimeFinish = clock();
double totalExecutionTime = (( executionTimeFinish - executionTimeStart )/double(CLOCKS_PER_SEC ));
cout << "Execution time: " << totalExecutionTime << endl;
statisticsFile.saveStatistics(&system, &statisticsSampler, totalExecutionTime);
statisticsFile.close();
return 0;
}