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;
}
