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) { 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; }