void test_connect_pipe() {
IO* lhs = IO::allocate(state, G(io));
IO* rhs = IO::allocate(state, G(io));
TS_ASSERT(IO::connect_pipe(state, lhs, rhs)->true_p());
TS_ASSERT_EQUALS(Fixnum::from(0), lhs->lineno());
TS_ASSERT_EQUALS(Fixnum::from(0), rhs->lineno());
TS_ASSERT(kind_of<IOBuffer>(lhs->ibuffer()));
TS_ASSERT(kind_of<IOBuffer>(rhs->ibuffer()));
int acc_mode = fcntl(lhs->to_fd(), F_GETFL);
TS_ASSERT(acc_mode >= 0);
TS_ASSERT_EQUALS(Fixnum::from(acc_mode), lhs->mode());
acc_mode = fcntl(rhs->to_fd(), F_GETFL);
TS_ASSERT(acc_mode >= 0);
TS_ASSERT_EQUALS(Fixnum::from(acc_mode), rhs->mode());
lhs->close(state);
rhs->close(state);
}
void test_connect_pipe() {
IO* lhs = IO::allocate(state, G(io));
IO* rhs = IO::allocate(state, G(io));
TS_ASSERT(IO::connect_pipe(state, lhs, rhs)->true_p());
TS_ASSERT_EQUALS(Fixnum::from(0), lhs->lineno());
TS_ASSERT_EQUALS(Fixnum::from(0), rhs->lineno());
TS_ASSERT(kind_of<IOBuffer>(lhs->ibuffer()));
TS_ASSERT(kind_of<IOBuffer>(rhs->ibuffer()));
TS_ASSERT_EQUALS(Fixnum::from(O_RDONLY), lhs->mode());
TS_ASSERT_EQUALS(Fixnum::from(O_WRONLY), rhs->mode());
rhs->write(state, String::create(state, "hello"), 0);
Object* obj = lhs->blocking_read(state, Fixnum::from(5));
TS_ASSERT(kind_of<String>(obj));
String* str = try_as<String>(obj);
TS_ASSERT_EQUALS(std::string("hello"), str->c_str(state));
lhs->close(state);
rhs->close(state);
}
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;
}
