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#include <cmath> #include <cmath> #include <cmath> #include <cmath>
#include <cstdlib> #include <cstdlib> #include <cstdlib> #include <cstdlib>
#include <fstream> #include <fstream> #include <fstream> #include <fstream>
#include <iostream> #include <iostream> #include <iostream> #include <iostream>
#include <string> #include <string> #include <string> #include <string>
using namespace std; using namespace std; using namespace std; using namespace std; using namespace std; using namespace std;
/********************************** /**********************************
Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D Basic MD of Lennard-Jonesium in 1D
**********************************/ **********************************/
/************************ /************************
declare global variables declare global variables declare global variables declare global variables declare global variables
************************/ ************************/
// values that stay fixed during the simulation
const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control) const int N = 36; // number of particles (integer for loop control)
const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths) const double dN = 36.; // number of particles (double for doing maths)
const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box const double L = 36.; // length of (1D) box
const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing const double a = L / dN; // lattice spacing
const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting) const int tsteps = 100; // number of time steps (integer for counting)
const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths) const double dtsteps = tsteps; // number of time steps (double for maths)
const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep const double dt = 0.01; // integration timestep
const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions const double rc = 18.; // distance cutoff for computing LJ interactions
const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared const double rc2 = rc * rc; // distance cutoff squared
const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6}) const double ecut = 4. * ((pow(rc,-12.)) - (pow(rc,-6.))); // value of LJ potential at r = rc: 4(1/rc^{12} - 1/rc^{6})
// values that change during the simulation
double en; // potential energy double en; // potential energy double en; // potential energy double en; // potential energy double en; // potential energy double en; // potential energy
double etot; // total energy (pot + kin) double etot; // total energy (pot + kin) double etot; // total energy (pot + kin) double etot; // total energy (pot + kin) double etot; // total energy (pot + kin) double etot; // total energy (pot + kin)
double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature double temp = 0.728; // temperature
// arrays for storing stuff
double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates double x[N]; // coordinates
double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates double xp[N]; // previous coordinates
double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities double v[N]; // velocities
double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces double f[N]; // forces
// store data for averaging
double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.; double sumTemp = 0.;
double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.; double sumEtot = 0.;
double temps[tsteps]; double temps[tsteps]; double temps[tsteps]; double temps[tsteps]; double temps[tsteps]; double temps[tsteps]; double temps[tsteps];
double etots[tsteps]; double etots[tsteps]; double etots[tsteps]; double etots[tsteps]; double etots[tsteps]; double etots[tsteps]; double etots[tsteps];
/********************* /*********************
function declarations function declarations function declarations
*********************/ *********************/
void void init(); (); ();
double double lattice_pos(int i); (int i); (int i); (int i); (int i); (int i);
void void force(); (); ();
void void integrate(int t); (int t); (int t); (int t); (int t); (int t);
void void printcoords(double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile); (double time, FILE* ofile);
void void statistics(FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile); (FILE* tfile, FILE* efile);
/********** /**********
MD program MD program MD program
**********/ **********/
int int main() { () { () { () {
//cout << "ecut = " << ecut << endl; //cout << "ecut = " << ecut << endl;
double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time double time = 0.; // initialise time
init(); // initialisation init(); // initialisation init(); // initialisation init(); // initialisation init(); // initialisation init(); // initialisation init(); // initialisation
// open coordinate output file // open coordinate output file
FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE; FILE * cfile = new FILE;
cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w"); cfile = fopen ("coords.xyz","w");
// open temperature output file // open temperature output file
FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE; FILE * tfile = new FILE;
tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w"); tfile = fopen ("temperature.dat","w");
fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature fprintf (tfile,"# time temperature\n"); "); ");
// open energy output file // open energy output file
FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE; FILE * efile = new FILE;
efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w"); efile = fopen ("energy.dat","w");
fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy fprintf (efile,"# time energy\n"); "); ");
// main MD loop // main MD loop
for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) { for (int t = 0; t < tsteps; t++) {

cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl; cout << "#---- Time = " << time << " ---- Steps = " << t << " ---- " << endl;
force(); // calculate forces force(); // calculate forces force(); // calculate forces force(); // calculate forces force(); // calculate forces force(); // calculate forces force(); // calculate forces
integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion integrate(t); // integrate equations of motion
// print current coordinates to file // print current coordinates to file
printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile); printcoords(time, cfile);
// print current temperature to file // print current temperature to file
fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f fprintf (tfile,"%10.10f %10.10f\n",time,temp); ",time,temp); ",time,temp); ",time,temp); ",time,temp); ",time,temp); ",time,temp);
// print current energy to file // print current energy to file
fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f fprintf (efile,"%10.10f %10.10f\n",time,etot); ",time,etot); ",time,etot); ",time,etot); ",time,etot); ",time,etot); ",time,etot);
time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt time += dt; // increase time by dt
} }
statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc statistics(tfile, efile); // calculate averages, SD, etc
// close output files // close output files
fclose(cfile); fclose(cfile); fclose(cfile); fclose(cfile); fclose(cfile); fclose(cfile);
fclose(tfile); fclose(tfile); fclose(tfile); fclose(tfile); fclose(tfile); fclose(tfile);
fclose(efile); fclose(efile); fclose(efile); fclose(efile); fclose(efile); fclose(efile);
}
/******************** /********************
1.1 of 3 2014.06.04 18:01:19
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/******************** /********************
function definitions function definitions function definitions
********************/ ********************/
// initialise positions and velocities
void void init() { () { () { () {
cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl; cout << endl << "#---- Initialising positions and velocities ----" << endl;
double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities double sumv = 0; // sum of velocities
double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared double sumv2 = 0; // sum of velocities squared
// loop over particles // loop over particles
for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) {
x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice x[i] = lattice_pos(i); // place particles on a lattice
v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5] v[i] = ((rand() % N) / dN) - 0.5; // assign velocities uniformly (but randomly) in range [-0.5,0.5]
sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities sumv += v[i]; // sum vlocities
sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities sumv2 += v[i]*v[i]; // sum squared velocities
} }
sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass sumv /= dN; // velocity centre of mass
sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity sumv2 /= dN; // mean-squared velocity
double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature double sf = sqrt(3. * temp / sumv2); // scale factor for velocities to achieve desired temperature
for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) {
v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities v[i] = (v[i] - sumv) * sf; // scale velocities
xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions xp[i] = x[i] - v[i] * dt; // set previous positions
} }
}
// place particle on a lattice
double double lattice_pos(int i) { (int i) { (int i) { (int i) { (int i) { (int i) { (int i) {

double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a; double pos = (i + 0.5) * a;
return pos; return pos; return pos; return pos; return pos;
}
// calculate forces
void void force() { () { () { () {
cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl; cout << endl << "#---- Calculating forces ----" << endl;
en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero en = 0; // (re)set energy to zero
// (re)set forces to zero // (re)set forces to zero
for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) {
f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0; f[i] = 0.0;
} }
// loop (inefficiently) over all pairs of atoms // loop (inefficiently) over all pairs of atoms
for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){ for (int i = 0; i < N-1; i++){
for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) { for (int j = i+1; j < N; j++) {
double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j double xr = x[i] - x[j]; // distance between atoms i and j
xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions xr -= L * rint(xr / L); // periodic boundary conditions
double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff double r2 = xr * xr; // square to compare to cutoff
if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff if (r2 < rc2) { // test cutoff
// compute Lennard-Jones interaction // compute Lennard-Jones interaction
double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2; double r2i = 1. / r2;
double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0); double r6i = pow(r2i, 3.0);
double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5); double ff = 48. * r2i * r6i * (r6i - 0.5);
// update forces // update forces
f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr; f[i] += ff * xr;
f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr; f[j] -= ff * xr;
// update energy // update energy
en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut; en += 4. * r6i * (r6i - 1.) - ecut;
} }
} }
} }
}
// integrate equations of motion
void void integrate(int t) { (int t) { (int t) { (int t) { (int t) { (int t) { (int t) {
cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl; cout << endl << "#---- Integrating equations of motion ----" << endl << endl;
double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0; double sumv = 0;
double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0; double sumv2 = 0;
for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) {
double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm double xx = 2. * x[i] - xp[i] + dt*dt*f[i]; // Verlet algorithm
double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity double vi = (xx - xp[i]) / (2. * dt); // velocity
sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass sumv += vi; // velocity centre of mass
sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy sumv2 += vi*vi; // total kinetic energy
xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions xp[i] = x[i]; // update previous positions
x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions x[i] = xx; // update current positions
} }
temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature temp = sumv2 / (3. * dN); // instantaneous temperature
// store for calculating SD // store for calculating SD
sumTemp += temp; sumTemp += temp; sumTemp += temp; sumTemp += temp; sumTemp += temp; sumTemp += temp; sumTemp += temp;
temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp; temps[t] = temp;
etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle etot = (en + 0.5 * sumv2) / dN; // total energy per particle
// store for calculating SD // store for calculating SD
sumEtot += etot; sumEtot += etot; sumEtot += etot; sumEtot += etot; sumEtot += etot; sumEtot += etot; sumEtot += etot;
etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot; etots[t] = etot;
}
// print coordinates
void void printcoords(double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) { (double time, FILE* cfile) {
fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d fprintf (cfile,"%d\n",N); ",N); ",N); ",N); ",N);
fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f fprintf (cfile,"time %10.10f\n",time); ",time); ",time); ",time); ",time);
for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) { for (int i = 0; i < N; i++) {
fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0 fprintf (cfile, "C %-8.8f 0.0 0.0\n",x[i]); ",x[i]); ",x[i]); ",x[i]); ",x[i]); ",x[i]); ",x[i]); ",x[i]);
} }
2.1 of 3 2014.06.04 18:01:19
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}
// calculate averages, etc and print to file
void void statistics(FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) { (FILE* tfile, FILE* efile) {
// averages // averages
double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps; double aveTemp = sumTemp / dtsteps;
double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps; double aveEtot = sumEtot / dtsteps;
// standard deviation // standard deviation
double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.; double varTemp = 0.;
double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.; double varEtot = 0.;
for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) { for (int i = 0; i < tsteps; i++) {
varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp); varTemp += (temps[i] - aveTemp)*(temps[i] - aveTemp);
varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot); varEtot += (etots[i] - aveEtot)*(etots[i] - aveEtot);
} }
double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps); double sdTemp = sqrt(varTemp / dtsteps);
double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps); double sdEtot = sqrt(varEtot / dtsteps);
fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f fprintf (tfile, "# Average temperature: %10.2f\n", aveTemp); ", aveTemp); ", aveTemp); ", aveTemp); ", aveTemp); ", aveTemp);
fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f fprintf (tfile, "# Standard deviation: %10.2f\n", sdTemp); ", sdTemp); ", sdTemp); ", sdTemp); ", sdTemp); ", sdTemp);
fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f fprintf (efile, "# Average total energy: %10.2f\n", aveEtot); ", aveEtot); ", aveEtot); ", aveEtot); ", aveEtot); ", aveEtot);
fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f fprintf (efile, "# Standard deviation: %10.2f\n", sdEtot); ", sdEtot); ", sdEtot); ", sdEtot); ", sdEtot); ", sdEtot);
}
3.1 of 3 2014.06.04 18:01:19