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#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <math.h>
#include "atoms.h"
#include "header.h"

#define XMUL 2
#define YMUL 1
#define ZMUL 4
#define N 100

#define TEMP 350.0

const double sqrt2 = 1.4142135623730950488016887242097;
const double sqrt3 = 1.7320508075688772935274463415059;
const double kB = 1.380658E-23;
const double RMo2 = (double)RAND_MAX / 2.0;

int main()
{
    Headerinfo tempheader;
    Atom* allatoms;
    int currentatom;
    int numatoms;
    FILE* file;
    int i,j,k,l,n;
    double currentT;
    double vMul;
    double netmx,netmy,netmz;
    double a;

    file = fopen("infile.atm", "wb");
    if(file == NULL)
    {
            printf("Failed to open infile.atm for writing\n\n");
            exit(6);
    }

    numatoms = (2+6*N)*XMUL*YMUL*ZMUL;

    allatoms = (Atom*)malloc(numatoms*sizeof(Atom));
    if(allatoms == NULL)
    {
            printf("unable to allocate memory for allatoms\n\n");
            fclose(file);
            exit(5);
    }

    /*srand((unsigned int)time(NULL));*/
    srand(2197);

    a = (elements[(enum AtomTypes)H].radius + elements[(enum AtomTypes)C].radius) * 2.0 / sqrt3;

    netmx = netmy = netmz = 0.0;
    currentT = 0.0;
    tempheader.iterations = 1000000;
    tempheader.mincutoff = 10.0 * a;
    tempheader.dt = 1.0E-15;
    tempheader.bigX = a + 6.4 * (double)XMUL * a + a*(double)N;
    tempheader.bigY = a + 8.4 * (double)YMUL * a + a*(double)N;
    tempheader.bigZ = a + 7.8 * (double)ZMUL * a + a*(double)(N/4);
    tempheader.T = TEMP;
    tempheader.desiredT = TEMP;
    tempheader.numatoms = numatoms;

    currentatom = 0;
    for(i=0; i<XMUL; i++)
    {
            for(j=0; j<YMUL; j++)
            {
                    for(k=0; k<ZMUL; k++)
                    {
                            allatoms[currentatom].type = C;
                            allatoms[currentatom].x = 2.0 * a + 6.4 * (double)i * a;
                            allatoms[currentatom].y = 2.0 * a + 8.4 * (double)j * a;
                            allatoms[currentatom].z = 2.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4);
                            allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                            allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                            allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                            allatoms[currentatom].ax = 0.0;
                            allatoms[currentatom].ay = 0.0;
                            allatoms[currentatom].az = 0.0;
                            allatoms[currentatom].ndx = 0.0;
                            allatoms[currentatom].ndy = 0.0;
                            allatoms[currentatom].ndz = 0.0;
                            allatoms[currentatom].potential = 0.0;
                            allatoms[currentatom].newpotential = 0.0;
                            for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                            allatoms[currentatom].bonds[0] = 1;
                            allatoms[currentatom].bonds[1] = 2;
                            allatoms[currentatom].bonds[2] = 3;
                            allatoms[currentatom].bonds[3] = 4;
                            currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                            netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                            netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                            netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                            currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 1.5 * a + 6.4 * (double)i * a;
                           allatoms[currentatom].y = 1.5 * a + 8.4 * (double)j * a;
                           allatoms[currentatom].z = 1.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -1;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 1.5 * a + 6.4 * (double)i * a;
                           allatoms[currentatom].y = 2.5 * a + 8.4 * (double)j * a;
                           allatoms[currentatom].z = 2.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -2;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 2.5 * a + 6.4 * (double)i * a;
                           allatoms[currentatom].y = 1.5 * a + 8.4 * (double)j * a;
                           allatoms[currentatom].z = 2.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -3;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           for(n=0; n<N-1; n++)
                           {
                                   allatoms[currentatom].type = C;
                                   allatoms[currentatom].x = 2.5 * a + 6.4 * (double)i * a + a*n;
                                   allatoms[currentatom].y = 2.5 * a + 8.4 * (double)j * a + a*n;
                                   allatoms[currentatom].z = 1.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -4;
                                   allatoms[currentatom].bonds[1] = 1;
                                   allatoms[currentatom].bonds[2] = 2;
                                   allatoms[currentatom].bonds[3] = 3;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;

                                   allatoms[currentatom].type = H;
                                   allatoms[currentatom].x = 2.0 * a + 6.4 * (double)i * a + a*n;
                                   allatoms[currentatom].y = 3.0 * a + 8.4 * (double)j * a + a*n;
                                   allatoms[currentatom].z = 1.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -1;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;

                                   allatoms[currentatom].type = H;
                                   allatoms[currentatom].x = 3.0 * a + 6.4 * (double)i * a + a*n;
                                   allatoms[currentatom].y = 2.0 * a + 8.4 * (double)j * a + a*n;
                                   allatoms[currentatom].z = 1.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -2;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;

                                   allatoms[currentatom].type = C;
                                   allatoms[currentatom].x = 2.0 * a + 6.4 * (double)i * a + a*(n+1);
                                   allatoms[currentatom].y = 2.0 * a + 8.4 * (double)j * a + a*(n+1);
                                   allatoms[currentatom].z = 2.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -3;
                                   allatoms[currentatom].bonds[1] = 1;
                                   allatoms[currentatom].bonds[2] = 2;
                                   allatoms[currentatom].bonds[3] = 3;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;

                                   allatoms[currentatom].type = H;
                                   allatoms[currentatom].x = 1.5 * a + 6.4 * (double)i * a + a*(n+1);
                                   allatoms[currentatom].y = 2.5 * a + 8.4 * (double)j * a + a*(n+1);
                                   allatoms[currentatom].z = 2.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -1;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;

                                   allatoms[currentatom].type = H;
                                   allatoms[currentatom].x = 2.5 * a + 6.4 * (double)i * a + a*(n+1);
                                   allatoms[currentatom].y = 1.5 * a + 8.4 * (double)j * a + a*(n+1);
                                   allatoms[currentatom].z = 2.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*n;
                                   allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                                   allatoms[currentatom].ax = 0.0;
                                   allatoms[currentatom].ay = 0.0;
                                   allatoms[currentatom].az = 0.0;
                                   allatoms[currentatom].ndx = 0.0;
                                   allatoms[currentatom].ndy = 0.0;
                                   allatoms[currentatom].ndz = 0.0;
                                   allatoms[currentatom].potential = 0.0;
                                   allatoms[currentatom].newpotential = 0.0;
                                   for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                                   allatoms[currentatom].bonds[0] = -2;
                                   currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                                   netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                                   netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                                   netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                                   currentatom++;
                           }

                           allatoms[currentatom].type = C;
                           allatoms[currentatom].x = 2.5 * a + 6.4 * (double)i * a + a*(N-1);
                           allatoms[currentatom].y = 2.5 * a + 8.4 * (double)j * a + a*(N-1);
                           allatoms[currentatom].z = 1.5 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*(N-1);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -4;
                           allatoms[currentatom].bonds[1] = 1;
                           allatoms[currentatom].bonds[2] = 2;
                           allatoms[currentatom].bonds[3] = 3;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 2.0 * a + 6.4 * (double)i * a + a*(N-1);
                           allatoms[currentatom].y = 3.0 * a + 8.4 * (double)j * a + a*(N-1);
                           allatoms[currentatom].z = 1.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*(N-1);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -1;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 3.0 * a + 6.4 * (double)i * a + a*(N-1);
                           allatoms[currentatom].y = 2.0 * a + 8.4 * (double)j * a + a*(N-1);
                           allatoms[currentatom].z = 1.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*(N-1);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -2;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;

                           allatoms[currentatom].type = H;
                           allatoms[currentatom].x = 3.0 * a + 6.4 * (double)i * a + a*(N-1);
                           allatoms[currentatom].y = 3.0 * a + 8.4 * (double)j * a + a*(N-1);
                           allatoms[currentatom].z = 2.0 * a + 7.8 * (double)k * a + 0.25 * a * (double)(N/4) + 0.00*a*(N-1);
                           allatoms[currentatom].vx = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vy = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].vz = ((double)rand()-RMo2)/RMo2;
                           allatoms[currentatom].ax = 0.0;
                           allatoms[currentatom].ay = 0.0;
                           allatoms[currentatom].az = 0.0;
                           allatoms[currentatom].ndx = 0.0;
                           allatoms[currentatom].ndy = 0.0;
                           allatoms[currentatom].ndz = 0.0;
                           allatoms[currentatom].potential = 0.0;
                           allatoms[currentatom].newpotential = 0.0;
                           for(l=0; l<NUMBONDS; l++) allatoms[currentatom].bonds[l] = 0;
                           allatoms[currentatom].bonds[0] = -3;
                           currentT += 0.5 * elements[allatoms[currentatom].type].mass * (allatoms[currentatom].vx*allatoms[currentatom].vx + allatoms[currentatom].vy*allatoms[currentatom].vy + allatoms[currentatom].vz*allatoms[currentatom].vz);
                           netmx += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vx;
                           netmy += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vy;
                           netmz += elements[allatoms[currentatom].type].mass * allatoms[currentatom].vz;
                           currentatom++;
                   }
           }
   }

   currentT /= (double)numatoms;
   currentT /= 1.5 * kB;

   netmx /= (double)numatoms;
   netmy /= (double)numatoms;
   netmz /= (double)numatoms;

   vMul = sqrt(TEMP/currentT);

   for(i=0; i<numatoms; i++)
   {
           while(allatoms[i].x > tempheader.bigX) allatoms[i].x -= tempheader.bigX;
           while(allatoms[i].x < 0.0) allatoms[i].x += tempheader.bigX;
           while(allatoms[i].y > tempheader.bigY) allatoms[i].y -= tempheader.bigY;
           while(allatoms[i].y < 0.0) allatoms[i].y += tempheader.bigY;
           while(allatoms[i].z > tempheader.bigZ) allatoms[i].z -= tempheader.bigZ;
           while(allatoms[i].z < 0.0) allatoms[i].z += tempheader.bigZ;

           allatoms[i].vx = (allatoms[i].vx - netmx/elements[allatoms[i].type].mass) * vMul;
           allatoms[i].vy = (allatoms[i].vy - netmy/elements[allatoms[i].type].mass) * vMul;
           allatoms[i].vz = (allatoms[i].vz - netmz/elements[allatoms[i].type].mass) * vMul;
   }

   fwrite(&tempheader, sizeof(Headerinfo), 1, file);
   fwrite(allatoms, sizeof(Atom), numatoms, file);

   free(allatoms);
   fclose(file);

   return 1;
}