1 |
xsun |
1185 |
#include<stdio.h> |
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#include<string.h> |
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#include<stdlib.h> |
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#include<math.h> |
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#include<fftw.h> |
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#include<mkl_lapack64.h> |
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//extern void dsyev(char *jobz, char *uplo, int *n, double *a, int *lda, |
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// double *w, double *work, int *lwork,int *info); |
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//void direct(double rcut, double box, int n, int nstep, int maxbin); |
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//double* dsyev_ctof(double **in, int rows, int cols); |
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//void dsyev_ftoc2(double *in, double **out, int rows, int cols); |
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// Structures to store our data: |
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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// coords holds the data for a single tethered dipole: |
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struct coords{ |
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double pos[3]; // cartesian coords |
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double theta; // orientational angle relative to z axis |
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double phi; // orientational angle in x-y plane |
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double mu; // dipole strength |
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char name[30]; // an identifier for the type of atom |
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}; |
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// state holds the current "configuration" of the entire system |
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struct system { |
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int nAtoms; // Number of Atoms in this configuration |
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struct coords *r; // The set of coordinates for all atoms |
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double beta; // beta = 1 /(kb*T) |
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double strength; // strength of the dipoles (Debye) |
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double z0; // default z axis position |
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double theta0; // default theta angle |
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double kz; // force constant for z displacement |
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double ktheta; // force constant for theta displacement |
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int nCycles; // How many cycles to do in total |
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int iCycle; // How many cycles have we done? |
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int nMoves; // How many MC moves in each cycle |
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int nSample; // How many cycles between samples |
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double Hmat[2][2]; // The information about the size of the per. box |
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double HmatI[2][2]; // The inverse box |
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double energy; // The current Energy |
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double dtheta; // maximum size of a theta move |
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double deltaz; // maximum size of a z move |
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double deltaphi; // maximum size of a phi move |
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int nAttempts; // number of MC moves that have been attempted |
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int nAccepts; // number of MC moves that have been accepted |
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int nx; // number of unit cells in x direction |
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int ny; // number of unit cells in y direction |
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struct system *next; // Next frame in the linked list |
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}; |
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char *program_name; /* the name of the program */ |
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// Function prototypes: |
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void usage(void); |
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void invertMat2(double a[2][2], double b[2][2]); |
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void wrapVector( double thePos[2], double Hmat[2][2], double HmatI[2][2]); |
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int main(argc, argv) |
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int argc; |
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char *argv[]; |
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{ |
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FILE *in_file; |
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char in_name[500]; |
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char *eof_test, *foo; |
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char read_buffer[1000]; |
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//int lineCount = 0; |
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int lineCount; |
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int nAtoms; |
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double *mag, *newmag; |
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int *present_in_old; |
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double *ux, *uy, *uz, p1; |
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double aLat, bLat; |
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int cells; |
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double sumZ, sumUx, sumUy, sumUz, sumP; |
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double interpsum, value; |
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int ninterp, px, py, newp; |
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int i, j, k, l, nloops; |
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int newx, newy, newindex, index; |
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int new_i, new_j, new_index; |
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int N, nframes; |
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double freq_x, freq_y, zero_freq_x, zero_freq_y, freq; |
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double maxfreqx, maxfreqy, maxfreq, dfreq; |
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double dx, dy, dx1, dy1, xTemp, yTemp, pt1x, pt1y, pt2x, pt2y; |
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int nx, ny; |
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int *samples; |
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double *bin, binmin, binmax, delr; |
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double *x, *y, *z; |
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double dh2, dh, sumh2, sumh, averh2, averh, t, delta, gamma, hi, proj; |
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double *corrhist, *h2hist; |
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double vrhist[100][500]; |
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double sum_vrhist[1000], ave_vrhist[1000]; |
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int vrsamp[1000][1000]; |
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int *ophist; |
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double d[2], hcorr; |
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double hsum, hsum_temp, h2sum, have, h2ave, fluc, bigL, smallA, areaPerMolecule, area, h, h2; |
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int nbins, nbins2, opbin, whichbinx, whichbiny, whichbin2, n1, n2, n3, n4, m, selfx, selfy; |
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int which; |
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double omat[3][3]; |
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double wrapMat[9]; |
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double onethird, ordvals[5000]; |
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double max; |
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double director[3][1000], vr[3][1000]; |
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double sum_director[3], ave_director[3], sum_vr[3], ave_vr[3]; |
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double orderpar[1000]; |
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double sum_orderpar, ave_orderpar; |
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char job, uplo; |
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int ndiag; |
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int nfilled; |
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double evals[100]; |
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int lwork; |
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double* work; |
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int ifail; |
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int done; |
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char current_flag; |
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lineCount = 0; |
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127 |
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program_name = argv[0]; |
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if (argc >= 2) |
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strcpy(in_name, argv[1]); |
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/* |
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for(i = 1; i < argc; i++){ |
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if(argv[i][0] == '-'){ |
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done = 0; |
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j = 1; |
135 |
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current_flag = argv[i][j]; |
136 |
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while( (current_flag != '\0') && ( !done ) ){ |
137 |
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switch(current_flag){ |
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case 'i': |
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i++; |
140 |
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strcpy( in_name, argv[i] ); |
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done = 1; |
142 |
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break; |
143 |
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} |
144 |
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} |
145 |
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} |
146 |
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} |
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*/ |
148 |
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149 |
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struct system* state; |
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struct system* temp_state; |
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struct coords* r; |
152 |
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153 |
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lwork = 9; |
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155 |
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work = (double *) malloc(lwork * sizeof(double)); |
156 |
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157 |
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onethird = 1.0 / 3.0; |
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ndiag = 3; |
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nfilled = 3; |
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job = 'V'; |
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uplo = 'U'; |
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ifail = 0; |
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164 |
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nbins = 30; |
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nbins2 = 30; |
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binmin = 0.0; |
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binmax = 1.0; |
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delr = (binmax - binmin) / (double) nbins2; |
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corrhist = (double *) calloc(nbins*nbins, sizeof(double)); |
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h2hist = (double *) calloc(nbins*nbins, sizeof(double)); |
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ophist = (int *) calloc(nbins2, sizeof(int)); |
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hsum = 0.0; |
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h2sum = 0.0; |
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sum_orderpar = 0.0; |
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ave_orderpar = 0.0; |
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for(i = 0; i < 3; i++){ |
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for(j = 0; j < 1000; j++){ |
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director[i][j] = 0.0; |
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vr[i][j] = 0.0; |
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} |
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} |
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for(i = 0; i < 1000; i++){ |
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sum_vrhist[i] = 0.0; |
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ave_vrhist[i] = 0.0; |
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} |
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189 |
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for(i = 0; i < 3; i++){ |
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sum_director[i] = 0.0; |
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ave_director[i] = 0.0; |
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sum_vr[i] = 0.0; |
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ave_vr[i] = 0.0; |
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} |
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for (i = 0; i < nbins; i++) { |
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for (j = 0; j < nbins; j++) { |
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corrhist[nbins * i + j] = 0.0; |
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h2hist[nbins * i + j] = 0.0; |
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} |
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} |
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203 |
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for (i = 0; i < 100; i++) { |
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for (j = 0; j < 500; j++) { |
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vrhist[i][j] = 0.0; |
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} |
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} |
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209 |
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for(i = 0; i < nbins2; i++){ |
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ophist[i] = 0; |
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} |
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213 |
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t = 300; |
214 |
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215 |
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in_file = fopen(in_name, "r"); |
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if(in_file == NULL){ |
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printf("Cannot open file \"%s\" for reading.\n", in_name); |
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exit(8); |
219 |
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} |
220 |
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221 |
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nframes = 0; |
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n1 = 0; |
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n2 = 0; |
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n3 = 0; |
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n4 = 0; |
226 |
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// start reading the first frame |
228 |
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229 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
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nAtoms = atoi(read_buffer); |
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ux = (double *) calloc(nAtoms, sizeof(double)); |
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uy = (double *) calloc(nAtoms, sizeof(double)); |
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uz = (double *) calloc(nAtoms, sizeof(double)); |
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lineCount++; |
235 |
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236 |
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for(i = 0; i < nAtoms; i++){ |
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ux[i] = 0.0; |
238 |
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uy[i] = 0.0; |
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uz[i] = 0.0; |
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} |
241 |
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242 |
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state = (struct system *) malloc(sizeof(struct system)); |
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state->next = NULL; |
244 |
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state->strength = 7.0; |
245 |
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246 |
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while(eof_test != NULL){ |
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248 |
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nframes++; |
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(void)sscanf(read_buffer, "%d", &state->nAtoms); |
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N = 2 * state->nAtoms; |
251 |
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252 |
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state->r = (struct coords *)calloc(N, sizeof(struct coords)); |
253 |
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254 |
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for(i = 0; i < 3; i++){ |
255 |
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for(j = 0; j < 3; j++){ |
256 |
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omat[i][j] = 0.0; |
257 |
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} |
258 |
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} |
259 |
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260 |
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// read and the comment line and grab the time and box dimensions |
261 |
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262 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
263 |
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lineCount++; |
264 |
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if(eof_test == NULL){ |
265 |
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printf("error in reading file at line: %d\n", lineCount); |
266 |
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exit(8); |
267 |
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} |
268 |
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269 |
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foo = strtok( read_buffer, " ,;\t\n" ); |
270 |
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(void)sscanf( read_buffer, "%d", &state->iCycle ); |
271 |
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272 |
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foo = strtok(NULL, " ,;\t\0"); |
273 |
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if(foo == NULL){ |
274 |
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printf("error in reading file at line: %d\n", lineCount); |
275 |
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exit(8); |
276 |
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} |
277 |
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(void)sscanf(foo, "%d", &state->nx); |
278 |
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279 |
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nx = state->nx; |
280 |
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281 |
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foo = strtok(NULL, " ,;\t\0"); |
282 |
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if(foo == NULL){ |
283 |
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printf("error in reading file at line: %d\n", lineCount); |
284 |
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exit(8); |
285 |
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} |
286 |
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(void)sscanf(foo, "%d", &state->ny); |
287 |
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288 |
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ny = state->ny; |
289 |
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290 |
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foo = strtok(NULL, " ,;\t\0"); |
291 |
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if(foo == NULL){ |
292 |
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printf("error in reading file at line: %d\n", lineCount); |
293 |
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exit(8); |
294 |
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} |
295 |
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(void)sscanf(foo, "%lf",&state->Hmat[0][0]); |
296 |
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297 |
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foo = strtok(NULL, " ,;\t\0"); |
298 |
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if(foo == NULL){ |
299 |
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printf("error in reading file at line: %d\n", lineCount); |
300 |
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exit(8); |
301 |
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} |
302 |
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(void)sscanf(foo, "%lf",&state->Hmat[1][0]); |
303 |
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304 |
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foo = strtok(NULL, " ,;\t\0"); |
305 |
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if(foo == NULL){ |
306 |
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printf("error in reading file at line: %d\n", lineCount); |
307 |
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exit(8); |
308 |
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} |
309 |
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(void)sscanf(foo, "%lf",&state->Hmat[0][1]); |
310 |
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311 |
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foo = strtok(NULL, " ,;\t\0"); |
312 |
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if(foo == NULL){ |
313 |
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printf("error in reading file at line: %d\n", lineCount); |
314 |
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exit(8); |
315 |
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} |
316 |
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(void)sscanf(foo, "%lf",&state->Hmat[1][1]); |
317 |
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318 |
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//Find HmatI: |
319 |
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320 |
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invertMat2(state->Hmat, state->HmatI); |
321 |
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322 |
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// Length of the two box vectors: |
323 |
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324 |
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dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
325 |
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dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
326 |
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327 |
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aLat = dx / (double)(state->nx); |
328 |
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bLat = dy / (double)(state->ny); |
329 |
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330 |
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// FFT stuff depends on nx and ny, so delay allocation until we have |
331 |
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// that information |
332 |
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333 |
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for (i=0;i<state->nAtoms;i++){ |
334 |
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335 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
336 |
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lineCount++; |
337 |
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if(eof_test == NULL){ |
338 |
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printf("error in reading file at line: %d\n", lineCount); |
339 |
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exit(8); |
340 |
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} |
341 |
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342 |
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foo = strtok(read_buffer, " ,;\t\0"); |
343 |
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(void)strcpy(state->r[i].name, foo); //copy the atom name |
344 |
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345 |
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// next we grab the positions |
346 |
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347 |
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foo = strtok(NULL, " ,;\t\0"); |
348 |
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if(foo == NULL){ |
349 |
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printf("error in reading postition x from %s\n" |
350 |
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"natoms = %d, line = %d\n", |
351 |
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in_name, state->nAtoms, lineCount ); |
352 |
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exit(8); |
353 |
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} |
354 |
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(void)sscanf( foo, "%lf", &state->r[i].pos[0] ); |
355 |
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356 |
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foo = strtok(NULL, " ,;\t\0"); |
357 |
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if(foo == NULL){ |
358 |
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printf("error in reading postition y from %s\n" |
359 |
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"natoms = %d, line = %d\n", |
360 |
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in_name, state->nAtoms, lineCount ); |
361 |
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exit(8); |
362 |
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} |
363 |
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(void)sscanf( foo, "%lf", &state->r[i].pos[1] ); |
364 |
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365 |
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foo = strtok(NULL, " ,;\t\0"); |
366 |
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if(foo == NULL){ |
367 |
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printf("error in reading postition z from %s\n" |
368 |
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"natoms = %d, line = %d\n", |
369 |
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in_name, state->nAtoms, lineCount ); |
370 |
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exit(8); |
371 |
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} |
372 |
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(void)sscanf( foo, "%lf", &state->r[i].pos[2] ); |
373 |
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374 |
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foo = strtok(NULL, " ,;\t\0"); |
375 |
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if(foo == NULL){ |
376 |
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printf("error in reading angle phi from %s\n" |
377 |
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"natoms = %d, line = %d\n", |
378 |
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in_name, state->nAtoms, lineCount ); |
379 |
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exit(8); |
380 |
|
|
} |
381 |
|
|
(void)sscanf( foo, "%lf", &state->r[i].phi ); |
382 |
|
|
|
383 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
384 |
|
|
if(foo == NULL){ |
385 |
|
|
printf("error in reading unit vector x from %s\n" |
386 |
|
|
"natoms = %d, line = %d\n", |
387 |
|
|
in_name, state->nAtoms, lineCount ); |
388 |
|
|
exit(8); |
389 |
|
|
} |
390 |
|
|
(void)sscanf( foo, "%lf", &ux[i] ); |
391 |
|
|
|
392 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
393 |
|
|
if(foo == NULL){ |
394 |
|
|
printf("error in reading unit vector y from %s\n" |
395 |
|
|
"natoms = %d, line = %d\n", |
396 |
|
|
in_name, state->nAtoms, lineCount ); |
397 |
|
|
exit(8); |
398 |
|
|
} |
399 |
|
|
(void)sscanf( foo, "%lf", &uy[i] ); |
400 |
|
|
|
401 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
402 |
|
|
if(foo == NULL){ |
403 |
|
|
printf("error in reading unit vector z from %s\n" |
404 |
|
|
"natoms = %d, line = %d\n", |
405 |
|
|
in_name, state->nAtoms, lineCount ); |
406 |
|
|
exit(8); |
407 |
|
|
} |
408 |
|
|
(void)sscanf( foo, "%lf", &uz[i] ); |
409 |
|
|
|
410 |
|
|
state->r[i].theta = acos(uz[i]); |
411 |
|
|
|
412 |
|
|
// The one parameter not stored in the dump file is the dipole strength |
413 |
|
|
state->r[i].mu = state->strength; |
414 |
|
|
} |
415 |
|
|
|
416 |
|
|
hsum_temp = 0.0; |
417 |
|
|
for (i = 0; i < state->nAtoms; i++) { |
418 |
|
|
|
419 |
|
|
h = state->r[i].pos[2]; |
420 |
|
|
h2 = pow(h,2); |
421 |
|
|
|
422 |
|
|
hsum_temp += h; |
423 |
|
|
hsum += h; |
424 |
|
|
h2sum += h2; |
425 |
|
|
|
426 |
|
|
n1++; |
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
for(i = 0; i < state->nAtoms; i++){ |
430 |
|
|
|
431 |
|
|
omat[0][0] += ux[i] * ux[i] - onethird; |
432 |
|
|
omat[0][1] += ux[i] * uy[i]; |
433 |
|
|
omat[0][2] += ux[i] * uz[i]; |
434 |
|
|
omat[1][0] += uy[i] * ux[i]; |
435 |
|
|
omat[1][1] += uy[i] * uy[i] - onethird; |
436 |
|
|
omat[1][2] += uy[i] * uz[i]; |
437 |
|
|
omat[2][0] += uz[i] * ux[i]; |
438 |
|
|
omat[2][1] += uz[i] * uy[i]; |
439 |
|
|
omat[2][2] += uz[i] * uz[i] - onethird; |
440 |
|
|
|
441 |
|
|
} |
442 |
|
|
|
443 |
|
|
for(i = 0; i < 3; i++){ |
444 |
|
|
for(j = 0; j < 3; j++){ |
445 |
|
|
omat[i][j] /= (double) state->nAtoms; |
446 |
|
|
} |
447 |
|
|
} |
448 |
|
|
|
449 |
|
|
// temp_array = dsyev_ctof(omat, nfilled, nfilled); |
450 |
|
|
|
451 |
|
|
for(j=0;j<3;j++) |
452 |
|
|
for(i=0;i<3;i++) |
453 |
|
|
wrapMat[i+j*3] = omat[i][j]; |
454 |
|
|
|
455 |
|
|
ifail = 0; |
456 |
|
|
dsyev(&job, &uplo, &nfilled, wrapMat, &ndiag, evals, work, &lwork, &ifail); |
457 |
|
|
|
458 |
|
|
for(j=0;j<3;j++) |
459 |
|
|
for(i=0;i<3;i++) |
460 |
|
|
omat[i][j] = wrapMat[i+j*3]; |
461 |
|
|
|
462 |
|
|
//dsyev_ftoc2(temp_array, omat, nfilled, nfilled); |
463 |
|
|
|
464 |
|
|
//free(temp_array); |
465 |
|
|
|
466 |
|
|
max = 0.0; |
467 |
|
|
for(j = 0; j < 3; j++){ |
468 |
|
|
if(fabs(evals[j]) > max){ |
469 |
|
|
which = j; |
470 |
|
|
max = fabs(evals[j]); |
471 |
|
|
} |
472 |
|
|
} |
473 |
|
|
|
474 |
|
|
director[0][nframes-1] = omat[0][which]; |
475 |
|
|
director[1][nframes-1] = omat[1][which]; |
476 |
|
|
director[2][nframes-1] = omat[2][which]; |
477 |
|
|
|
478 |
|
|
vr[0][nframes-1] = fabs(director[1][nframes-1]); |
479 |
|
|
vr[1][nframes-1] = fabs(-director[0][nframes-1]); |
480 |
|
|
vr[2][nframes-1] = 0; |
481 |
|
|
|
482 |
|
|
orderpar[nframes-1] = 1.5 * max; |
483 |
|
|
printf("%d\t%lf\n", state->iCycle, orderpar[nframes-1]); |
484 |
|
|
|
485 |
|
|
opbin = (int) (orderpar[nframes-1] / delr); |
486 |
|
|
if(opbin < nbins2) ophist[opbin] += 1; |
487 |
|
|
|
488 |
|
|
/* for(i = 0; i < state->nAtoms; i++){ */ |
489 |
|
|
/* proj = vr[0][nframes-1] * state->r[i].pos[0] + vr[1][nframes-1] * state->r[i].pos[1]; */ |
490 |
|
|
/* hi = state->r[i].pos[2] - hsum_temp / (double) state->nAtoms; */ |
491 |
|
|
|
492 |
|
|
/* whichbin2 = (int) ((proj / (vr[0][nframes-1] * dx + vr[1][nframes-1] * dy)) * nbins2); */ |
493 |
|
|
/* vrhist[whichbin2][nframes-1] += hi; */ |
494 |
|
|
/* vrsamp[whichbin2][nframes-1]++; */ |
495 |
|
|
/* } */ |
496 |
|
|
|
497 |
|
|
/* for(i = 0; i < state->nAtoms; i++){ */ |
498 |
|
|
/* for(j = 0; j < state->nAtoms; j++){ */ |
499 |
|
|
|
500 |
|
|
/* d[0] = state->r[j].pos[0] - state->r[i].pos[0]; */ |
501 |
|
|
/* d[1] = state->r[j].pos[1] - state->r[i].pos[1]; */ |
502 |
|
|
|
503 |
|
|
/* wrapVector(d, state->Hmat, state->HmatI); */ |
504 |
|
|
|
505 |
|
|
/* whichbinx = (int) ((nbins-1) * (dx/2.0 + d[0]) / dx); */ |
506 |
|
|
/* whichbiny = (int) ((nbins-1) * (dy/2.0 + d[1]) / dy); */ |
507 |
|
|
|
508 |
|
|
/* //if (i == j) { */ |
509 |
|
|
/* //printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
510 |
|
|
/* //} */ |
511 |
|
|
|
512 |
|
|
/* //printf("d0 = %lf, d1 = %lf\n", d[0], d[1]); */ |
513 |
|
|
/* //printf("wx = %d, wy = %d\n", whichbinx, whichbiny); */ |
514 |
|
|
|
515 |
|
|
/* if (whichbinx >= nbins || whichbiny >= nbins) { */ |
516 |
|
|
/* printf("off by one error\n"); */ |
517 |
|
|
/* printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
518 |
|
|
/* exit(0); */ |
519 |
|
|
/* } */ |
520 |
|
|
/* if (whichbinx < 0 || whichbiny < 0) { */ |
521 |
|
|
/* printf("off by one error\n"); */ |
522 |
|
|
/* printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); */ |
523 |
|
|
/* exit(0); */ |
524 |
|
|
/* } */ |
525 |
|
|
|
526 |
|
|
/* hcorr = state->r[j].pos[2] * state->r[i].pos[2]; */ |
527 |
|
|
|
528 |
|
|
/* corrhist[nbins * whichbinx + whichbiny] += hcorr; */ |
529 |
|
|
|
530 |
|
|
/* dh = state->r[j].pos[2] - state->r[i].pos[2]; */ |
531 |
|
|
/* dh2 = pow(dh, 2); */ |
532 |
|
|
|
533 |
|
|
/* h2hist[nbins * whichbinx + whichbiny] += dh2; */ |
534 |
|
|
|
535 |
|
|
/* n2++; */ |
536 |
|
|
/* } */ |
537 |
|
|
/* } */ |
538 |
|
|
|
539 |
|
|
temp_state = state->next; |
540 |
|
|
state->next = NULL; |
541 |
|
|
|
542 |
|
|
if (temp_state != NULL) { |
543 |
|
|
free(temp_state->r); |
544 |
|
|
free(temp_state); |
545 |
|
|
} |
546 |
|
|
|
547 |
|
|
// Make a new frame |
548 |
|
|
|
549 |
|
|
temp_state = (struct system *) malloc(sizeof(struct system)); |
550 |
|
|
temp_state->next = state; |
551 |
|
|
state = temp_state; |
552 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
553 |
|
|
lineCount++; |
554 |
|
|
} |
555 |
|
|
|
556 |
|
|
|
557 |
|
|
/* have = hsum / (double) n1; */ |
558 |
|
|
/* h2ave = h2sum / (double) n1; */ |
559 |
|
|
/* fluc = h2ave - pow(have, 2); */ |
560 |
|
|
|
561 |
|
|
/* printf("# <h> = %lf\n", have); */ |
562 |
|
|
/* printf("# <h2> = %lf\n", h2ave); */ |
563 |
|
|
/* printf("# sigma(h) = %lf\n", sqrt(h2ave - have * have)); */ |
564 |
|
|
/* printf("# fluctuation = %lf\n", fluc); */ |
565 |
|
|
|
566 |
|
|
/* for(i = 0; i < nframes; i++){ */ |
567 |
|
|
/* sum_orderpar += orderpar[i]; */ |
568 |
|
|
/* } */ |
569 |
|
|
/* ave_orderpar = sum_orderpar / (double) nframes; */ |
570 |
|
|
|
571 |
|
|
/* for(i = 0; i < nframes; i++){ */ |
572 |
|
|
/* sum_director[0] += director[0][i]; */ |
573 |
|
|
/* sum_director[1] += director[1][i]; */ |
574 |
|
|
/* sum_director[2] += director[2][i]; */ |
575 |
|
|
/* } */ |
576 |
|
|
/* ave_director[0] = sum_director[0] / (double) nframes; */ |
577 |
|
|
/* ave_director[1] = sum_director[1] / (double) nframes; */ |
578 |
|
|
/* ave_director[2] = sum_director[2] / (double) nframes; */ |
579 |
|
|
|
580 |
|
|
/* for(i = 0; i < nframes; i++){ */ |
581 |
|
|
/* sum_vr[0] += vr[0][i]; */ |
582 |
|
|
/* sum_vr[1] += vr[1][i]; */ |
583 |
|
|
/* sum_vr[2] += vr[2][i]; */ |
584 |
|
|
/* } */ |
585 |
|
|
/* ave_vr[0] = sum_vr[0] / (double) nframes; */ |
586 |
|
|
/* ave_vr[1] = sum_vr[1] / (double) nframes; */ |
587 |
|
|
/* ave_vr[2] = sum_vr[2] / (double) nframes; */ |
588 |
|
|
|
589 |
|
|
/* printf("# orderparameter = %lf\n", ave_orderpar); */ |
590 |
|
|
/* printf("# director axis is ( %lf\t%lf\t%lf )\n", */ |
591 |
|
|
/* ave_director[0], ave_director[1], ave_director[2]); */ |
592 |
|
|
/* printf("# vr axis is ( %lf\t%lf\t%lf )\n", ave_vr[0], ave_vr[1], ave_vr[2]); */ |
593 |
|
|
|
594 |
|
|
/* for(i = 0; i < nbins2; i++){ */ |
595 |
|
|
/* for(j = 0; j < nframes; j++){ */ |
596 |
|
|
/* sum_vrhist[i] += vrhist[i][j]; */ |
597 |
|
|
/* } */ |
598 |
|
|
/* } */ |
599 |
|
|
|
600 |
|
|
/* dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); */ |
601 |
|
|
/* dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); */ |
602 |
|
|
|
603 |
|
|
/* area = dx * dy; */ |
604 |
|
|
|
605 |
|
|
/* bigL = sqrt(area); */ |
606 |
|
|
|
607 |
|
|
/* areaPerMolecule = area / (double) state->nAtoms; */ |
608 |
|
|
|
609 |
|
|
/* smallA = sqrt(areaPerMolecule); */ |
610 |
|
|
|
611 |
|
|
/* gamma = t * log(bigL / smallA) / (2.0 * M_PI * fluc); */ |
612 |
|
|
|
613 |
|
|
/* printf("# first gamma estimate = %lf\n", gamma); */ |
614 |
|
|
|
615 |
|
|
/* printf("# \n"); */ |
616 |
|
|
|
617 |
|
|
/* for(i = 0; i < nbins2; i++){ */ |
618 |
|
|
/* ave_vrhist[i] = sum_vrhist[i] / (double) nframes; */ |
619 |
|
|
/* printf("%lf\t%lf\n", (double) i * (ave_vr[0] * dx + ave_vr[1] * dy) / (double) nbins2, */ |
620 |
|
|
/* ave_vrhist[i]); */ |
621 |
|
|
/* } */ |
622 |
|
|
|
623 |
|
|
/* selfx = (int) ((double)nbins / 2.0); */ |
624 |
|
|
/* selfy = (int) ((double)nbins / 2.0); */ |
625 |
|
|
|
626 |
|
|
/* for (i = 0; i < nbins; i++) { */ |
627 |
|
|
/* for (j = 0; j < nbins; j++) { */ |
628 |
|
|
/* printf("%lf\t", h2hist[nbins * i + j] / (double) n2); */ |
629 |
|
|
/* } */ |
630 |
|
|
/* printf("\n"); */ |
631 |
|
|
/* } */ |
632 |
|
|
|
633 |
|
|
free(work); |
634 |
|
|
free(corrhist); |
635 |
|
|
free(h2hist); |
636 |
|
|
free(ux); |
637 |
|
|
free(uy); |
638 |
|
|
free(uz); |
639 |
|
|
return 1; |
640 |
|
|
|
641 |
|
|
} |
642 |
|
|
|
643 |
|
|
double matDet2(double a[2][2]) { |
644 |
|
|
|
645 |
|
|
double determinant; |
646 |
|
|
|
647 |
|
|
determinant = (a[0][0] * a[1][1]) - (a[0][1] * a[1][0]); |
648 |
|
|
|
649 |
|
|
return determinant; |
650 |
|
|
} |
651 |
|
|
|
652 |
|
|
|
653 |
|
|
void invertMat2(double a[2][2], double b[2][2]) { |
654 |
|
|
|
655 |
|
|
double determinant; |
656 |
|
|
|
657 |
|
|
determinant = matDet2( a ); |
658 |
|
|
|
659 |
|
|
if (determinant == 0.0) { |
660 |
|
|
printf("Can't invert a matrix with a zero determinant!\n"); |
661 |
|
|
} |
662 |
|
|
|
663 |
|
|
b[0][0] = a[1][1] / determinant; |
664 |
|
|
b[0][1] = -a[0][1] / determinant; |
665 |
|
|
b[1][0] = -a[1][0] / determinant; |
666 |
|
|
b[1][1] = a[0][0] / determinant; |
667 |
|
|
} |
668 |
|
|
|
669 |
|
|
void matVecMul2(double m[2][2], double inVec[2], double outVec[2]) { |
670 |
|
|
double a0, a1, a2; |
671 |
|
|
|
672 |
|
|
a0 = inVec[0]; a1 = inVec[1]; |
673 |
|
|
|
674 |
|
|
outVec[0] = m[0][0]*a0 + m[0][1]*a1; |
675 |
|
|
outVec[1] = m[1][0]*a0 + m[1][1]*a1; |
676 |
|
|
} |
677 |
|
|
|
678 |
|
|
void wrapVector( double thePos[2], double Hmat[2][2], double HmatInv[2][2]){ |
679 |
|
|
|
680 |
|
|
int i; |
681 |
|
|
double scaled[2]; |
682 |
|
|
|
683 |
|
|
// calc the scaled coordinates. |
684 |
|
|
|
685 |
|
|
matVecMul2(HmatInv, thePos, scaled); |
686 |
|
|
|
687 |
|
|
for(i=0; i<2; i++) |
688 |
|
|
scaled[i] -= roundMe(scaled[i]); |
689 |
|
|
|
690 |
|
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
691 |
|
|
|
692 |
|
|
matVecMul2(Hmat, scaled, thePos); |
693 |
|
|
|
694 |
|
|
} |
695 |
|
|
|
696 |
|
|
/* double* dsyev_ctof(double **in, int rows, int cols) */ |
697 |
|
|
/* { */ |
698 |
|
|
/* double *out; */ |
699 |
|
|
/* int i, j; */ |
700 |
|
|
|
701 |
|
|
/* out = (double *) calloc(rows * cols, sizeof(double)); */ |
702 |
|
|
|
703 |
|
|
/* if (!out){ */ |
704 |
|
|
/* printf("Fail to allocate memory\n"); */ |
705 |
|
|
/* exit(1); */ |
706 |
|
|
/* } */ |
707 |
|
|
|
708 |
|
|
/* for (i = 0; i < rows; i++) */ |
709 |
|
|
/* for (j = 0; j < cols; j++) */ |
710 |
|
|
/* out[i+j*cols] = in[i][j]; */ |
711 |
|
|
|
712 |
|
|
/* return(out); */ |
713 |
|
|
/* } */ |
714 |
|
|
|
715 |
|
|
/* void dsyev_ftoc2(double *in, double **out, int rows, int cols) */ |
716 |
|
|
/* { */ |
717 |
|
|
/* int i, j; */ |
718 |
|
|
|
719 |
|
|
/* for (i = 0; i < rows; i++) */ |
720 |
|
|
/* for (j = 0; j < cols; j++) */ |
721 |
|
|
/* out[i][j] = in[i+j*cols]; */ |
722 |
|
|
/* } */ |
723 |
|
|
/* void direct(double rcut, double box, int n, int nstep, int maxbin){ */ |
724 |
|
|
|
725 |
|
|
/* int bin, maxbin, nbins, i, j, k, n, bind, which; */ |
726 |
|
|
/* int hist[maxbin], histd[maxbin], startstep; */ |
727 |
|
|
/* int nstep, stopstep, ndiag, nfilled, ifail, lwork; */ |
728 |
|
|
/* double delr, rijsp, rxij, ryij, rzij, rij; */ |
729 |
|
|
/* double delrd, rijsqd, rijd, orderpar[1000], nideal; */ |
730 |
|
|
/* double omat[3][3], evals[100], cons, rlower; */ |
731 |
|
|
/* double rcut, box, dens, director[3][1000], rupper; */ |
732 |
|
|
/* double rx[1000][1000], ry[1000][1000], rz[1000][1000]; */ |
733 |
|
|
/* double ux[1000][1000], uy[1000][1000], uz[1000][1000]; */ |
734 |
|
|
/* double vx[1000][1000], vy[1000][1000], vz[1000][1000]; */ |
735 |
|
|
/* double jx[1000][1000], jy[1000][1000], jz[1000][1000]; */ |
736 |
|
|
/* double grd[5000], gr[5000], max, binmin, binmax; */ |
737 |
|
|
/* double onethird, ordvals[5000]; */ |
738 |
|
|
/* char job, uplo; */ |
739 |
|
|
/* int ndiag; */ |
740 |
|
|
/* int nfilled; */ |
741 |
|
|
/* double omat[3][3]; */ |
742 |
|
|
/* double evals[100]; */ |
743 |
|
|
/* double work[]; */ |
744 |
|
|
/* int lwork; */ |
745 |
|
|
/* int ifail; */ |
746 |
|
|
|
747 |
|
|
/* lwork = 9; */ |
748 |
|
|
/* work = (double *)calloc(lwork, sizeof(double)); */ |
749 |
|
|
|
750 |
|
|
/* onethird = 1.0 / 3.0; */ |
751 |
|
|
/* ndiag = 3; */ |
752 |
|
|
/* nfilled = 3; */ |
753 |
|
|
/* job = 'V'; */ |
754 |
|
|
/* uplo = 'U'; */ |
755 |
|
|
/* ifail = 0; */ |
756 |
|
|
|
757 |
|
|
/* binmin = 0.0; */ |
758 |
|
|
/* binmax = 1.0; */ |
759 |
|
|
/* delr = (binmax - binmin) / (double) maxbin; */ |
760 |
|
|
|
761 |
|
|
/* for(i = 0; i < maxbin; i++){ */ |
762 |
|
|
|
763 |
|
|
/* ordvals(i) = 0.0; */ |
764 |
|
|
/* hist(i) = 0.0; */ |
765 |
|
|
|
766 |
|
|
/* } */ |
767 |
|
|
|
768 |
|
|
/* for(i = 0; i < stopstep; i++){ */ |
769 |
|
|
|
770 |
|
|
/* for(j = 0; j < 3; j++){ */ |
771 |
|
|
/* for(k = 0; k < 3; k++){ */ |
772 |
|
|
/* omat[j][k] = 0.0; */ |
773 |
|
|
/* } */ |
774 |
|
|
/* } */ |
775 |
|
|
|
776 |
|
|
/* for(j = 0; j < n; j++){ */ |
777 |
|
|
|
778 |
|
|
/* omat[1][1] = omat[1][1] + ux[j][i] * ux[j][i] - onethird; */ |
779 |
|
|
/* omat[1][2] = omat[1][2] + ux[j][i] * uy[j][i]; */ |
780 |
|
|
/* omat[1][3] = omat[1][3] + ux[j][i] * uz[j][i]; */ |
781 |
|
|
/* omat[2][1] = omat[2][1] + uy[j][i] * ux[j][i]; */ |
782 |
|
|
/* omat[2][2] = omat[2][2] + uy[j][i] * uy[j][i] - onethird; */ |
783 |
|
|
/* omat[2][3] = omat[2][3] + uy[j][i] * uz[j][i]; */ |
784 |
|
|
/* omat[3][1] = omat[3][1] + uz[j][i] * ux[j][i]; */ |
785 |
|
|
/* omat[3][2] = omat[3][2] + uz[j][i] * uy[j][i]; */ |
786 |
|
|
/* omat[3][3] = omat[3][3] + uz[j][i] * uz[j][i] - onethird; */ |
787 |
|
|
|
788 |
|
|
/* } */ |
789 |
|
|
|
790 |
|
|
|
791 |
|
|
/* for(j = 0; j < 3; j++){ */ |
792 |
|
|
/* for(k = 0; k < 3; k++){ */ |
793 |
|
|
/* omat[j][k] = omat[j][k] / (double) n; */ |
794 |
|
|
/* } */ |
795 |
|
|
/* } */ |
796 |
|
|
|
797 |
|
|
/* dsyev_(job, uplo, nfilled, omat, ndiag, evals, work, lwork, ifail); */ |
798 |
|
|
|
799 |
|
|
/* max = 0.0; */ |
800 |
|
|
/* for(j = 0; j < 3; j++){ */ |
801 |
|
|
/* if(fabs(evals(j)) > max){ */ |
802 |
|
|
/* which = j; */ |
803 |
|
|
/* max = fabs(evals(j)); */ |
804 |
|
|
/* } */ |
805 |
|
|
/* } */ |
806 |
|
|
|
807 |
|
|
/* director[1][i] = omat[1][which]; */ |
808 |
|
|
/* director[2][i] = omat[2][which]; */ |
809 |
|
|
/* director[3][i] = omat[3][which]; */ |
810 |
|
|
|
811 |
|
|
/* orderpar(i) = 1.5 * max; */ |
812 |
|
|
|
813 |
|
|
/* bin = (int) (orderpar(i) / delr) + 1; */ |
814 |
|
|
|
815 |
|
|
/* if(bin < maxbin) */ |
816 |
|
|
/* hist(bin) = hist(bin) + 1; */ |
817 |
|
|
/* } */ |
818 |
|
|
|
819 |
|
|
/* cons = 1.0; */ |
820 |
|
|
/* for(bin = 0; bin < maxbin; bin++){ */ |
821 |
|
|
|
822 |
|
|
/* rlower = (double) (bin - 1) * delr; */ |
823 |
|
|
/* rupper = rlower + delr; */ |
824 |
|
|
/* ordvals(bin) = rlower + (delr / 2.0); */ |
825 |
|
|
/* nideal = cons * (pow(rupper, 3) - pow(rlower, 3)); */ |
826 |
|
|
/* gr(bin) = (double) (hist(bin)) / (double) nstep /nideal; */ |
827 |
|
|
|
828 |
|
|
/* } */ |
829 |
|
|
/* } */ |