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#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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inline double min( double a, double b ){ |
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return (a < b ) ? a : b; |
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} |
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inline double max( double a, double b ){ |
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return (a > b ) ? a : b; |
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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[1000]; |
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double sum_vrhist[1000]; |
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int vrsamp[1000]; |
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int *ophist; |
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double d[2], hcorr; |
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double hsum, hsum_frame, h2sum, have, h2ave, h_ave_frame; |
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double 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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int highestAtom; |
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double highestZ; |
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double omat[3][3]; |
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double myPerp[3]; |
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double myDir[3]; |
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double myVec[2]; |
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double lperp; |
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double ldir; |
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double dot; |
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double maxProj, maxProjOut; |
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double avgHeightAtProj; |
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double wrapMat[9]; |
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double onethird, ordvals[5000]; |
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double maxEval; |
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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, sum2_orderpar, ave_orderpar, ave2_orderpar, err_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, lastData, firstData; |
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char current_flag; |
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lineCount = 0; |
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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; |
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current_flag = argv[i][j]; |
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while( (current_flag != '\0') && ( !done ) ){ |
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switch(current_flag){ |
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case 'i': |
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i++; |
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strcpy( in_name, argv[i] ); |
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done = 1; |
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break; |
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} |
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} |
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} |
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} |
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*/ |
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struct system* state; |
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struct system* temp_state; |
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struct coords* r; |
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lwork = 9; |
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work = (double *) malloc(lwork * sizeof(double)); |
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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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nbins = 30; |
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nbins2 = 100; |
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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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sum2_orderpar = 0.0; |
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ave_orderpar = 0.0; |
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ave2_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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} |
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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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for (i = 0; i < 1000; i++) { |
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vrhist[i] = 0.0; |
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} |
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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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t = 300; |
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in_file = fopen(in_name, "r"); |
233 |
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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); |
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} |
237 |
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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; |
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// start reading the first frame |
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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++; |
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for(i = 0; i < nAtoms; i++){ |
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ux[i] = 0.0; |
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uy[i] = 0.0; |
256 |
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uz[i] = 0.0; |
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} |
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state = (struct system *) malloc(sizeof(struct system)); |
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state->next = NULL; |
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state->strength = 7.0; |
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while(eof_test != NULL){ |
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highestAtom = -1; |
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highestZ = 0.0; |
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1185 |
nframes++; |
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(void)sscanf(read_buffer, "%d", &state->nAtoms); |
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N = 2 * state->nAtoms; |
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state->r = (struct coords *)calloc(N, sizeof(struct coords)); |
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274 |
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for(i = 0; i < 3; i++){ |
275 |
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for(j = 0; j < 3; j++){ |
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omat[i][j] = 0.0; |
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} |
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} |
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280 |
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// read and the comment line and grab the time and box dimensions |
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282 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
283 |
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lineCount++; |
284 |
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if(eof_test == NULL){ |
285 |
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printf("error in reading file at line: %d\n", lineCount); |
286 |
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exit(8); |
287 |
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} |
288 |
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289 |
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foo = strtok( read_buffer, " ,;\t\n" ); |
290 |
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(void)sscanf( read_buffer, "%d", &state->iCycle ); |
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292 |
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foo = strtok(NULL, " ,;\t\0"); |
293 |
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if(foo == NULL){ |
294 |
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printf("error in reading file at line: %d\n", lineCount); |
295 |
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exit(8); |
296 |
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} |
297 |
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(void)sscanf(foo, "%d", &state->nx); |
298 |
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299 |
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nx = state->nx; |
300 |
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301 |
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foo = strtok(NULL, " ,;\t\0"); |
302 |
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if(foo == NULL){ |
303 |
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printf("error in reading file at line: %d\n", lineCount); |
304 |
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exit(8); |
305 |
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} |
306 |
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(void)sscanf(foo, "%d", &state->ny); |
307 |
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308 |
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ny = state->ny; |
309 |
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310 |
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foo = strtok(NULL, " ,;\t\0"); |
311 |
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if(foo == NULL){ |
312 |
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printf("error in reading file at line: %d\n", lineCount); |
313 |
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exit(8); |
314 |
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} |
315 |
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(void)sscanf(foo, "%lf",&state->Hmat[0][0]); |
316 |
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317 |
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foo = strtok(NULL, " ,;\t\0"); |
318 |
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if(foo == NULL){ |
319 |
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printf("error in reading file at line: %d\n", lineCount); |
320 |
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exit(8); |
321 |
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} |
322 |
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(void)sscanf(foo, "%lf",&state->Hmat[1][0]); |
323 |
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324 |
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foo = strtok(NULL, " ,;\t\0"); |
325 |
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if(foo == NULL){ |
326 |
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printf("error in reading file at line: %d\n", lineCount); |
327 |
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exit(8); |
328 |
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} |
329 |
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(void)sscanf(foo, "%lf",&state->Hmat[0][1]); |
330 |
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331 |
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foo = strtok(NULL, " ,;\t\0"); |
332 |
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if(foo == NULL){ |
333 |
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printf("error in reading file at line: %d\n", lineCount); |
334 |
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exit(8); |
335 |
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} |
336 |
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(void)sscanf(foo, "%lf",&state->Hmat[1][1]); |
337 |
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338 |
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//Find HmatI: |
339 |
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340 |
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invertMat2(state->Hmat, state->HmatI); |
341 |
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342 |
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// Length of the two box vectors: |
343 |
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344 |
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dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
345 |
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dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
346 |
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347 |
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aLat = dx / (double)(state->nx); |
348 |
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bLat = dy / (double)(state->ny); |
349 |
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350 |
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// FFT stuff depends on nx and ny, so delay allocation until we have |
351 |
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// that information |
352 |
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353 |
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for (i=0;i<state->nAtoms;i++){ |
354 |
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355 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
356 |
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lineCount++; |
357 |
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if(eof_test == NULL){ |
358 |
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printf("error in reading file at line: %d\n", lineCount); |
359 |
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exit(8); |
360 |
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} |
361 |
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362 |
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foo = strtok(read_buffer, " ,;\t\0"); |
363 |
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(void)strcpy(state->r[i].name, foo); //copy the atom name |
364 |
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365 |
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// next we grab the positions |
366 |
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367 |
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foo = strtok(NULL, " ,;\t\0"); |
368 |
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if(foo == NULL){ |
369 |
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printf("error in reading postition x from %s\n" |
370 |
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"natoms = %d, line = %d\n", |
371 |
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in_name, state->nAtoms, lineCount ); |
372 |
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exit(8); |
373 |
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} |
374 |
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(void)sscanf( foo, "%lf", &state->r[i].pos[0] ); |
375 |
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376 |
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foo = strtok(NULL, " ,;\t\0"); |
377 |
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if(foo == NULL){ |
378 |
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printf("error in reading postition y from %s\n" |
379 |
|
|
"natoms = %d, line = %d\n", |
380 |
|
|
in_name, state->nAtoms, lineCount ); |
381 |
|
|
exit(8); |
382 |
|
|
} |
383 |
|
|
(void)sscanf( foo, "%lf", &state->r[i].pos[1] ); |
384 |
|
|
|
385 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
386 |
|
|
if(foo == NULL){ |
387 |
|
|
printf("error in reading postition z from %s\n" |
388 |
|
|
"natoms = %d, line = %d\n", |
389 |
|
|
in_name, state->nAtoms, lineCount ); |
390 |
|
|
exit(8); |
391 |
|
|
} |
392 |
|
|
(void)sscanf( foo, "%lf", &state->r[i].pos[2] ); |
393 |
xsun |
1333 |
if (state->r[i].pos[2] > highestZ) { |
394 |
|
|
highestAtom = i; |
395 |
|
|
highestZ = state->r[i].pos[2]; |
396 |
|
|
} |
397 |
xsun |
1185 |
|
398 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
399 |
|
|
if(foo == NULL){ |
400 |
|
|
printf("error in reading angle phi from %s\n" |
401 |
|
|
"natoms = %d, line = %d\n", |
402 |
|
|
in_name, state->nAtoms, lineCount ); |
403 |
|
|
exit(8); |
404 |
|
|
} |
405 |
|
|
(void)sscanf( foo, "%lf", &state->r[i].phi ); |
406 |
|
|
|
407 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
408 |
|
|
if(foo == NULL){ |
409 |
|
|
printf("error in reading unit vector x from %s\n" |
410 |
|
|
"natoms = %d, line = %d\n", |
411 |
|
|
in_name, state->nAtoms, lineCount ); |
412 |
|
|
exit(8); |
413 |
|
|
} |
414 |
|
|
(void)sscanf( foo, "%lf", &ux[i] ); |
415 |
|
|
|
416 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
417 |
|
|
if(foo == NULL){ |
418 |
|
|
printf("error in reading unit vector y from %s\n" |
419 |
|
|
"natoms = %d, line = %d\n", |
420 |
|
|
in_name, state->nAtoms, lineCount ); |
421 |
|
|
exit(8); |
422 |
|
|
} |
423 |
|
|
(void)sscanf( foo, "%lf", &uy[i] ); |
424 |
|
|
|
425 |
|
|
foo = strtok(NULL, " ,;\t\0"); |
426 |
|
|
if(foo == NULL){ |
427 |
|
|
printf("error in reading unit vector z from %s\n" |
428 |
|
|
"natoms = %d, line = %d\n", |
429 |
|
|
in_name, state->nAtoms, lineCount ); |
430 |
|
|
exit(8); |
431 |
|
|
} |
432 |
|
|
(void)sscanf( foo, "%lf", &uz[i] ); |
433 |
|
|
|
434 |
|
|
state->r[i].theta = acos(uz[i]); |
435 |
|
|
|
436 |
|
|
// The one parameter not stored in the dump file is the dipole strength |
437 |
|
|
state->r[i].mu = state->strength; |
438 |
|
|
} |
439 |
|
|
|
440 |
xsun |
1333 |
hsum_frame = 0.0; |
441 |
xsun |
1185 |
for (i = 0; i < state->nAtoms; i++) { |
442 |
|
|
|
443 |
|
|
h = state->r[i].pos[2]; |
444 |
|
|
h2 = pow(h,2); |
445 |
xsun |
1333 |
|
446 |
|
|
hsum_frame += h; |
447 |
xsun |
1185 |
hsum += h; |
448 |
|
|
h2sum += h2; |
449 |
xsun |
1333 |
|
450 |
xsun |
1185 |
n1++; |
451 |
|
|
} |
452 |
|
|
|
453 |
xsun |
1333 |
h_ave_frame = hsum_frame / (double) state->nAtoms; |
454 |
|
|
|
455 |
xsun |
1185 |
for(i = 0; i < state->nAtoms; i++){ |
456 |
|
|
|
457 |
|
|
omat[0][0] += ux[i] * ux[i] - onethird; |
458 |
|
|
omat[0][1] += ux[i] * uy[i]; |
459 |
|
|
omat[0][2] += ux[i] * uz[i]; |
460 |
|
|
omat[1][0] += uy[i] * ux[i]; |
461 |
|
|
omat[1][1] += uy[i] * uy[i] - onethird; |
462 |
|
|
omat[1][2] += uy[i] * uz[i]; |
463 |
|
|
omat[2][0] += uz[i] * ux[i]; |
464 |
|
|
omat[2][1] += uz[i] * uy[i]; |
465 |
|
|
omat[2][2] += uz[i] * uz[i] - onethird; |
466 |
|
|
|
467 |
|
|
} |
468 |
|
|
|
469 |
|
|
for(i = 0; i < 3; i++){ |
470 |
|
|
for(j = 0; j < 3; j++){ |
471 |
|
|
omat[i][j] /= (double) state->nAtoms; |
472 |
|
|
} |
473 |
|
|
} |
474 |
|
|
|
475 |
|
|
// temp_array = dsyev_ctof(omat, nfilled, nfilled); |
476 |
|
|
|
477 |
|
|
for(j=0;j<3;j++) |
478 |
xsun |
1333 |
for(i=0;i<3;i++) |
479 |
|
|
wrapMat[i+j*3] = omat[i][j]; |
480 |
xsun |
1185 |
|
481 |
|
|
ifail = 0; |
482 |
|
|
dsyev(&job, &uplo, &nfilled, wrapMat, &ndiag, evals, work, &lwork, &ifail); |
483 |
xsun |
1333 |
|
484 |
xsun |
1185 |
for(j=0;j<3;j++) |
485 |
xsun |
1333 |
for(i=0;i<3;i++) |
486 |
|
|
omat[i][j] = wrapMat[i+j*3]; |
487 |
|
|
|
488 |
xsun |
1185 |
//dsyev_ftoc2(temp_array, omat, nfilled, nfilled); |
489 |
xsun |
1333 |
|
490 |
xsun |
1185 |
//free(temp_array); |
491 |
|
|
|
492 |
xsun |
1333 |
maxEval = 0.0; |
493 |
xsun |
1185 |
for(j = 0; j < 3; j++){ |
494 |
xsun |
1333 |
if(fabs(evals[j]) > maxEval){ |
495 |
xsun |
1185 |
which = j; |
496 |
xsun |
1333 |
maxEval = fabs(evals[j]); |
497 |
xsun |
1185 |
} |
498 |
|
|
} |
499 |
|
|
|
500 |
xsun |
1333 |
orderpar[nframes-1] = 1.5 * maxEval; |
501 |
xsun |
1185 |
opbin = (int) (orderpar[nframes-1] / delr); |
502 |
|
|
if(opbin < nbins2) ophist[opbin] += 1; |
503 |
|
|
|
504 |
xsun |
1333 |
for(i = 0; i < 3; i++){ |
505 |
|
|
myDir[i] = 0.0; |
506 |
|
|
myPerp[i] = 0.0; |
507 |
|
|
} |
508 |
|
|
|
509 |
|
|
myDir[0] = omat[0][which]; |
510 |
|
|
myDir[1] = omat[1][which]; |
511 |
|
|
myDir[2] = omat[2][which]; |
512 |
xsun |
1185 |
|
513 |
xsun |
1333 |
if (myDir[0] < 0.0) { |
514 |
|
|
myDir[0] = -myDir[0]; |
515 |
|
|
myDir[1] = -myDir[1]; |
516 |
xsun |
1185 |
} |
517 |
xsun |
1333 |
|
518 |
|
|
ldir = sqrt(myDir[0]*myDir[0] + myDir[1]*myDir[1] + myDir[2]*myDir[2]); |
519 |
|
|
|
520 |
|
|
myDir[0] /= ldir; |
521 |
|
|
myDir[1] /= ldir; |
522 |
|
|
myDir[2] /= ldir; |
523 |
|
|
|
524 |
|
|
//printf("%f\t%f\t%f\n", myDir[0], myDir[1], myDir[2]); |
525 |
|
|
|
526 |
|
|
director[0][nframes-1] = myDir[0]; |
527 |
|
|
director[1][nframes-1] = myDir[1]; |
528 |
|
|
director[2][nframes-1] = myDir[2]; |
529 |
|
|
|
530 |
|
|
//printf("%f\t%f\t%f\n", director[0][nframes-1], director[1][nframes-1], director[2][nframes-1]); |
531 |
|
|
|
532 |
|
|
myPerp[0] = myDir[1]; |
533 |
|
|
myPerp[1] = -myDir[0]; |
534 |
|
|
myPerp[2] = 0.0; |
535 |
|
|
|
536 |
|
|
if (myPerp[0] < 0.0) { |
537 |
|
|
myPerp[0] = -myPerp[0]; |
538 |
|
|
myPerp[1] = -myPerp[1]; |
539 |
|
|
} |
540 |
|
|
|
541 |
|
|
lperp = sqrt(myPerp[0]*myPerp[0] + myPerp[1]*myPerp[1] + myPerp[2]*myPerp[2]); |
542 |
|
|
|
543 |
|
|
myPerp[0] /= lperp; |
544 |
|
|
myPerp[1] /= lperp; |
545 |
|
|
myPerp[2] /= lperp; |
546 |
|
|
|
547 |
|
|
vr[0][nframes-1] = myPerp[0]; |
548 |
|
|
vr[1][nframes-1] = myPerp[1]; |
549 |
|
|
vr[2][nframes-1] = myPerp[2]; |
550 |
|
|
|
551 |
|
|
maxProj = 0.5 * sqrt(dx*dx + dy*dy); |
552 |
|
|
//maxProj = myPerp[0]*dx + myPerp[1]*dy; |
553 |
|
|
// for now, assume highest atom is atom 0 |
554 |
|
|
highestAtom = 0; |
555 |
xsun |
1185 |
|
556 |
|
|
for(i = 0; i < state->nAtoms; i++){ |
557 |
xsun |
1333 |
|
558 |
|
|
// difference vector from highest point: |
559 |
|
|
myVec[0] = state->r[i].pos[0] - state->r[highestAtom].pos[0]; |
560 |
|
|
myVec[1] = state->r[i].pos[1] - state->r[highestAtom].pos[1]; |
561 |
|
|
// wrapped in periodic boundary conditions: |
562 |
|
|
wrapVector(myVec, state->Hmat, state->HmatI); |
563 |
|
|
|
564 |
|
|
// then projected onto myPerp: |
565 |
|
|
proj = myPerp[0]*myVec[0] + myPerp[1]*myVec[1]; |
566 |
|
|
// and binned: |
567 |
|
|
|
568 |
|
|
whichbin2 = (int) (((1.0 + (proj/maxProj)) / 2.0) * (double) nbins2); |
569 |
|
|
// printf( "proj/maxProj = %f\twhichbin2 = %d\n", proj/maxProj, whichbin2); |
570 |
|
|
|
571 |
|
|
hi = state->r[i].pos[2] - h_ave_frame; |
572 |
|
|
// for(i = 0; i < nbins2; i++) printf("%f\t%d\n", vrhist[i], vrsamp[i]); |
573 |
|
|
vrhist[whichbin2] += hi; |
574 |
|
|
vrsamp[whichbin2] ++; |
575 |
|
|
} |
576 |
|
|
|
577 |
|
|
for(i = 0; i < state->nAtoms; i++){ |
578 |
xsun |
1185 |
for(j = 0; j < state->nAtoms; j++){ |
579 |
|
|
|
580 |
|
|
d[0] = state->r[j].pos[0] - state->r[i].pos[0]; |
581 |
|
|
d[1] = state->r[j].pos[1] - state->r[i].pos[1]; |
582 |
|
|
|
583 |
|
|
wrapVector(d, state->Hmat, state->HmatI); |
584 |
|
|
|
585 |
|
|
whichbinx = (int) ((nbins-1) * (dx/2.0 + d[0]) / dx); |
586 |
|
|
whichbiny = (int) ((nbins-1) * (dy/2.0 + d[1]) / dy); |
587 |
|
|
|
588 |
|
|
//if (i == j) { |
589 |
|
|
//printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
590 |
|
|
//} |
591 |
|
|
|
592 |
|
|
//printf("d0 = %lf, d1 = %lf\n", d[0], d[1]); |
593 |
|
|
//printf("wx = %d, wy = %d\n", whichbinx, whichbiny); |
594 |
|
|
|
595 |
|
|
if (whichbinx >= nbins || whichbiny >= nbins) { |
596 |
|
|
printf("off by one error\n"); |
597 |
|
|
printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
598 |
|
|
exit(0); |
599 |
|
|
} |
600 |
|
|
if (whichbinx < 0 || whichbiny < 0) { |
601 |
|
|
printf("off by one error\n"); |
602 |
|
|
printf("whichbinx = %i, whichbiny = %i\n", whichbinx, whichbiny); |
603 |
|
|
exit(0); |
604 |
|
|
} |
605 |
|
|
|
606 |
|
|
hcorr = state->r[j].pos[2] * state->r[i].pos[2]; |
607 |
|
|
|
608 |
|
|
corrhist[nbins * whichbinx + whichbiny] += hcorr; |
609 |
|
|
|
610 |
|
|
dh = state->r[j].pos[2] - state->r[i].pos[2]; |
611 |
|
|
dh2 = pow(dh, 2); |
612 |
|
|
|
613 |
|
|
h2hist[nbins * whichbinx + whichbiny] += dh2; |
614 |
|
|
|
615 |
|
|
n2++; |
616 |
|
|
} |
617 |
|
|
} |
618 |
|
|
|
619 |
|
|
temp_state = state->next; |
620 |
|
|
state->next = NULL; |
621 |
|
|
|
622 |
|
|
if (temp_state != NULL) { |
623 |
|
|
free(temp_state->r); |
624 |
|
|
free(temp_state); |
625 |
|
|
} |
626 |
|
|
|
627 |
|
|
// Make a new frame |
628 |
|
|
|
629 |
|
|
temp_state = (struct system *) malloc(sizeof(struct system)); |
630 |
|
|
temp_state->next = state; |
631 |
|
|
state = temp_state; |
632 |
|
|
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
633 |
|
|
lineCount++; |
634 |
|
|
} |
635 |
|
|
|
636 |
|
|
|
637 |
|
|
have = hsum / (double) n1; |
638 |
|
|
h2ave = h2sum / (double) n1; |
639 |
|
|
fluc = h2ave - pow(have, 2); |
640 |
|
|
|
641 |
|
|
printf("# <h> = %lf\n", have); |
642 |
|
|
printf("# <h2> = %lf\n", h2ave); |
643 |
|
|
printf("# sigma(h) = %lf\n", sqrt(h2ave - have * have)); |
644 |
|
|
printf("# fluctuation = %lf\n", fluc); |
645 |
|
|
|
646 |
|
|
for(i = 0; i < nframes; i++){ |
647 |
|
|
sum_orderpar += orderpar[i]; |
648 |
|
|
sum2_orderpar += pow(orderpar[i], 2); |
649 |
|
|
} |
650 |
|
|
ave_orderpar = sum_orderpar / (double) nframes; |
651 |
|
|
ave2_orderpar = sum2_orderpar / (double) nframes; |
652 |
|
|
err_orderpar = ave2_orderpar - pow(ave_orderpar, 2); |
653 |
xsun |
1333 |
|
654 |
|
|
for(i = 0; i < 3; i++){ |
655 |
|
|
sum_director[i] = 0.0; |
656 |
|
|
ave_director[i] = 0.0; |
657 |
|
|
sum_vr[i] = 0.0; |
658 |
|
|
ave_vr[i] = 0.0; |
659 |
|
|
} |
660 |
xsun |
1185 |
|
661 |
|
|
for(i = 0; i < nframes; i++){ |
662 |
|
|
sum_director[0] += director[0][i]; |
663 |
|
|
sum_director[1] += director[1][i]; |
664 |
|
|
sum_director[2] += director[2][i]; |
665 |
|
|
} |
666 |
|
|
ave_director[0] = sum_director[0] / (double) nframes; |
667 |
|
|
ave_director[1] = sum_director[1] / (double) nframes; |
668 |
|
|
ave_director[2] = sum_director[2] / (double) nframes; |
669 |
|
|
|
670 |
|
|
for(i = 0; i < nframes; i++){ |
671 |
|
|
sum_vr[0] += vr[0][i]; |
672 |
|
|
sum_vr[1] += vr[1][i]; |
673 |
|
|
sum_vr[2] += vr[2][i]; |
674 |
|
|
} |
675 |
|
|
ave_vr[0] = sum_vr[0] / (double) nframes; |
676 |
|
|
ave_vr[1] = sum_vr[1] / (double) nframes; |
677 |
|
|
ave_vr[2] = sum_vr[2] / (double) nframes; |
678 |
|
|
|
679 |
|
|
printf("# orderparameter = %lf\n", ave_orderpar); |
680 |
|
|
printf("# error = %lf\n", err_orderpar); |
681 |
|
|
printf("# director axis is ( %lf\t%lf\t%lf )\n", |
682 |
|
|
ave_director[0], ave_director[1], ave_director[2]); |
683 |
xsun |
1333 |
printf("# vr axis is ( %lf\t%lf\t%lf )\n", ave_vr[0], ave_vr[1], ave_vr[2]); |
684 |
xsun |
1185 |
|
685 |
|
|
dx = sqrt(pow(state->Hmat[0][0], 2) + pow(state->Hmat[1][0], 2)); |
686 |
|
|
dy = sqrt(pow(state->Hmat[0][1], 2) + pow(state->Hmat[1][1], 2)); |
687 |
|
|
|
688 |
|
|
area = dx * dy; |
689 |
|
|
|
690 |
|
|
bigL = sqrt(area); |
691 |
|
|
|
692 |
|
|
areaPerMolecule = area / (double) state->nAtoms; |
693 |
|
|
|
694 |
|
|
smallA = sqrt(areaPerMolecule); |
695 |
|
|
|
696 |
|
|
gamma = t * log(bigL / smallA) / (2.0 * M_PI * fluc); |
697 |
|
|
|
698 |
|
|
printf("# first gamma estimate = %lf\n", gamma); |
699 |
|
|
|
700 |
xsun |
1333 |
firstData = -1; |
701 |
|
|
lastData = -1; |
702 |
|
|
|
703 |
|
|
for (i=0; i< nbins2; i++) { |
704 |
|
|
if (vrsamp[i] > 0) { |
705 |
|
|
if (firstData == -1) firstData = i; |
706 |
|
|
lastData = i; |
707 |
|
|
} |
708 |
|
|
} |
709 |
|
|
|
710 |
|
|
maxProj = 0.5*sqrt(dx*dx + dy*dy); |
711 |
|
|
maxProjOut = 2.0*maxProj*(double)(lastData - firstData)/(double)nbins2; |
712 |
|
|
|
713 |
|
|
printf("# maximum projection = %lf\n", maxProjOut); |
714 |
xsun |
1185 |
printf("# \n"); |
715 |
xsun |
1333 |
|
716 |
|
|
for (i = firstData ; i < lastData; i++) { |
717 |
|
|
//proj = maxProj * ((double)i / (double)nbins2); |
718 |
|
|
|
719 |
|
|
proj = maxProj*( (2.0 * (double)i / (double)nbins2) -1.0); |
720 |
|
|
|
721 |
|
|
if (vrsamp[i] > 0) { |
722 |
|
|
avgHeightAtProj = vrhist[i]/(double)vrsamp[i]; |
723 |
|
|
} else { |
724 |
|
|
avgHeightAtProj = 0.0; |
725 |
|
|
} |
726 |
|
|
printf("%lf\t%lf\n", proj, avgHeightAtProj); |
727 |
xsun |
1185 |
} |
728 |
|
|
|
729 |
|
|
selfx = (int) ((double)nbins / 2.0); |
730 |
|
|
selfy = (int) ((double)nbins / 2.0); |
731 |
|
|
|
732 |
|
|
/* for (i = 0; i < nbins; i++) { */ |
733 |
|
|
/* for (j = 0; j < nbins; j++) { */ |
734 |
|
|
/* printf("%lf\t", h2hist[nbins * i + j] / (double) n2); */ |
735 |
|
|
/* } */ |
736 |
|
|
/* printf("\n"); */ |
737 |
|
|
/* } */ |
738 |
|
|
|
739 |
|
|
free(work); |
740 |
|
|
free(corrhist); |
741 |
|
|
free(h2hist); |
742 |
|
|
free(ux); |
743 |
|
|
free(uy); |
744 |
|
|
free(uz); |
745 |
|
|
return 1; |
746 |
|
|
|
747 |
|
|
} |
748 |
|
|
|
749 |
|
|
double matDet2(double a[2][2]) { |
750 |
|
|
|
751 |
|
|
double determinant; |
752 |
|
|
|
753 |
|
|
determinant = (a[0][0] * a[1][1]) - (a[0][1] * a[1][0]); |
754 |
|
|
|
755 |
|
|
return determinant; |
756 |
|
|
} |
757 |
|
|
|
758 |
|
|
|
759 |
|
|
void invertMat2(double a[2][2], double b[2][2]) { |
760 |
|
|
|
761 |
|
|
double determinant; |
762 |
|
|
|
763 |
|
|
determinant = matDet2( a ); |
764 |
|
|
|
765 |
|
|
if (determinant == 0.0) { |
766 |
|
|
printf("Can't invert a matrix with a zero determinant!\n"); |
767 |
|
|
} |
768 |
|
|
|
769 |
|
|
b[0][0] = a[1][1] / determinant; |
770 |
|
|
b[0][1] = -a[0][1] / determinant; |
771 |
|
|
b[1][0] = -a[1][0] / determinant; |
772 |
|
|
b[1][1] = a[0][0] / determinant; |
773 |
|
|
} |
774 |
|
|
|
775 |
|
|
void matVecMul2(double m[2][2], double inVec[2], double outVec[2]) { |
776 |
|
|
double a0, a1, a2; |
777 |
|
|
|
778 |
|
|
a0 = inVec[0]; a1 = inVec[1]; |
779 |
|
|
|
780 |
|
|
outVec[0] = m[0][0]*a0 + m[0][1]*a1; |
781 |
|
|
outVec[1] = m[1][0]*a0 + m[1][1]*a1; |
782 |
|
|
} |
783 |
|
|
|
784 |
|
|
void wrapVector( double thePos[2], double Hmat[2][2], double HmatInv[2][2]){ |
785 |
|
|
|
786 |
|
|
int i; |
787 |
|
|
double scaled[2]; |
788 |
|
|
|
789 |
|
|
// calc the scaled coordinates. |
790 |
|
|
|
791 |
|
|
matVecMul2(HmatInv, thePos, scaled); |
792 |
|
|
|
793 |
|
|
for(i=0; i<2; i++) |
794 |
|
|
scaled[i] -= roundMe(scaled[i]); |
795 |
|
|
|
796 |
|
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
797 |
|
|
|
798 |
|
|
matVecMul2(Hmat, scaled, thePos); |
799 |
|
|
|
800 |
|
|
} |
801 |
|
|
|
802 |
|
|
/* double* dsyev_ctof(double **in, int rows, int cols) */ |
803 |
|
|
/* { */ |
804 |
|
|
/* double *out; */ |
805 |
|
|
/* int i, j; */ |
806 |
|
|
|
807 |
|
|
/* out = (double *) calloc(rows * cols, sizeof(double)); */ |
808 |
|
|
|
809 |
|
|
/* if (!out){ */ |
810 |
|
|
/* printf("Fail to allocate memory\n"); */ |
811 |
|
|
/* exit(1); */ |
812 |
|
|
/* } */ |
813 |
|
|
|
814 |
|
|
/* for (i = 0; i < rows; i++) */ |
815 |
|
|
/* for (j = 0; j < cols; j++) */ |
816 |
|
|
/* out[i+j*cols] = in[i][j]; */ |
817 |
|
|
|
818 |
|
|
/* return(out); */ |
819 |
|
|
/* } */ |
820 |
|
|
|
821 |
|
|
/* void dsyev_ftoc2(double *in, double **out, int rows, int cols) */ |
822 |
|
|
/* { */ |
823 |
|
|
/* int i, j; */ |
824 |
|
|
|
825 |
|
|
/* for (i = 0; i < rows; i++) */ |
826 |
|
|
/* for (j = 0; j < cols; j++) */ |
827 |
|
|
/* out[i][j] = in[i+j*cols]; */ |
828 |
|
|
/* } */ |
829 |
|
|
/* void direct(double rcut, double box, int n, int nstep, int maxbin){ */ |
830 |
|
|
|
831 |
|
|
/* int bin, maxbin, nbins, i, j, k, n, bind, which; */ |
832 |
|
|
/* int hist[maxbin], histd[maxbin], startstep; */ |
833 |
|
|
/* int nstep, stopstep, ndiag, nfilled, ifail, lwork; */ |
834 |
|
|
/* double delr, rijsp, rxij, ryij, rzij, rij; */ |
835 |
|
|
/* double delrd, rijsqd, rijd, orderpar[1000], nideal; */ |
836 |
|
|
/* double omat[3][3], evals[100], cons, rlower; */ |
837 |
|
|
/* double rcut, box, dens, director[3][1000], rupper; */ |
838 |
|
|
/* double rx[1000][1000], ry[1000][1000], rz[1000][1000]; */ |
839 |
|
|
/* double ux[1000][1000], uy[1000][1000], uz[1000][1000]; */ |
840 |
|
|
/* double vx[1000][1000], vy[1000][1000], vz[1000][1000]; */ |
841 |
|
|
/* double jx[1000][1000], jy[1000][1000], jz[1000][1000]; */ |
842 |
|
|
/* double grd[5000], gr[5000], max, binmin, binmax; */ |
843 |
|
|
/* double onethird, ordvals[5000]; */ |
844 |
|
|
/* char job, uplo; */ |
845 |
|
|
/* int ndiag; */ |
846 |
|
|
/* int nfilled; */ |
847 |
|
|
/* double omat[3][3]; */ |
848 |
|
|
/* double evals[100]; */ |
849 |
|
|
/* double work[]; */ |
850 |
|
|
/* int lwork; */ |
851 |
|
|
/* int ifail; */ |
852 |
|
|
|
853 |
|
|
/* lwork = 9; */ |
854 |
|
|
/* work = (double *)calloc(lwork, sizeof(double)); */ |
855 |
|
|
|
856 |
|
|
/* onethird = 1.0 / 3.0; */ |
857 |
|
|
/* ndiag = 3; */ |
858 |
|
|
/* nfilled = 3; */ |
859 |
|
|
/* job = 'V'; */ |
860 |
|
|
/* uplo = 'U'; */ |
861 |
|
|
/* ifail = 0; */ |
862 |
|
|
|
863 |
|
|
/* binmin = 0.0; */ |
864 |
|
|
/* binmax = 1.0; */ |
865 |
|
|
/* delr = (binmax - binmin) / (double) maxbin; */ |
866 |
|
|
|
867 |
|
|
/* for(i = 0; i < maxbin; i++){ */ |
868 |
|
|
|
869 |
|
|
/* ordvals(i) = 0.0; */ |
870 |
|
|
/* hist(i) = 0.0; */ |
871 |
|
|
|
872 |
|
|
/* } */ |
873 |
|
|
|
874 |
|
|
/* for(i = 0; i < stopstep; i++){ */ |
875 |
|
|
|
876 |
|
|
/* for(j = 0; j < 3; j++){ */ |
877 |
|
|
/* for(k = 0; k < 3; k++){ */ |
878 |
|
|
/* omat[j][k] = 0.0; */ |
879 |
|
|
/* } */ |
880 |
|
|
/* } */ |
881 |
|
|
|
882 |
|
|
/* for(j = 0; j < n; j++){ */ |
883 |
|
|
|
884 |
|
|
/* omat[1][1] = omat[1][1] + ux[j][i] * ux[j][i] - onethird; */ |
885 |
|
|
/* omat[1][2] = omat[1][2] + ux[j][i] * uy[j][i]; */ |
886 |
|
|
/* omat[1][3] = omat[1][3] + ux[j][i] * uz[j][i]; */ |
887 |
|
|
/* omat[2][1] = omat[2][1] + uy[j][i] * ux[j][i]; */ |
888 |
|
|
/* omat[2][2] = omat[2][2] + uy[j][i] * uy[j][i] - onethird; */ |
889 |
|
|
/* omat[2][3] = omat[2][3] + uy[j][i] * uz[j][i]; */ |
890 |
|
|
/* omat[3][1] = omat[3][1] + uz[j][i] * ux[j][i]; */ |
891 |
|
|
/* omat[3][2] = omat[3][2] + uz[j][i] * uy[j][i]; */ |
892 |
|
|
/* omat[3][3] = omat[3][3] + uz[j][i] * uz[j][i] - onethird; */ |
893 |
|
|
|
894 |
|
|
/* } */ |
895 |
|
|
|
896 |
|
|
|
897 |
|
|
/* for(j = 0; j < 3; j++){ */ |
898 |
|
|
/* for(k = 0; k < 3; k++){ */ |
899 |
|
|
/* omat[j][k] = omat[j][k] / (double) n; */ |
900 |
|
|
/* } */ |
901 |
|
|
/* } */ |
902 |
|
|
|
903 |
|
|
/* dsyev_(job, uplo, nfilled, omat, ndiag, evals, work, lwork, ifail); */ |
904 |
|
|
|
905 |
|
|
/* max = 0.0; */ |
906 |
|
|
/* for(j = 0; j < 3; j++){ */ |
907 |
|
|
/* if(fabs(evals(j)) > max){ */ |
908 |
|
|
/* which = j; */ |
909 |
|
|
/* max = fabs(evals(j)); */ |
910 |
|
|
/* } */ |
911 |
|
|
/* } */ |
912 |
|
|
|
913 |
|
|
/* director[1][i] = omat[1][which]; */ |
914 |
|
|
/* director[2][i] = omat[2][which]; */ |
915 |
|
|
/* director[3][i] = omat[3][which]; */ |
916 |
|
|
|
917 |
|
|
/* orderpar(i) = 1.5 * max; */ |
918 |
|
|
|
919 |
|
|
/* bin = (int) (orderpar(i) / delr) + 1; */ |
920 |
|
|
|
921 |
|
|
/* if(bin < maxbin) */ |
922 |
|
|
/* hist(bin) = hist(bin) + 1; */ |
923 |
|
|
/* } */ |
924 |
|
|
|
925 |
|
|
/* cons = 1.0; */ |
926 |
|
|
/* for(bin = 0; bin < maxbin; bin++){ */ |
927 |
|
|
|
928 |
|
|
/* rlower = (double) (bin - 1) * delr; */ |
929 |
|
|
/* rupper = rlower + delr; */ |
930 |
|
|
/* ordvals(bin) = rlower + (delr / 2.0); */ |
931 |
|
|
/* nideal = cons * (pow(rupper, 3) - pow(rlower, 3)); */ |
932 |
|
|
/* gr(bin) = (double) (hist(bin)) / (double) nstep /nideal; */ |
933 |
|
|
|
934 |
|
|
/* } */ |
935 |
|
|
/* } */ |