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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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|
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#include "cosCorr.h" |
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|
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void cosCorr( char* out_prefix, char* atom1, char* atom2, |
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struct xyz_frame* frames, int nFrames, |
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int startFrame, int endFrame ){ |
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|
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|
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int i,j,k; |
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|
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double atom1Dens; |
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double atom2Dens; |
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|
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double atom1Constant; |
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double atom2Constant; |
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|
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double nAtom1; |
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double nAtom2; |
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|
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double delR; |
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double boxVol; |
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double shortBox; |
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|
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double dx, dy, dz; |
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double rxj, ryj, rzj; |
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double uxj, uyj, uzj; |
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double uxk, uyk, uzk; |
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double uj, uk; |
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double distSqr; |
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double dist; |
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double dotProd; |
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|
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double rLower, rUpper; |
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double nIdeal; |
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double volSlice; |
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|
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int bin; |
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int histogram[histBins]; |
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double the_cosCorr[histBins]; |
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double rValue[histBins]; |
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|
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char out_name[500]; |
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char tempString[100]; |
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FILE *out_file; |
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|
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// find the box size and delR; |
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|
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shortBox = frames[0].boxX; |
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if( shortBox > frames[0].boxY ) shortBox = frames[0].boxY; |
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if( shortBox > frames[0].boxZ ) shortBox = frames[0].boxZ; |
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|
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delR = ( shortBox / 2.0 ) / histBins; |
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boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ; |
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|
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// zero the histograms; |
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|
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for(i=0; i<histBins; i++ ){ |
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|
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rValue[i] = 0.0; |
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the_cosCorr[i] = 0.0; |
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histogram[i] = 0; |
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} |
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|
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// find the number of each type; |
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|
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nAtom1 = 0; |
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nAtom2 = 0; |
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for( i=0; i<frames[0].nAtoms; i++ ){ |
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|
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if( !strcmp( frames[0].names[i], atom1 ) ) nAtom1++; |
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if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++; |
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} |
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|
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if( !nAtom1 ){ |
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|
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fprintf( stderr, |
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"\n" |
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"cosCorr error, \"%s\" was not found in the trajectory.\n", |
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atom1 ); |
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exit(8); |
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} |
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|
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if( !nAtom2 ){ |
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|
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fprintf( stderr, |
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"\n" |
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"cosCorr error, \"%s\" was not found in the trajectory.\n", |
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atom2 ); |
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exit(8); |
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} |
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|
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// calculate some of the constants; |
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|
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atom1Dens = nAtom1 / boxVol; |
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atom2Dens = nAtom2 / boxVol; |
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|
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atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0; |
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atom2Constant = ( 4.0 * M_PI * atom2Dens ) / 3.0; |
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|
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// calculate the histogram |
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|
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for( i=startFrame; i<endFrame; i++){ |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
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|
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if( !strcmp( frames[0].names[j], atom1 ) ){ |
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|
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rxj = frames[i].r[j].x; |
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ryj = frames[i].r[j].y; |
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rzj = frames[i].r[j].z; |
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|
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// normalize the unit vector |
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|
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uxj = frames[i].v[j].x; |
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uyj = frames[i].v[j].y; |
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uzj = frames[i].v[j].z; |
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|
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uj = sqrt( (uxj * uxj) + (uyj * uyj) + (uzj * uzj) ); |
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|
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uxj /= uj; |
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uyj /= uj; |
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uzj /= uj; |
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|
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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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|
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if( !strcmp( frames[0].names[k], atom2 ) ){ |
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|
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// normalize the unit vector |
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|
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uxk = frames[i].v[k].x; |
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uyk = frames[i].v[k].y; |
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uzk = frames[i].v[k].z; |
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|
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uk = sqrt( (uxk * uxk) + (uyk * uyk) + (uzk * uzk) ); |
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|
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uxk /= uk; |
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uyk /= uk; |
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uzk /= uk; |
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|
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// calculate the distance |
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|
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dx = rxj - frames[i].r[k].x; |
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dy = ryj - frames[i].r[k].y; |
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dz = rzj - frames[i].r[k].z; |
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|
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map( &dx, &dy, &dz, |
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frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
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|
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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
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dist = sqrt( distSqr ); |
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|
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// calculate the cos correllation |
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|
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dotProd = (uxj * uxk) + (uyj * uyk) + (uzj * uzk); |
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|
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// add to the appropriate bin |
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bin = (int)( dist / delR ); |
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if( bin < histBins ){ |
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histogram[bin] += 2; |
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the_cosCorr[bin] += 2.0 * dotProd; |
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} |
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} |
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} |
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} |
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else if( !strcmp( frames[0].names[j], atom2 ) ){ |
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|
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rxj = frames[i].r[j].x; |
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ryj = frames[i].r[j].y; |
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rzj = frames[i].r[j].z; |
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|
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// normalize the unit vector |
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|
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uxj = frames[i].v[j].x; |
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uyj = frames[i].v[j].y; |
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uzj = frames[i].v[j].z; |
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|
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uj = sqrt( (uxj * uxj) + (uyj * uyj) + (uzj * uzj) ); |
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|
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uxj /= uj; |
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uyj /= uj; |
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uzj /= uj; |
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|
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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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|
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if( !strcmp( frames[0].names[k], atom1 ) ){ |
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|
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// normalize the unit vector |
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|
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uxk = frames[i].v[k].x; |
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uyk = frames[i].v[k].y; |
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uzk = frames[i].v[k].z; |
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|
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uk = sqrt( (uxk * uxk) + (uyk * uyk) + (uzk * uzk) ); |
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|
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uxk /= uk; |
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uyk /= uk; |
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uzk /= uk; |
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|
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// calculate the distance |
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|
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dx = rxj - frames[i].r[k].x; |
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dy = ryj - frames[i].r[k].y; |
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dz = rzj - frames[i].r[k].z; |
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|
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map( &dx, &dy, &dz, |
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frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
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|
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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
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dist = sqrt( distSqr ); |
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|
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// calculate the cos correllation |
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|
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dotProd = (uxj * uxk) + (uyj * uyk) + (uzj * uzk); |
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|
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// add to the appropriate bin |
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bin = (int)( dist / delR ); |
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if( bin < histBins ){ |
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histogram[bin] += 2; |
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the_cosCorr[bin] += 2.0 * dotProd; |
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} |
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} |
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} |
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} |
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} |
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} |
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|
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// calculate the cosCorr |
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|
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for( i=0; i<histBins; i++ ){ |
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|
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rLower = i * delR; |
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rUpper = rLower + delR; |
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|
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if( histogram[i] != 0 ) the_cosCorr[i] /= histogram[i]; |
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|
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rValue[i] = rLower + ( delR / 2.0 ); |
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} |
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|
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// make the out_name; |
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|
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strcpy( out_name, out_prefix ); |
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sprintf( tempString, "-%s-%s.cosCorr", atom1, atom2 ); |
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strcat( out_name, tempString ); |
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|
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out_file = fopen( out_name, "w" ); |
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if( out_file == NULL ){ |
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fprintf( stderr, |
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"\n" |
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"cosCorr error, unable to open \"%s\" for writing.\n", |
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out_name ); |
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exit(8); |
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} |
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|
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// write out the findings |
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|
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for( i=0; i<histBins; i++ ){ |
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fprintf( out_file, |
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"%lf\t%lf\n", |
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rValue[i], the_cosCorr[i] ); |
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} |
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|
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fclose( out_file ); |
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|
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} |
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