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mmeineke |
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#include <math.h> |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include "GofR.h" |
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void map( double *x, double *y, double *z, |
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double boxX, double boxY, double boxZ ); |
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// this algoritm assumes constant number of atoms between frames, and |
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// constant boxSize |
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void GofR( char* out_prefix, char* atom1, char* atom2, |
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mmeineke |
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struct xyz_frame* frames, int nFrames, |
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int startFrame, int endFrame ){ |
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mmeineke |
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mmeineke |
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int i,j,k; |
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mmeineke |
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enum g_types { all_all, atom_all, atom_atom }; |
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enum g_types the_type; |
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char* allAtom; |
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double atom1Dens; |
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double atom2Dens; |
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double allDens; |
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double atom1Constant; |
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double atom2Constant; |
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double allConstant; |
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double nAtom1; |
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double nAtom2; |
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double nAtoms; |
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double delR; |
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double boxVol; |
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double shortBox; |
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mmeineke |
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double rxj, ryj, rzj; |
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mmeineke |
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double dx, dy, dz; |
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double distSqr; |
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double dist; |
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double rLower, rUpper; |
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double nIdeal; |
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double volSlice; |
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int bin; |
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int histogram[GofRBins]; |
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double the_GofR[GofRBins]; |
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double rValue[GofRBins]; |
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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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// figure out the type of GofR we are calculating |
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if( !strcmp( atom1, "all" ) ){ |
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if( !strcmp( atom2, "all" ) ) the_type = all_all; |
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else{ |
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the_type = atom_all; |
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allAtom = atom2; |
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} |
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} |
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else{ |
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if( !strcmp( atom2, "all" ) ){ |
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the_type = atom_all; |
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allAtom = atom1; |
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} |
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else the_type = atom_atom; |
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} |
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// find the box size and delR; |
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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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delR = ( shortBox / 2.0 ) / GofRBins; |
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boxVol = frames[0].boxX * frames[0].boxY * frames[0].boxZ; |
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// zero the histograms; |
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for(i=0; i<GofRBins; i++ ){ |
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rValue[i] = 0.0; |
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the_GofR[i] = 0.0; |
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histogram[i] = 0; |
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} |
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switch( the_type ){ |
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case atom_atom: |
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// find the number of each type; |
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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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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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if( !nAtom1 ){ |
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fprintf( stderr, |
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"\n" |
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"GofR 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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if( !nAtom2 ){ |
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fprintf( stderr, |
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"\n" |
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"GofR 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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// calculate some of the constants; |
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atom1Dens = nAtom1 / boxVol; |
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atom2Dens = nAtom2 / boxVol; |
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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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// calculate the histogram |
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mmeineke |
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for( i=startFrame; i<endFrame; i++){ |
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mmeineke |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
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mmeineke |
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if( !strcmp( frames[0].names[j], atom1 ) ){ |
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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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mmeineke |
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mmeineke |
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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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mmeineke |
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if( !strcmp( frames[0].names[k], atom2 ) ){ |
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mmeineke |
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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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mmeineke |
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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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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
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dist = sqrt( distSqr ); |
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// add to the appropriate bin |
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bin = (int)( dist / delR ); |
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if( bin < GofRBins ) histogram[bin] += 2; |
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} |
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} |
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mmeineke |
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} |
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else if( !strcmp( frames[0].names[j], atom2 ) ){ |
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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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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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mmeineke |
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if( !strcmp( frames[0].names[k], atom1 ) ){ |
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mmeineke |
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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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mmeineke |
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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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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
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dist = sqrt( distSqr ); |
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// add to the appropriate bin |
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bin = (int)( dist / delR ); |
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if( bin < GofRBins ) histogram[bin] += 2; |
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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 GofR |
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for( i=0; i<GofRBins; i++ ){ |
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rLower = i * delR; |
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rUpper = rLower + delR; |
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
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nIdeal = volSlice * ( atom1Constant + atom2Constant ); |
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the_GofR[i] = histogram[i] / ( nFrames * ( nAtom1 + nAtom2 ) * nIdeal ); |
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rValue[i] = rLower + ( delR / 2.0 ); |
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} |
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// make the out_name; |
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strcpy( out_name, out_prefix ); |
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sprintf( tempString, "-%s-%s.GofR", atom1, atom2 ); |
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strcat( out_name, tempString ); |
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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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"GofR 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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break; |
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case atom_all: |
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// find the number of AllAtoms; |
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nAtom1 = 0; |
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for( i=0; i<frames[0].nAtoms; i++ ){ |
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if( !strcmp( frames[0].names[i], allAtom ) ) nAtom1++; |
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} |
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if( !nAtom1 ){ |
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fprintf( stderr, |
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"\n" |
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"GofR error, \"%s\" was not found in the trajectory.\n", |
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atom1 ); |
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exit(8); |
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} |
245 |
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// calculate some of the constants; |
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atom1Dens = nAtom1 / boxVol; |
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allDens = frames[0].nAtoms / boxVol; |
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atom1Constant = ( 4.0 * M_PI * atom1Dens ) / 3.0; |
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allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
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// calculate the histogram |
255 |
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mmeineke |
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for( i=startFrame; i<endFrame; i++){ |
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mmeineke |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
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mmeineke |
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if( !strcmp( frames[0].names[j], allAtom ) ){ |
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mmeineke |
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mmeineke |
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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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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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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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mmeineke |
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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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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
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dist = sqrt( distSqr ); |
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// add to the appropriate bin |
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bin = (int)( dist / delR ); |
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if( bin < GofRBins ) histogram[bin] += 2; |
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} |
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mmeineke |
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} |
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mmeineke |
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283 |
mmeineke |
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else{ |
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rxj = frames[i].r[j].x; |
286 |
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ryj = frames[i].r[j].y; |
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rzj = frames[i].r[j].z; |
288 |
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289 |
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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
290 |
mmeineke |
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291 |
mmeineke |
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if( !strcmp( frames[0].names[k], allAtom ) ){ |
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293 |
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dx = rxj - frames[i].r[k].x; |
294 |
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dy = ryj - frames[i].r[k].y; |
295 |
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dz = rzj - frames[i].r[k].z; |
296 |
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297 |
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map( &dx, &dy, &dz, |
298 |
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frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
299 |
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300 |
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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
301 |
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dist = sqrt( distSqr ); |
302 |
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303 |
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// add to the appropriate bin |
304 |
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bin = (int)( dist / delR ); |
305 |
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if( bin < GofRBins ) histogram[bin] += 2; |
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} |
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mmeineke |
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} |
308 |
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} |
309 |
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} |
310 |
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} |
311 |
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312 |
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// calculate the GofR |
313 |
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314 |
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for( i=0; i<GofRBins; i++ ){ |
315 |
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316 |
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rLower = i * delR; |
317 |
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rUpper = rLower + delR; |
318 |
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319 |
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
320 |
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nIdeal = volSlice * ( allConstant ); |
321 |
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322 |
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
323 |
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rValue[i] = rLower + ( delR / 2.0 ); |
324 |
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} |
325 |
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326 |
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// make the out_name; |
327 |
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328 |
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strcpy( out_name, out_prefix ); |
329 |
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sprintf( tempString, "-%s-%s.GofR", allAtom, "all" ); |
330 |
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strcat( out_name, tempString ); |
331 |
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332 |
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out_file = fopen( out_name, "w" ); |
333 |
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if( out_file == NULL ){ |
334 |
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fprintf( stderr, |
335 |
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"\n" |
336 |
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"GofR error, unable to open \"%s\" for writing.\n", |
337 |
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out_name ); |
338 |
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exit(8); |
339 |
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} |
340 |
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break; |
341 |
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342 |
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case all_all: |
343 |
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344 |
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// calculate some of the constants; |
345 |
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346 |
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allDens = frames[0].nAtoms / boxVol; |
347 |
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348 |
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allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
349 |
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350 |
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// calculate the histogram |
351 |
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352 |
mmeineke |
82 |
for( i=startFrame; i<endFrame; i++){ |
353 |
mmeineke |
45 |
for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
354 |
mmeineke |
46 |
|
355 |
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rxj = frames[i].r[j].x; |
356 |
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ryj = frames[i].r[j].y; |
357 |
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rzj = frames[i].r[j].z; |
358 |
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359 |
mmeineke |
45 |
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
360 |
mmeineke |
46 |
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361 |
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dx = rxj - frames[i].r[k].x; |
362 |
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dy = ryj - frames[i].r[k].y; |
363 |
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dz = rzj - frames[i].r[k].z; |
364 |
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365 |
mmeineke |
45 |
map( &dx, &dy, &dz, |
366 |
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frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
367 |
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368 |
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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
369 |
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dist = sqrt( distSqr ); |
370 |
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371 |
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// add to the appropriate bin |
372 |
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bin = (int)( dist / delR ); |
373 |
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if( bin < GofRBins ) histogram[bin] += 2; |
374 |
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} |
375 |
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} |
376 |
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} |
377 |
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378 |
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// calculate the GofR |
379 |
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380 |
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for( i=0; i<GofRBins; i++ ){ |
381 |
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382 |
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rLower = i * delR; |
383 |
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rUpper = rLower + delR; |
384 |
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385 |
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
386 |
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nIdeal = volSlice * ( allConstant ); |
387 |
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388 |
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
389 |
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rValue[i] = rLower + ( delR / 2.0 ); |
390 |
|
|
} |
391 |
|
|
|
392 |
|
|
// make the out_name; |
393 |
|
|
|
394 |
|
|
strcpy( out_name, out_prefix ); |
395 |
|
|
sprintf( tempString, "-%s-%s.GofR", "all", "all" ); |
396 |
|
|
strcat( out_name, tempString ); |
397 |
|
|
|
398 |
|
|
out_file = fopen( out_name, "w" ); |
399 |
|
|
if( out_file == NULL ){ |
400 |
|
|
fprintf( stderr, |
401 |
|
|
"\n" |
402 |
|
|
"GofR error, unable to open \"%s\" for writing.\n", |
403 |
|
|
out_name ); |
404 |
|
|
exit(8); |
405 |
|
|
} |
406 |
|
|
break; |
407 |
|
|
} |
408 |
|
|
|
409 |
|
|
for( i=0; i<GofRBins; i++ ){ |
410 |
|
|
fprintf( out_file, |
411 |
|
|
"%lf\t%lf\n", |
412 |
|
|
rValue[i], the_GofR[i] ); |
413 |
|
|
} |
414 |
|
|
|
415 |
|
|
fclose( out_file ); |
416 |
|
|
} |
417 |
|
|
|