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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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mmeineke |
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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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struct xyz_frame* frames, int nFrames ){ |
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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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mmeineke |
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if( !strcmp( frames[0].names[i], atom2 ) ) nAtom2++; |
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mmeineke |
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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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for( i=0; i<nFrames; i++){ |
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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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} |
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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 |
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for( i=0; i<nFrames; i++){ |
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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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mmeineke |
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else{ |
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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; |
287 |
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288 |
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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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mmeineke |
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290 |
mmeineke |
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if( !strcmp( frames[0].names[k], allAtom ) ){ |
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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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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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302 |
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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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} |
308 |
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} |
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} |
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311 |
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// calculate the GofR |
312 |
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313 |
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for( i=0; i<GofRBins; i++ ){ |
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315 |
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rLower = i * delR; |
316 |
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rUpper = rLower + delR; |
317 |
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318 |
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
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nIdeal = volSlice * ( allConstant ); |
320 |
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321 |
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
322 |
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rValue[i] = rLower + ( delR / 2.0 ); |
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} |
324 |
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325 |
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// make the out_name; |
326 |
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strcpy( out_name, out_prefix ); |
328 |
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sprintf( tempString, "-%s-%s.GofR", allAtom, "all" ); |
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strcat( out_name, tempString ); |
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out_file = fopen( out_name, "w" ); |
332 |
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if( out_file == NULL ){ |
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fprintf( stderr, |
334 |
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"\n" |
335 |
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"GofR error, unable to open \"%s\" for writing.\n", |
336 |
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out_name ); |
337 |
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exit(8); |
338 |
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} |
339 |
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break; |
340 |
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case all_all: |
342 |
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343 |
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// calculate some of the constants; |
344 |
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345 |
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allDens = frames[0].nAtoms / boxVol; |
346 |
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347 |
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allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
348 |
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349 |
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// calculate the histogram |
350 |
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351 |
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for( i=0; i<nFrames; i++){ |
352 |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
353 |
mmeineke |
46 |
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354 |
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rxj = frames[i].r[j].x; |
355 |
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ryj = frames[i].r[j].y; |
356 |
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rzj = frames[i].r[j].z; |
357 |
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358 |
mmeineke |
45 |
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
359 |
mmeineke |
46 |
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360 |
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dx = rxj - frames[i].r[k].x; |
361 |
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dy = ryj - frames[i].r[k].y; |
362 |
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dz = rzj - frames[i].r[k].z; |
363 |
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364 |
mmeineke |
45 |
map( &dx, &dy, &dz, |
365 |
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frames[i].boxX, frames[i].boxY, frames[i].boxZ ); |
366 |
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367 |
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distSqr = (dx * dx) + (dy * dy) + (dz * dz); |
368 |
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dist = sqrt( distSqr ); |
369 |
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370 |
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// add to the appropriate bin |
371 |
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bin = (int)( dist / delR ); |
372 |
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if( bin < GofRBins ) histogram[bin] += 2; |
373 |
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} |
374 |
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} |
375 |
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} |
376 |
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377 |
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// calculate the GofR |
378 |
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379 |
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for( i=0; i<GofRBins; i++ ){ |
380 |
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381 |
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rLower = i * delR; |
382 |
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rUpper = rLower + delR; |
383 |
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384 |
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
385 |
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nIdeal = volSlice * ( allConstant ); |
386 |
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387 |
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
388 |
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rValue[i] = rLower + ( delR / 2.0 ); |
389 |
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} |
390 |
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391 |
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// make the out_name; |
392 |
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393 |
|
|
strcpy( out_name, out_prefix ); |
394 |
|
|
sprintf( tempString, "-%s-%s.GofR", "all", "all" ); |
395 |
|
|
strcat( out_name, tempString ); |
396 |
|
|
|
397 |
|
|
out_file = fopen( out_name, "w" ); |
398 |
|
|
if( out_file == NULL ){ |
399 |
|
|
fprintf( stderr, |
400 |
|
|
"\n" |
401 |
|
|
"GofR error, unable to open \"%s\" for writing.\n", |
402 |
|
|
out_name ); |
403 |
|
|
exit(8); |
404 |
|
|
} |
405 |
|
|
break; |
406 |
|
|
} |
407 |
|
|
|
408 |
|
|
for( i=0; i<GofRBins; i++ ){ |
409 |
|
|
fprintf( out_file, |
410 |
|
|
"%lf\t%lf\n", |
411 |
|
|
rValue[i], the_GofR[i] ); |
412 |
|
|
} |
413 |
|
|
|
414 |
|
|
fclose( out_file ); |
415 |
|
|
} |
416 |
|
|
|