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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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|
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#include "GofR.h" |
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|
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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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|
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// this algoritm assumes constant number of atoms between frames, and |
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// constant boxSize |
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|
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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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|
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int i,j,k,l; |
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|
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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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|
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double atom1Dens; |
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double atom2Dens; |
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double allDens; |
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|
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double atom1Constant; |
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double atom2Constant; |
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double allConstant; |
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|
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double nAtom1; |
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double nAtom2; |
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double nAtoms; |
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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 distSqr; |
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double dist; |
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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[GofRBins]; |
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double the_GofR[GofRBins]; |
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double rValue[GofRBins]; |
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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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|
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// figure out the type of GofR we are calculating |
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|
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if( !strcmp( atom1, "all" ) ){ |
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|
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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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|
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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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|
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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 ) / GofRBins; |
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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<GofRBins; i++ ){ |
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|
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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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|
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switch( the_type ){ |
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|
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case atom_atom: |
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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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else 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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"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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|
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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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"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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|
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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=0; i<nFrames; i++){ |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
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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[j], atom1 ) ){ |
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if( !strcmp( frames[0].names[k], atom2 ) ){ |
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|
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dx = frames[i].r[j].x - frames[i].r[k].x; |
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dy = frames[i].r[j].y - frames[i].r[k].y; |
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dz = frames[i].r[j].z - 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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// 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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else if( !strcmp( frames[0].names[j], atom2 ) ){ |
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if( !strcmp( frames[0].names[k], atom1 ) ){ |
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|
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dx = frames[i].r[j].x - frames[i].r[k].x; |
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dy = frames[i].r[j].y - frames[i].r[k].y; |
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dz = frames[i].r[j].z - 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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// 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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|
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// calculate the GofR |
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|
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for( i=0; i<GofRBins; 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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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
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nIdeal = volSlice * ( atom1Constant + atom2Constant ); |
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|
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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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|
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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.GofR", 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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"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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|
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case atom_all: |
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|
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// find the number of AllAtoms; |
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|
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nAtom1 = 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], allAtom ) ) nAtom1++; |
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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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"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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|
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// calculate some of the constants; |
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|
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atom1Dens = nAtom1 / boxVol; |
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allDens = frames[0].nAtoms / boxVol; |
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|
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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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|
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// calculate the histogram |
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|
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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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for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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|
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if( !strcmp( frames[0].names[j], allAtom ) ){ |
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|
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dx = frames[i].r[j].x - frames[i].r[k].x; |
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dy = frames[i].r[j].y - frames[i].r[k].y; |
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dz = frames[i].r[j].z - 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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// 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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else if( !strcmp( frames[0].names[k], allAtom ) ){ |
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|
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dx = frames[i].r[j].x - frames[i].r[k].x; |
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dy = frames[i].r[j].y - frames[i].r[k].y; |
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dz = frames[i].r[j].z - 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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// 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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|
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for( i=0; i<GofRBins; 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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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
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nIdeal = volSlice * ( allConstant ); |
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|
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
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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.GofR", allAtom, "all" ); |
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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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"GofR error, unable to open \"%s\" for writing.\n", |
| 306 |
out_name ); |
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exit(8); |
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} |
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break; |
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|
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case all_all: |
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|
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// calculate some of the constants; |
| 314 |
|
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allDens = frames[0].nAtoms / boxVol; |
| 316 |
|
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allConstant = ( 4.0 * M_PI * allDens ) / 3.0; |
| 318 |
|
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// calculate the histogram |
| 320 |
|
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for( i=0; i<nFrames; i++){ |
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for( j=0; j<(frames[i].nAtoms-1); j++ ){ |
| 323 |
for( k=j+1; k< frames[i].nAtoms; k++ ){ |
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|
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dx = frames[i].r[j].x - frames[i].r[k].x; |
| 326 |
dy = frames[i].r[j].y - frames[i].r[k].y; |
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dz = frames[i].r[j].z - 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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// 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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// calculate the GofR |
| 343 |
|
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for( i=0; i<GofRBins; i++ ){ |
| 345 |
|
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rLower = i * delR; |
| 347 |
rUpper = rLower + delR; |
| 348 |
|
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volSlice = pow( rUpper, 3.0 ) - pow( rLower, 3.0 ); |
| 350 |
nIdeal = volSlice * ( allConstant ); |
| 351 |
|
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the_GofR[i] = histogram[i] / ( nFrames * frames[0].nAtoms * nIdeal ); |
| 353 |
rValue[i] = rLower + ( delR / 2.0 ); |
| 354 |
} |
| 355 |
|
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// make the out_name; |
| 357 |
|
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strcpy( out_name, out_prefix ); |
| 359 |
sprintf( tempString, "-%s-%s.GofR", "all", "all" ); |
| 360 |
strcat( out_name, tempString ); |
| 361 |
|
| 362 |
out_file = fopen( out_name, "w" ); |
| 363 |
if( out_file == NULL ){ |
| 364 |
fprintf( stderr, |
| 365 |
"\n" |
| 366 |
"GofR error, unable to open \"%s\" for writing.\n", |
| 367 |
out_name ); |
| 368 |
exit(8); |
| 369 |
} |
| 370 |
break; |
| 371 |
} |
| 372 |
|
| 373 |
for( i=0; i<GofRBins; i++ ){ |
| 374 |
fprintf( out_file, |
| 375 |
"%lf\t%lf\n", |
| 376 |
rValue[i], the_GofR[i] ); |
| 377 |
} |
| 378 |
|
| 379 |
fclose( out_file ); |
| 380 |
} |
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|
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|
| 383 |
void map( double *x, double *y, double *z, |
| 384 |
double boxX, double boxY, double boxZ ){ |
| 385 |
|
| 386 |
*x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5 ); |
| 387 |
*y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5 ); |
| 388 |
*z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5 ); |
| 389 |
|
| 390 |
} |
