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#include <stdio.h> |
| 2 |
#include <stdlib.h> |
| 3 |
#include <string.h> |
| 4 |
#include <math.h> |
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|
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|
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#include "madProps.h" |
| 8 |
#include "frameCount.h" |
| 9 |
|
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char *program_name; /*the name of the program */ |
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|
| 12 |
void usage(void); |
| 13 |
|
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int main(argc, argv) |
| 15 |
int argc; |
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char *argv[]; |
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{ |
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|
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|
| 20 |
struct xyz_frame *dumpArray; |
| 21 |
int nFrames; // the nu8mvber of frames |
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int lineNum = 0; // keeps track of the line number |
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int n_atoms; // the number of atoms |
| 24 |
int i,j; // loop counters |
| 25 |
int isFirst; |
| 26 |
|
| 27 |
char read_buffer[2000]; /*the line buffer for reading */ |
| 28 |
char *foo; /*the pointer to the current string token */ |
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FILE *in_file; /* the input file */ |
| 30 |
char *in_name = NULL; /*the name of the input file */ |
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char *out_prefix; // the output prefix |
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char current_flag; // used in parseing the flags |
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|
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|
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|
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int done = 0; // multipurpose boolean |
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int have_prefix = 0; // prefix boolean |
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int calcRMSD = 0; |
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|
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int calcGofR = 0; |
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char gofR1[30]; |
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char gofR2[30]; |
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|
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int calcMuCorr = 0; |
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char muCorr[30]; |
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|
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int calcCosCorr = 0; |
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char cosCorr1[30]; |
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char cosCorr2[30]; |
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|
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int startFrame = 0; |
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int haveStartFrame = 0; |
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int endFrame = 0; |
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int haveEndFrame = 0; |
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|
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program_name = argv[0]; /*save the program name in case we need it*/ |
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|
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for( i = 1; i < argc; i++){ |
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|
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if(argv[i][0] =='-'){ |
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|
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// parse the option |
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|
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if(argv[i][1] == '-' ){ |
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|
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// parse long word options |
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|
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if( !strcmp( argv[i], "--GofR" ) ){ |
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calcGofR = 1; |
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i++; |
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strcpy( gofR1, argv[i] ); |
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i++; |
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strcpy( gofR2, argv[i] ); |
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} |
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|
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else if( !strcmp( argv[i], "--MuCorr") ){ |
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calcMuCorr = 1; |
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i++; |
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strcpy( muCorr, argv[i] ); |
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} |
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|
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else if( !strcmp( argv[i], "--startFrame" ) ){ |
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haveStartFrame = 1; |
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i++; |
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startFrame = atoi(argv[i]); |
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} |
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|
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else if( !strcmp( argv[i], "--endFrame" ) ){ |
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haveEndFrame = 1; |
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i++; |
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endFrame = atoi(argv[i]); |
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} |
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|
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else{ |
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fprintf( stderr, |
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"Invalid option \"%s\"\n", argv[i] ); |
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usage(); |
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} |
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} |
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|
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else{ |
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|
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// parse single character options |
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|
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done =0; |
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j = 1; |
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current_flag = argv[i][j]; |
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while( (current_flag != '\0') && (!done) ){ |
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|
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switch(current_flag){ |
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|
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case 'o': |
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// -o <prefix> => the output prefix. |
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|
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i++; |
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out_prefix = argv[i]; |
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have_prefix = 1; |
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done = 1; |
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break; |
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|
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case 'h': |
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// -h => give the usage |
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|
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usage(); |
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break; |
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|
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case 'r': |
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// calculates the rmsd |
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|
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calcRMSD = 1; |
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break; |
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|
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case 'g': |
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// calculate all to all g(r) |
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|
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calcGofR = 1; |
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strcpy( gofR1, "all" ); |
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strcpy( gofR2, "all" ); |
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break; |
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|
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default: |
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|
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fprintf( stderr, "about to print bad option\n" ); |
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|
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(void)fprintf(stderr, "Bad option \"-%s\"\n", current_flag); |
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usage(); |
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} |
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j++; |
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current_flag = argv[i][j]; |
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} |
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} |
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} |
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|
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else{ |
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|
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if( in_name != NULL ){ |
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fprintf( stderr, |
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"Error at \"%s\", program does not currently support\n" |
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"more than one input file.\n" |
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"\n", |
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argv[i]); |
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usage(); |
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} |
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|
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in_name = argv[i]; |
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} |
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} |
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|
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if(in_name == NULL){ |
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usage(); |
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} |
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|
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if( !have_prefix ) out_prefix = in_name; |
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|
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printf( "Counting number of frames..." ); |
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fflush( stdout ); |
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|
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nFrames = frameCount( in_name ); |
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if( !haveEndFrame ) endFrame = nFrames; |
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|
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printf( "done.\n" |
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"nframes = %d\n" |
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"\n", |
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nFrames ); |
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fflush( stdout ); |
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|
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in_file = fopen(in_name, "r"); |
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if(in_file == NULL){ |
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printf("Cannot open file: %s\n", in_name); |
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exit(8); |
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} |
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|
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// create and initialize the array of frames |
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|
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dumpArray = (struct xyz_frame*)calloc( nFrames, |
| 196 |
sizeof( struct xyz_frame ) ); |
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for( i=0; i<nFrames; i++ ){ |
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dumpArray[i].nAtoms = 0; |
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dumpArray[i].time = 0.0; |
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dumpArray[i].boxX = 0.0; |
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dumpArray[i].boxY = 0.0; |
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dumpArray[i].boxZ = 0.0; |
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dumpArray[i].r = NULL; |
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dumpArray[i].v = NULL; |
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dumpArray[i].names = NULL; |
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} |
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|
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// read the frames |
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|
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printf( "Reading the frames into the coordinate arrays..." ); |
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fflush( stdout ); |
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|
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isFirst = 1; |
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for(j =0; j<nFrames; j++ ){ |
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|
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// read the number of atoms |
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|
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fgets(read_buffer, sizeof(read_buffer), in_file); |
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lineNum++; |
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|
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n_atoms = atoi( read_buffer ); |
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dumpArray[j].nAtoms = n_atoms; |
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|
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dumpArray[j].r = |
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(struct coords *)calloc(n_atoms, sizeof(struct coords)); |
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|
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if( isFirst ) { |
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dumpArray[0].names = |
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(atomID *)calloc( n_atoms, sizeof(atomID) ); |
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isFirst = 0; |
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} |
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|
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if( calcMuCorr || calcCosCorr ){ |
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dumpArray[j].v = |
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(struct vect *)calloc(n_atoms, sizeof(struct vect)); |
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} |
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|
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//read the time and the box sizes |
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|
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fgets(read_buffer, sizeof(read_buffer), in_file); |
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lineNum++; |
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|
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foo = strtok(read_buffer, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading time at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].time = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading boxX at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].boxX = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading boxY at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].boxY = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading boxZ at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].boxZ = atof( foo ); |
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|
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|
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for( i=0; i < n_atoms; i++){ |
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|
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fgets(read_buffer, sizeof(read_buffer), in_file); |
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lineNum++; |
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|
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// get the name and positions |
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|
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foo = strtok(read_buffer, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading atom name at line %d\n", lineNum ); |
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exit(8); |
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} |
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|
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strcpy(dumpArray[0].names[i], foo); /*copy the atom name */ |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("error in reading position x at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].r[i].x = atof( foo ); |
| 298 |
|
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foo = strtok(NULL, " ,;\t"); |
| 300 |
if(foo == NULL){ |
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printf("error in reading position y at line %d\n", lineNum); |
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exit(8); |
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} |
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|
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dumpArray[j].r[i].y = atof( foo ); |
| 306 |
|
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foo = strtok(NULL, " ,;\t"); |
| 308 |
if(foo == NULL){ |
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printf("error in reading position z at line %d\n", lineNum); |
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exit(8); |
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} |
| 312 |
|
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dumpArray[j].r[i].z = atof( foo ); |
| 314 |
|
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if( calcCosCorr || calcMuCorr ){ |
| 316 |
|
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foo = strtok(NULL, " ,;\t"); |
| 318 |
if(foo == NULL){ |
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|
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dumpArray[j].v[i].x = 0.0; |
| 321 |
dumpArray[j].v[i].y = 0.0; |
| 322 |
dumpArray[j].v[i].z = 0.0; |
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} |
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else{ |
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|
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dumpArray[j].v[i].x = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
| 329 |
if(foo == NULL){ |
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printf("error in reading vector y at line %d\n", lineNum); |
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exit(8); |
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} |
| 333 |
|
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dumpArray[j].v[i].y = atof( foo ); |
| 335 |
|
| 336 |
foo = strtok(NULL, " ,;\t"); |
| 337 |
if(foo == NULL){ |
| 338 |
printf("error in reading vector z at line %d\n", lineNum); |
| 339 |
exit(8); |
| 340 |
} |
| 341 |
|
| 342 |
dumpArray[j].v[i].z = atof( foo ); |
| 343 |
} |
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} |
| 345 |
|
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} |
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} |
| 348 |
|
| 349 |
(void)fclose(in_file); |
| 350 |
|
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printf( "done\n" |
| 352 |
"\n" ); |
| 353 |
fflush( stdout ); |
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|
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|
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|
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// do calculations here. |
| 358 |
|
| 359 |
if( calcGofR ){ |
| 360 |
|
| 361 |
fprintf( stdout, |
| 362 |
"Calculating the g(r) between atoms \"%s\" and \"%s\"...", |
| 363 |
gofR1, gofR2 ); |
| 364 |
fflush( stdout ); |
| 365 |
|
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// gofr call |
| 367 |
GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame ); |
| 368 |
|
| 369 |
fprintf( stdout, |
| 370 |
" done.\n" |
| 371 |
"\n"); |
| 372 |
fflush(stdout); |
| 373 |
} |
| 374 |
|
| 375 |
if( calcRMSD ){ |
| 376 |
|
| 377 |
fprintf( stdout, |
| 378 |
"Calculating the RMSD..." ); |
| 379 |
fflush( stdout ); |
| 380 |
|
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// RMSD call |
| 382 |
|
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|
| 384 |
fprintf( stdout, |
| 385 |
" done.\n" |
| 386 |
"\n"); |
| 387 |
fflush(stdout); |
| 388 |
} |
| 389 |
|
| 390 |
if( calcMuCorr ){ |
| 391 |
|
| 392 |
fprintf( stdout, |
| 393 |
"Calculating the mu correlation for \"%s\"...", |
| 394 |
muCorr); |
| 395 |
fflush( stdout ); |
| 396 |
|
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// muCorr call |
| 398 |
|
| 399 |
|
| 400 |
fprintf( stdout, |
| 401 |
" done.\n" |
| 402 |
"\n"); |
| 403 |
fflush(stdout); |
| 404 |
} |
| 405 |
|
| 406 |
if( calcCosCorr ){ |
| 407 |
|
| 408 |
fprintf( stdout, |
| 409 |
"Calculating the cos correlation between \"%s\" and \"%s\"...", |
| 410 |
cosCorr1, cosCorr2 ); |
| 411 |
fflush( stdout ); |
| 412 |
|
| 413 |
cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame, |
| 414 |
endFrame ); |
| 415 |
|
| 416 |
fprintf( stdout, |
| 417 |
" done.\n" |
| 418 |
"\n"); |
| 419 |
fflush(stdout); |
| 420 |
} |
| 421 |
|
| 422 |
return 0; |
| 423 |
|
| 424 |
} |
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|
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|
| 427 |
void map( double *x, double *y, double *z, |
| 428 |
double boxX, double boxY, double boxZ ){ |
| 429 |
|
| 430 |
*x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5 ); |
| 431 |
*y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5 ); |
| 432 |
*z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5 ); |
| 433 |
|
| 434 |
} |
| 435 |
|
| 436 |
|
| 437 |
/*************************************************************************** |
| 438 |
* prints out the usage for the command line arguments, then exits. |
| 439 |
***************************************************************************/ |
| 440 |
|
| 441 |
void usage(){ |
| 442 |
(void)fprintf(stdout, |
| 443 |
"The proper usage is: %s [options] <xyz_file>\n" |
| 444 |
"\n" |
| 445 |
"Options:\n" |
| 446 |
"\n" |
| 447 |
" short:\n" |
| 448 |
" ------\n" |
| 449 |
" -h Display this message\n" |
| 450 |
" -o <prefix> The output prefix\n" |
| 451 |
" -r Calculate the RMSD\n" |
| 452 |
" -g Calculate all to all g(r)\n" |
| 453 |
|
| 454 |
"\n" |
| 455 |
" long:\n" |
| 456 |
" -----\n" |
| 457 |
" --GofR <atom1> <atom2> Calculates g(r) between atom1 and atom 2\n" |
| 458 |
" -note: \"all\" will do all atoms\n" |
| 459 |
" --MuCorr <atom> Calculate mu correlation of atom\n" |
| 460 |
" --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n" |
| 461 |
" --startFrame <frame#> Specifies a frame to start correlating\n" |
| 462 |
" --endFrame <frame#> Specifies a frame to stop correlating.\n" |
| 463 |
|
| 464 |
"\n" |
| 465 |
"\n", |
| 466 |
program_name); |
| 467 |
exit(8); |
| 468 |
} |
