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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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|
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#include "frameCount.h" |
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|
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struct coords{ |
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double x; |
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double y; |
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double z; |
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char name[30]; |
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}; |
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|
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|
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struct xyz_frame{ |
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int nAtoms; |
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double time; |
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double boxX, boxY, boxZ; |
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struct coords *r; |
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}; |
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|
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char *program_name; /*the name of the program */ |
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|
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void usage(void); |
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|
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int main(argc, argv) |
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int argc; |
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char *argv[]; |
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{ |
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|
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|
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struct xyz_frame *dumpArray; |
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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 |
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int i,j; // loop counters |
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|
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char read_buffer[2000]; /*the line buffer for reading */ |
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char *foo; /*the pointer to the current string token */ |
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FILE *in_file; /* the input file */ |
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char *in_name = NULL; /*the name of the input file */ |
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|
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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 = 0; i < argc; i++){ |
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|
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if(argv[i][0] =='-'){ |
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|
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/* argv[i][1] is the actual option character */ |
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|
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switch(argv[i][1]){ |
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|
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/* -f <name> => the xyz input file |
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* [i+1] actually starts the name |
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*/ |
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|
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case 'f': |
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in_name = argv[i+1]; |
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break; |
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|
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default: |
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(void)fprintf(stderr, "Bad 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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|
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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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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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|
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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 the array of frames |
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|
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dumpArray = (struct xyz_frame*)calloc( nFrames, |
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sizeof( struct xyz_frame ) ); |
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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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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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//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[j].r[i].name, 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 ); |
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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 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 ); |
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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 z 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].z = atof( foo ); |
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|
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} |
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} |
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|
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(void)fclose(in_file); |
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|
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printf( "done\n" |
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"\n" ); |
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fflush( stdout ); |
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|
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|
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|
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// do calculations here. |
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|
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|
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|
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|
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|
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|
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|
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return 0; |
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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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* prints out the usage for the command line arguments, then exits. |
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***************************************************************************/ |
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|
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void usage(){ |
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(void)fprintf(stderr, |
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"The proper usage is: %s [options] -f <xyz_file>\n\n" |
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"Options:\n", |
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program_name); |
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exit(8); |
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} |
