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#define _FILE_OFFSET_BITS 64 |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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|
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|
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#include "params.h" |
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#include "tcProps.h" |
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#include "readWrite.h" |
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#include "scdCorr.h" |
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|
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|
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#define VERSION_MAJOR 0 |
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#define VERSION_MINOR 1 |
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|
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char *programName; /*the name of the program */ |
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void usage(void); |
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|
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int main( int argC, char *argV[] ){ |
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|
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// list of 'a priori' constants |
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|
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const int nLipAtoms = NL_ATOMS; |
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const int nBonds = NBONDS; |
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const int nLipids = NLIPIDS; |
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const int nSSD = NSSD; |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
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|
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// different needed variables |
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|
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struct atomCoord atoms[nAtoms]; |
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int i,j,k; |
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char* inName; |
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int nFrames; |
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|
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char* outPrefix; // the output prefix |
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char currentFlag; // used in parsing the flags |
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int done = 0; // multipurpose boolean |
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int havePrefix; // boolean for the output prefix |
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char* conversionCheck; |
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int conversionError; |
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int optionError; |
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char* pair1; |
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char* pair2; |
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int scdCorr; |
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double startTime; |
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|
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// system initialization |
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|
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isScanned = 0; |
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fileOpen = 0; |
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nFrames = 0; |
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frameTimes = NULL; |
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|
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outPrefix = NULL; |
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inName = NULL; |
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|
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conversionError = 0; |
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optionError = 0; |
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havePrefix = 0; |
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scdCorr = 0; |
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startTime = 0.0; |
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|
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|
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// parse the command line |
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|
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programName = 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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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofr\n"); |
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usage(); |
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exit(0); |
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} |
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pair1 = argV[i]; |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofr\n"); |
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usage(); |
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exit(0); |
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} |
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pair2 = argV[i]; |
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|
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} |
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|
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else if( !strcmp( argV[i], "--gofrTheta" ) ){ |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrTheta\n"); |
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usage(); |
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exit(0); |
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} |
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pair1 = argV[i]; |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrTheta\n"); |
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usage(); |
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exit(0); |
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} |
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pair2 = argV[i]; |
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|
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} |
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|
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else if( !strcmp( argV[i], "--gofrOmega" ) ){ |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrOmega\n"); |
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usage(); |
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exit(0); |
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} |
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pair1 = argV[i]; |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrOmega\n"); |
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usage(); |
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exit(0); |
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} |
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pair2 = argV[i]; |
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|
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} |
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|
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else if( !strcmp( argV[i], "--version") ){ |
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|
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printf("\n" |
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"tcProps version %d.%d\n" |
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"\n", |
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VERSION_MAJOR, VERSION_MINOR ); |
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exit(0); |
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|
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} |
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|
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else if( !strcmp( argV[i], "--help") ){ |
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|
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usage(); |
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exit(0); |
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} |
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|
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// anything else is an error |
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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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exit(0); |
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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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currentFlag = argV[i][j]; |
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while( (currentFlag != '\0') && (!done) ){ |
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|
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switch(currentFlag){ |
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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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j++; |
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currentFlag = argV[i][j]; |
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|
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if( currentFlag != '\0' ) optionError = 1; |
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|
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"The -o flag should end an option sequence.\n" |
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" example: -r <outname> *NOT* -or <outname>\n" ); |
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usage(); |
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exit(0); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for -o\n"); |
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usage(); |
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exit(0); |
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} |
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|
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outPrefix = argV[i]; |
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if( outPrefix[0] == '-' ) optionError = 1; |
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|
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"\"%s\" is not a valid out prefix/name.\n" |
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"Out prefix/name should not begin with a dash.\n", |
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outPrefix ); |
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usage(); |
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exit(0); |
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} |
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|
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havePrefix = 1; |
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done = 1; |
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break; |
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|
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case 'l': |
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// -l <double> set <double> to the maxLength |
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|
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haveMaxLength = true; |
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j++; |
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currentFlag = argV[i][j]; |
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|
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if( currentFlag != '\0' ) optionError = 1; |
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|
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"The -l flag should end an option sequence.\n" |
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" example: -sl <double> *NOT* -ls <double>\n" ); |
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usage(); |
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exit(0); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for -l\n"); |
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usage(); |
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exit(0); |
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} |
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|
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maxLength = atof( argV[i] ); |
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|
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done = 1; |
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|
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break; |
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|
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case 't': |
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// -t <double> set <double> to the startTime |
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|
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j++; |
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currentFlag = argV[i][j]; |
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|
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if( currentFlag != '\0' ) optionError = 1; |
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|
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"The -t flag should end an option sequence.\n" |
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" example: -st <double> *NOT* -ts <double>\n" ); |
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usage(); |
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exit(0); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for -t\n"); |
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usage(); |
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exit(0); |
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} |
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|
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startTime = atof( argV[i] ); |
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done = 1; |
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break; |
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|
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case 's': |
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// -s turn on separate output files |
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|
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scdCorr = 1; |
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break; |
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|
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|
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default: |
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|
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sprintf(painCave.errMsg, |
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"\n" |
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"Bad option \"-%c\"\n", currentFlag); |
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usage(); |
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exit(0); |
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} |
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j++; |
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currentFlag = 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( inName != 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 dump file.\n" |
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"\n", |
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argV[i]); |
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usage(); |
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exit(0); |
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} |
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|
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inName = argV[i]; |
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|
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} |
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} |
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|
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if( inName == NULL ){ |
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fprintf( stderr, |
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"Error, dump file is needed to run.\n" ); |
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usage(); |
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exit(0); |
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} |
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|
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|
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// initialize the arrays |
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|
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for(i=0;i<nLipids;i++){ |
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|
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atoms[nLipAtoms*i+0].type = HEAD; |
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atoms[nLipAtoms*i+0].u[0] = 0.0; |
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atoms[nLipAtoms*i+0].u[1] = 0.0; |
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atoms[nLipAtoms*i+0].u[2] = 1.0; |
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|
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|
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atoms[nLipAtoms*i+1].type = CH2; |
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|
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atoms[nLipAtoms*i+2].type = CH; |
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|
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atoms[nLipAtoms*i+3].type = CH2; |
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|
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atoms[nLipAtoms*i+4].type = CH2; |
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|
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atoms[nLipAtoms*i+5].type = CH2; |
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|
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atoms[nLipAtoms*i+6].type = CH2; |
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|
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atoms[nLipAtoms*i+7].type = CH2; |
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|
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atoms[nLipAtoms*i+8].type = CH2; |
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|
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atoms[nLipAtoms*i+9].type = CH2; |
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|
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atoms[nLipAtoms*i+10].type = CH3; |
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|
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atoms[nLipAtoms*i+11].type = CH2; |
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|
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atoms[nLipAtoms*i+12].type = CH2; |
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|
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atoms[nLipAtoms*i+13].type = CH2; |
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|
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atoms[nLipAtoms*i+14].type = CH2; |
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|
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atoms[nLipAtoms*i+15].type = CH2; |
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|
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atoms[nLipAtoms*i+16].type = CH2; |
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|
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atoms[nLipAtoms*i+17].type = CH2; |
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|
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atoms[nLipAtoms*i+18].type = CH3; |
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} |
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|
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for(i=(nLipAtoms*nLipids);i<nAtoms;i++){ |
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atoms[i].type = SSD; |
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atoms[i].u[0] = 0.0; |
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atoms[i].u[1] = 0.0; |
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atoms[i].u[2] = 1.0; |
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} |
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|
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// read and set the frames |
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|
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openFile( inName ); |
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|
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fprintf( stdout, |
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"\n" |
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"Counting the number of frames in \"%s\"...", |
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inName ); |
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fflush(stdout); |
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|
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setFrames( inName ); |
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|
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fprintf( stdout, |
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"done.\n" |
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"nFrames = %d\n.", |
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nFrames ); |
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fflush(stdout); |
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|
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if(scdCorr){ |
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|
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fprintf ( stdout, |
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"Calculating the Scd correlation\n" ); |
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fflush( stdout ); |
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|
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calcScdCorr( startTime ); |
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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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* 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(stdout, |
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"\n" |
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"The proper usage is: %s [options] <input_file>\n" |
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"\n" |
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"Options:\n" |
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"\n" |
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" short:\n" |
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" ------\n" |
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" -o <name> The output prefix\n" |
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" -t <time> Set the start time for correlations\n" |
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" -l <maxLength> set the maximum value of r\n" |
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" *Defaults to 1/2 smallest length of first frame.\n" |
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" -s Calculate the Scd chain correlation.\n" |
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"\n" |
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" long:\n" |
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" -----\n" |
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" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n" |
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" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
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" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
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" --version displays the version number\n" |
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" --help displays this help message.\n" |
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|
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"\n" |
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"\n", |
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programName); |
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} |
