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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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#include <string.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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#include "directorHead.h" |
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#include "directorWhole.h" |
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#include "rmsd.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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|
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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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int haveMaxLength; |
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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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double maxLength; |
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int directorHead, directorWhole, doRMSD; |
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enum atomNames rmsdType; |
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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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haveMaxLength = 0; |
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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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directorHead = 0; |
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directorWhole = 0; |
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doRMSD = 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], "--rmsd" ) ){ |
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|
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doRMSD = 1; |
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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 --rmsd\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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if( !strcmp(pair1, "HEAD") ) rmsdType = HEAD; |
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else if( !strcmp(pair1, "CH") ) rmsdType = CH; |
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else if( !strcmp(pair1, "CH2") )rmsdType = CH2; |
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else if( !strcmp(pair1, "CH3") )rmsdType = CH3; |
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else if( !strcmp(pair1, "SSD") )rmsdType = SSD; |
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else if( !strcmp(pair1, "COM") )rmsdType = COM; |
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else{ |
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fprintf( stderr, |
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"Unrecognized rmsd atom type \"%s\"\n", |
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pair1 ); |
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exit(0); |
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} |
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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 = 1; |
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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 Scd corr |
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|
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scdCorr = 1; |
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break; |
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|
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case 'h': |
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// -h turn on director head |
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|
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directorHead = 1; |
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break; |
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|
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case 'w': |
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// -h turn on director head |
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|
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directorWhole = 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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fprintf( stderr, |
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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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if( outPrefix == NULL ) |
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outPrefix = inName; |
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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].mass = 72; |
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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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|
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atoms[nLipAtoms*i+1].type = CH2; |
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atoms[nLipAtoms*i+1].mass = 14.03; |
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|
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atoms[nLipAtoms*i+2].type = CH; |
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atoms[nLipAtoms*i+2].mass = 13.02; |
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|
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atoms[nLipAtoms*i+3].type = CH2; |
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atoms[nLipAtoms*i+3].mass = 14.03; |
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|
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atoms[nLipAtoms*i+4].type = CH2; |
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atoms[nLipAtoms*i+4].mass = 14.03; |
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|
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atoms[nLipAtoms*i+5].type = CH2; |
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atoms[nLipAtoms*i+5].mass = 14.03; |
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|
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atoms[nLipAtoms*i+6].type = CH2; |
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atoms[nLipAtoms*i+6].mass = 14.03; |
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|
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atoms[nLipAtoms*i+7].type = CH2; |
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atoms[nLipAtoms*i+7].mass = 14.03; |
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|
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atoms[nLipAtoms*i+8].type = CH2; |
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atoms[nLipAtoms*i+8].mass = 14.03; |
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|
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atoms[nLipAtoms*i+9].type = CH2; |
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atoms[nLipAtoms*i+9].mass = 14.03; |
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|
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atoms[nLipAtoms*i+10].type = CH3; |
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atoms[nLipAtoms*i+10].mass = 15.04; |
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|
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atoms[nLipAtoms*i+11].type = CH2; |
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atoms[nLipAtoms*i+11].mass = 14.03; |
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|
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atoms[nLipAtoms*i+12].type = CH2; |
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atoms[nLipAtoms*i+12].mass = 14.03; |
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|
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atoms[nLipAtoms*i+13].type = CH2; |
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atoms[nLipAtoms*i+13].mass = 14.03; |
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|
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atoms[nLipAtoms*i+14].type = CH2; |
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atoms[nLipAtoms*i+14].mass = 14.03; |
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|
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atoms[nLipAtoms*i+15].type = CH2; |
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atoms[nLipAtoms*i+15].mass = 14.03; |
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|
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atoms[nLipAtoms*i+16].type = CH2; |
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atoms[nLipAtoms*i+16].mass = 14.03; |
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|
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atoms[nLipAtoms*i+17].type = CH2; |
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atoms[nLipAtoms*i+17].mass = 14.03; |
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|
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atoms[nLipAtoms*i+18].type = CH3; |
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atoms[nLipAtoms*i+18].mass = 15.04; |
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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].mass = 18.03; |
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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(); |
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|
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fprintf( stdout, |
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"\n" |
450 |
"Counting the number of frames in \"%s\"...", |
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inName ); |
452 |
fflush(stdout); |
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|
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setFrames(); |
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|
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fprintf( stdout, |
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"done.\n" |
458 |
"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, atoms, outPrefix ); |
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} |
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|
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if(directorHead){ |
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|
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fprintf ( stdout, |
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"Calculating the Head director\n" ); |
475 |
fflush( stdout ); |
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|
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calcDirHeadCorr( startTime, atoms, outPrefix ); |
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} |
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|
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if(directorWhole){ |
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|
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fprintf ( stdout, |
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"Calculating the bilayer director\n" ); |
484 |
fflush( stdout ); |
485 |
|
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calcDirWholeCorr( startTime, atoms, outPrefix ); |
487 |
} |
488 |
|
489 |
if(doRMSD){ |
490 |
|
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fprintf ( stdout, |
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"Calculating the RMSD\n" ); |
493 |
fflush( stdout ); |
494 |
|
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rmsd( rmsdType, startTime, outPrefix ); |
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} |
497 |
|
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|
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closeFile(); |
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|
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} |
502 |
|
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|
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/*************************************************************************** |
505 |
* prints out the usage for the command line arguments, then exits. |
506 |
***************************************************************************/ |
507 |
|
508 |
void usage(){ |
509 |
(void)fprintf(stdout, |
510 |
"\n" |
511 |
"The proper usage is: %s [options] <input_file>\n" |
512 |
"\n" |
513 |
"Options:\n" |
514 |
"\n" |
515 |
" short:\n" |
516 |
" ------\n" |
517 |
" -o <name> The output prefix\n" |
518 |
" -t <time> Set the start time for correlations\n" |
519 |
" -l <maxLength> set the maximum value of r\n" |
520 |
" *Defaults to 1/2 smallest length of first frame.\n" |
521 |
" -s Calculate the Scd chain correlation.\n" |
522 |
" -h Calculate the directors for the head groups\n" |
523 |
" -w Calculate the director fro the bilayers\n" |
524 |
"\n" |
525 |
" long:\n" |
526 |
" -----\n" |
527 |
" --rmsd <atom1> rmsd for atom1\n" |
528 |
" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
529 |
" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
530 |
" --version displays the version number\n" |
531 |
" --help displays this help message.\n" |
532 |
|
533 |
"\n" |
534 |
"\n", |
535 |
programName); |
536 |
} |