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#define _FILE_OFFSET_BITS 64 |
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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 "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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#include "gofz.h" |
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|
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#define VERSION_MAJOR 0 |
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#define VERSION_MINOR 1 |
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char *programName; /*the name of the program */ |
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void usage(void); |
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int main( int argC, char *argV[] ){ |
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// list of 'a priori' constants |
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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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struct atomCoord atoms[nAtoms]; |
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int i,j,k; |
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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, doGofz; |
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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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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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doGofz = 0; |
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|
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|
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// parse the command line |
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programName = argV[0]; /*save the program name in case we need it*/ |
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for( i = 1; i < argC; i++){ |
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if(argV[i][0] =='-'){ |
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// parse the option |
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if(argV[i][1] == '-' ){ |
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// parse long word options |
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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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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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else if( !strcmp( argV[i], "--gofrTheta" ) ){ |
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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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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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else if( !strcmp( argV[i], "--gofrOmega" ) ){ |
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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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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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else if( !strcmp( argV[i], "--version") ){ |
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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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else if( !strcmp( argV[i], "--help") ){ |
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usage(); |
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exit(0); |
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} |
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// anything else is an error |
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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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else{ |
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// parse single character options |
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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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switch(currentFlag){ |
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case 'o': |
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// -o <prefix> => the output prefix. |
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j++; |
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currentFlag = argV[i][j]; |
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if( currentFlag != '\0' ) optionError = 1; |
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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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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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outPrefix = argV[i]; |
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if( outPrefix[0] == '-' ) optionError = 1; |
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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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havePrefix = 1; |
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done = 1; |
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break; |
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case 'l': |
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// -l <double> set <double> to the maxLength |
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mmeineke |
1060 |
haveMaxLength = 1; |
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mmeineke |
1058 |
j++; |
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currentFlag = argV[i][j]; |
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if( currentFlag != '\0' ) optionError = 1; |
255 |
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256 |
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if( optionError ){ |
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fprintf( stderr, |
258 |
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"\n" |
259 |
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"The -l flag should end an option sequence.\n" |
260 |
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" example: -sl <double> *NOT* -ls <double>\n" ); |
261 |
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usage(); |
262 |
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exit(0); |
263 |
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} |
264 |
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265 |
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i++; |
266 |
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if( i>=argC ){ |
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fprintf( stderr, |
268 |
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"\n" |
269 |
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"not enough arguments for -l\n"); |
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usage(); |
271 |
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exit(0); |
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} |
273 |
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274 |
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maxLength = atof( argV[i] ); |
275 |
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276 |
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done = 1; |
277 |
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278 |
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break; |
279 |
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280 |
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case 't': |
281 |
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// -t <double> set <double> to the startTime |
282 |
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283 |
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j++; |
284 |
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currentFlag = argV[i][j]; |
285 |
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286 |
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if( currentFlag != '\0' ) optionError = 1; |
287 |
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288 |
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if( optionError ){ |
289 |
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fprintf( stderr, |
290 |
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"\n" |
291 |
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"The -t flag should end an option sequence.\n" |
292 |
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" example: -st <double> *NOT* -ts <double>\n" ); |
293 |
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usage(); |
294 |
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exit(0); |
295 |
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} |
296 |
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297 |
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i++; |
298 |
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if( i>=argC ){ |
299 |
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fprintf( stderr, |
300 |
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"\n" |
301 |
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"not enough arguments for -t\n"); |
302 |
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usage(); |
303 |
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exit(0); |
304 |
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} |
305 |
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306 |
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startTime = atof( argV[i] ); |
307 |
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done = 1; |
308 |
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break; |
309 |
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310 |
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case 's': |
311 |
mmeineke |
1060 |
// -s turn on Scd corr |
312 |
mmeineke |
1058 |
|
313 |
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scdCorr = 1; |
314 |
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break; |
315 |
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316 |
mmeineke |
1060 |
case 'h': |
317 |
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// -h turn on director head |
318 |
mmeineke |
1058 |
|
319 |
mmeineke |
1060 |
directorHead = 1; |
320 |
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break; |
321 |
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322 |
mmeineke |
1062 |
case 'w': |
323 |
mmeineke |
1080 |
// -w turn on director head |
324 |
mmeineke |
1060 |
|
325 |
mmeineke |
1062 |
directorWhole = 1; |
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break; |
327 |
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328 |
mmeineke |
1080 |
case 'g': |
329 |
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// -g turn on gofZ |
330 |
mmeineke |
1062 |
|
331 |
mmeineke |
1080 |
doGofz = 1; |
332 |
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break; |
333 |
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334 |
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335 |
mmeineke |
1058 |
default: |
336 |
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337 |
mmeineke |
1060 |
fprintf( stderr, |
338 |
mmeineke |
1058 |
"\n" |
339 |
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"Bad option \"-%c\"\n", currentFlag); |
340 |
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usage(); |
341 |
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exit(0); |
342 |
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} |
343 |
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j++; |
344 |
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currentFlag = argV[i][j]; |
345 |
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} |
346 |
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} |
347 |
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} |
348 |
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349 |
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else{ |
350 |
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351 |
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if( inName != NULL ){ |
352 |
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fprintf( stderr, |
353 |
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"Error at \"%s\", program does not currently support\n" |
354 |
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"more than one input dump file.\n" |
355 |
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"\n", |
356 |
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argV[i]); |
357 |
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usage(); |
358 |
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exit(0); |
359 |
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} |
360 |
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361 |
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inName = argV[i]; |
362 |
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363 |
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} |
364 |
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} |
365 |
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366 |
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if( inName == NULL ){ |
367 |
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fprintf( stderr, |
368 |
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"Error, dump file is needed to run.\n" ); |
369 |
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usage(); |
370 |
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exit(0); |
371 |
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} |
372 |
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|
373 |
mmeineke |
1060 |
if( outPrefix == NULL ) |
374 |
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outPrefix = inName; |
375 |
mmeineke |
1058 |
|
376 |
mmeineke |
1060 |
|
377 |
mmeineke |
1049 |
// initialize the arrays |
378 |
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|
379 |
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for(i=0;i<nLipids;i++){ |
380 |
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|
381 |
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atoms[nLipAtoms*i+0].type = HEAD; |
382 |
mmeineke |
1062 |
atoms[nLipAtoms*i+0].mass = 72; |
383 |
mmeineke |
1052 |
atoms[nLipAtoms*i+0].u[0] = 0.0; |
384 |
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atoms[nLipAtoms*i+0].u[1] = 0.0; |
385 |
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atoms[nLipAtoms*i+0].u[2] = 1.0; |
386 |
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|
387 |
mmeineke |
1062 |
|
388 |
mmeineke |
1049 |
|
389 |
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atoms[nLipAtoms*i+1].type = CH2; |
390 |
mmeineke |
1062 |
atoms[nLipAtoms*i+1].mass = 14.03; |
391 |
mmeineke |
1049 |
|
392 |
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atoms[nLipAtoms*i+2].type = CH; |
393 |
mmeineke |
1062 |
atoms[nLipAtoms*i+2].mass = 13.02; |
394 |
mmeineke |
1049 |
|
395 |
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atoms[nLipAtoms*i+3].type = CH2; |
396 |
mmeineke |
1062 |
atoms[nLipAtoms*i+3].mass = 14.03; |
397 |
mmeineke |
1049 |
|
398 |
|
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atoms[nLipAtoms*i+4].type = CH2; |
399 |
mmeineke |
1062 |
atoms[nLipAtoms*i+4].mass = 14.03; |
400 |
mmeineke |
1049 |
|
401 |
|
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atoms[nLipAtoms*i+5].type = CH2; |
402 |
mmeineke |
1062 |
atoms[nLipAtoms*i+5].mass = 14.03; |
403 |
mmeineke |
1049 |
|
404 |
|
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atoms[nLipAtoms*i+6].type = CH2; |
405 |
mmeineke |
1062 |
atoms[nLipAtoms*i+6].mass = 14.03; |
406 |
mmeineke |
1049 |
|
407 |
|
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atoms[nLipAtoms*i+7].type = CH2; |
408 |
mmeineke |
1062 |
atoms[nLipAtoms*i+7].mass = 14.03; |
409 |
mmeineke |
1049 |
|
410 |
|
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atoms[nLipAtoms*i+8].type = CH2; |
411 |
mmeineke |
1062 |
atoms[nLipAtoms*i+8].mass = 14.03; |
412 |
mmeineke |
1049 |
|
413 |
|
|
atoms[nLipAtoms*i+9].type = CH2; |
414 |
mmeineke |
1062 |
atoms[nLipAtoms*i+9].mass = 14.03; |
415 |
mmeineke |
1049 |
|
416 |
|
|
atoms[nLipAtoms*i+10].type = CH3; |
417 |
mmeineke |
1062 |
atoms[nLipAtoms*i+10].mass = 15.04; |
418 |
mmeineke |
1049 |
|
419 |
|
|
atoms[nLipAtoms*i+11].type = CH2; |
420 |
mmeineke |
1062 |
atoms[nLipAtoms*i+11].mass = 14.03; |
421 |
mmeineke |
1049 |
|
422 |
|
|
atoms[nLipAtoms*i+12].type = CH2; |
423 |
mmeineke |
1062 |
atoms[nLipAtoms*i+12].mass = 14.03; |
424 |
mmeineke |
1049 |
|
425 |
mmeineke |
1062 |
atoms[nLipAtoms*i+13].type = CH2; |
426 |
|
|
atoms[nLipAtoms*i+13].mass = 14.03; |
427 |
mmeineke |
1049 |
|
428 |
|
|
atoms[nLipAtoms*i+14].type = CH2; |
429 |
mmeineke |
1062 |
atoms[nLipAtoms*i+14].mass = 14.03; |
430 |
mmeineke |
1049 |
|
431 |
|
|
atoms[nLipAtoms*i+15].type = CH2; |
432 |
mmeineke |
1062 |
atoms[nLipAtoms*i+15].mass = 14.03; |
433 |
mmeineke |
1049 |
|
434 |
|
|
atoms[nLipAtoms*i+16].type = CH2; |
435 |
mmeineke |
1062 |
atoms[nLipAtoms*i+16].mass = 14.03; |
436 |
mmeineke |
1049 |
|
437 |
|
|
atoms[nLipAtoms*i+17].type = CH2; |
438 |
mmeineke |
1062 |
atoms[nLipAtoms*i+17].mass = 14.03; |
439 |
mmeineke |
1049 |
|
440 |
|
|
atoms[nLipAtoms*i+18].type = CH3; |
441 |
mmeineke |
1062 |
atoms[nLipAtoms*i+18].mass = 15.04; |
442 |
mmeineke |
1049 |
} |
443 |
|
|
|
444 |
mmeineke |
1052 |
for(i=(nLipAtoms*nLipids);i<nAtoms;i++){ |
445 |
mmeineke |
1049 |
atoms[i].type = SSD; |
446 |
mmeineke |
1062 |
atoms[i].mass = 18.03; |
447 |
mmeineke |
1052 |
atoms[i].u[0] = 0.0; |
448 |
|
|
atoms[i].u[1] = 0.0; |
449 |
|
|
atoms[i].u[2] = 1.0; |
450 |
mmeineke |
1049 |
} |
451 |
mmeineke |
1052 |
|
452 |
|
|
// read and set the frames |
453 |
|
|
|
454 |
mmeineke |
1060 |
openFile(); |
455 |
mmeineke |
1058 |
|
456 |
|
|
fprintf( stdout, |
457 |
|
|
"\n" |
458 |
|
|
"Counting the number of frames in \"%s\"...", |
459 |
|
|
inName ); |
460 |
|
|
fflush(stdout); |
461 |
|
|
|
462 |
mmeineke |
1060 |
setFrames(); |
463 |
mmeineke |
1052 |
|
464 |
mmeineke |
1058 |
fprintf( stdout, |
465 |
|
|
"done.\n" |
466 |
mmeineke |
1060 |
"nFrames = %d.\n", |
467 |
mmeineke |
1058 |
nFrames ); |
468 |
|
|
fflush(stdout); |
469 |
|
|
|
470 |
|
|
if(scdCorr){ |
471 |
|
|
|
472 |
|
|
fprintf ( stdout, |
473 |
|
|
"Calculating the Scd correlation\n" ); |
474 |
|
|
fflush( stdout ); |
475 |
|
|
|
476 |
mmeineke |
1060 |
calcScdCorr( startTime, atoms, outPrefix ); |
477 |
mmeineke |
1058 |
} |
478 |
mmeineke |
1060 |
|
479 |
|
|
if(directorHead){ |
480 |
|
|
|
481 |
|
|
fprintf ( stdout, |
482 |
|
|
"Calculating the Head director\n" ); |
483 |
|
|
fflush( stdout ); |
484 |
|
|
|
485 |
|
|
calcDirHeadCorr( startTime, atoms, outPrefix ); |
486 |
|
|
} |
487 |
mmeineke |
1062 |
|
488 |
|
|
if(directorWhole){ |
489 |
|
|
|
490 |
|
|
fprintf ( stdout, |
491 |
|
|
"Calculating the bilayer director\n" ); |
492 |
|
|
fflush( stdout ); |
493 |
|
|
|
494 |
|
|
calcDirWholeCorr( startTime, atoms, outPrefix ); |
495 |
|
|
} |
496 |
mmeineke |
1073 |
|
497 |
|
|
if(doRMSD){ |
498 |
|
|
|
499 |
|
|
fprintf ( stdout, |
500 |
|
|
"Calculating the RMSD\n" ); |
501 |
|
|
fflush( stdout ); |
502 |
|
|
|
503 |
|
|
rmsd( rmsdType, startTime, outPrefix ); |
504 |
|
|
} |
505 |
mmeineke |
1080 |
|
506 |
|
|
if(doGofz){ |
507 |
|
|
|
508 |
|
|
fprintf ( stdout, |
509 |
|
|
"Calculating the gofZ\n" ); |
510 |
|
|
fflush( stdout ); |
511 |
|
|
|
512 |
|
|
calcGofz( startTime, atoms, outPrefix ); |
513 |
|
|
} |
514 |
mmeineke |
1058 |
|
515 |
|
|
|
516 |
mmeineke |
1060 |
closeFile(); |
517 |
|
|
|
518 |
mmeineke |
1058 |
} |
519 |
|
|
|
520 |
|
|
|
521 |
|
|
/*************************************************************************** |
522 |
|
|
* prints out the usage for the command line arguments, then exits. |
523 |
|
|
***************************************************************************/ |
524 |
|
|
|
525 |
|
|
void usage(){ |
526 |
|
|
(void)fprintf(stdout, |
527 |
|
|
"\n" |
528 |
|
|
"The proper usage is: %s [options] <input_file>\n" |
529 |
|
|
"\n" |
530 |
|
|
"Options:\n" |
531 |
|
|
"\n" |
532 |
|
|
" short:\n" |
533 |
|
|
" ------\n" |
534 |
|
|
" -o <name> The output prefix\n" |
535 |
|
|
" -t <time> Set the start time for correlations\n" |
536 |
|
|
" -l <maxLength> set the maximum value of r\n" |
537 |
|
|
" *Defaults to 1/2 smallest length of first frame.\n" |
538 |
|
|
" -s Calculate the Scd chain correlation.\n" |
539 |
mmeineke |
1062 |
" -h Calculate the directors for the head groups\n" |
540 |
mmeineke |
1080 |
" -w Calculate the director from the bilayers\n" |
541 |
|
|
" -g Calculate the gofz profile\n" |
542 |
mmeineke |
1058 |
"\n" |
543 |
|
|
" long:\n" |
544 |
|
|
" -----\n" |
545 |
mmeineke |
1073 |
" --rmsd <atom1> rmsd for atom1\n" |
546 |
mmeineke |
1058 |
" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
547 |
|
|
" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
548 |
|
|
" --version displays the version number\n" |
549 |
|
|
" --help displays this help message.\n" |
550 |
|
|
|
551 |
|
|
"\n" |
552 |
|
|
"\n", |
553 |
|
|
programName); |
554 |
|
|
} |