| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <stdio.h> |
| 4 |
#include <stdlib.h> |
| 5 |
#include <string.h> |
| 6 |
|
| 7 |
|
| 8 |
#include "params.h" |
| 9 |
#include "tcProps.h" |
| 10 |
#include "readWrite.h" |
| 11 |
#include "scdCorr.h" |
| 12 |
#include "directorHead.h" |
| 13 |
#include "directorWhole.h" |
| 14 |
#include "rmsd.h" |
| 15 |
#include "gofz.h" |
| 16 |
|
| 17 |
|
| 18 |
#define VERSION_MAJOR 0 |
| 19 |
#define VERSION_MINOR 1 |
| 20 |
|
| 21 |
char *programName; /*the name of the program */ |
| 22 |
void usage(void); |
| 23 |
|
| 24 |
int main( int argC, char *argV[] ){ |
| 25 |
|
| 26 |
// list of 'a priori' constants |
| 27 |
|
| 28 |
const int nLipAtoms = NL_ATOMS; |
| 29 |
const int nBonds = NBONDS; |
| 30 |
const int nLipids = NLIPIDS; |
| 31 |
const int nSSD = NSSD; |
| 32 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 33 |
|
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// different needed variables |
| 35 |
|
| 36 |
struct atomCoord atoms[nAtoms]; |
| 37 |
int i,j,k; |
| 38 |
|
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char* outPrefix; // the output prefix |
| 40 |
char currentFlag; // used in parsing the flags |
| 41 |
int done = 0; // multipurpose boolean |
| 42 |
int havePrefix; // boolean for the output prefix |
| 43 |
int haveMaxLength; |
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char* conversionCheck; |
| 45 |
int conversionError; |
| 46 |
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; |
| 51 |
double maxLength; |
| 52 |
int directorHead, directorWhole, doRMSD, doGofz; |
| 53 |
enum atomNames rmsdType; |
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|
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// system initialization |
| 56 |
|
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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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doGofz = 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 |
| 282 |
|
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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; |
| 287 |
|
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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" |
| 292 |
" example: -st <double> *NOT* -ts <double>\n" ); |
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usage(); |
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exit(0); |
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} |
| 296 |
|
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
| 301 |
"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; |
| 309 |
|
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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; |
| 321 |
|
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case 'w': |
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// -w turn on director head |
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|
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directorWhole = 1; |
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break; |
| 327 |
|
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case 'g': |
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// -g turn on gofZ |
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|
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doGofz = 1; |
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break; |
| 333 |
|
| 334 |
|
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default: |
| 336 |
|
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fprintf( stderr, |
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"\n" |
| 339 |
"Bad option \"-%c\"\n", currentFlag); |
| 340 |
usage(); |
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exit(0); |
| 342 |
} |
| 343 |
j++; |
| 344 |
currentFlag = argV[i][j]; |
| 345 |
} |
| 346 |
} |
| 347 |
} |
| 348 |
|
| 349 |
else{ |
| 350 |
|
| 351 |
if( inName != NULL ){ |
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fprintf( stderr, |
| 353 |
"Error at \"%s\", program does not currently support\n" |
| 354 |
"more than one input dump file.\n" |
| 355 |
"\n", |
| 356 |
argV[i]); |
| 357 |
usage(); |
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exit(0); |
| 359 |
} |
| 360 |
|
| 361 |
inName = argV[i]; |
| 362 |
|
| 363 |
} |
| 364 |
} |
| 365 |
|
| 366 |
if( inName == NULL ){ |
| 367 |
fprintf( stderr, |
| 368 |
"Error, dump file is needed to run.\n" ); |
| 369 |
usage(); |
| 370 |
exit(0); |
| 371 |
} |
| 372 |
|
| 373 |
if( outPrefix == NULL ) |
| 374 |
outPrefix = inName; |
| 375 |
|
| 376 |
|
| 377 |
// initialize the arrays |
| 378 |
|
| 379 |
for(i=0;i<nLipids;i++){ |
| 380 |
|
| 381 |
atoms[nLipAtoms*i+0].type = HEAD; |
| 382 |
atoms[nLipAtoms*i+0].mass = 72; |
| 383 |
atoms[nLipAtoms*i+0].u[0] = 0.0; |
| 384 |
atoms[nLipAtoms*i+0].u[1] = 0.0; |
| 385 |
atoms[nLipAtoms*i+0].u[2] = 1.0; |
| 386 |
|
| 387 |
|
| 388 |
|
| 389 |
atoms[nLipAtoms*i+1].type = CH2; |
| 390 |
atoms[nLipAtoms*i+1].mass = 14.03; |
| 391 |
|
| 392 |
atoms[nLipAtoms*i+2].type = CH; |
| 393 |
atoms[nLipAtoms*i+2].mass = 13.02; |
| 394 |
|
| 395 |
atoms[nLipAtoms*i+3].type = CH2; |
| 396 |
atoms[nLipAtoms*i+3].mass = 14.03; |
| 397 |
|
| 398 |
atoms[nLipAtoms*i+4].type = CH2; |
| 399 |
atoms[nLipAtoms*i+4].mass = 14.03; |
| 400 |
|
| 401 |
atoms[nLipAtoms*i+5].type = CH2; |
| 402 |
atoms[nLipAtoms*i+5].mass = 14.03; |
| 403 |
|
| 404 |
atoms[nLipAtoms*i+6].type = CH2; |
| 405 |
atoms[nLipAtoms*i+6].mass = 14.03; |
| 406 |
|
| 407 |
atoms[nLipAtoms*i+7].type = CH2; |
| 408 |
atoms[nLipAtoms*i+7].mass = 14.03; |
| 409 |
|
| 410 |
atoms[nLipAtoms*i+8].type = CH2; |
| 411 |
atoms[nLipAtoms*i+8].mass = 14.03; |
| 412 |
|
| 413 |
atoms[nLipAtoms*i+9].type = CH2; |
| 414 |
atoms[nLipAtoms*i+9].mass = 14.03; |
| 415 |
|
| 416 |
atoms[nLipAtoms*i+10].type = CH3; |
| 417 |
atoms[nLipAtoms*i+10].mass = 15.04; |
| 418 |
|
| 419 |
atoms[nLipAtoms*i+11].type = CH2; |
| 420 |
atoms[nLipAtoms*i+11].mass = 14.03; |
| 421 |
|
| 422 |
atoms[nLipAtoms*i+12].type = CH2; |
| 423 |
atoms[nLipAtoms*i+12].mass = 14.03; |
| 424 |
|
| 425 |
atoms[nLipAtoms*i+13].type = CH2; |
| 426 |
atoms[nLipAtoms*i+13].mass = 14.03; |
| 427 |
|
| 428 |
atoms[nLipAtoms*i+14].type = CH2; |
| 429 |
atoms[nLipAtoms*i+14].mass = 14.03; |
| 430 |
|
| 431 |
atoms[nLipAtoms*i+15].type = CH2; |
| 432 |
atoms[nLipAtoms*i+15].mass = 14.03; |
| 433 |
|
| 434 |
atoms[nLipAtoms*i+16].type = CH2; |
| 435 |
atoms[nLipAtoms*i+16].mass = 14.03; |
| 436 |
|
| 437 |
atoms[nLipAtoms*i+17].type = CH2; |
| 438 |
atoms[nLipAtoms*i+17].mass = 14.03; |
| 439 |
|
| 440 |
atoms[nLipAtoms*i+18].type = CH3; |
| 441 |
atoms[nLipAtoms*i+18].mass = 15.04; |
| 442 |
} |
| 443 |
|
| 444 |
for(i=(nLipAtoms*nLipids);i<nAtoms;i++){ |
| 445 |
atoms[i].type = SSD; |
| 446 |
atoms[i].mass = 18.03; |
| 447 |
atoms[i].u[0] = 0.0; |
| 448 |
atoms[i].u[1] = 0.0; |
| 449 |
atoms[i].u[2] = 1.0; |
| 450 |
} |
| 451 |
|
| 452 |
// read and set the frames |
| 453 |
|
| 454 |
openFile(); |
| 455 |
|
| 456 |
fprintf( stdout, |
| 457 |
"\n" |
| 458 |
"Counting the number of frames in \"%s\"...", |
| 459 |
inName ); |
| 460 |
fflush(stdout); |
| 461 |
|
| 462 |
setFrames(); |
| 463 |
|
| 464 |
fprintf( stdout, |
| 465 |
"done.\n" |
| 466 |
"nFrames = %d.\n", |
| 467 |
nFrames ); |
| 468 |
fflush(stdout); |
| 469 |
|
| 470 |
if(scdCorr){ |
| 471 |
|
| 472 |
fprintf ( stdout, |
| 473 |
"Calculating the Scd correlation\n" ); |
| 474 |
fflush( stdout ); |
| 475 |
|
| 476 |
calcScdCorr( startTime, atoms, outPrefix ); |
| 477 |
} |
| 478 |
|
| 479 |
if(directorHead){ |
| 480 |
|
| 481 |
fprintf ( stdout, |
| 482 |
"Calculating the Head director\n" ); |
| 483 |
fflush( stdout ); |
| 484 |
|
| 485 |
calcDirHeadCorr( startTime, atoms, outPrefix ); |
| 486 |
} |
| 487 |
|
| 488 |
if(directorWhole){ |
| 489 |
|
| 490 |
fprintf ( stdout, |
| 491 |
"Calculating the bilayer director\n" ); |
| 492 |
fflush( stdout ); |
| 493 |
|
| 494 |
calcDirWholeCorr( startTime, atoms, outPrefix ); |
| 495 |
} |
| 496 |
|
| 497 |
if(doRMSD){ |
| 498 |
|
| 499 |
fprintf ( stdout, |
| 500 |
"Calculating the RMSD\n" ); |
| 501 |
fflush( stdout ); |
| 502 |
|
| 503 |
rmsd( rmsdType, startTime, outPrefix ); |
| 504 |
} |
| 505 |
|
| 506 |
if(doGofz){ |
| 507 |
|
| 508 |
fprintf ( stdout, |
| 509 |
"Calculating the gofZ\n" ); |
| 510 |
fflush( stdout ); |
| 511 |
|
| 512 |
calcGofz( startTime, atoms, outPrefix ); |
| 513 |
} |
| 514 |
|
| 515 |
|
| 516 |
closeFile(); |
| 517 |
|
| 518 |
} |
| 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 |
" -h Calculate the directors for the head groups\n" |
| 540 |
" -w Calculate the director from the bilayers\n" |
| 541 |
" -g Calculate the gofz profile\n" |
| 542 |
"\n" |
| 543 |
" long:\n" |
| 544 |
" -----\n" |
| 545 |
" --rmsd <atom1> rmsd for atom1\n" |
| 546 |
" --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 |
} |
