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#include <iostream> |
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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 <vector> |
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|
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#include "simError.h" |
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#include "SimSetup.hpp" |
| 9 |
#include "SimInfo.hpp" |
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#include "Atom.hpp" |
| 11 |
#include "Integrator.hpp" |
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#include "Thermo.hpp" |
| 13 |
#include "ReadWrite.hpp" |
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|
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#include "PairCorrList.hpp" |
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#include "AllCorr.hpp" |
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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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using namespace std; |
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|
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int main(int argC,char* argV[]){ |
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|
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int i,j; // loop counters |
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|
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char* outPrefix; // the output prefix |
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|
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char* conversionCheck; |
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bool conversionError; |
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bool optionError; |
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|
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char currentFlag; // used in parsing the flags |
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bool done = false; // multipurpose boolean |
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bool havePrefix; // boolean for the output prefix |
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|
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bool haveMaxLength; |
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double maxLength; |
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|
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bool separateOut; |
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bool havePairCorrs; |
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bool haveStaticCorrs; |
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|
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int nBins; |
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|
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vector<PairCorrList> theList; |
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pairCorrEnum pairType; |
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|
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char* pair1; |
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char* pair2; |
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|
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char dumpName[2000]; |
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char* endTest; |
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int nameLength; |
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int nFrames; |
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char* inName; |
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SimSetup* startMe; |
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SimInfo* infoArray; |
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DumpReader* reader; |
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AllCorr theCorrs; |
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|
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// first things first, all of the initializations |
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|
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fflush(stdout); |
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srand48( 1337 ); // the random number generator. |
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initSimError(); // the error handler |
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|
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outPrefix = NULL; |
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inName = NULL; |
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|
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conversionError = false; |
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optionError = false; |
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|
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havePrefix = false; |
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haveMaxLength = false; |
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|
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haveStaticCorrs = false; |
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havePairCorrs = false; |
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separateOut = false; |
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|
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maxLength = 1.0; |
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nBins = 100; |
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|
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programName = argV[0]; /*save the program name in case we need it*/ |
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|
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for( i = 1; i < argC; i++){ |
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|
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if(argV[i][0] =='-'){ |
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|
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// parse the option |
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|
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if(argV[i][1] == '-' ){ |
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|
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// parse long word options |
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|
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if( !strcmp( argV[i], "--gofr" ) ){ |
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|
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i++; |
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if( i>=argC ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for --gofr\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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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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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for --gofr\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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pair2 = argV[i]; |
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|
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pairType = gofr; |
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theList.push_back(PairCorrList( pairType, pair1, pair2 )); |
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havePairCorrs = true; |
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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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"staticProps 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 = true; |
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|
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for -o\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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outPrefix = argV[i]; |
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if( outPrefix[0] == '-' ) optionError = true; |
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|
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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havePrefix = true; |
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done = true; |
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break; |
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|
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case 'l': |
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// -l <double> set <double> to the maxLength |
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|
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haveMaxLength = true; |
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j++; |
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currentFlag = argV[i][j]; |
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|
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if( currentFlag != '\0' ) optionError = true; |
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|
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for -l\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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maxLength = strtod( argV[i], &conversionCheck); |
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if( conversionCheck == argV[i] ) conversionError = true; |
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if( *conversionCheck != '\0' ) conversionError = true; |
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|
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if( conversionError ){ |
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sprintf( painCave.errMsg, |
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"Error converting \"%s\" to a double for maxLength.\n", |
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argV[i] ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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done = true; |
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|
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break; |
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|
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case 's': |
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// -s turn on separate output files |
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|
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separateOut = true; |
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break; |
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|
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case 'n': |
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// -n <int> set <int> to the nBins |
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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 = true; |
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|
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if( optionError ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"The -n flag should end an option sequence.\n" |
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" example: -sn <int> *NOT* -ns <int>\n" ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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i++; |
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if( i>=argC ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"not enough arguments for -n\n"); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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nBins = strtol( argV[i], &conversionCheck, 10 ); |
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if( conversionCheck == argV[i] ) conversionError = true; |
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if( *conversionCheck != '\0' ) conversionError = true; |
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|
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if( conversionError ){ |
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sprintf( painCave.errMsg, |
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"Error converting \"%s\" to an int for nBins.\n", |
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argV[i] ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if( nBins < 1 ){ |
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sprintf( painCave.errMsg, |
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"nBins error: nBins = %d is less than 1.\n", |
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nBins ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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done = true; |
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|
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break; |
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|
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default: |
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|
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sprintf(painCave.errMsg, |
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"\n" |
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"Bad option \"-%c\"\n", currentFlag); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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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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sprintf( painCave.errMsg, |
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"Error at \"%s\", program does not currently support\n" |
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"more than one input bass file.\n" |
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"\n", |
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argV[i]); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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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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sprintf( painCave.errMsg, |
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"Error, bass file is needed to run.\n" ); |
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usage(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// make the dump name |
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|
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strcpy( dumpName, inName ); |
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nameLength = strlen( dumpName ); |
| 361 |
endTest = &(dumpName[nameLength - 5]); |
| 362 |
if( !strcmp( endTest, ".bass" ) ){ |
| 363 |
strcpy( endTest, ".dump" ); |
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} |
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else if( !strcmp( endTest, ".BASS" ) ){ |
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strcpy( endTest, ".dump" ); |
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} |
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else{ |
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strcat( dumpName, ".dump" ); |
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} |
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|
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// count the number of frames in the dump file. |
| 373 |
|
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printf("Counting the number of frames in \"%s\"... ", dumpName ); |
| 375 |
fflush(stdout); |
| 376 |
|
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reader = new DumpReader( dumpName ); |
| 378 |
nFrames = reader->getNframes(); |
| 379 |
|
| 380 |
printf("done.\n" |
| 381 |
"\tFound %d frames.\n" |
| 382 |
"\n", |
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nFrames ); |
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fflush(stdout); |
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|
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infoArray = new SimInfo[nFrames]; |
| 387 |
|
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printf("Parsing the bass file, and initializing the " |
| 389 |
"Simulation Frames..." ); |
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fflush(stdout); |
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|
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startMe = new SimSetup(); |
| 393 |
startMe->setSimInfo( infoArray, nFrames ); |
| 394 |
startMe->parseFile( inName ); |
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startMe->createSim(); |
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|
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delete startMe; |
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|
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printf("done.\n"); |
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fflush(stdout); |
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|
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printf("Initializing the pair correlations..." ); |
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fflush(stdout); |
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|
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if(haveMaxLength) |
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theCorrs.setMaxLength( maxLength ); |
| 407 |
|
| 408 |
theCorrs.setNbins( nBins ); |
| 409 |
theCorrs.setFrames( infoArray, nFrames, reader ); |
| 410 |
theCorrs.setPairCorrList( theList ); |
| 411 |
theCorrs.initCorrelations( outPrefix, separateOut, havePairCorrs, |
| 412 |
haveStaticCorrs ); |
| 413 |
|
| 414 |
printf("done\n"); |
| 415 |
fflush(stdout); |
| 416 |
|
| 417 |
theCorrs.calcCorrelations(); |
| 418 |
|
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return 0 ; |
| 420 |
} |
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|
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|
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/*************************************************************************** |
| 424 |
* prints out the usage for the command line arguments, then exits. |
| 425 |
***************************************************************************/ |
| 426 |
|
| 427 |
void usage(){ |
| 428 |
(void)fprintf(stdout, |
| 429 |
"\n" |
| 430 |
"The proper usage is: %s [options] <input_file>\n" |
| 431 |
"\n" |
| 432 |
"Options:\n" |
| 433 |
"\n" |
| 434 |
" short:\n" |
| 435 |
" ------\n" |
| 436 |
" -o <name> The output prefix\n" |
| 437 |
" -n <nBins> Set the number of bins in the Histogram.\n" |
| 438 |
" *Defaults to 100\n" |
| 439 |
" -l <maxLength> set the maximum value of r\n" |
| 440 |
" *Defaults to 1/2 smallest length of first frame.\n" |
| 441 |
" -s Turn on separate output files\n" |
| 442 |
" *Defaults to single output file.\n" |
| 443 |
"\n" |
| 444 |
" long:\n" |
| 445 |
" -----\n" |
| 446 |
" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n" |
| 447 |
" *note: \"_ALL_\" matches all atoms\n" |
| 448 |
" --version displays the version number\n" |
| 449 |
" --help displays this help message.\n" |
| 450 |
|
| 451 |
"\n" |
| 452 |
"\n", |
| 453 |
programName); |
| 454 |
} |
