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#include <stdlib.h> |
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#include <vector> |
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|
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#include "AllCorr.hpp" |
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|
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|
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AllCorr::AllCorr(){ |
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|
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pairCorrs = NULL; |
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haveFrames = false; |
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pairCorrSet = false; |
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haveLength = false; |
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haveNbins = false; |
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} |
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|
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AllCorr::~AllCorr(){ |
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int i; |
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|
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if( pairCorrs != NULL ){ |
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for(i=0; i<nPairs; i++) |
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delete pairCorrs[i]; |
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delete[] pairCorrs; |
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} |
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} |
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|
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void AllCorr::setMaxLength( double theLength ){ |
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maxLength = theLength; |
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haveLength = true; |
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} |
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|
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void AllCorr::setNbins( double theNbins ){ |
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nBins = theNbins; |
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haveNbins = true; |
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} |
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|
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void AllCorr::setFrames( SimInfo* theInfoArray, int theNframes, |
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DumpReader* theReader ){ |
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int i; |
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|
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|
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infoArray = theInfoArray; |
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nFrames = theNframes; |
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reader = theReader; |
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|
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nAtoms = infoArray[0].n_atoms; |
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|
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|
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// allocate the first frame's atom arrays |
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|
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(infoArray[0].getConfiguration())->createArrays(infoArray[0].n_atoms); |
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for (i = 0; i < infoArray[0].n_atoms; i++) |
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infoArray[0].atoms[i]->setCoords(); |
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|
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// read in the first frame's positions |
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|
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reader->readFrame( &(infoArray[0]), 0 ); |
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|
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if( !haveLength ){ |
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maxLength = infoArray[0].getMaxCutoff(); |
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haveLength = true; |
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} |
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|
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haveFrames = true; |
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} |
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|
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void AllCorr::setPairCorrList( vector <PairCorrList> &theList ){ |
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|
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int i; |
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char pair1[PCL_NAME_LENGTH]; |
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char pair2[PCL_NAME_LENGTH]; |
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|
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if( !haveFrames ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"AllCorr Error: attempt to create the pair correlations without" |
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" first setting the Frames\n" ); |
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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( !haveNbins ){ |
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sprintf( painCave.errMsg, |
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"\n" |
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"AllCorr Error: attempt to create the pair correlations without" |
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" first setting nBins\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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theList.sort(); |
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|
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nPairs = (int)theList.size(); |
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pairCorrs = new PairCorrType*[nPairs]; |
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|
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for(i=0;i<nPairs;i++){ |
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|
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theList[i].getAtom1( pair1 ); |
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theList[i].getAtom2( pair2 ); |
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|
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switch( theList[i].getType() ){ |
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|
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case gofr: |
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pairCorrs[i] = new GofR(pair1, pair2, nAtoms, nBins); |
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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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"AllCorr Error: Unrecognized pair corr type in " |
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" setPairCorrList()->theList[%d]\n", |
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i ); |
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painCave.isFatal = 1; |
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simError(); |
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break; |
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} |
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} |
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|
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pairCorrSet = true; |
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} |
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|
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void AllCorr::initCorrelations( char* theOutPrefix, bool theIsSeparateOut, |
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bool theHavePairCorrs, |
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bool theHaveStaticCorrs ){ |
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int i; |
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atomName* theNames = new atomNames[nAtoms]; |
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|
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havePairCorrs = theHavePairCorrs; |
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haveStaticCorrs = theHaveStaticCorrs; |
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|
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if( havePairCorrs){ |
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|
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if(!pairCorrSet){ |
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sprintf( painCave.errMsg, |
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"AllCorr error: Attempt to initialize pair correlations " |
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" without first setting the pair correlation list.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(i=0;i<nAtoms;i++){ |
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|
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strcpy(theNames[i].name, infoArray[0].atoms[i]->getType() ); |
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} |
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|
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for(i=0;i<nPairs;i++){ |
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pairCorrs[i]->initCoor(maxLength, theNames ); |
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} |
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} |
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|
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if( haveStaticCorrs ){ |
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|
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// empty for now |
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} |
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|
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strcpy(outPrefix, theOutPrefix); |
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isSeparateOut = theIsSeparateOut; |
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} |
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|
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|
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void AllCorr::calcCorrelations(){ |
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|
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SimInfor* currInfo; |
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int i,j,k,l; |
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double rij[3], rDist, uHatI[3], uHatJ[3]; |
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double* grndOut = NULL; |
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double dSqr, ri[3], rj[3]; |
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DirectionalAtom* dAtom; |
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double frameVolume; |
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|
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|
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for(k=0; k<nFrames; k++){ |
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|
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currInfo = &(infoArray[k]); |
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|
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// skip the first frame, as it is already initialized |
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if( k != 0 ){ |
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|
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// allocate the frame's atom arrays |
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|
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(currInfo->getConfiguration())->createArrays(currInfo->n_atoms); |
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for (i = 0; i < currInfo->n_atoms; i++) |
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currInfo->atoms[i]->setCoords(); |
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|
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// read in the frame's positions |
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|
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reader->readFrame( &(infoArray[k]), 0 ); |
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} |
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|
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frameVolume = currInfo->boxVol; |
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this->setFrameVolume( frameVolume ); |
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|
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if(havePairCorrs){ |
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|
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// do the pair loop |
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|
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for(i=0;i<(nAtoms-1);i++){ |
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|
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if( this->matchI(i) ){ |
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|
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for(j=i+1;j<nAtoms;j++){ |
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|
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if( this->matchJ(j) ){ |
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|
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// calc rdist and rij; |
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|
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currInfo->atoms[i]->getPos( ri ); |
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currInfo->wrapVector( ri ); |
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|
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currInfo->atoms[i]->getPos( rj ); |
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currInfo->wrapVector( rj ); |
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|
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for(l=0;l<3;l++) |
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rij[l] = rj[l] - ri[l]; |
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|
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dSqr=0; |
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for(l=0;l<3;l++) |
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dSqr += rj[l] * rj[l]; |
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|
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rDist = sqrt( dSqr ); |
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|
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if( currInfo->atoms[i]->isDirectional() ){ |
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|
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dAtom = (directionalAtom*)currInfo->atoms[i]; |
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dAtom->getU( uHatI ); |
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|
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if( currInfo->atoms[j]->isDirectional() ){ |
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|
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dAtom = (directionalAtom*)currInfo->atoms[j]; |
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dAtom->getU( uHatJ ); |
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|
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this->pairCorrelate( rij, rDist, uHatI, uHatJ ); |
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} |
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else{ |
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|
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this->pairCorrelate( rij, rDist, uHatI, grndOut ); |
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} |
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} |
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else if( currInfo->atoms[j]->isDirectional() ){ |
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|
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dAtom = (directionalAtom*)currInfo->atoms[j]; |
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dAtom->getU( uHatJ ); |
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|
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this->pairCorrelate( rij, rDist, grndOut, uHatJ ); |
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} |
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else{ |
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this->pairCorrelate( rij, rDist, grndOut, grndOut ); |
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} |
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} |
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} |
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} |
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} |
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} |
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|
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if( haveStaticCorrs ){ |
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|
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// empty for now |
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|
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} |
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|
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// accumulate the averages for this frame |
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|
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this->accumulateFrame(); |
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|
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// de-allocate the frame |
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|
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(currInfo->getConfiguration())->destroyArrays(); |
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} |
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|
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this->writeCorrs(); |
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} |
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|
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bool AllCorr::matchI(int i){ |
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|
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int k; |
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bool result; |
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|
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result = false; |
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|
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for(k=0;k<nPairs;k++) |
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result = (result || pairCorrs[k]->matchI(i) ); |
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|
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return result; |
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} |
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|
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bool AllCorr::matchJ(int j){ |
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|
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int k; |
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bool result; |
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|
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result = false; |
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|
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for(k=0;k<nPairs;k++) |
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result = (result || pairCorrs[k]->matchJ(j) ); |
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|
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return result; |
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} |
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|
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void AllCorr::pairCorrelate( double[3] Rij, double dist, |
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double[3] uHatI, double[3] uHatJ ){ |
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|
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int i; |
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|
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for(i=0;i<nPairs;i++) |
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pairCorrs[i]->correlate( Rij, dist, uHatI, uHatj ); |
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} |
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|
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void AllCorr::setFrameVolume( double theVolume ){ |
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|
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int i; |
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|
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if( havePairCorrs ){ |
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|
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for(i=0;i<nPairs;i++) |
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pairCorrs[i]->setFrameVolume( theVolume ); |
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} |
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|
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if( haveStaticCorrs ){ |
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|
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// empty for now |
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} |
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} |
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|
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void AllCorr::accumulateFrame( void ){ |
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|
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int i; |
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|
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if( havePairCorrs ){ |
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|
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for(i=0;i<nPair;i++) |
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pairCorrs[i]->accumulateFrame(); |
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} |
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|
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if( haveStaticCorrs ){ |
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|
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// empty for now |
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} |
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} |
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|
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void AllCorr::writeCorrs( void ){ |
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int i; |
| 342 |
|
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if( isSeparateOut ){ |
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|
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if( havePairCorrs ){ |
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|
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for(i=0;i<nPairs;i++) |
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pairCorrs[i]->writeCorrs( outPrefix ); |
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} |
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|
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if( haveStaticCorrs ){ |
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|
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// empty for now |
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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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// empty for now |
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} |
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|
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} |
