1 |
tim |
658 |
#include "Integrator.hpp" |
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#include "simError.h" |
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
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: T(theInfo, the_ff), fz(NULL), indexOfZConsMols(NULL) |
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{ |
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//get properties from SimInfo |
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GenericData* data; |
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IndexData* index; |
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DoubleData* sampleTime; |
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StringData* filename; |
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data = info->getProperty("zconsindex"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set index of z-constraint molecules.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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index = dynamic_cast<IndexData*>(data); |
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if(!index){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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indexOfAllZConsMols = index->getIndexData(); |
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} |
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} |
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//retrive sample time of z-contraint |
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data = info->getProperty("zconstime"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set sample time.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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sampleTime = dynamic_cast<DoubleData*>(data); |
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if(!sampleTime){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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this->zconsTime = sampleTime->getData(); |
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} |
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} |
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//retrive output filename of z force |
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data = info->getProperty("zconsfilename"); |
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if(!data) { |
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sprintf( painCave.errMsg, |
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"ZConstraint error: If you use an ZConstraint\n" |
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" , you must set output filename of z-force.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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filename = dynamic_cast<StringData*>(data); |
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if(!filename){ |
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sprintf( painCave.errMsg, |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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else{ |
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this->zconsOutput = filename->getData(); |
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} |
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} |
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//calculate reference z coordinate for z-constraint molecules |
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double totalMass_local; |
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double totalMass; |
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double totalMZ_local; |
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double totalMZ; |
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double massOfUncons_local; |
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double massOfCurMol; |
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double COM[3]; |
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totalMass_local = 0; |
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totalMass = 0; |
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totalMZ_local = 0; |
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totalMZ = 0; |
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massOfUncons_local = 0; |
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for(int i = 0; i < nMols; i++){ |
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massOfCurMol = molecules[i].getTotalMass(); |
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molecules[i].getCOM(COM); |
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totalMass_local += massOfCurMol; |
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totalMZ_local += massOfCurMol * COM[2]; |
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if(isZConstraintMol(&molecules[i]) == -1){ |
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massOfUncons_local += massOfCurMol; |
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} |
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} |
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#ifdef IS_MPI |
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MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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totalMass = totalMass_local; |
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totalMZ = totalMZ_local; |
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totalMassOfUncons = massOfUncons_local; |
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#endif |
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double zsys; |
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zsys = totalMZ / totalMass; |
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#ifndef IS_MPI |
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for(int i = 0; i < nMols; i++){ |
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if(isZConstraintMol(&molecules[i]) > -1 ){ |
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molecules[i].getCOM(COM); |
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allRefZ.push_back(COM[2] - zsys); |
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} |
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} |
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#else |
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int whichNode; |
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enum CommType { RequestMolZPos, EndOfRequest} status; |
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//int status; |
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double zpos; |
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int localIndex; |
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MPI_Status ierr; |
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int tag = 0; |
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if(worldRank == 0){ |
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int globalIndexOfCurMol; |
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int *MolToProcMap; |
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MolToProcMap = mpiSim->getMolToProcMap(); |
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for(int i = 0; i < indexOfAllZConsMols.size(); i++){ |
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whichNode = MolToProcMap[indexOfAllZConsMols[i]]; |
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globalIndexOfCurMol = indexOfAllZConsMols[i]; |
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if(whichNode == 0){ |
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for(int j = 0; j < nMols; j++) |
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if(molecules[j].getGlobalIndex() == globalIndexOfCurMol){ |
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localIndex = j; |
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break; |
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} |
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molecules[localIndex].getCOM(COM); |
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allRefZ.push_back(COM[2] - zsys); |
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188 |
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} |
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else{ |
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status = RequestMolZPos; |
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MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
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MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
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MPI_Recv(&zpos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
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allRefZ.push_back(zpos - zsys); |
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} |
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} //End of Request Loop |
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//Send ending request message to slave nodes |
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status = EndOfRequest; |
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for(int i =1; i < mpiSim->getNumberProcessors(); i++) |
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MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD); |
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} |
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else{ |
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int whichMol; |
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bool done = false; |
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while (!done){ |
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MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr); |
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switch (status){ |
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case RequestMolZPos : |
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MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr); |
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for(int i = 0; i < nMols; i++) |
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if(molecules[i].getGlobalIndex() == whichMol){ |
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localIndex = i; |
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break; |
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} |
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molecules[localIndex].getCOM(COM); |
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zpos = COM[2]; |
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MPI_Send(&zpos, 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD); |
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break; |
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case EndOfRequest : |
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done = true; |
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break; |
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} |
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} |
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} |
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//Brocast the allRefZ to slave nodes; |
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double* allRefZBuf; |
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int nZConsMols; |
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nZConsMols = indexOfAllZConsMols.size(); |
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allRefZBuf = new double[nZConsMols]; |
250 |
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if(worldRank == 0){ |
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for(int i = 0; i < nZConsMols; i++) |
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allRefZBuf[i] = allRefZ[i]; |
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} |
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MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD); |
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259 |
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if(worldRank != 0){ |
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for(int i = 0; i < nZConsMols; i++) |
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allRefZ.push_back(allRefZBuf[i]); |
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} |
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delete[] allRefZBuf; |
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#endif |
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268 |
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269 |
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#ifdef IS_MPI |
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update(); |
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#else |
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int searchResult; |
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refZ = allRefZ; |
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for(int i = 0; i < nMols; i++){ |
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searchResult = isZConstraintMol(&molecules[i]); |
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280 |
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if(searchResult > -1){ |
281 |
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zconsMols.push_back(&molecules[i]); |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
284 |
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285 |
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molecules[i].getCOM(COM); |
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} |
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else |
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{ |
289 |
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unconsMols.push_back(&molecules[i]); |
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massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
292 |
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} |
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} |
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fz = new double[zconsMols.size()]; |
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indexOfZConsMols = new int [zconsMols.size()]; |
298 |
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if(!fz || !indexOfZConsMols){ |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
305 |
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306 |
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for(int i = 0; i < zconsMols.size(); i++) |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
308 |
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309 |
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#endif |
310 |
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311 |
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fzOut = new ZConsWriter(zconsOutput.c_str()); |
312 |
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313 |
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if(!fzOut){ |
314 |
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sprintf( painCave.errMsg, |
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"Memory allocation failure in class Zconstraint\n"); |
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painCave.isFatal = 1; |
317 |
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simError(); |
318 |
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} |
319 |
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320 |
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fzOut->writeRefZ(indexOfAllZConsMols, allRefZ); |
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} |
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template<typename T> ZConstraint<T>::~ZConstraint() |
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{ |
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if(fz) |
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delete[] fz; |
327 |
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328 |
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if(indexOfZConsMols) |
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delete[] indexOfZConsMols; |
330 |
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331 |
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if(fzOut) |
332 |
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delete fzOut; |
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} |
334 |
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335 |
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#ifdef IS_MPI |
336 |
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template<typename T> void ZConstraint<T>::update() |
337 |
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{ |
338 |
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double COM[3]; |
339 |
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int index; |
340 |
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341 |
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zconsMols.clear(); |
342 |
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massOfZConsMols.clear(); |
343 |
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refZ.clear(); |
344 |
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345 |
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unconsMols.clear(); |
346 |
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massOfUnconsMols.clear(); |
347 |
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348 |
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349 |
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//creat zconsMol and unconsMol lists |
350 |
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for(int i = 0; i < nMols; i++){ |
351 |
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352 |
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index = isZConstraintMol(&molecules[i]); |
353 |
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354 |
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if(index > -1){ |
355 |
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356 |
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zconsMols.push_back(&molecules[i]); |
357 |
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massOfZConsMols.push_back(molecules[i].getTotalMass()); |
358 |
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359 |
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molecules[i].getCOM(COM); |
360 |
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refZ.push_back(allRefZ[index]); |
361 |
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} |
362 |
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else |
363 |
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{ |
364 |
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365 |
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unconsMols.push_back(&molecules[i]); |
366 |
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massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
367 |
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368 |
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} |
369 |
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} |
370 |
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371 |
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//The reason to declare fz and indexOfZconsMols as pointer to array is |
372 |
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// that we want to make the MPI communication simple |
373 |
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if(fz) |
374 |
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delete[] fz; |
375 |
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376 |
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if(indexOfZConsMols) |
377 |
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delete[] indexOfZConsMols; |
378 |
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379 |
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if (zconsMols.size() > 0){ |
380 |
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fz = new double[zconsMols.size()]; |
381 |
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indexOfZConsMols = new int[zconsMols.size()]; |
382 |
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383 |
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if(!fz || !indexOfZConsMols){ |
384 |
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sprintf( painCave.errMsg, |
385 |
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"Memory allocation failure in class Zconstraint\n"); |
386 |
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painCave.isFatal = 1; |
387 |
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simError(); |
388 |
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} |
389 |
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390 |
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for(int i = 0; i < zconsMols.size(); i++){ |
391 |
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indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
392 |
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} |
393 |
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394 |
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} |
395 |
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else{ |
396 |
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fz = NULL; |
397 |
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indexOfZConsMols = NULL; |
398 |
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} |
399 |
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400 |
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} |
401 |
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402 |
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#endif |
403 |
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404 |
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/** Function Name: isZConstraintMol |
405 |
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** Parameter |
406 |
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** Molecule* mol |
407 |
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** Return value: |
408 |
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** -1, if the molecule is not z-constraint molecule, |
409 |
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** other non-negative values, its index in indexOfAllZConsMols vector |
410 |
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*/ |
411 |
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412 |
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template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
413 |
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{ |
414 |
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int index; |
415 |
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int low; |
416 |
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int high; |
417 |
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int mid; |
418 |
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419 |
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index = mol->getGlobalIndex(); |
420 |
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421 |
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low = 0; |
422 |
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high = indexOfAllZConsMols.size() - 1; |
423 |
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424 |
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//Binary Search (we have sorted the array) |
425 |
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while(low <= high){ |
426 |
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mid = (low + high) /2; |
427 |
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|
if (indexOfAllZConsMols[mid] == index) |
428 |
|
|
return mid; |
429 |
|
|
else if (indexOfAllZConsMols[mid] > index ) |
430 |
|
|
high = mid -1; |
431 |
|
|
else |
432 |
|
|
low = mid + 1; |
433 |
|
|
} |
434 |
|
|
|
435 |
|
|
return -1; |
436 |
|
|
} |
437 |
|
|
|
438 |
|
|
/** Function Name: integrateStep |
439 |
|
|
** Parameter: |
440 |
|
|
** int calcPot; |
441 |
|
|
** int calcStress; |
442 |
|
|
** Description: |
443 |
|
|
** Advance One Step. |
444 |
|
|
** Memo: |
445 |
|
|
** The best way to implement z-constraint is to override integrateStep |
446 |
|
|
** Overriding constrainB is not a good choice, since in integrateStep, |
447 |
|
|
** constrainB is invoked by below line, |
448 |
|
|
** if(nConstrained) constrainB(); |
449 |
|
|
** For instance, we would like to apply z-constraint without bond contrain, |
450 |
|
|
** In that case, if we override constrainB, Z-constrain method will never be executed; |
451 |
|
|
*/ |
452 |
|
|
template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress ) |
453 |
|
|
{ |
454 |
|
|
T::integrateStep( calcPot, calcStress ); |
455 |
|
|
resetZ(); |
456 |
|
|
|
457 |
|
|
double currZConsTime = 0; |
458 |
|
|
|
459 |
|
|
//write out forces of z constraint |
460 |
|
|
if( info->getTime() >= currZConsTime){ |
461 |
|
|
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
462 |
|
|
} |
463 |
|
|
} |
464 |
|
|
|
465 |
|
|
/** Function Name: resetZ |
466 |
|
|
** Description: |
467 |
|
|
** Reset the z coordinates |
468 |
|
|
*/ |
469 |
|
|
|
470 |
|
|
template<typename T> void ZConstraint<T>::resetZ() |
471 |
|
|
{ |
472 |
|
|
double deltaZ; |
473 |
|
|
double mzOfZCons; //total sum of m*z of z-constrain molecules |
474 |
|
|
double mzOfUncons; //total sum of m*z of unconstrain molecuels; |
475 |
|
|
double totalMZOfZCons; |
476 |
|
|
double totalMZOfUncons; |
477 |
|
|
double COM[3]; |
478 |
|
|
double zsys; |
479 |
|
|
Atom** zconsAtoms; |
480 |
|
|
|
481 |
|
|
mzOfZCons = 0; |
482 |
|
|
mzOfUncons = 0; |
483 |
|
|
|
484 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
485 |
|
|
mzOfZCons += massOfZConsMols[i] * refZ[i]; |
486 |
|
|
} |
487 |
|
|
|
488 |
|
|
#ifdef IS_MPI |
489 |
|
|
MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
490 |
|
|
#else |
491 |
|
|
totalMZOfZCons = mzOfZCons; |
492 |
|
|
#endif |
493 |
|
|
|
494 |
|
|
for(int i = 0; i < unconsMols.size(); i++){ |
495 |
|
|
unconsMols[i]->getCOM(COM); |
496 |
|
|
mzOfUncons += massOfUnconsMols[i] * COM[2]; |
497 |
|
|
} |
498 |
|
|
|
499 |
|
|
#ifdef IS_MPI |
500 |
|
|
MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
501 |
|
|
#else |
502 |
|
|
totalMZOfUncons = mzOfUncons; |
503 |
|
|
#endif |
504 |
|
|
|
505 |
|
|
zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons; |
506 |
|
|
|
507 |
|
|
cout << "current time: " << info->getTime() <<endl; |
508 |
|
|
for(int i = 0; i < zconsMols.size(); i++){ |
509 |
|
|
|
510 |
|
|
zconsMols[i]->getCOM(COM); |
511 |
|
|
|
512 |
|
|
cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t"; |
513 |
|
|
deltaZ = zsys + refZ[i] - COM[2]; |
514 |
|
|
cout << "\tdistance: " << COM[2] +deltaZ - zsys; |
515 |
|
|
//update z coordinate |
516 |
|
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
517 |
|
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
518 |
|
|
zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ); |
519 |
|
|
} |
520 |
|
|
|
521 |
|
|
//calculate z constrain force |
522 |
|
|
fz[i] = massOfZConsMols[i]* deltaZ / dt2; |
523 |
|
|
|
524 |
|
|
cout << "\tforce: " << fz[i] << endl; |
525 |
|
|
} |
526 |
|
|
|
527 |
|
|
|
528 |
|
|
} |