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using namespace std; |
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ZConsWriter::ZConsWriter(const char* filename) |
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ZConsWriter::ZConsWriter(const char* filename, vector<ZConsParaItem>* thePara) |
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{ |
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//use master - slave mode, only master node writes to disk |
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#ifdef IS_MPI |
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if(!output){ |
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sprintf( painCave.errMsg, |
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"Could not open \"s\" for z constrain output \n", |
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filename); |
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filename); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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output << "#number of z constrain molecules" << endl; |
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output << "#global Index of molecule\trefZ" << endl; |
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|
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output << "#global Index of molecule\tzPos" << endl; |
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output << "#every frame will contain below data" <<endl; |
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output << "#time(fs)" << endl; |
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output << "#number of z constrain molecules" << endl; |
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output << "#global Index of molecule\tzconstrain force" << endl; |
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output << "#number of fixed z-constrain molecules" << endl; |
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output << "#global Index of molecule\tzconstrain force\tcurrentZPos" << endl; |
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|
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parameters = thePara; |
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writeZPos(); |
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|
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#ifdef IS_MPI |
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} |
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#endif |
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#endif |
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} |
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void ZConsWriter::writeFZ(double time, int num, int* index, double* fz) |
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{ |
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/** |
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* |
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*/ |
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void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos){ |
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#ifndef IS_MPI |
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vector<pair<int, double> > data; // The space between two ">" is needed. Otherwise, compileer |
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// will take it as redirect symbol ">>" |
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|
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for(int i = 0; i < num ; i++) |
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data.push_back(pair<int, double>(index[i], fz[i])); |
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output << time << endl; |
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output << num << endl; |
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//sort data by index |
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sort(data.begin(), data.end()); |
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|
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for(int i=0; i < data.size(); i++) |
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output << data[i].first << "\t" << data[i].second << endl; |
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|
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#else |
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for(int i = 0; i < num; i++) |
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output << index[i] <<"\t" << fz[i] << "\t" << curZPos[i] << endl; |
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//master node will be responsible for receiving, assembling and writing data |
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if(worldRank == 0) |
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{ |
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#else |
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int totalNum; |
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MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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vector<pair<int,double> > data; |
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int numProcessors; |
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int recvCount; |
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int* indexBuf; |
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double* fzBuf; |
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MPI_Status istatus; |
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//process the data in master |
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for(int i=0; i < num; i++){ |
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data.push_back(pair<int, double>(index[i], fz[i])); |
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} |
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if(worldRank == 0){ |
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output << time << endl; |
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output << totalNum << endl; |
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} |
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|
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int whichNode; |
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enum CommType { RequesPosAndForce, EndOfRequest} status; |
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double pos; |
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double force; |
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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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numProcessors = mpiSim->getNumberProcessors(); |
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int globalIndexOfCurMol; |
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int *MolToProcMap; |
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MolToProcMap = mpiSim->getMolToProcMap(); |
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//acquire the data from other nodes; |
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for(int whichNode = 1; whichNode < numProcessors; whichNode++){ |
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for(int i = 0; i < parameters->size(); i++){ |
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MPI_Recv(&recvCount, 1, MPI_INT, whichNode, |
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0, MPI_COMM_WORLD, &istatus); |
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globalIndexOfCurMol = (*parameters)[i].zconsIndex; |
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whichNode = MolToProcMap[globalIndexOfCurMol]; |
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if(recvCount > 0){ |
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indexBuf = new int[recvCount]; |
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fzBuf = new double[recvCount]; |
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if(whichNode == 0){ |
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if(!indexBuf || !fzBuf){ |
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sprintf(painCave.errMsg, |
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"Memory Allocation inside class ZConsWriter\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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MPI_Recv(indexBuf, recvCount, MPI_INT, whichNode, |
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0, MPI_COMM_WORLD, &istatus); |
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for(int j = 0; j < num; j++) |
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if(index[j] == globalIndexOfCurMol){ |
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localIndex = j; |
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break; |
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} |
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MPI_Recv(fzBuf, recvCount, MPI_DOUBLE_PRECISION, whichNode, |
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0, MPI_COMM_WORLD, &istatus); |
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//assemble the data |
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for(int i = 0; i < recvCount; i++){ |
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data.push_back(pair<int, double>(indexBuf[i], fzBuf[i])); |
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} |
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delete[] indexBuf; |
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delete[] fzBuf; |
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force = fz[localIndex]; |
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pos = curZPos[localIndex]; |
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} |
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} |
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else{ |
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status = RequesPosAndForce; |
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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(&force, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
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MPI_Recv(&pos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
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} |
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output << globalIndexOfCurMol << "\t" << force << "\t" << pos << endl; |
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} //End of Request Loop |
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// sort the data by index |
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sort(data.begin(), data.end()); |
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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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} |
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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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output << time << endl; |
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output << data.size() << endl; |
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switch (status){ |
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case RequesPosAndForce : |
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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 < data.size(); i++){ |
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for(int i = 0; i < num; i++) |
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if(index[i] == whichMol){ |
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localIndex = i; |
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break; |
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} |
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output << data[i].first << "\t" << data[i].second << endl; |
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MPI_Send(&fz[localIndex], 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD); |
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MPI_Send(&curZPos[localIndex], 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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} |
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else |
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{ |
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MPI_Send(&num, 1, MPI_INT, 0, 0, MPI_COMM_WORLD); |
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if(num > 0){ |
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MPI_Send(index, num, MPI_INT, 0, 0, MPI_COMM_WORLD); |
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MPI_Send(fz, num, MPI_DOUBLE_PRECISION, 0, 0, MPI_COMM_WORLD); |
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} |
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} |
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#endif |
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} |
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< |
void ZConsWriter::writeRefZ(const vector<int>& index, const vector<double>& refZ){ |
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/* |
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* |
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*/ |
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void ZConsWriter::writeZPos(){ |
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#ifdef IS_MPI |
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if(worldRank == 0){ |
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#endif |
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output << index.size() << endl; |
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output << parameters->size() << endl; |
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< |
for(int i =0 ; i < index.size(); i++) |
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output << index[i] << "\t" << refZ[i] << endl; |
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for(int i =0 ; i < parameters->size(); i++) |
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output << (*parameters)[i].zconsIndex << "\t" << (*parameters)[i].zPos << endl; |
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#ifdef IS_MPI |
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} |
