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#include "simpleBuilderCmd.hpp" |
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#include "StringUtils.hpp" |
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#include "LatticeFactory.hpp" |
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#include "Vector3d.hpp" |
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using namespace std; |
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BaseLattice* simpleLat; |
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int numMol; |
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double latticeConstant; |
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vector lc; |
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double mass; |
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double density; |
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int nx, ny, nz; |
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double Hmat[3][3]; |
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MoLocator *locator; |
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double* posX; |
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double* posY; |
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double* posZ; |
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vector<Vector3d> latticePos; |
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vector<Vector3d> latticeOrt; |
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int numMolPerCell; |
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int curMolIndex; |
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DumpWriter* writer; |
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} |
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//creat lattice |
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simpleLat = LatticeFactory::getInstance() ->createLattice(latticeType); |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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if(simpleLat == NULL){ |
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cerr << "Error in creating lattice" << endl; |
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exit(1); |
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latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0); |
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//set lattice constant |
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simpleLat->setLatticeConstant(latticeConstant); |
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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//calculate the total |
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numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell; |
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newSimSetup->parseFile(&outMdFileName[0] ); |
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newSimSetup->createSim(); |
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//set Hamt |
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//set Hmat |
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newInfo->setBoxM(Hmat); |
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//allocat memory for storing pos, vel and etc |
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newInfo.atoms[i]->setCoords(); |
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//creat Molocator |
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locator = new MoLocator(newInfo->compStamps[0]); |
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//allocate memory for posX, posY, posZ |
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posX = new doule[numMolPerCell]; |
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if(posX == NULL){ |
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cerr << "memory allocation error" << endl; |
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exit(1); |
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} |
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posY = new doule[numMolPerCell]; |
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if(posX == NULL){ |
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cerr << "memory allocation error" << endl; |
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exit(1); |
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} |
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locator = new MoLocator(newInfo->compStamps[0], newSimSetup->the_ff); |
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posZ = new doule[numMolPerCell]; |
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if(posX == NULL){ |
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cerr << "memory allocation error" << endl; |
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exit(1); |
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} |
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//place the molecules |
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curMolIndex = 0; |
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//get the orientation of the cell sites |
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//for the same type of molecule in same lattice, it will not change |
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latticeOrt = simpleLat->getLatticePointsOrt(); |
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for(int i =0; i < nx; i++){ |
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for(int j=0; j < ny; j++){ |
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for(int k = 0; k < nz; k++){ |
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simpleLat->getLatticePoints(&posX, &posY, &posZ, i, j, k); |
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//get the position of the cell sites |
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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for(int l = 0; l < numMolPerCell; l++) |
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locator->placeMol(posX[l], posY[l], posZ[l], newInfo->molecules[curMolIndex++]); |
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locator->placeMol(latticePos[l], latticeOrt[l], newInfo->molecules[curMolIndex++]); |
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} |
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} |
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} |
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if(!newSimSetup) |
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delete newSimSetup; |
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if (posX) |
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delete[] posX; |
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if (posY) |
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delete[] posY; |
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if (posZ) |
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delete[] posZ; |
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if (writer != NULL) |
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delete writer; |
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return 0; |
