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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <cmath> |
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#include <iostream> |
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#include <string> |
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#include <map> |
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#include <fstream> |
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|
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#include "io/Globals.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimSetup.hpp" |
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#include "applications/simpleBuilder/simpleBuilderCmd.h" |
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#include "utils/StringUtils.hpp" |
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#include "applications/simpleBuilder/LatticeFactory.hpp" |
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#include "math/Vector3.hpp" |
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#include "applications/simpleBuilder/MoLocator.hpp" |
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#include "applications/simpleBuilder/Lattice.hpp" |
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|
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|
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|
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void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
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int numMol); |
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double getMolMass(MoleculeStamp * molStamp, ForceFields * myFF); |
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|
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int main(int argc, char *argv []) { |
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gengetopt_args_info args_info; |
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std::string latticeType; |
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std::string inputFileName; |
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std::string outPrefix; |
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std::string outMdFileName; |
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std::string outInitFileName; |
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SimInfo *oldInfo; |
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SimSetup *oldSimSetup; |
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BaseLattice *simpleLat; |
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int numMol; |
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double latticeConstant; |
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vector < double > lc; |
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double mass; |
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const double rhoConvertConst = 1.661; |
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double density; |
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int nx, |
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ny, |
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nz; |
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double Hmat[3][3]; |
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MoLocator *locator; |
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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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// parse command line arguments |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
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|
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density = args_info.density_arg; |
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|
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//get lattice type |
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latticeType = UpperCase(args_info.latticetype_arg); |
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|
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if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
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std::cerr << latticeType << " is an invalid lattice type" << std::endl; |
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std::cerr << LatticeFactory::getInstance()->toString() << std::endl; |
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exit(1); |
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} |
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|
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//get the number of unit cell |
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nx = args_info.nx_arg; |
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|
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if (nx <= 0) { |
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std::cerr << "The number of unit cell in h direction must be greater than 0" |
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<< std::endl; |
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exit(1); |
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} |
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|
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ny = args_info.ny_arg; |
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|
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if (ny <= 0) { |
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std::cerr << "The number of unit cell in l direction must be greater than 0" |
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<< std::endl; |
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exit(1); |
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} |
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|
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nz = args_info.nz_arg; |
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|
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if (nz <= 0) { |
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std::cerr << "The number of unit cell in k direction must be greater than 0" |
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<< std::endl; |
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exit(1); |
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} |
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|
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//get input file name |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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std::cerr << "You must specify a input file name.\n" << std::endl; |
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cmdline_parser_print_help(); |
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exit(1); |
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} |
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|
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//parse md file and set up the system |
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oldInfo = new SimInfo; |
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|
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if (oldInfo == NULL) { |
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std::cerr << "error in creating SimInfo" << std::endl; |
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exit(1); |
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} |
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|
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oldSimSetup = new SimSetup(); |
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|
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if (oldSimSetup == NULL) { |
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std::cerr << "error in creating SimSetup" << std::endl; |
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exit(1); |
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} |
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|
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oldSimSetup->suspendInit(); |
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oldSimSetup->setSimInfo(oldInfo); |
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oldSimSetup->parseFile(&inputFileName[0]); |
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oldSimSetup->createSim(); |
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|
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if (oldInfo->nComponents >= 2) { |
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std::cerr << "can not build the system with more than two components" |
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<< std::endl; |
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exit(1); |
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} |
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|
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//get mass of molecule. |
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//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
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mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
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|
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
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if (simpleLat == NULL) { |
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std::cerr << "Error in creating lattice" << std::endl; |
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exit(1); |
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} |
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|
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
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//calculate lattice constant (in Angstrom) |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
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1.0 / 3.0); |
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|
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//set lattice constant |
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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|
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//calculate the total number of molecules |
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numMol = nx * ny * nz * numMolPerCell; |
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|
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if (oldInfo->n_mol != numMol) { |
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outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
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outMdFileName = outPrefix + ".md"; |
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|
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//creat new .md file on fly which corrects the number of molecule |
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createMdFile(inputFileName, outMdFileName, numMol); |
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std::cerr |
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<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
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<< std::endl; |
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std::cerr << "A new .md file: " << outMdFileName |
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<< " is generated, use it to rerun the simpleBuilder" << std::endl; |
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exit(1); |
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} |
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|
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//determine the output file names |
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if (args_info.output_given) |
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outInitFileName = args_info.output_arg; |
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else |
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outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
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|
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//allocat memory for storing pos, vel and etc |
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oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
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|
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for(int i = 0; i < oldInfo->n_atoms; i++) |
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oldInfo->atoms[i]->setCoords(); |
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|
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//creat Molocator |
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locator = new MoLocator(oldInfo->compStamps[0], |
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oldSimSetup->getForceField()); |
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|
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//fill Hmat |
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Hmat[0][0] = nx * latticeConstant; |
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Hmat[0][1] = 0.0; |
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Hmat[0][2] = 0.0; |
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|
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Hmat[1][0] = 0.0; |
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Hmat[1][1] = ny * latticeConstant; |
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Hmat[1][2] = 0.0; |
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|
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Hmat[2][0] = 0.0; |
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Hmat[2][1] = 0.0; |
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Hmat[2][2] = nz * latticeConstant; |
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|
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//set Hmat |
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oldInfo->setBoxM(Hmat); |
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|
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//place the molecules |
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|
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curMolIndex = 0; |
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|
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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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|
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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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|
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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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|
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for(int l = 0; l < numMolPerCell; l++) |
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locator->placeMol(latticePos[l], latticeOrt[l], |
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&(oldInfo->molecules[curMolIndex++])); |
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} |
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} |
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} |
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|
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//create dumpwriter and write out the coordinates |
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oldInfo->finalName = outInitFileName; |
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writer = new DumpWriter(oldInfo); |
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|
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if (writer == NULL) { |
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std::cerr << "error in creating DumpWriter" << std::endl; |
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exit(1); |
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} |
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|
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writer->writeFinal(0); |
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cout << "new initial configuration file: " << outInitFileName |
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<< " is generated." << std::endl; |
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|
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//delete objects |
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|
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//delete oldInfo and oldSimSetup |
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if (oldInfo != NULL) |
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delete oldInfo; |
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|
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if (oldSimSetup != NULL) |
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delete oldSimSetup; |
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|
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if (writer != NULL) |
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delete writer; |
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|
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return 0; |
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} |
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|
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void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
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int numMol) { |
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ifstream oldMdFile; |
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ofstream newMdFile; |
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const int MAXLEN = 65535; |
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char buffer[MAXLEN]; |
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|
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//create new .md file based on old .md file |
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oldMdFile.open(oldMdFileName.c_str()); |
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newMdFile.open(newMdFileName.c_str()); |
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|
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oldMdFile.getline(buffer, MAXLEN); |
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|
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while (!oldMdFile.eof()) { |
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|
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//correct molecule number |
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if (strstr(buffer, "nMol") != NULL) { |
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sprintf(buffer, "\t\tnMol = %d;", numMol); |
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newMdFile << buffer << std::endl; |
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} else |
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newMdFile << buffer << std::endl; |
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|
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oldMdFile.getline(buffer, MAXLEN); |
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} |
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|
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oldMdFile.close(); |
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newMdFile.close(); |
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} |
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|
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double getMolMass(MoleculeStamp *molStamp, ForceFields *myFF) { |
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int nAtoms; |
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AtomStamp *currAtomStamp; |
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double totMass; |
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|
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totMass = 0; |
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nAtoms = molStamp->getNAtoms(); |
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|
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for(size_t i = 0; i < nAtoms; i++) { |
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currAtomStamp = molStamp->getAtom(i); |
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totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
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} |
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|
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return totMass; |
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} |
