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tim |
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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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#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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using namespace std;
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void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
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double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF);
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int main( int argc, char* argv[]){
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gengetopt_args_info args_info;
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string latticeType;
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string inputFileName;
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string outPrefix;
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string outMdFileName;
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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, ny, 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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// 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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density = args_info.density_arg;
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//get lattice type
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latticeType = UpperCase(args_info.latticetype_arg);
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if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
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cerr << latticeType << " is an invalid lattice type" << endl;
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cerr << LatticeFactory::getInstance()->toString() << endl;
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exit(1);
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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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if(nx <= 0){
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cerr << "The number of unit cell in h direction must be greater than 0" << endl;
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exit(1);
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}
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ny = args_info.ny_arg;
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if(ny <= 0){
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cerr << "The number of unit cell in l direction must be greater than 0" << endl;
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exit(1);
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}
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nz = args_info.nz_arg;
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if(nz <= 0){
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cerr << "The number of unit cell in k direction must be greater than 0" << endl;
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exit(1);
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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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cerr <<"You must specify a input file name.\n" << endl;
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cmdline_parser_print_help();
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exit(1);
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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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if(oldInfo == NULL){
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cerr << "error in creating SimInfo" << endl;
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exit(1);
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}
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oldSimSetup = new SimSetup();
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if(oldSimSetup == NULL){
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cerr << "error in creating SimSetup" << endl;
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exit(1);
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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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if(oldInfo->nComponents >=2){
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cerr << "can not build the system with more than two components" << endl;
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exit(1);
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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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//creat lattice
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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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}
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numMolPerCell = simpleLat->getNumSitesPerCell();
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//calculate lattice constant (in Angstrom)
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
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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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//calculate the total number of molecules
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numMol = nx * ny * nz * numMolPerCell;
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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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//creat new .md file on fly which corrects the number of molecule
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createMdFile(inputFileName, outMdFileName, numMol);
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cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
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cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
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exit(1);
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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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//allocat memory for storing pos, vel and etc
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oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
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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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//creat Molocator
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locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
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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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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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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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//set Hmat
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oldInfo->setBoxM(Hmat);
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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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//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(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
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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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if(writer == NULL){
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cerr << "error in creating DumpWriter" << endl;
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exit(1);
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}
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writer->writeFinal(0);
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cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl;
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//delete objects
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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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if(oldSimSetup != NULL)
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delete oldSimSetup;
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if (writer != NULL)
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delete writer;
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return 0;
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}
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void createMdFile(const string& oldMdFileName, const string& newMdFileName, 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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//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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oldMdFile.getline(buffer, MAXLEN);
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while(!oldMdFile.eof()){
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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 << endl;
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}
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else
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newMdFile << buffer << endl;
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oldMdFile.getline(buffer, MAXLEN);
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}
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oldMdFile.close();
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newMdFile.close();
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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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totMass = 0;
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nAtoms = molStamp->getNAtoms();
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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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return totMass;
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}
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