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root/group/trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp
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Comparing trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp (file contents):
Revision 1424 by tim, Wed Jul 28 04:59:35 2004 UTC vs.
Revision 1436 by tim, Thu Jul 29 19:12:00 2004 UTC

# Line 7 | Line 7
7   #include <map>
8   #include <fstream>
9  
10 – #include "simError.h"
10   #include "Globals.hpp"
11   #include "SimInfo.hpp"
12   #include "SimSetup.hpp"
13 < #include "simpleBuilderCmd.hpp"
13 > #include "simpleBuilderCmd.h"
14   #include "StringUtils.hpp"
15   #include "LatticeFactory.hpp"
16 + #include "Vector3d.hpp"
17 + #include "MoLocator.hpp"
18 + #include "Lattice.hpp"
19  
20   using namespace std;
21  
22 + void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
23 + double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF);
24  
25   int main( int argc, char* argv[]){
26  
# Line 27 | Line 31 | int main( int argc, char* argv[]){
31    string outMdFileName;
32    string outInitFileName;
33    SimInfo* oldInfo;
30 –  SimInfo* newInfo;
34    SimSetup* oldSimSetup;
32 –  SimSetup* newSimSetup;
35    BaseLattice* simpleLat;
36    int numMol;
37    double latticeConstant;
38 +  vector<double> lc;
39    double mass;
40 +  const double rhoConvertConst = 1.661;
41    double density;
42    int nx, ny, nz;
43    double Hmat[3][3];
44    MoLocator *locator;
45 <  double* posX;
46 <  double* posY;
43 <  double* posZ;
45 >  vector<Vector3d> latticePos;
46 >  vector<Vector3d> latticeOrt;
47    int numMolPerCell;
48    int curMolIndex;
49    DumpWriter* writer;
50 <
50 >  
51    // parse command line arguments
49 –
52    if (cmdline_parser (argc, argv, &args_info) != 0)
53      exit(1) ;
54 +  
55 +  density = args_info.density_arg;
56  
57 <  if(!args_info.density_given && !args_info.ndensity_given){
54 <    cerr << "density or number density must be given" << endl;
55 <    return false;
56 <  }
57 <
57 >  //get lattice type
58    latticeType = UpperCase(args_info.latticetype_arg);
59    if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
60      cerr << latticeType << " is an invalid lattice type" << endl;
61 <    cerr << LatticeFactory::getInstance()->oString << endl;
61 >    cerr << LatticeFactory::getInstance()->toString() << endl;
62      exit(1);
63    }
64 <        
65 <  nx = args_info.nx_args;
64 >
65 >  //get the number of unit cell
66 >  nx = args_info.nx_arg;
67    if(nx <= 0){
68      cerr << "The number of unit cell in h direction must be greater than 0" << endl;
69      exit(1);
70    }
71  
72 <  nx = args_info.nx_args;
73 <  if(nx <= 0){
72 >  ny = args_info.ny_arg;
73 >  if(ny <= 0){
74      cerr << "The number of unit cell in l direction must be greater than 0" << endl;
75      exit(1);
76    }
77  
78 <  nx = args_info.nx_args;
79 <  if(nx <= 0){
78 >  nz = args_info.nz_arg;
79 >  if(nz <= 0){
80      cerr << "The number of unit cell in k direction must be greater than 0" << endl;
81      exit(1);
82    }
83          
84    //get input file name
85 <  if (args_info.inputs_num) {
85 >  if (args_info.inputs_num)
86      inputFileName = args_info.inputs[0];
86 –    cerr << in_name << "\n";      }
87    else {                
88      cerr <<"You must specify a input file name.\n" << endl;
89      cmdline_parser_print_help();
90      exit(1);
91    }
92  
93 –  //determine the output file names
93    
95 –  if (args_info.output_given){
96 –    outPrefix = args_info.output_arg;
97 –  }
98 –  else
99 –    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
100 –  
101 –  outMdFileName = outPrefix + ".md";
102 –  outInitFileName = outPrefix + ".in";
103 –
94    //parse md file and set up the system
95    oldInfo = new SimInfo;
96    if(oldInfo == NULL){
# Line 108 | Line 98 | int main( int argc, char* argv[]){
98       exit(1);
99    }
100  
101 <  oldSimSetup = new SimSetup(oldInfo);  
101 >  oldSimSetup = new SimSetup();  
102    if(oldSimSetup == NULL){
103       cerr << "error in creating SimSetup" << endl;
104       exit(1);
105    }
106 <    
106 >
107 >  oldSimSetup->suspendInit();
108    oldSimSetup->setSimInfo(oldInfo );
109    oldSimSetup->parseFile(&inputFileName[0] );
110 <  oldSimSetup->createSim();
111 <
112 <
122 <  if(oldInfo->nComponets >=2){
110 >  oldSimSetup->createSim();
111 >  
112 >  if(oldInfo->nComponents >=2){
113        cerr << "can not build the system with more than two components" << endl;
114        exit(1);
115    }
116 <
116 >  
117 >  //get mass of molecule.
118 >  //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
119 >  mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());
120 >  
121    //creat lattice
122 <        simpleLat = LatticeFactory::getInstance()       ->createLattice(latticeType);
122 >        simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
123          if(simpleLat == NULL){
124                  cerr << "Error in creating lattice" << endl;
125                  exit(1);
126          }
127  
128 <
135 <  numMolPerCell = simpleLat->getNpoints();
136 <  //calculate lattice constant
137 <  latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
128 >  numMolPerCell = simpleLat->getNumSitesPerCell();
129    
130 +  //calculate lattice constant (in Angstrom)
131 +  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
132 +  
133    //set lattice constant
134 <  simpleLat->setLatticeConstant(latticeConstant);
134 >  lc.push_back(latticeConstant);
135 >  simpleLat->setLatticeConstant(lc);
136    
137 <  //calculate the total
138 <  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
137 >  //calculate the total number of molecules
138 >  numMol = nx * ny * nz * numMolPerCell;
139  
140 +  if (oldInfo->n_mol != numMol){
141 +
142 +    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
143 +    outMdFileName = outPrefix + ".md";
144 +
145 +    //creat new .md file on fly which corrects the number of molecule    
146 +    createMdFile(inputFileName, outMdFileName, numMol);
147 +    cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
148 +    cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
149 +    exit(1);
150 +  }
151 +  
152 +  //determine the output file names  
153 +  if (args_info.output_given)
154 +    outInitFileName = args_info.output_arg;
155 +  else
156 +    outInitFileName = getPrefix(inputFileName.c_str())  + ".in";
157 +  
158 +  
159 +  //allocat memory for storing pos, vel and etc
160 +  oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
161 +  for (int i = 0; i < oldInfo->n_atoms; i++)
162 +    oldInfo->atoms[i]->setCoords();  
163 +
164 +  //creat Molocator
165 +  locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
166 +
167    //fill Hmat
168    Hmat[0][0] = nx * latticeConstant;
169    Hmat[0][1] = 0.0;
170    Hmat[0][2] = 0.0;
171  
172 <  Hmat[1][0] = ny * latticeConstant;
173 <  Hmat[1][1] = 0.0;
172 >  Hmat[1][0] = 0.0;
173 >  Hmat[1][1] = ny * latticeConstant;
174    Hmat[1][2] = 0.0;
175  
176 <  Hmat[2][0] = nz * latticeConstant;
176 >  Hmat[2][0] = 0.0;
177    Hmat[2][1] = 0.0;
178 <  Hmat[2][2] = 0.0;
157 <  
158 <  //creat new .md file on fly
159 <  createMdFile(inputFileName, outMdFileName, numMol);
178 >  Hmat[2][2] = nz * latticeConstant ;
179  
180 <  //parse new .md file and set up the system
181 <  newInfo = new SimInfo;
182 <  if(newInfo == NULL){
164 <     cerr << "error in creating SimInfo" << endl;
165 <     exit(1);
166 <  }
167 <
168 <  newSimSetup = new SimSetup(newInfo);  
169 <  if(newSimSetup == NULL){
170 <     cerr << "error in creating SimSetup" << endl;
171 <     exit(1);
172 <  }
173 <    
174 <  newSimSetup->setSimInfo(newInfo );
175 <  newSimSetup->parseFile(&outMdFileName[0] );
176 <  newSimSetup->createSim();
177 <
178 <  //set Hamt
179 <  newInfo->setBoxM(Hmat);
180 <
181 <  //allocat memory for storing pos, vel and etc
182 <  newInfo.getConfiguration()->createArrays(newInfo.n_atoms);
183 <  for (int i = 0; i < newInfo.n_atoms; i++)
184 <    newInfo.atoms[i]->setCoords();  
185 <
186 <  //creat Molocator
187 <  locator = new MoLocator(newInfo->compStamps[0]);
188 <
189 <  //allocate memory for posX, posY, posZ
190 <
191 <  posX = new doule[numMolPerCell];
192 <  if(posX == NULL){
193 <    cerr << "memory allocation error" << endl;
194 <    exit(1);
195 <  }
196 <
197 <  posY = new doule[numMolPerCell];
198 <  if(posX == NULL){
199 <    cerr << "memory allocation error" << endl;
200 <    exit(1);
201 <  }
202 <
203 <  posZ = new doule[numMolPerCell];
204 <  if(posX == NULL){
205 <    cerr << "memory allocation error" << endl;
206 <    exit(1);
207 <  }
208 <
180 >  //set Hmat
181 >  oldInfo->setBoxM(Hmat);
182 >  
183    //place the molecules
184  
185    curMolIndex = 0;
186 +
187 +  //get the orientation of the cell sites
188 +  //for the same type of molecule in same lattice, it will not change
189 +  latticeOrt = simpleLat->getLatticePointsOrt();
190 +
191    for(int i =0; i < nx; i++){
192      for(int j=0; j < ny; j++){
193         for(int k = 0; k < nz; k++){
215 –        
216 –          simpleLat->getLatticePoints(&posX, &posY, &posZ, i, j, k);
194  
195 +          //get the position of the cell sites
196 +          simpleLat->getLatticePointsPos(latticePos, i, j, k);
197 +
198            for(int l = 0; l < numMolPerCell; l++)
199 <            locator->placeMol(posX[l], posY[l], posZ[l], newInfo->molecules[curMolIndex++]);
199 >            locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
200         }
201      }
202    }
203  
204    //create dumpwriter and write out the coordinates
205 <  writer = new DumpWriter( newInfo );
205 >  oldInfo->finalName = outInitFileName;
206 >  writer = new DumpWriter( oldInfo );
207    if(writer == NULL){
208      cerr << "error in creating DumpWriter" << endl;
209      exit(1);    
210    }
211 <  writer->writeFinal();
212 <
232 <  
211 >  writer->writeFinal(0);
212 >  cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl;
213    //delete objects
214 <  if(!oldInfo)
214 >
215 >  //delete oldInfo and oldSimSetup
216 >  if(oldInfo != NULL)
217       delete oldInfo;
218    
219 <  if(!oldSimSetup)
220 <     delete oldSimSetup;
239 <
240 <  if(!newInfo)
241 <     delete newInfo;
219 >  if(oldSimSetup != NULL)
220 >     delete oldSimSetup;
221    
243 –  if(!newSimSetup)
244 –     delete newSimSetup;
245 –
246 –  if (posX)
247 –     delete[] posX;
248 –
249 –  if (posY)
250 –     delete[] posY;
251 –
252 –  if (posZ)
253 –   delete[] posZ;
254 –
222    if (writer != NULL)
223      delete writer;
224    return 0;
# Line 263 | Line 230 | void createMdFile(const string& oldMdFileName, const s
230    const int MAXLEN = 65535;
231    char buffer[MAXLEN];
232  
266 –
233    //create new .md file based on old .md file
234 <  oldMdFile.open(oldMdFileName.c_str())
235 <  newMdFile.open(newMdFileName);
234 >  oldMdFile.open(oldMdFileName.c_str());
235 >  newMdFile.open(newMdFileName.c_str());
236  
237    oldMdFile.getline(buffer, MAXLEN);
238    while(!oldMdFile.eof()){
239  
240 <    if(line.find("nMol") < line.size())
241 <      sprintf(buffer, "nMol = %s;", numMol);
240 >    //correct molecule number
241 >    if(strstr(buffer, "nMol") !=NULL){      
242 >      sprintf(buffer, "\t\tnMol = %d;", numMol);
243 >      newMdFile << buffer << endl;
244 >    }
245      else
246        newMdFile << buffer << endl;
247  
# Line 283 | Line 252 | void createMdFile(const string& oldMdFileName, const s
252    newMdFile.close();
253  
254   }
255 +
256 + double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){
257 +  int nAtoms;
258 +  AtomStamp* currAtomStamp;
259 +  double totMass;
260 +  
261 +  totMass = 0;
262 +  nAtoms = molStamp->getNAtoms();
263 +
264 +  for(size_t i=0; i<nAtoms; i++){
265 +    currAtomStamp = molStamp->getAtom(i);
266 +    totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
267 +  }
268 +
269 +  return totMass;
270 + }

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