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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 1435 by tim, Thu Jul 29 18:16:16 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 25 | Line 29 | int main( int argc, char* argv[]){
29    string inputFileName;
30    string outPrefix;
31    string outMdFileName;
28 –  string outInitFileName;
32    SimInfo* oldInfo;
30 –  SimInfo* newInfo;
33    SimSetup* oldSimSetup;
32 –  SimSetup* newSimSetup;
34    BaseLattice* simpleLat;
35    int numMol;
36    double latticeConstant;
37 +  vector<double> lc;
38    double mass;
39 +  const double rhoConvertConst = 1.661;
40    double density;
41    int nx, ny, nz;
42    double Hmat[3][3];
43    MoLocator *locator;
44 <  double* posX;
45 <  double* posY;
43 <  double* posZ;
44 >  vector<Vector3d> latticePos;
45 >  vector<Vector3d> latticeOrt;
46    int numMolPerCell;
47    int curMolIndex;
48    DumpWriter* writer;
49 <
49 >  
50    // parse command line arguments
49 –
51    if (cmdline_parser (argc, argv, &args_info) != 0)
52      exit(1) ;
53  
54 +  //process density
55    if(!args_info.density_given && !args_info.ndensity_given){
56 <    cerr << "density or number density must be given" << endl;
57 <    return false;
56 >    cerr << "SimpleBuilder Error: density or number density must be given" << endl;
57 >    cmdline_parser_print_help();
58 >    exit(1);
59    }
60 +  else if(args_info.density_given){
61 +    if( args_info.ndensity_given)
62 +      cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl;
63 +    
64 +    density = args_info.density_arg;
65 +  }
66 +  else if(args_info.ndensity_given){
67 +    //convert number density to density
68 +  }
69  
70 +
71 +  //get lattice type
72    latticeType = UpperCase(args_info.latticetype_arg);
73    if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
74      cerr << latticeType << " is an invalid lattice type" << endl;
75 <    cerr << LatticeFactory::getInstance()->oString << endl;
75 >    cerr << LatticeFactory::getInstance()->toString() << endl;
76      exit(1);
77    }
78 <        
79 <  nx = args_info.nx_args;
78 >
79 >  //get the number of unit cell
80 >  nx = args_info.nx_arg;
81    if(nx <= 0){
82      cerr << "The number of unit cell in h direction must be greater than 0" << endl;
83      exit(1);
84    }
85  
86 <  nx = args_info.nx_args;
87 <  if(nx <= 0){
86 >  ny = args_info.ny_arg;
87 >  if(ny <= 0){
88      cerr << "The number of unit cell in l direction must be greater than 0" << endl;
89      exit(1);
90    }
91  
92 <  nx = args_info.nx_args;
93 <  if(nx <= 0){
92 >  nz = args_info.nz_arg;
93 >  if(nz <= 0){
94      cerr << "The number of unit cell in k direction must be greater than 0" << endl;
95      exit(1);
96    }
97          
98    //get input file name
99 <  if (args_info.inputs_num) {
99 >  if (args_info.inputs_num)
100      inputFileName = args_info.inputs[0];
86 –    cerr << in_name << "\n";      }
101    else {                
102      cerr <<"You must specify a input file name.\n" << endl;
103      cmdline_parser_print_help();
# Line 99 | Line 113 | int main( int argc, char* argv[]){
113      outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
114    
115    outMdFileName = outPrefix + ".md";
102 –  outInitFileName = outPrefix + ".in";
116  
117    //parse md file and set up the system
118    oldInfo = new SimInfo;
# Line 108 | Line 121 | int main( int argc, char* argv[]){
121       exit(1);
122    }
123  
124 <  oldSimSetup = new SimSetup(oldInfo);  
124 >  oldSimSetup = new SimSetup();  
125    if(oldSimSetup == NULL){
126       cerr << "error in creating SimSetup" << endl;
127       exit(1);
128    }
129 <    
129 >
130 >  oldSimSetup->suspendInit();
131    oldSimSetup->setSimInfo(oldInfo );
132    oldSimSetup->parseFile(&inputFileName[0] );
133 <  oldSimSetup->createSim();
134 <
135 <
122 <  if(oldInfo->nComponets >=2){
133 >  oldSimSetup->createSim();
134 >  
135 >  if(oldInfo->nComponents >=2){
136        cerr << "can not build the system with more than two components" << endl;
137        exit(1);
138    }
139 <
139 >  
140 >  //get mass of molecule.
141 >  //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
142 >  mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField());
143 >  
144    //creat lattice
145 <        simpleLat = LatticeFactory::getInstance()       ->createLattice(latticeType);
145 >        simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
146          if(simpleLat == NULL){
147                  cerr << "Error in creating lattice" << endl;
148                  exit(1);
149          }
150  
151 <
135 <  numMolPerCell = simpleLat->getNpoints();
136 <  //calculate lattice constant
137 <  latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
151 >  numMolPerCell = simpleLat->getNumSitesPerCell();
152    
153 +  //calculate lattice constant (in Angstrom)
154 +  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0);
155 +  
156    //set lattice constant
157 <  simpleLat->setLatticeConstant(latticeConstant);
157 >  lc.push_back(latticeConstant);
158 >  simpleLat->setLatticeConstant(lc);
159    
160 <  //calculate the total
161 <  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
160 >  //calculate the total number of molecules
161 >  numMol = nx * ny * nz * numMolPerCell;
162  
163 +  if (oldInfo->n_mol != numMol){
164 +    //creat new .md file on fly which corrects the number of molecule
165 +    createMdFile(inputFileName, outMdFileName, numMol);
166 +    cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
167 +    cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
168 +    exit(1);
169 +  }
170 +
171 +  //allocat memory for storing pos, vel and etc
172 +  oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
173 +  for (int i = 0; i < oldInfo->n_atoms; i++)
174 +    oldInfo->atoms[i]->setCoords();  
175 +
176 +  //creat Molocator
177 +  locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
178 +
179    //fill Hmat
180    Hmat[0][0] = nx * latticeConstant;
181    Hmat[0][1] = 0.0;
182    Hmat[0][2] = 0.0;
183  
184 <  Hmat[1][0] = ny * latticeConstant;
185 <  Hmat[1][1] = 0.0;
184 >  Hmat[1][0] = 0.0;
185 >  Hmat[1][1] = ny * latticeConstant;
186    Hmat[1][2] = 0.0;
187  
188 <  Hmat[2][0] = nz * latticeConstant;
188 >  Hmat[2][0] = 0.0;
189    Hmat[2][1] = 0.0;
190 <  Hmat[2][2] = 0.0;
190 >  Hmat[2][2] = nz * latticeConstant ;
191 >
192 >  //set Hmat
193 >  oldInfo->setBoxM(Hmat);
194    
195 <  //creat new .md file on fly
196 <  createMdFile(inputFileName, outMdFileName, numMol);
195 >  //place the molecules
196 >
197 >  curMolIndex = 0;
198  
199 <  //parse new .md file and set up the system
200 <  newInfo = new SimInfo;
201 <  if(newInfo == NULL){
164 <     cerr << "error in creating SimInfo" << endl;
165 <     exit(1);
166 <  }
199 >  //get the orientation of the cell sites
200 >  //for the same type of molecule in same lattice, it will not change
201 >  latticeOrt = simpleLat->getLatticePointsOrt();
202  
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 –
209 –  //place the molecules
210 –
211 –  curMolIndex = 0;
203    for(int i =0; i < nx; i++){
204      for(int j=0; j < ny; j++){
205         for(int k = 0; k < nz; k++){
215 –        
216 –          simpleLat->getLatticePoints(&posX, &posY, &posZ, i, j, k);
206  
207 +          //get the position of the cell sites
208 +          simpleLat->getLatticePointsPos(latticePos, i, j, k);
209 +
210            for(int l = 0; l < numMolPerCell; l++)
211 <            locator->placeMol(posX[l], posY[l], posZ[l], newInfo->molecules[curMolIndex++]);
211 >            locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
212         }
213      }
214    }
215  
216    //create dumpwriter and write out the coordinates
217 <  writer = new DumpWriter( newInfo );
217 >  writer = new DumpWriter( oldInfo );
218    if(writer == NULL){
219      cerr << "error in creating DumpWriter" << endl;
220      exit(1);    
221    }
222 <  writer->writeFinal();
231 <
222 >  writer->writeFinal(0);
223    
224    //delete objects
225 <  if(!oldInfo)
225 >
226 >  //delete oldInfo and oldSimSetup
227 >  if(oldInfo != NULL)
228       delete oldInfo;
229    
230 <  if(!oldSimSetup)
231 <     delete oldSimSetup;
239 <
240 <  if(!newInfo)
241 <     delete newInfo;
230 >  if(oldSimSetup != NULL)
231 >     delete oldSimSetup;
232    
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 –
233    if (writer != NULL)
234      delete writer;
235    return 0;
# Line 263 | Line 241 | void createMdFile(const string& oldMdFileName, const s
241    const int MAXLEN = 65535;
242    char buffer[MAXLEN];
243  
266 –
244    //create new .md file based on old .md file
245 <  oldMdFile.open(oldMdFileName.c_str())
246 <  newMdFile.open(newMdFileName);
245 >  oldMdFile.open(oldMdFileName.c_str());
246 >  newMdFile.open(newMdFileName.c_str());
247  
248    oldMdFile.getline(buffer, MAXLEN);
249    while(!oldMdFile.eof()){
250  
251 <    if(line.find("nMol") < line.size())
252 <      sprintf(buffer, "nMol = %s;", numMol);
251 >    //correct molecule number
252 >    if(strstr(buffer, "nMol") !=NULL){      
253 >      sprintf(buffer, "\t\tnMol = %d;", numMol);
254 >      newMdFile << buffer << endl;
255 >    }
256      else
257        newMdFile << buffer << endl;
258  
# Line 283 | Line 263 | void createMdFile(const string& oldMdFileName, const s
263    newMdFile.close();
264  
265   }
266 +
267 + double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){
268 +  int nAtoms;
269 +  AtomStamp* currAtomStamp;
270 +  double totMass;
271 +  
272 +  totMass = 0;
273 +  nAtoms = molStamp->getNAtoms();
274 +
275 +  for(size_t i=0; i<nAtoms; i++){
276 +    currAtomStamp = molStamp->getAtom(i);
277 +    totMass += myFF->getAtomTypeMass(currAtomStamp->getType());
278 +  }
279 +
280 +  return totMass;
281 + }

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