ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp
(Generate patch)

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 1429 by tim, Wed Jul 28 20:29:49 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  
24   int main( int argc, char* argv[]){
25  
# Line 33 | Line 36 | int main( int argc, char* argv[]){
36    BaseLattice* simpleLat;
37    int numMol;
38    double latticeConstant;
39 +  vector<double> lc;
40    double mass;
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;
# Line 58 | Line 61 | int main( int argc, char* argv[]){
61    latticeType = UpperCase(args_info.latticetype_arg);
62    if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
63      cerr << latticeType << " is an invalid lattice type" << endl;
64 <    cerr << LatticeFactory::getInstance()->oString << endl;
64 >    cerr << LatticeFactory::getInstance()->toString() << endl;
65      exit(1);
66    }
67          
68 <  nx = args_info.nx_args;
68 >  nx = args_info.nx_arg;
69    if(nx <= 0){
70      cerr << "The number of unit cell in h direction must be greater than 0" << endl;
71      exit(1);
72    }
73  
74 <  nx = args_info.nx_args;
75 <  if(nx <= 0){
74 >  ny = args_info.ny_arg;
75 >  if(ny <= 0){
76      cerr << "The number of unit cell in l direction must be greater than 0" << endl;
77      exit(1);
78    }
79  
80 <  nx = args_info.nx_args;
81 <  if(nx <= 0){
80 >  nz = args_info.nz_arg;
81 >  if(nz <= 0){
82      cerr << "The number of unit cell in k direction must be greater than 0" << endl;
83      exit(1);
84    }
85          
86    //get input file name
87 <  if (args_info.inputs_num) {
87 >  if (args_info.inputs_num)
88      inputFileName = args_info.inputs[0];
86 –    cerr << in_name << "\n";      }
89    else {                
90      cerr <<"You must specify a input file name.\n" << endl;
91      cmdline_parser_print_help();
# Line 108 | Line 110 | int main( int argc, char* argv[]){
110       exit(1);
111    }
112  
113 <  oldSimSetup = new SimSetup(oldInfo);  
113 >  oldSimSetup = new SimSetup();  
114    if(oldSimSetup == NULL){
115       cerr << "error in creating SimSetup" << endl;
116       exit(1);
# Line 116 | Line 118 | int main( int argc, char* argv[]){
118      
119    oldSimSetup->setSimInfo(oldInfo );
120    oldSimSetup->parseFile(&inputFileName[0] );
119 –  oldSimSetup->createSim();
121  
122  
123 <  if(oldInfo->nComponets >=2){
123 >  if(oldInfo->nComponents >=2){
124        cerr << "can not build the system with more than two components" << endl;
125        exit(1);
126    }
127  
128    //creat lattice
129 <        simpleLat = LatticeFactory::getInstance()       ->createLattice(latticeType);
129 >        simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
130          if(simpleLat == NULL){
131                  cerr << "Error in creating lattice" << endl;
132                  exit(1);
133          }
134  
135  
136 <  numMolPerCell = simpleLat->getNpoints();
136 >  numMolPerCell = simpleLat->getNumSitesPerCell();
137    //calculate lattice constant
138    latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
139    
140    //set lattice constant
141 <  simpleLat->setLatticeConstant(latticeConstant);
141 >  lc.push_back(latticeConstant);
142 >  simpleLat->setLatticeConstant(lc);
143    
144    //calculate the total
145    numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
# Line 165 | Line 167 | int main( int argc, char* argv[]){
167       exit(1);
168    }
169  
170 <  newSimSetup = new SimSetup(newInfo);  
170 >  newSimSetup = new SimSetup();  
171    if(newSimSetup == NULL){
172       cerr << "error in creating SimSetup" << endl;
173       exit(1);
# Line 175 | Line 177 | int main( int argc, char* argv[]){
177    newSimSetup->parseFile(&outMdFileName[0] );
178    newSimSetup->createSim();
179  
180 <  //set Hamt
180 >  //set Hmat
181    newInfo->setBoxM(Hmat);
182  
183    //allocat memory for storing pos, vel and etc
184 <  newInfo.getConfiguration()->createArrays(newInfo.n_atoms);
185 <  for (int i = 0; i < newInfo.n_atoms; i++)
186 <    newInfo.atoms[i]->setCoords();  
184 >  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
185 >  for (int i = 0; i < newInfo->n_atoms; i++)
186 >    newInfo->atoms[i]->setCoords();  
187  
188    //creat Molocator
189 <  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 <  }
189 >  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
190  
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 –
191    //place the molecules
192  
193    curMolIndex = 0;
194 +
195 +  //get the orientation of the cell sites
196 +  //for the same type of molecule in same lattice, it will not change
197 +  latticeOrt = simpleLat->getLatticePointsOrt();
198 +
199    for(int i =0; i < nx; i++){
200      for(int j=0; j < ny; j++){
201         for(int k = 0; k < nz; k++){
215 –        
216 –          simpleLat->getLatticePoints(&posX, &posY, &posZ, i, j, k);
202  
203 +          //get the position of the cell sites
204 +          simpleLat->getLatticePointsPos(latticePos, i, j, k);
205 +
206            for(int l = 0; l < numMolPerCell; l++)
207 <            locator->placeMol(posX[l], posY[l], posZ[l], newInfo->molecules[curMolIndex++]);
207 >            locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
208         }
209      }
210    }
# Line 227 | Line 215 | int main( int argc, char* argv[]){
215      cerr << "error in creating DumpWriter" << endl;
216      exit(1);    
217    }
218 <  writer->writeFinal();
218 >  writer->writeFinal(0);
219  
220    
221    //delete objects
# Line 243 | Line 231 | int main( int argc, char* argv[]){
231    if(!newSimSetup)
232       delete newSimSetup;
233  
246 –  if (posX)
247 –     delete[] posX;
248 –
249 –  if (posY)
250 –     delete[] posY;
251 –
252 –  if (posZ)
253 –   delete[] posZ;
254 –
234    if (writer != NULL)
235      delete writer;
236    return 0;
# Line 262 | Line 241 | void createMdFile(const string& oldMdFileName, const s
241    ofstream newMdFile;
242    const int MAXLEN = 65535;
243    char buffer[MAXLEN];
244 +  string line;
245  
266 –
246    //create new .md file based on old .md file
247 <  oldMdFile.open(oldMdFileName.c_str())
248 <  newMdFile.open(newMdFileName);
247 >  oldMdFile.open(oldMdFileName.c_str());
248 >  newMdFile.open(newMdFileName.c_str());
249  
250    oldMdFile.getline(buffer, MAXLEN);
251    while(!oldMdFile.eof()){
252  
253 <    if(line.find("nMol") < line.size())
254 <      sprintf(buffer, "nMol = %s;", numMol);
253 >    if(line.find("nMol") < line.size()){
254 >      
255 >      sprintf(buffer, "\t\tnMol = %d;", numMol);
256 >      newMdFile << buffer << endl;
257 >    }
258      else
259        newMdFile << buffer << endl;
260  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines