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root/group/trunk/OOPSE/utils/bilayerSys.cpp
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Comparing trunk/OOPSE/utils/bilayerSys.cpp (file contents):
Revision 503 by mmeineke, Tue Apr 15 21:47:54 2003 UTC vs.
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC

# Line 1 | Line 1
1 + #include <iostream>
2 +
3   #include <cstdlib>
4   #include <cstring>
5   #include <cmath>
# Line 37 | Line 39 | int buildRandomBilayer( void ){
39    int nAtoms, atomIndex, molIndex, molID;
40    int* molSeq;
41    int* molMap;
42 +  int* molStart;
43    int* cardDeck;
44    int deckSize;
45    int rSite, rCard;
# Line 54 | Line 57 | int buildRandomBilayer( void ){
57    
58    srand48( RAND_SEED );
59    molSeq = NULL;
60 +  molStart = NULL;
61    molMap = NULL;
62    cardDeck = NULL;
63    atoms = NULL;
# Line 102 | Line 106 | int buildRandomBilayer( void ){
106    molIndex = 0;
107    locate = new MoLocator*[bsInfo.nComponents];
108    molSeq = new int[bsInfo.totNmol];
109 +  molStart = new int[bsInfo.totNmol];  
110    for(i=0; i<bsInfo.nComponents; i++){
111      locate[i] = new MoLocator( bsInfo.compStamps[i] );
112      for(j=0; j<bsInfo.componentsNmol[i]; j++){
113        molSeq[molIndex] = i;
114 +      molStart[molIndex] = nAtoms;
115        molIndex++;
116        nAtoms += bsInfo.compStamps[i]->getNAtoms();
117      }
# Line 124 | Line 130 | int buildRandomBilayer( void ){
130    cell *= M_SQRT2;
131  
132    siteIndex = 0;
127 –  atomIndex = 0;
133    for(i=0; i<nCells; i++){
134      for(j=0; j<nCells; j++){
135        for(k=0; k<nCells; k++){
# Line 136 | Line 141 | int buildRandomBilayer( void ){
141            
142            getRandomRot( rot );
143            molID = molSeq[molMap[siteIndex]];
144 <          locate[molID]->placeMol( pos, rot, &atoms[atomIndex] );
145 <          
141 <          atomIndex += bsInfo.compStamps[molID]->getNAtoms();
144 >          atomIndex = molStart[ molMap[siteIndex] ];
145 >          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
146          }
147          siteIndex++;
148  
# Line 146 | Line 150 | int buildRandomBilayer( void ){
150            pos[0] = i * cell + (0.5 * cell);
151            pos[1] = j * cell;
152            pos[2] = k * cell + (0.5 * cell);
153 <          
153 >
154            getRandomRot( rot );
155            molID = molSeq[molMap[siteIndex]];
156 <          locate[molID]->placeMol( pos, rot, &atoms[atomIndex] );
157 <          
154 <          atomIndex += bsInfo.compStamps[molID]->getNAtoms();
156 >          atomIndex = molStart[ molMap[siteIndex] ];
157 >          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
158          }
159          siteIndex++;
160  
# Line 162 | Line 165 | int buildRandomBilayer( void ){
165            
166            getRandomRot( rot );
167            molID = molSeq[molMap[siteIndex]];
168 <          locate[molID]->placeMol( pos, rot, &atoms[atomIndex] );
169 <          
167 <          atomIndex += bsInfo.compStamps[molID]->getNAtoms();
168 >          atomIndex = molStart[ molMap[siteIndex] ];
169 >          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
170          }
171          siteIndex++;
172  
# Line 172 | Line 174 | int buildRandomBilayer( void ){
174            pos[0] = i * cell;
175            pos[1] = j * cell + (0.5 * cell);
176            pos[2] = k * cell + (0.5 * cell);
177 <          
177 >
178            getRandomRot( rot );
179            molID = molSeq[molMap[siteIndex]];
180 <          locate[molID]->placeMol( pos, rot, &atoms[atomIndex] );
181 <          
180 <          atomIndex += bsInfo.compStamps[molID]->getNAtoms();
180 >          atomIndex = molStart[ molMap[siteIndex] ];
181 >          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
182          }
183          siteIndex++;
184        }
# Line 196 | Line 197 | int buildRandomBilayer( void ){
197    simnfo->box_y = bsInfo.boxY;
198    simnfo->box_z = bsInfo.boxZ;
199    
200 <  sprintf( simnfo->statusName, "%s.dump", bsInfo.outPrefix );
200 >  sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
201    sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
202 <  
202 >
203    simnfo->atoms = atoms;
204    
205    // set up the writer and write out

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