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root/group/trunk/OOPSE/utils/bilayerSys.cpp
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Comparing trunk/OOPSE/utils/bilayerSys.cpp (file contents):
Revision 538 by mmeineke, Sat May 17 16:57:08 2003 UTC vs.
Revision 573 by mmeineke, Thu Jul 3 19:41:26 2003 UTC

# Line 48 | Line 48 | int buildRandomBilayer( void ){
48    const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
49    const double waterCell = 4.929; // fcc unit cell length
50  
51 <  const double water_padding = 2.5;
52 <  const double lipid_spaceing = 5.0;
51 >  const double water_padding = 6.0;
52 >  const double lipid_spaceing = 8.0;
53  
54  
55    int i,j,k, l;
# Line 224 | Line 224 | int buildRandomBilayer( void ){
224    
225    int targetWaters = nWaters + n_deleted * nLipids;
226  
227 +  targetWaters = (int) ( targetWaters * 1.2 );
228 +
229    // find the best box size for the sim
230  
231    int testTot;
# Line 468 | Line 470 | int buildRandomBilayer( void ){
470    bsInfo.boxY = box_y;
471    bsInfo.boxZ = box_z;
472    
473 +  double boxVector[3];
474    simnfo = new SimInfo();
475    simnfo->n_atoms = nAtoms;
476 <  simnfo->box_x = bsInfo.boxX;
477 <  simnfo->box_y = bsInfo.boxY;
478 <  simnfo->box_z = bsInfo.boxZ;
479 <  
476 >  boxVector[0] = bsInfo.boxX;
477 >  boxVector[1] = bsInfo.boxY;
478 >  boxVector[2] = bsInfo.boxZ;
479 >  simnfo->setBox( boxVector );
480 >
481    sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
482    sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
483  
# Line 482 | Line 486 | int buildRandomBilayer( void ){
486    // set up the writer and write out
487    
488    writer = new DumpWriter( simnfo );
489 <  writer->writeFinal();
489 >  writer->writeFinal( 0.0 );
490      
491    // clean up the memory
492    
# Line 670 | Line 674 | int Old_buildRandomBilayer( void ){
674    bsInfo.boxY = nCells * cell;
675    bsInfo.boxZ = nCells * cell;
676    
677 +  double boxVector[3];
678    simnfo = new SimInfo();
679    simnfo->n_atoms = nAtoms;
680 <  simnfo->box_x = bsInfo.boxX;
681 <  simnfo->box_y = bsInfo.boxY;
682 <  simnfo->box_z = bsInfo.boxZ;
683 <  
680 >  boxVector[0] = bsInfo.boxX;
681 >  boxVector[1] = bsInfo.boxY;
682 >  boxVector[2] = bsInfo.boxZ;
683 >  simnfo->setBox( boxVector );
684 >
685    sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
686    sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
687  
# Line 684 | Line 690 | int Old_buildRandomBilayer( void ){
690    // set up the writer and write out
691    
692    writer = new DumpWriter( simnfo );
693 <  writer->writeFinal();
693 >  writer->writeFinal(0.0);
694      
695    // clean up the memory
696    

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