| 549 |
|
simInit->setSimInfo( mainInfo ); |
| 550 |
|
simInit->suspendInit(); |
| 551 |
|
simInit->parseFile( inName ); |
| 552 |
< |
simInit->createSim(); |
| 552 |
> |
simInit->createSim(); |
| 553 |
|
|
| 554 |
|
delete simInit; |
| 555 |
|
|
| 581 |
|
double *posX, *posY, *posZ; |
| 582 |
|
double pos[3], posA[3], posB[3]; |
| 583 |
|
|
| 584 |
< |
const double waterFudge = 5.0; |
| 584 |
> |
const double waterFudge = 6.0; |
| 585 |
|
|
| 586 |
|
int i,j,k,l; |
| 587 |
|
int nAtoms, atomIndex, molIndex, molID; |
| 597 |
|
int targetWaters; |
| 598 |
|
|
| 599 |
|
Atom** atoms; |
| 600 |
– |
SimInfo* simnfo; |
| 600 |
|
SimInfo* testInfo; |
| 601 |
|
coord testSite; |
| 602 |
|
SimState* theConfig; |
| 616 |
|
|
| 617 |
|
molStart = NULL; |
| 618 |
|
|
| 620 |
– |
// create the simInfo objects |
| 621 |
– |
|
| 622 |
– |
simnfo = new SimInfo; |
| 623 |
– |
|
| 619 |
|
// set the the lipidStamp |
| 620 |
|
|
| 621 |
|
foundLipid = 0; |
| 689 |
|
} |
| 690 |
|
zHeight = maxZ - minZ; |
| 691 |
|
|
| 692 |
< |
nCells = (int) sqrt( (double)targetNlipids * bLat / (4.0 * aLat) ); |
| 692 |
> |
std::cerr << "aLat = " << aLat << "; bLat = " << bLat << "\n"; |
| 693 |
|
|
| 694 |
+ |
nCells = (int)ceil( sqrt( (double)targetNlipids * bLat / (4.0 * aLat) )); |
| 695 |
+ |
|
| 696 |
|
nx = nCells; |
| 697 |
|
ny = (int) ((double)nCells * aLat / bLat); |
| 698 |
|
|
| 699 |
+ |
std::cerr << "nx = " << nx << "; ny = " << ny << "\n"; |
| 700 |
+ |
|
| 701 |
|
boxX = nx * aLat; |
| 702 |
|
boxY = ny * bLat; |
| 703 |
|
|
| 903 |
|
|
| 904 |
|
// create the real Atom arrays |
| 905 |
|
|
| 906 |
< |
theConfig = simnfo->getConfiguration(); |
| 906 |
> |
delete[] (mainInfo->atoms); |
| 907 |
> |
theConfig = mainInfo->getConfiguration(); |
| 908 |
|
theConfig->createArrays( nAtoms ); |
| 909 |
< |
simnfo->atoms = new Atom*[nAtoms]; |
| 910 |
< |
simnfo->n_atoms = nAtoms; |
| 911 |
< |
atoms = simnfo->atoms; |
| 909 |
> |
mainInfo->atoms = new Atom*[nAtoms]; |
| 910 |
> |
mainInfo->n_atoms = nAtoms; |
| 911 |
> |
atoms = mainInfo->atoms; |
| 912 |
|
|
| 913 |
|
// wrap back to <0,0,0> as center |
| 914 |
|
|
| 927 |
|
Hmat[2][2] = boxZ; |
| 928 |
|
|
| 929 |
|
mainInfo->setBoxM( Hmat ); |
| 930 |
– |
simnfo->setBoxM( Hmat ); |
| 930 |
|
|
| 931 |
|
for(j=0;j<nLipids;j++){ |
| 932 |
|
|
| 934 |
|
lipidSites[j].pos[1] -= centerY; |
| 935 |
|
lipidSites[j].pos[2] -= centerZ; |
| 936 |
|
|
| 937 |
< |
simnfo->wrapVector( lipidSites[j].pos ); |
| 937 |
> |
mainInfo->wrapVector( lipidSites[j].pos ); |
| 938 |
|
} |
| 939 |
|
|
| 940 |
|
for(j=0;j<nWaters;j++){ |
| 943 |
|
waterSites[j].pos[1] -= centerY; |
| 944 |
|
waterSites[j].pos[2] -= centerZ; |
| 945 |
|
|
| 946 |
< |
simnfo->wrapVector( waterSites[j].pos ); |
| 946 |
> |
mainInfo->wrapVector( waterSites[j].pos ); |
| 947 |
|
} |
| 948 |
|
|
| 949 |
|
// initialize lipid positions |
| 965 |
|
molIndex++; |
| 966 |
|
} |
| 967 |
|
|
| 969 |
– |
strcpy( simnfo->sampleName, mainInfo->sampleName ); |
| 970 |
– |
strcpy( simnfo->finalName, mainInfo->finalName ); |
| 971 |
– |
|
| 968 |
|
// set up the writer and write out |
| 969 |
|
|
| 970 |
< |
writer = new DumpWriter( simnfo ); |
| 970 |
> |
writer = new DumpWriter( mainInfo ); |
| 971 |
|
writer->writeFinal( 0.0 ); |
| 972 |
|
|
| 973 |
|
std::cout << "\n" |
