513 |
|
theConfig = testInfo->getConfiguration(); |
514 |
|
theConfig->createArrays( lipidNatoms ); |
515 |
|
testInfo->atoms = new Atom*[lipidNatoms]; |
516 |
+ |
for (i=0; i < lipidNatoms; i++) { |
517 |
+ |
testInfo->atoms[i] = new Atom(i, theConfig); |
518 |
+ |
testInfo->atoms[i]->setCoords(); |
519 |
+ |
} |
520 |
|
atoms = testInfo->atoms; |
521 |
|
|
522 |
|
// create the test box for initial water displacement |
679 |
|
theConfig = testInfo2->getConfiguration(); |
680 |
|
theConfig->createArrays( nAtoms ); |
681 |
|
testInfo2->atoms = new Atom*[nAtoms]; |
682 |
+ |
for (i=0; i < nAtoms; i++) { |
683 |
+ |
testInfo2->atoms[i] = new Atom(i, theConfig); |
684 |
+ |
testInfo2->atoms[i]->setCoords(); |
685 |
+ |
} |
686 |
|
atoms = testInfo2->atoms; |
687 |
|
|
688 |
|
rCutSqr = lipid_spaceing * lipid_spaceing; |
859 |
|
nAtoms += waterNatoms; |
860 |
|
} |
861 |
|
|
862 |
+ |
std::cerr << "Flag-1\n"; |
863 |
|
theConfig = mainInfo->getConfiguration(); |
864 |
+ |
mainInfo->n_atoms = nAtoms; |
865 |
|
theConfig->createArrays( nAtoms ); |
866 |
|
mainInfo->atoms = new Atom*[nAtoms]; |
867 |
+ |
for (i=0; i < nAtoms; i++) { |
868 |
+ |
mainInfo->atoms[i] = new Atom(i, theConfig); |
869 |
+ |
mainInfo->atoms[i]->setCoords(); |
870 |
+ |
} |
871 |
|
atoms = mainInfo->atoms; |
872 |
< |
mainInfo->n_atoms = nAtoms; |
872 |
> |
std::cerr << "Flag0\n"; |
873 |
|
|
874 |
|
// set up the SimInfo object |
875 |
|
|
903 |
|
|
904 |
|
// initialize lipid positions |
905 |
|
|
906 |
+ |
std::cerr << "Flag1\n"; |
907 |
+ |
|
908 |
|
molIndex = 0; |
909 |
|
for(i=0; i<nLipids; i++ ){ |
910 |
|
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
913 |
|
} |
914 |
|
|
915 |
|
// initialize the water positions |
916 |
+ |
std::cerr << "Flag2\n"; |
917 |
|
|
918 |
|
for(i=0; i<newWaters; i++){ |
919 |
|
|
926 |
|
} |
927 |
|
} |
928 |
|
|
929 |
+ |
std::cerr << "Flag3\n"; |
930 |
|
|
931 |
|
|
932 |
|
// set up the writer and write out |
933 |
|
|
934 |
|
writer = new DumpWriter( mainInfo ); |
935 |
+ |
std::cerr << "Flag4\n"; |
936 |
|
writer->writeFinal( 0.0 ); |
937 |
+ |
std::cerr << "Flag5\n"; |
938 |
|
|
939 |
|
return 1; |
940 |
|
} |