| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 50 |
+ |
#ifdef IS_MPI |
| 51 |
+ |
#include <mpi.h> |
| 52 |
+ |
#endif |
| 53 |
|
#include <algorithm> |
| 54 |
|
#include <set> |
| 55 |
|
#include <map> |
| 64 |
|
#include "io/ForceFieldOptions.hpp" |
| 65 |
|
#include "brains/ForceField.hpp" |
| 66 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 64 |
– |
#ifdef IS_MPI |
| 65 |
– |
#include <mpi.h> |
| 66 |
– |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 91 |
|
for (vector<Component*>::iterator i = components.begin(); |
| 92 |
|
i !=components.end(); ++i) { |
| 93 |
|
molStamp = (*i)->getMoleculeStamp(); |
| 94 |
+ |
if ( (*i)->haveRegion() ) { |
| 95 |
+ |
molStamp->setRegion( (*i)->getRegion() ); |
| 96 |
+ |
} else { |
| 97 |
+ |
// set the region to a disallowed value: |
| 98 |
+ |
molStamp->setRegion( -1 ); |
| 99 |
+ |
} |
| 100 |
+ |
|
| 101 |
|
nMolWithSameStamp = (*i)->getNMol(); |
| 102 |
|
|
| 103 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
| 372 |
|
|
| 373 |
|
void SimInfo::addInteractionPairs(Molecule* mol) { |
| 374 |
|
ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); |
| 375 |
+ |
vector<Atom*>::iterator atomIter; |
| 376 |
|
vector<Bond*>::iterator bondIter; |
| 377 |
|
vector<Bend*>::iterator bendIter; |
| 378 |
|
vector<Torsion*>::iterator torsionIter; |
| 379 |
|
vector<Inversion*>::iterator inversionIter; |
| 380 |
+ |
Atom* atom; |
| 381 |
|
Bond* bond; |
| 382 |
|
Bend* bend; |
| 383 |
|
Torsion* torsion; |
| 420 |
|
atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 421 |
|
} |
| 422 |
|
} |
| 423 |
+ |
|
| 424 |
|
|
| 425 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; |
| 426 |
|
bond = mol->nextBond(bondIter)) { |
| 790 |
|
#endif |
| 791 |
|
|
| 792 |
|
return atomTypes; |
| 793 |
+ |
} |
| 794 |
+ |
|
| 795 |
+ |
|
| 796 |
+ |
int getGlobalCountOfType(AtomType* atype) { |
| 797 |
+ |
/* |
| 798 |
+ |
set<AtomType*> atypes = getSimulatedAtomTypes(); |
| 799 |
+ |
map<AtomType*, int> counts_; |
| 800 |
+ |
|
| 801 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 802 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 803 |
+ |
atom = mol->nextAtom(ai)) { |
| 804 |
+ |
atom->getAtomType(); |
| 805 |
+ |
} |
| 806 |
+ |
} |
| 807 |
+ |
*/ |
| 808 |
+ |
return 0; |
| 809 |
|
} |
| 810 |
|
|
| 811 |
|
void SimInfo::setupSimVariables() { |
| 941 |
|
} |
| 942 |
|
} |
| 943 |
|
|
| 944 |
< |
// Build the identArray_ |
| 944 |
> |
// Build the identArray_ and regions_ |
| 945 |
|
|
| 946 |
|
identArray_.clear(); |
| 947 |
< |
identArray_.reserve(getNAtoms()); |
| 948 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 947 |
> |
identArray_.reserve(getNAtoms()); |
| 948 |
> |
regions_.clear(); |
| 949 |
> |
regions_.reserve(getNAtoms()); |
| 950 |
> |
|
| 951 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 952 |
> |
int reg = mol->getRegion(); |
| 953 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 954 |
|
identArray_.push_back(atom->getIdent()); |
| 955 |
+ |
regions_.push_back(reg); |
| 956 |
|
} |
| 957 |
|
} |
| 958 |
< |
|
| 928 |
< |
//scan topology |
| 929 |
< |
|
| 930 |
< |
int* excludeList = excludedInteractions_.getPairList(); |
| 931 |
< |
int* oneTwoList = oneTwoInteractions_.getPairList(); |
| 932 |
< |
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 933 |
< |
int* oneFourList = oneFourInteractions_.getPairList(); |
| 934 |
< |
|
| 958 |
> |
|
| 959 |
|
topologyDone_ = true; |
| 960 |
|
} |
| 961 |
|
|
| 1027 |
|
|
| 1028 |
|
|
| 1029 |
|
StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
| 1030 |
< |
if (index >= IOIndexToIntegrableObject.size()) { |
| 1030 |
> |
if (index >= int(IOIndexToIntegrableObject.size())) { |
| 1031 |
|
sprintf(painCave.errMsg, |
| 1032 |
|
"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n" |
| 1033 |
|
"\tindex exceeds number of known objects!\n"); |
