| 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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "selection/SelectionManager.hpp" |
| 61 |
|
#include "io/ForceFieldOptions.hpp" |
| 62 |
< |
#include "UseTheForce/ForceField.hpp" |
| 62 |
> |
#include "brains/ForceField.hpp" |
| 63 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 64 |
+ |
#ifdef IS_MPI |
| 65 |
+ |
#include <mpi.h> |
| 66 |
+ |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 72 |
|
forceField_(ff), simParams_(simParams), |
| 73 |
|
ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
| 74 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
| 75 |
< |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 75 |
> |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0), |
| 76 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
| 77 |
|
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
| 78 |
< |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
| 78 |
> |
nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
| 79 |
|
calcBoxDipole_(false), useAtomicVirial_(true) { |
| 80 |
|
|
| 81 |
|
MoleculeStamp* molStamp; |
| 225 |
|
|
| 226 |
|
|
| 227 |
|
void SimInfo::calcNdf() { |
| 228 |
< |
int ndf_local; |
| 228 |
> |
int ndf_local, nfq_local; |
| 229 |
|
MoleculeIterator i; |
| 230 |
|
vector<StuntDouble*>::iterator j; |
| 231 |
+ |
vector<Atom*>::iterator k; |
| 232 |
+ |
|
| 233 |
|
Molecule* mol; |
| 234 |
|
StuntDouble* integrableObject; |
| 235 |
+ |
Atom* atom; |
| 236 |
|
|
| 237 |
|
ndf_local = 0; |
| 238 |
+ |
nfq_local = 0; |
| 239 |
|
|
| 240 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 241 |
|
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 250 |
|
ndf_local += 3; |
| 251 |
|
} |
| 252 |
|
} |
| 245 |
– |
|
| 253 |
|
} |
| 254 |
+ |
for (atom = mol->beginFluctuatingCharge(k); atom != NULL; |
| 255 |
+ |
atom = mol->nextFluctuatingCharge(k)) { |
| 256 |
+ |
if (atom->isFluctuatingCharge()) { |
| 257 |
+ |
nfq_local++; |
| 258 |
+ |
} |
| 259 |
+ |
} |
| 260 |
|
} |
| 261 |
|
|
| 262 |
+ |
ndfLocal_ = ndf_local; |
| 263 |
+ |
|
| 264 |
|
// n_constraints is local, so subtract them on each processor |
| 265 |
|
ndf_local -= nConstraints_; |
| 266 |
|
|
| 267 |
|
#ifdef IS_MPI |
| 268 |
|
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 269 |
+ |
MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 270 |
|
#else |
| 271 |
|
ndf_ = ndf_local; |
| 272 |
+ |
nGlobalFluctuatingCharges_ = nfq_local; |
| 273 |
|
#endif |
| 274 |
|
|
| 275 |
|
// nZconstraints_ is global, as are the 3 COM translations for the |
| 793 |
|
int usesElectrostatic = 0; |
| 794 |
|
int usesMetallic = 0; |
| 795 |
|
int usesDirectional = 0; |
| 796 |
+ |
int usesFluctuatingCharges = 0; |
| 797 |
|
//loop over all of the atom types |
| 798 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 799 |
|
usesElectrostatic |= (*i)->isElectrostatic(); |
| 800 |
|
usesMetallic |= (*i)->isMetal(); |
| 801 |
|
usesDirectional |= (*i)->isDirectional(); |
| 802 |
+ |
usesFluctuatingCharges |= (*i)->isFluctuatingCharge(); |
| 803 |
|
} |
| 804 |
< |
|
| 804 |
> |
|
| 805 |
|
#ifdef IS_MPI |
| 806 |
|
int temp; |
| 807 |
|
temp = usesDirectional; |
| 812 |
|
|
| 813 |
|
temp = usesElectrostatic; |
| 814 |
|
MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 815 |
+ |
|
| 816 |
+ |
temp = usesFluctuatingCharges; |
| 817 |
+ |
MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 818 |
|
#else |
| 819 |
|
|
| 820 |
|
usesDirectionalAtoms_ = usesDirectional; |
| 821 |
|
usesMetallicAtoms_ = usesMetallic; |
| 822 |
|
usesElectrostaticAtoms_ = usesElectrostatic; |
| 823 |
+ |
usesFluctuatingCharges_ = usesFluctuatingCharges; |
| 824 |
|
|
| 825 |
|
#endif |
| 826 |
|
|
| 842 |
|
|
| 843 |
|
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 844 |
|
GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
| 822 |
– |
cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n"; |
| 845 |
|
} |
| 846 |
|
} |
| 847 |
|
return GlobalAtomIndices; |
| 863 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 864 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 865 |
|
GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
| 844 |
– |
cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n"; |
| 866 |
|
} |
| 867 |
|
} |
| 868 |
|
return GlobalGroupIndices; |
| 1213 |
|
|
| 1214 |
|
det = intTensor.determinant(); |
| 1215 |
|
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1216 |
< |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1216 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det); |
| 1217 |
|
return; |
| 1218 |
|
} |
| 1219 |
|
|
| 1229 |
|
|
| 1230 |
|
detI = intTensor.determinant(); |
| 1231 |
|
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1232 |
< |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1232 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI); |
| 1233 |
|
return; |
| 1234 |
|
} |
| 1235 |
|
/* |
