| 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 |
|
// n_constraints is local, so subtract them on each processor |
| 264 |
|
|
| 265 |
|
#ifdef IS_MPI |
| 266 |
|
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 267 |
+ |
MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 268 |
|
#else |
| 269 |
|
ndf_ = ndf_local; |
| 270 |
+ |
nGlobalFluctuatingCharges_ = nfq_local; |
| 271 |
|
#endif |
| 272 |
|
|
| 273 |
|
// nZconstraints_ is global, as are the 3 COM translations for the |
| 709 |
|
Atom* atom; |
| 710 |
|
set<AtomType*> atomTypes; |
| 711 |
|
|
| 712 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 713 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 712 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 713 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 714 |
> |
atom = mol->nextAtom(ai)) { |
| 715 |
|
atomTypes.insert(atom->getAtomType()); |
| 716 |
|
} |
| 717 |
|
} |
| 718 |
< |
|
| 718 |
> |
|
| 719 |
|
#ifdef IS_MPI |
| 720 |
|
|
| 721 |
|
// loop over the found atom types on this processor, and add their |
| 722 |
|
// numerical idents to a vector: |
| 723 |
< |
|
| 723 |
> |
|
| 724 |
|
vector<int> foundTypes; |
| 725 |
|
set<AtomType*>::iterator i; |
| 726 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) |
| 729 |
|
// count_local holds the number of found types on this processor |
| 730 |
|
int count_local = foundTypes.size(); |
| 731 |
|
|
| 732 |
< |
// count holds the total number of found types on all processors |
| 717 |
< |
// (some will be redundant with the ones found locally): |
| 718 |
< |
int count; |
| 719 |
< |
MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
| 732 |
> |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 733 |
|
|
| 734 |
< |
// create a vector to hold the globally found types, and resize it: |
| 735 |
< |
vector<int> ftGlobal; |
| 736 |
< |
ftGlobal.resize(count); |
| 737 |
< |
vector<int> counts; |
| 734 |
> |
// we need arrays to hold the counts and displacement vectors for |
| 735 |
> |
// all processors |
| 736 |
> |
vector<int> counts(nproc, 0); |
| 737 |
> |
vector<int> disps(nproc, 0); |
| 738 |
|
|
| 739 |
< |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 740 |
< |
counts.resize(nproc); |
| 741 |
< |
vector<int> disps; |
| 742 |
< |
disps.resize(nproc); |
| 739 |
> |
// fill the counts array |
| 740 |
> |
MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], |
| 741 |
> |
1, MPI::INT); |
| 742 |
> |
|
| 743 |
> |
// use the processor counts to compute the displacement array |
| 744 |
> |
disps[0] = 0; |
| 745 |
> |
int totalCount = counts[0]; |
| 746 |
> |
for (int iproc = 1; iproc < nproc; iproc++) { |
| 747 |
> |
disps[iproc] = disps[iproc-1] + counts[iproc-1]; |
| 748 |
> |
totalCount += counts[iproc]; |
| 749 |
> |
} |
| 750 |
|
|
| 751 |
< |
// now spray out the foundTypes to all the other processors: |
| 751 |
> |
// we need a (possibly redundant) set of all found types: |
| 752 |
> |
vector<int> ftGlobal(totalCount); |
| 753 |
|
|
| 754 |
+ |
// now spray out the foundTypes to all the other processors: |
| 755 |
|
MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, |
| 756 |
< |
&ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
| 756 |
> |
&ftGlobal[0], &counts[0], &disps[0], |
| 757 |
> |
MPI::INT); |
| 758 |
|
|
| 759 |
+ |
vector<int>::iterator j; |
| 760 |
+ |
|
| 761 |
|
// foundIdents is a stl set, so inserting an already found ident |
| 762 |
|
// will have no effect. |
| 763 |
|
set<int> foundIdents; |
| 764 |
< |
vector<int>::iterator j; |
| 764 |
> |
|
| 765 |
|
for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) |
| 766 |
|
foundIdents.insert((*j)); |
| 767 |
|
|
| 768 |
|
// now iterate over the foundIdents and get the actual atom types |
| 769 |
|
// that correspond to these: |
| 770 |
|
set<int>::iterator it; |
| 771 |
< |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 771 |
> |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 772 |
|
atomTypes.insert( forceField_->getAtomType((*it)) ); |
| 773 |
|
|
| 774 |
|
#endif |
| 775 |
< |
|
| 775 |
> |
|
| 776 |
|
return atomTypes; |
| 777 |
|
} |
| 778 |
|
|
| 784 |
|
if ( simParams_->getAccumulateBoxDipole() ) { |
| 785 |
|
calcBoxDipole_ = true; |
| 786 |
|
} |
| 787 |
< |
|
| 787 |
> |
|
| 788 |
|
set<AtomType*>::iterator i; |
| 789 |
|
set<AtomType*> atomTypes; |
| 790 |
|
atomTypes = getSimulatedAtomTypes(); |
| 791 |
|
int usesElectrostatic = 0; |
| 792 |
|
int usesMetallic = 0; |
| 793 |
|
int usesDirectional = 0; |
| 794 |
+ |
int usesFluctuatingCharges = 0; |
| 795 |
|
//loop over all of the atom types |
| 796 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 797 |
|
usesElectrostatic |= (*i)->isElectrostatic(); |
| 798 |
|
usesMetallic |= (*i)->isMetal(); |
| 799 |
|
usesDirectional |= (*i)->isDirectional(); |
| 800 |
+ |
usesFluctuatingCharges |= (*i)->isFluctuatingCharge(); |
| 801 |
|
} |
| 802 |
< |
|
| 802 |
> |
|
| 803 |
|
#ifdef IS_MPI |
| 804 |
|
int temp; |
| 805 |
|
temp = usesDirectional; |
| 806 |
|
MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 807 |
< |
|
| 807 |
> |
|
| 808 |
|
temp = usesMetallic; |
| 809 |
|
MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 810 |
< |
|
| 810 |
> |
|
| 811 |
|
temp = usesElectrostatic; |
| 812 |
|
MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 813 |
+ |
|
| 814 |
+ |
temp = usesFluctuatingCharges; |
| 815 |
+ |
MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 816 |
+ |
#else |
| 817 |
+ |
|
| 818 |
+ |
usesDirectionalAtoms_ = usesDirectional; |
| 819 |
+ |
usesMetallicAtoms_ = usesMetallic; |
| 820 |
+ |
usesElectrostaticAtoms_ = usesElectrostatic; |
| 821 |
+ |
usesFluctuatingCharges_ = usesFluctuatingCharges; |
| 822 |
+ |
|
| 823 |
|
#endif |
| 824 |
+ |
|
| 825 |
+ |
requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
| 826 |
+ |
requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 827 |
+ |
requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 828 |
|
} |
| 829 |
|
|
| 830 |
|
|
| 1211 |
|
|
| 1212 |
|
det = intTensor.determinant(); |
| 1213 |
|
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1214 |
< |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1214 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det); |
| 1215 |
|
return; |
| 1216 |
|
} |
| 1217 |
|
|
| 1227 |
|
|
| 1228 |
|
detI = intTensor.determinant(); |
| 1229 |
|
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1230 |
< |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1230 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI); |
| 1231 |
|
return; |
| 1232 |
|
} |
| 1233 |
|
/* |
