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ATC version 2.0, date: Aug21

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10638 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
2013-08-21 23:06:07 +00:00
parent 0f69054d68
commit d77ab2f96a
161 changed files with 3811 additions and 2548 deletions
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53
lib/atc/ExtrinsicModelElectrostatic.cpp
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@ -11,6 +11,13 @@
#include "AtomToMoleculeTransfer.h"
#include "MoleculeSet.h"
#include "ChargeRegulator.h"
#include <set>
using std::string;
using std::vector;
using std::map;
using std::pair;
using std::set;
static const double kTol_ = 1.0e-8;
static const double tol_sparse = 1.e-30;//tolerance for compaction from dense
@ -164,6 +171,15 @@ namespace ATC {
// add charge density transfer operator
if (atc_->track_charge()) {
InterscaleManager & interscaleManager(atc_->interscale_manager());
// make sure we have gradients at atoms
VectorDependencyManager<SPAR_MAT * > * interpolantGradient = interscaleManager.vector_sparse_matrix("InterpolantGradient");
if (!interpolantGradient) {
interpolantGradient = new PerAtomShapeFunctionGradient(atc_);
interscaleManager.add_vector_sparse_matrix(interpolantGradient,
"InterpolantGradient");
}
FundamentalAtomQuantity * atomicCharge =
interscaleManager.fundamental_atom_quantity(LammpsInterface::ATOM_CHARGE);
AtfShapeFunctionRestriction * nodalAtomicCharge =
@ -173,20 +189,6 @@ namespace ATC {
new AtfShapeFunctionMdProjection(atc_,nodalAtomicCharge,MASS_DENSITY);
interscaleManager.add_dense_matrix(nodalAtomicChargeDensity,"NodalAtomicChargeDensity");
// add species charge density transfer operators
const map<string,pair<IdType,int> > & speciesIds(atc_->species_ids());
map<string,pair<IdType,int> >::const_iterator specid;
for (specid = speciesIds.begin(); specid != speciesIds.end(); specid++) {
const string specie = specid->first;
AtfShapeFunctionRestriction * nodalAtomicSpeciesCharge =
new AtfShapeFunctionRestriction(atc_,atomicCharge,
interscaleManager.sparse_matrix("Accumulant"+specie));
interscaleManager.add_dense_matrix(nodalAtomicSpeciesCharge,"NodalAtomicSpeciesCharge"+specie);
AtfShapeFunctionMdProjection * nodalAtomicSpeciesChargeDensity =
new AtfShapeFunctionMdProjection(atc_,nodalAtomicSpeciesCharge,MASS_DENSITY);
interscaleManager.add_dense_matrix(nodalAtomicSpeciesChargeDensity,"NodalAtomicSpeciesChargeDensity"+specie);
}
// get the total charge and dipole moment at the node per molecule
// small molecules require per atom quantities with ghosts
@ -312,8 +314,18 @@ namespace ATC {
nodalAtomicGhostCharge_ = interscaleManager.dense_matrix("NodalAtomicGhostCharge");
if (! nodalAtomicGhostCharge_) {
FundamentalAtomQuantity * ghostCharge = interscaleManager.fundamental_atom_quantity(LammpsInterface::ATOM_CHARGE, GHOST);
PerAtomSparseMatrix<double> * ghostShapeFunctions = interscaleManager.per_atom_sparse_matrix("InterpolantGhost");
if (!ghostShapeFunctions) {
ghostShapeFunctions = new PerAtomShapeFunction(atc_,
interscaleManager.per_atom_quantity("AtomicGhostCoarseGrainingPositions"),
interscaleManager.per_atom_int_quantity("AtomGhostElement"),
GHOST);
interscaleManager.add_per_atom_sparse_matrix(ghostShapeFunctions,"InterpolantGhost");
}
nodalAtomicGhostCharge_ = new AtfShapeFunctionRestriction(atc_,ghostCharge,
interscaleManager.per_atom_sparse_matrix("InterpolantGhost"));
ghostShapeFunctions);
interscaleManager.add_dense_matrix(nodalAtomicGhostCharge_,"NodalAtomicGhostCharge");
}
}
@ -446,14 +458,6 @@ namespace ATC {
}
}
const map<string,pair<IdType,int> > & speciesIds(atc_->species_ids());
map<string,pair<IdType,int> >::const_iterator specie;
for (specie = speciesIds.begin(); specie != speciesIds.end(); specie++) {
DENS_MAN & nodalAtomicSpeciesChargeDensityOut(atc_->tagged_dens_man("NodalAtomicSpeciesChargeDensity"+specie->first));
DENS_MAN * nodalAtomicSpeciesChargeDensity((atc_->interscale_manager()).dense_matrix("NodalAtomicSpeciesChargeDensity"+specie->first));
nodalAtomicSpeciesChargeDensityOut = nodalAtomicSpeciesChargeDensity->quantity();
}
const map<string,pair<MolSize,int> > & moleculeIds(atc_->molecule_ids());
map<string,pair<MolSize,int> >::const_iterator molecule;
for (molecule = moleculeIds.begin(); molecule != moleculeIds.end(); molecule++) {
@ -540,10 +544,11 @@ namespace ATC {
int nsd = atc_->nsd();
int nLocal = atc_->nlocal();
DENS_MAT E(nLocal,nsd);
const SPAR_MAT_VEC & shapeFucntionDerivatives(((atc_->interscale_manager()).vector_sparse_matrix("InterpolantGradient"))->quantity());
if (nLocal > 0) {
for (int i=0; i < nsd; i++) {
CLON_VEC Ei = column(E,i);
Ei = -1.*(*(((atc_->shpFcnDerivs_)->quantity())[i])*potential);
Ei = -1.*(*(shapeFucntionDerivatives[i])*potential);
}
}