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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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588
lib/atc/ATC_Coupling.cpp
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@ -10,6 +10,12 @@
#include "PhysicsModel.h"
#include "AtomToMoleculeTransfer.h"
#include "MoleculeSet.h"
#include "FieldManager.h"
using std::string;
using std::map;
using std::pair;
using std::set;
namespace ATC {
//--------------------------------------------------
@ -26,6 +32,8 @@ namespace ATC {
atomicRegulator_(NULL),
atomQuadForInternal_(true),
elementMask_(NULL),
elementMaskMass_(NULL),
elementMaskMassMd_(NULL),
internalToMask_(NULL),
internalElement_(NULL),
ghostElement_(NULL),
@ -46,6 +54,8 @@ namespace ATC {
mdMassNormalization_ = true;
// check to see if lammps has any charges
if (lammpsInterface_->atom_charge()) trackCharge_ = true;
// default: perform velocity verlet
integrateInternalAtoms_ = true;
}
//--------------------------------------------------
ATC_Coupling::~ATC_Coupling()
@ -93,7 +103,7 @@ namespace ATC {
\section syntax
fix_modify AtC initial <field> <nodeset> <constant | function>
- <field> = field name valid for type of physics, temperature | electron_temperature
- <nodeset> = name of set of nodes to apply boundary condition
- <nodeset> = name of set of nodes to apply initial condition
- <constant | function> = value or name of function followed by its
parameters
\section examples
@ -102,8 +112,6 @@ namespace ATC {
Sets the initial values for the specified field at the specified nodes.
\section restrictions
keyword 'all' reserved in nodeset name
\section related
see \ref man_internal
\section default
none
*/
@ -150,15 +158,29 @@ namespace ATC {
parse_field(arg,argIdx,thisField,thisIndex);
string nsetName(arg[argIdx++]);
XT_Function * f = NULL;
// fix current value
if (narg == argIdx) {
set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nsetName);
set<int>::const_iterator iset;
const DENS_MAT & field =(fields_.find(thisField)->second).quantity();
for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
int inode = *iset;
double v = field(inode,thisIndex);
f = XT_Function_Mgr::instance()->constant_function(v);
set<int> one; one.insert(inode);
prescribedDataMgr_->fix_field(one,thisField,thisIndex,f);
}
}
// parse constant
if (narg == argIdx+1) {
else if (narg == argIdx+1) {
f = XT_Function_Mgr::instance()->constant_function(atof(arg[argIdx]));
prescribedDataMgr_->fix_field(nsetName,thisField,thisIndex,f);
}
// parse function
else {
f = XT_Function_Mgr::instance()->function(&(arg[argIdx]),narg-argIdx);
prescribedDataMgr_->fix_field(nsetName,thisField,thisIndex,f);
}
prescribedDataMgr_->fix_field(nsetName,thisField,thisIndex,f);
match = true;
}
@ -314,9 +336,13 @@ namespace ATC {
\section examples
<TT> fix_modify atc fe_md_boundary interpolate </TT> \n
\section description
Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed.
\section restrictions
If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.
\section related
see \man_boundary_faceset for how to specify the faceset name.
\section default
Interpolate.
*/
else if (strcmp(arg[argIdx],"fe_md_boundary")==0) {
bndyIntType_ = FE_INTERPOLATION;// default
@ -346,8 +372,11 @@ namespace ATC {
\section examples
fix_modify AtC boundary_faceset is obndy
\section description
\section restrictions
This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist.
\section restrictions
This is only valid when fe_md_boundary is set to faceset.
\section related
\man_fe_md_boundary
\section default
*/
else if (strcmp(arg[argIdx],"boundary_faceset")==0) {
@ -373,7 +402,7 @@ namespace ATC {
\section examples
<TT> fix_modify atc internal_quadrature off </TT>
\section description
Command use or not use atomic quadrature on internal elements
Command to use or not use atomic quadrature on internal elements
fully filled with atoms. By turning the internal quadrature off
these elements do not contribute to the governing PDE and the fields
at the internal nodes follow the weighted averages of the atomic data.
@ -446,7 +475,9 @@ namespace ATC {
match = true;
}
/*! \page man_atomic_charge fix_modify AtC <include | omit> atomic_charge
/*! \page man_atomic_charge fix_modify AtC atomic_charge
\section syntax
fix_modify AtC <include | omit> atomic_charge
- <include | omit> = switch to activiate/deactiviate inclusion of intrinsic atomic charge in ATC
\section examples
<TT> fix_modify atc compute include atomic_charge </TT>
@ -475,7 +506,9 @@ namespace ATC {
}
}
/*! \page man_source_integration fix_modify AtC source_integration < fe | atom>
/*! \page man_source_integration fix_modify AtC source_integration
\section syntax
fix_modify AtC source_integration < fe | atom>
\section examples
<TT> fix_modify atc source_integration atom </TT>
\section description
@ -495,16 +528,17 @@ namespace ATC {
match = true;
}
/*! \page man_consistent_fe_initialization fix_modify AtC consistent_fe_initialization <on | off>
- <include | omit> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
/*! \page man_consistent_fe_initialization fix_modify AtC consistent_fe_initialization
\section syntax
fix_modify AtC consistent_fe_initialization <on | off>
- <on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
\section examples
<TT> fix_modify atc compute include atomic_charge </TT>
<TT> fix_modify atc consistent_fe_initialization on </TT>
\section description
Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.
\section restrictions
Can be used with: thermal, two_temperature
Cannot be used with time filtering on
Does not include boundary nodes
Can be used with: thermal, two_temperature.
Cannot be used with time filtering on. Does not include boundary nodes.
\section related
\section default
Default is off
@ -555,15 +589,16 @@ namespace ATC {
}
}
/*! \page man_mass_matrix fix_modify AtC mass_matrix <fe | md_fe>
/*! \page man_mass_matrix fix_modify AtC mass_matrix
\section syntax
fix_modify AtC mass_matrix <fe | md_fe>
- <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
\section examples
<TT> fix_modify atc mass_matrix fe </TT>
\section description
Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency.
\section restrictions
Should not be used unless the FE region is contained within the MD region,
otherwise the method will be unstable and inaccurate
Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate
\section related
\section default
Default is off
@ -590,9 +625,12 @@ namespace ATC {
\section examples
<TT> fix_modify AtC material gap_region 2</TT>
\section description
Sets the material model in elementset_name to be of type material_id.
\section restrictions
The element set must already be created and the material must be specified in the material file given the the atc fix on construction
\section related
\section default
All elements default to the first material in the material file.
*/
else if (strcmp(arg[argIdx],"material")==0) {
argIdx++;
@ -693,43 +731,12 @@ namespace ATC {
throw ATC_Error("Unknown physics type in ATC_Coupling::create_physics_model");
}
}
//--------------------------------------------------------
void ATC_Coupling::init_integrate_velocity()
{
const DENS_MAT & m(atomMasses_->quantity());
double dt = 0.5 * lammpsInterface_->dt();
_deltaQuantity_ = atomForces_->quantity();
for (int i = 0; i < nLocal_; i++)
for (int j = 0; j < nsd_; j ++)
_deltaQuantity_(i,j) *= dt/m(i,0);
(*atomVelocities_) += _deltaQuantity_;
}
//--------------------------------------------------------
void ATC_Coupling::init_integrate_position()
{
double dt = lammpsInterface_->dt();
_deltaQuantity_ = atomVelocities_->quantity();
_deltaQuantity_ *= dt;
(*atomPositions_) += _deltaQuantity_;
}
//--------------------------------------------------------
void ATC_Coupling::final_integrate()
{
const DENS_MAT & m(atomMasses_->quantity());
double dt = 0.5 * lammpsInterface_->dt();
_deltaQuantity_ = atomForces_->quantity();
for (int i = 0; i < nLocal_; i++)
for (int j = 0; j < nsd_; j ++)
_deltaQuantity_(i,j) *= dt/m(i,0);
(*atomVelocities_) += _deltaQuantity_;
}
//--------------------------------------------------------
void ATC_Coupling::construct_methods()
{
ATC_Method::construct_methods();
// construct needed time filters for mass matrices
if (timeFilterManager_.need_reset()) {
init_filter();
@ -807,10 +814,11 @@ namespace ATC {
//-----------------------------------------------------------------
// this is w_a source_a
void ATC_Coupling::compute_sources_at_atoms(const RHS_MASK & rhsMask,
const FIELDS & fields,
const PhysicsModel * physicsModel,
FIELD_MATS & atomicSources)
const FIELDS & fields,
const PhysicsModel * physicsModel,
FIELD_MATS & atomicSources)
{
if (shpFcnMask_) {
feEngine_->compute_source(rhsMask,
fields,
physicsModel,
@ -819,7 +827,16 @@ namespace ATC {
shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),
atomicSources);
}
else {
for (FIELDS::const_iterator field = fields.begin();
field != fields.end(); field++) {
FieldName thisFieldName = field->first;
FIELDS::const_iterator fieldItr = fields.find(thisFieldName);
const DENS_MAT & field = (fieldItr->second).quantity();
atomicSources[thisFieldName].reset(field.nRows(),field.nCols());
}
}
}
//-----------------------------------------------------------------
@ -849,6 +866,24 @@ namespace ATC {
}
}
//-----------------------------------------------------------------
void ATC_Coupling::masked_atom_domain_rhs_tangent(
const pair<FieldName,FieldName> row_col,
const RHS_MASK & rhsMask,
const FIELDS & fields,
SPAR_MAT & stiffness,
const PhysicsModel * physicsModel)
{
if (shpFcnMask_) {
feEngine_->compute_tangent_matrix(rhsMask, row_col,
fields, physicsModel, atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(), shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),stiffness);
}
else {
stiffness.reset(nNodes_,nNodes_);
}
}
//-----------------------------------------------------------------
void ATC_Coupling::compute_rhs_tangent(
const pair<FieldName,FieldName> row_col,
const RHS_MASK & rhsMask,
@ -871,10 +906,11 @@ namespace ATC {
}
feEngine_->compute_tangent_matrix(rhsMaskFE, row_col,
fields , physicsModel, elementToMaterialMap_, stiffness);
feEngine_->compute_tangent_matrix(rhsMaskMD, row_col,
fields, physicsModel, atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(), shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),stiffnessAtomDomain_);
masked_atom_domain_rhs_tangent(row_col,
rhsMaskMD,
fields,
stiffnessAtomDomain_,
physicsModel);
stiffness += stiffnessAtomDomain_;
}
@ -925,6 +961,32 @@ namespace ATC {
feEngine_->add_robin_fluxes(rhsMask, fields, time(), robinFcn, rhs);
}
//-----------------------------------------------------------------
void ATC_Coupling::masked_atom_domain_rhs_integral(
const Array2D<bool> & rhsMask,
const FIELDS & fields, FIELDS & rhs,
const PhysicsModel * physicsModel)
{
if (shpFcnMask_) {
feEngine_->compute_rhs_vector(rhsMask,
fields,
physicsModel,
atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),
shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),
rhs);
}
else {
for (FIELDS::const_iterator field = fields.begin();
field != fields.end(); field++) {
FieldName thisFieldName = field->first;
FIELDS::const_iterator fieldItr = fields.find(thisFieldName);
const DENS_MAT & field = (fieldItr->second).quantity();
(rhs[thisFieldName].set_quantity()).reset(field.nRows(),field.nCols());
}
}
}
//-----------------------------------------------------------------
void ATC_Coupling::evaluate_rhs_integral(
const Array2D<bool> & rhsMask,
const FIELDS & fields, FIELDS & rhs,
@ -942,14 +1004,10 @@ namespace ATC {
elementToMaterialMap_,
rhs,
&(elementMask_->quantity()));
feEngine_->compute_rhs_vector(rhsMask,
fields,
physicsModel,
atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),
shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),
rhsAtomDomain_);
masked_atom_domain_rhs_integral(rhsMask,
fields,
rhsAtomDomain_,
physicsModel);
for (FIELDS::const_iterator field = fields.begin();
field != fields.end(); field++) {
FieldName thisFieldName = field->first;
@ -958,14 +1016,10 @@ namespace ATC {
}
else if (integrationType == ATOM_DOMAIN) {
feEngine_->compute_rhs_vector(rhsMask,
fields,
physicsModel,
atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),
shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),
rhs);
masked_atom_domain_rhs_integral(rhsMask,
fields,
rhs,
physicsModel);
}
else if (integrationType == FULL_DOMAIN_ATOMIC_QUADRATURE_SOURCE) {
RHS_MASK rhsMaskFE = rhsMask;
@ -983,14 +1037,10 @@ namespace ATC {
physicsModel,
elementToMaterialMap_,
rhs);
feEngine_->compute_rhs_vector(rhsMaskMD,
fields,
physicsModel,
atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),
shpFcnMask_->quantity(),
shpFcnDerivsMask_->quantity(),
rhsAtomDomain_);
masked_atom_domain_rhs_integral(rhsMaskMD,
fields,
rhsAtomDomain_,
physicsModel);
for (FIELDS::const_iterator field = fields.begin();
field != fields.end(); field++) {
FieldName thisFieldName = field->first;
@ -1123,6 +1173,52 @@ namespace ATC {
}
}
//--------------------------------------------------------
// create_full_element_mask
// constructs element mask which only masks out
// null elements
//--------------------------------------------------------
MatrixDependencyManager<DenseMatrix, bool> * ATC_Coupling::create_full_element_mask()
{
MatrixDependencyManager<DenseMatrix, bool> * elementMaskMan = new MatrixDependencyManager<DenseMatrix, bool>(feEngine_->num_elements(),1);
DenseMatrix<bool> & elementMask(elementMaskMan->set_quantity());
elementMask = true;
const set<int> & nullElements = feEngine_->null_elements();
set<int>::const_iterator iset;
for (iset = nullElements.begin(); iset != nullElements.end(); iset++) {
int ielem = *iset;
elementMask(ielem,0) = false;
}
return elementMaskMan;
}
//--------------------------------------------------------
// create_element_set_mask
// constructs element mask based on an element set,
// uses ints for MPI communication later
//--------------------------------------------------------
MatrixDependencyManager<DenseMatrix, int> * ATC_Coupling::create_element_set_mask(const string & elementSetName)
{
MatrixDependencyManager<DenseMatrix, int> * elementMaskMan = new MatrixDependencyManager<DenseMatrix, int>(feEngine_->num_elements(),1);
DenseMatrix<int> & elementMask(elementMaskMan->set_quantity());
elementMask = false;
const set<int> & elementSet((feEngine_->fe_mesh())->elementset(elementSetName));
set<int>::const_iterator iset;
for (iset = elementSet.begin(); iset != elementSet.end(); ++iset) {
int ielem = *iset;
elementMask(ielem,0) = true;
}
const set<int> & nullElements = feEngine_->null_elements();
for (iset = nullElements.begin(); iset != nullElements.end(); iset++) {
int ielem = *iset;
elementMask(ielem,0) = false;
}
return elementMaskMan;
}
//--------------------------------------------------------
// set_computational_geometry
// constructs needed transfer operators which define
// hybrid atom/FE computational geometry
@ -1131,70 +1227,85 @@ namespace ATC {
{
ATC_Method::set_computational_geometry();
// does element contain internal atoms
if (internalElementSet_.size()) {
// set up elements and maps based on prescribed element sets
internalElement_ = create_element_set_mask(internalElementSet_);
}
else {
internalElement_ = new AtomTypeElement(this,atomElement_);
}
interscaleManager_.add_dense_matrix_int(internalElement_,
"ElementHasInternal");
if (groupbitGhost_) {
atomGhostElement_ = new AtomToElementMap(this,
atomGhostCoarseGrainingPositions_,
GHOST);
interscaleManager_.add_per_atom_int_quantity(atomGhostElement_,
"AtomGhostElement");
}
// does element contain internal atoms
internalElement_ = new AtomTypeElement(this,atomElement_);
interscaleManager_.add_dense_matrix_int(internalElement_,
"ElementHasInternal");
// does element contain ghost atoms
if (atomGhostElement_) {
// does element contain ghost atoms
ghostElement_ = new AtomTypeElement(this,atomGhostElement_);
interscaleManager_.add_dense_matrix_int(ghostElement_,
"ElementHasGhost");
}
// element masking for FE quadrature
// element masking for approximate right-hand side FE atomic quadrature
if (atomQuadForInternal_) {
elementMask_ = new MatrixDependencyManager<DenseMatrix, bool>(feEngine_->num_elements(),1);
DenseMatrix<bool> & elementMask(elementMask_->set_quantity());
elementMask = true;
const set<int> & nullElements = feEngine_->null_elements();
set<int>::const_iterator iset;
for (iset = nullElements.begin(); iset != nullElements.end(); iset++) {
int ielem = *iset;
elementMask(ielem,0) = false;
}
elementMask_ = create_full_element_mask();
}
else {
elementMask_ = new ElementMask(this);
if (internalElementSet_.size()) {
// when geometry is based on elements, there are no mixed elements
elementMask_ = new MatrixDependencyManager<DenseMatrix, bool>;
(elementMask_->set_quantity()).reset(feEngine_->num_elements(),1,false);
}
else {
elementMask_ = new ElementMask(this);
}
internalToMask_ = new AtomToElementset(this,elementMask_);
interscaleManager_.add_per_atom_int_quantity(internalToMask_,
"InternalToMaskMap");
}
interscaleManager_.add_dense_matrix_bool(elementMask_,
"ElementMask");
// node type
nodalGeometryType_ = new NodalGeometryType(this);
"ElementMask");
if (useFeMdMassMatrix_) {
if (atomQuadForInternal_) {
elementMaskMass_ = elementMask_;
}
else {
elementMaskMass_ = create_full_element_mask();
interscaleManager_.add_dense_matrix_bool(elementMaskMass_,
"NonNullElementMask");
}
elementMaskMassMd_ = new AtomElementMask(this);
interscaleManager_.add_dense_matrix_bool(elementMaskMassMd_,
"InternalElementMask");
}
// assign element and node types for computational geometry
if (internalElementSet_.size()) {
nodalGeometryType_ = new NodalGeometryTypeElementSet(this);
}
else {
nodalGeometryType_ = new NodalGeometryType(this);
}
interscaleManager_.add_dense_matrix_int(nodalGeometryType_,
"NodalGeometryType");
"NodalGeometryType");
}
//--------------------------------------------------------
// construct_transfers
// constructs needed transfer operators
// construct_interpolant
// constructs: interpolatn, accumulant, weights, and spatial derivatives
//--------------------------------------------------------
void ATC_Coupling::construct_transfers()
void ATC_Coupling::construct_interpolant()
{
ATC_Method::construct_transfers();
// finite element shape functions for interpolants
PerAtomShapeFunction * atomShapeFunctions = new PerAtomShapeFunction(this);
interscaleManager_.add_per_atom_sparse_matrix(atomShapeFunctions,"Interpolant");
shpFcn_ = atomShapeFunctions;
if (groupbitGhost_) {
atomShapeFunctions = new PerAtomShapeFunction(this,
atomGhostCoarseGrainingPositions_,
atomGhostElement_,
GHOST);
interscaleManager_.add_per_atom_sparse_matrix(atomShapeFunctions,"InterpolantGhost");
shpFcnGhost_ = atomShapeFunctions;
}
// use shape functions for accumulants if no kernel function is provided
if (!kernelFunction_) {
@ -1209,30 +1320,64 @@ namespace ATC {
accumulantWeights_ = new AccumulantWeights(accumulant_);
mdMassNormalization_ = false;
}
// add species transfer operators
map<string,pair<IdType,int> >::const_iterator specid;
for (specid = speciesIds_.begin(); specid != speciesIds_.end(); specid++) {
const string specie = specid->first;
LargeToSmallAtomMap * specieMap;
if ((specid->second).first == ATOM_TYPE) {
specieMap = new AtomToType(this,(specid->second).second);
interscaleManager_.add_per_atom_int_quantity(specieMap,
"AtomMap"+specie);
}
else { // if ((specie->second).first == ATOM_GROUP)
specieMap = new AtomToGroup(this,(specid->second).second);
interscaleManager_.add_per_atom_int_quantity(specieMap,
"AtomMap"+specie);
}
ReducedSparseMatrix * accumulantSpecie = new ReducedSparseMatrix(this,
accumulant_,
specieMap);
interscaleManager_.add_sparse_matrix(accumulantSpecie,"Accumulant"+specie);
}
this->create_atom_volume();
// add molecule transfer operators
// masked atom weights
if (atomQuadForInternal_) {
atomicWeightsMask_ = atomVolume_;
}
else {
atomicWeightsMask_ = new MappedDiagonalMatrix(this,
atomVolume_,
internalToMask_);
interscaleManager_.add_diagonal_matrix(atomicWeightsMask_,
"AtomWeightsMask");
}
// nodal volumes for mass matrix, relies on atomVolumes constructed in base class construct_transfers
nodalAtomicVolume_ = new AdmtfShapeFunctionRestriction(this,atomVolume_,shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicVolume_,"NodalAtomicVolume");
// shape function derivatives, masked shape function and derivatives if needed for FE quadrature in atomic domain
if (atomQuadForInternal_) {
shpFcnDerivs_ = new PerAtomShapeFunctionGradient(this);
interscaleManager_.add_vector_sparse_matrix(shpFcnDerivs_,
"InterpolantGradient");
shpFcnMask_ = shpFcn_;
shpFcnDerivsMask_ = shpFcnDerivs_;
}
else {
bool hasMaskedElt = false;
const DenseMatrix<bool> & elementMask(elementMask_->quantity());
for (int i = 0; i < elementMask.size(); ++i) {
if (elementMask(i,0)) {
hasMaskedElt = true;
break;
}
}
if (hasMaskedElt) {
shpFcnDerivs_ = new PerAtomShapeFunctionGradient(this);
interscaleManager_.add_vector_sparse_matrix(shpFcnDerivs_,
"InterpolantGradient");
shpFcnMask_ = new RowMappedSparseMatrix(this,
shpFcn_,
internalToMask_);
interscaleManager_.add_sparse_matrix(shpFcnMask_,
"ShapeFunctionMask");
shpFcnDerivsMask_ = new RowMappedSparseMatrixVector(this,
shpFcnDerivs_,
internalToMask_);
interscaleManager_.add_vector_sparse_matrix(shpFcnDerivsMask_,"ShapeFunctionGradientMask");
}
}
}
//--------------------------------------------------------
// construct_molecule_transfers
//--------------------------------------------------------
void ATC_Coupling::construct_molecule_transfers()
{
map<string,pair<MolSize,int> >::const_iterator molecule;
PerAtomQuantity<double> * atomProcGhostCoarseGrainingPositions = interscaleManager_.per_atom_quantity("AtomicProcGhostCoarseGrainingPositions");
@ -1258,58 +1403,16 @@ namespace ATC {
interscaleManager_.add_sparse_matrix(shpFcnMol,
"ShapeFunction"+moleculeName);
}
}
//--------------------------------------------------------
// construct_transfers
// constructs needed transfer operators
//--------------------------------------------------------
void ATC_Coupling::construct_transfers()
{
ATC_Method::construct_transfers();
this->create_atom_volume();
// masked atom weights
if (atomQuadForInternal_) {
atomicWeightsMask_ = atomVolume_;
}
else {
atomicWeightsMask_ = new MappedDiagonalMatrix(this,
atomVolume_,
internalToMask_);
interscaleManager_.add_diagonal_matrix(atomicWeightsMask_,
"AtomWeightsMask");
}
// shape function derivatives
PerAtomShapeFunctionGradient * atomShapeFunctionGradients = new PerAtomShapeFunctionGradient(this);
interscaleManager_.add_vector_sparse_matrix(atomShapeFunctionGradients,
"InterpolantGradient");
shpFcnDerivs_ = atomShapeFunctionGradients;
if (groupbitGhost_) {
atomShapeFunctionGradients = new PerAtomShapeFunctionGradient(this,
atomGhostElement_,
atomGhostCoarseGrainingPositions_,
"InterpolantGradientGhost",
GHOST);
interscaleManager_.add_vector_sparse_matrix(atomShapeFunctionGradients,
"InterpolantGradientGhost");
shpFcnDerivsGhost_ = atomShapeFunctionGradients;
}
// masked shape function and derivatives
if (atomQuadForInternal_) {
shpFcnMask_ = shpFcn_;
shpFcnDerivsMask_ = shpFcnDerivs_;
}
else {
shpFcnMask_ = new RowMappedSparseMatrix(this,
shpFcn_,
internalToMask_);
interscaleManager_.add_sparse_matrix(shpFcnMask_,
"ShapeFunctionMask");
shpFcnDerivsMask_ = new RowMappedSparseMatrixVector(this,
shpFcnDerivs_,
internalToMask_);
interscaleManager_.add_vector_sparse_matrix(shpFcnDerivsMask_,"ShapeFunctionGradientMask");
}
// nodal volumes for mass matrix, relies on atomVolumes constructed in base class construct_transfers
nodalAtomicVolume_ = new AdmtfShapeFunctionRestriction(this,atomVolume_,shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicVolume_,"NodalAtomicVolume");
extrinsicModelManager_.construct_transfers();
}
@ -1387,11 +1490,15 @@ namespace ATC {
if (useFeMdMassMatrix_) {
feEngine_->compute_lumped_mass_matrix(massMask,fields_,physicsModel,
elementToMaterialMap_,massMats_,
&(elementMask_->quantity()));
&(elementMaskMass_->quantity()));
const DIAG_MAT & myMassMat(massMats_[thisField].quantity());
DIAG_MAT & myMassMatInv(massMatsInv_[thisField].set_quantity());
DIAG_MAT & myMassMatMDInv(massMatsMdInv_[thisField].set_quantity());
(massMatsMd_[thisField].set_quantity()) = myMassMat;
DIAG_MAT & myMassMatMdInv(massMatsMdInv_[thisField].set_quantity());
feEngine_->compute_lumped_mass_matrix(massMask,fields_,physicsModel,
elementToMaterialMap_,massMatsMd_,
&(elementMaskMassMd_->quantity()));
const DIAG_MAT & myMassMatMd(massMatsMd_[thisField].quantity());
// compute inverse mass matrices since we're using lumped masses
for (int iNode = 0; iNode < nNodes_; iNode++) {
@ -1399,7 +1506,11 @@ namespace ATC {
myMassMatInv(iNode,iNode) = 1./myMassMat(iNode,iNode);
else
myMassMatInv(iNode,iNode) = 0.;
myMassMatMDInv = myMassMatInv;
if (fabs(myMassMatMd(iNode,iNode))>0)
myMassMatMdInv(iNode,iNode) = 1./myMassMatMd(iNode,iNode);
else
myMassMatMdInv(iNode,iNode) = 0.;
}
}
else {
@ -1418,10 +1529,14 @@ namespace ATC {
}
// atomic quadrature for FE mass matrix in atomic domain
feEngine_->compute_lumped_mass_matrix(massMask,fields_,physicsModel,atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),shpFcnMask_->quantity(),
massMatsAqInstantaneous_);
if (shpFcnMask_) {
feEngine_->compute_lumped_mass_matrix(massMask,fields_,physicsModel,atomMaterialGroupsMask_,
atomicWeightsMask_->quantity(),shpFcnMask_->quantity(),
massMatsAqInstantaneous_);
}
else {
(massMatsAqInstantaneous_[thisField].set_quantity()).reset(nNodes_,nNodes_);
}
// set up mass MD matrices
compute_md_mass_matrix(thisField,massMatsMdInstantaneous_[thisField].set_quantity());
@ -1489,12 +1604,81 @@ namespace ATC {
}
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// pre_init_integrate
// time integration before the lammps atomic
// integration of the Verlet step 1
//--------------------------------------------------------
void ATC_Coupling::pre_init_integrate()
{
ATC_Method::pre_init_integrate();
double dt = lammpsInterface_->dt();
// Perform any initialization, no actual integration
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate1(dt);
}
// Apply controllers to atom velocities, if needed
atomicRegulator_->apply_pre_predictor(dt,lammpsInterface_->ntimestep());
// predict nodal fields and time derivatives
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate2(dt);
}
extrinsicModelManager_.pre_init_integrate();
}
//--------------------------------------------------------
// mid_init_integrate
// time integration between the velocity update and
// the position lammps update of Verlet step 1
//--------------------------------------------------------
void ATC_Coupling::mid_init_integrate()
{
double dt = lammpsInterface_->dt();
// Compute nodal velocity at n+1/2, if needed
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->mid_initial_integrate1(dt);
}
atomicRegulator_->apply_mid_predictor(dt,lammpsInterface_->ntimestep());
extrinsicModelManager_.mid_init_integrate();
}
///--------------------------------------------------------
// post_init_integrate
// time integration after the lammps atomic updates of
// Verlet step 1
//--------------------------------------------------------
void ATC_Coupling::post_init_integrate()
{
double dt = lammpsInterface_->dt();
// Compute nodal velocity at n+1
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->post_initial_integrate1(dt);
}
// Update kinetostat quantities if displacement is being regulated
atomicRegulator_->apply_post_predictor(dt,lammpsInterface_->ntimestep());
// Update extrisic model
extrinsicModelManager_.post_init_integrate();
// fixed values, non-group bcs handled through FE
set_fixed_nodes();
update_time(0.5);
// ghost update, if needed
ATC_Method::post_init_integrate();
// Apply time filtering to mass matrices, if needed
if (timeFilterManager_.filter_dynamics() && !useFeMdMassMatrix_) {
double dt = lammpsInterface_->dt();
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;