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lammps/lib/atc/PrescribedDataManager.cpp
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PrescribedDataManager.cpp
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#include "PrescribedDataManager.h"
#include "FE_Engine.h"
#include "ATC_Error.h"
#include <sstream>
#include <iostream>
using std::stringstream;
using std::make_pair;
using std::map;
using std::set;
using std::pair;
using std::string;
using std::cout;
namespace ATC {
//-------------------------------------------------------------------------
// PrescribedDataManager
//-------------------------------------------------------------------------
PrescribedDataManager::PrescribedDataManager
(FE_Engine * feEngine,
const map<FieldName,int> & fieldSize) :
fieldSizes_(fieldSize), feEngine_(feEngine)
{
// construct & initialize internal data
nNodes_ = feEngine_->num_nodes();
nElems_ = feEngine_->num_elements();
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
int thisSize = field->second;
// nodal ics & essential bcs
ics_[thisField].reset(nNodes_,thisSize);
bcs_[thisField].reset(nNodes_,thisSize);
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int idof = 0; idof < thisSize ; ++idof) {
ics_[thisField](inode,idof) = NULL;
bcs_[thisField](inode,idof) = NULL;
}
}
// compact inode, value lists
(bcValues_[thisField]).resize(thisSize);
// element based sources
elementSources_[thisField].reset(nElems_,thisSize);
for (int ielem = 0; ielem < nElems_ ; ++ielem) {
for (int idof = 0; idof < thisSize ; ++idof) {
elementSources_[thisField](ielem,idof) = NULL;
}
}
// node based sources
nodalSources_[thisField].reset(nNodes_,thisSize);
}
}
//-------------------------------------------------------------------------
// ~PrescribedDataManager
//-------------------------------------------------------------------------
PrescribedDataManager::~PrescribedDataManager()
{
}
//-------------------------------------------------------------------------
// add_field
//-------------------------------------------------------------------------
void PrescribedDataManager::add_field(FieldName fieldName, int size)
{
// check to see if field exists
if (fieldSizes_.find(fieldName) == fieldSizes_.end()) return;
// construct & initialize internal data
nNodes_ = feEngine_->num_nodes();
nElems_ = feEngine_->num_elements();
// nodal ics & essential bcs
ics_[fieldName].reset(nNodes_,size);
bcs_[fieldName].reset(nNodes_,size);
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int idof = 0; idof < size ; ++idof) {
ics_[fieldName](inode,idof) = NULL;
bcs_[fieldName](inode,idof) = NULL;
}
}
// element based sources
elementSources_[fieldName].reset(nElems_,size);
for (int ielem = 0; ielem < nElems_ ; ++ielem) {
for (int idof = 0; idof < size ; ++idof) {
elementSources_[fieldName](ielem,idof) = NULL;
}
}
}
//-------------------------------------------------------------------------
// remove_field
//-------------------------------------------------------------------------
void PrescribedDataManager::remove_field(FieldName fieldName)
{
// check to see if field exists
if (fieldSizes_.find(fieldName) == fieldSizes_.end())
return;
// delete field in maps
fieldSizes_.erase(fieldName);
ics_.erase(fieldName);
bcs_.erase(fieldName);
elementSources_.erase(fieldName);
}
//-------------------------------------------------------------------------
// fix_initial_field
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_initial_field
(const string nodesetName,
const FieldName thisField,
const int thisIndex,
const XT_Function * f)
{
set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nodesetName);
set<int>::const_iterator iset;
for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
int inode = *iset;
ics_[thisField](inode,thisIndex) = (XT_Function*) f;
}
}
//-------------------------------------------------------------------------
// fix_field
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_field
(const std::set<int> nodeSet,
const FieldName thisField,
const int thisIndex,
const XT_Function * f)
{
// fix fields
set<int>::const_iterator iset;
for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
int inode = *iset;
bcs_[thisField](inode,thisIndex) = (XT_Function*) f;
}
}
void PrescribedDataManager::fix_field
(const string nodesetName,
const FieldName thisField,
const int thisIndex,
const XT_Function * f)
{
set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nodesetName);
fix_field(nodeSet,thisField,thisIndex,f);
}
//-------------------------------------------------------------------------
// unfix_field
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_field
(const string nodesetName,
const FieldName thisField,
const int thisIndex)
{
set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nodesetName);
set<int>::const_iterator iset;
for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
int inode = *iset;
bcs_[thisField](inode,thisIndex) = NULL;
}
}
//-------------------------------------------------------------------------
// fix_field
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_field
(const int nodeId,
const FieldName thisField,
const int thisIndex,
const XT_Function * f)
{
bcs_[thisField](nodeId,thisIndex) = (XT_Function*) f;
}
//-------------------------------------------------------------------------
// unfix_field
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_field
(const int nodeId,
const FieldName thisField,
const int thisIndex)
{
bcs_[thisField](nodeId,thisIndex) = NULL;
}
//-------------------------------------------------------------------------
// fix_flux
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_flux
(const string facesetName,
const FieldName thisField,
const int thisIndex,
const XT_Function * f)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
// allocate, if necessary
Array < XT_Function * > & dof = faceSources_[thisField][face];
if (dof.size() == 0) {
int ndof = (fieldSizes_.find(thisField))->second;
dof.reset(ndof);
for(int i = 0; i < ndof; i++) dof(i) = NULL;
}
dof(thisIndex) = (XT_Function*) f;
}
}
//-------------------------------------------------------------------------
// unfix_flux
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_flux
(const string facesetName,
const FieldName thisField,
const int thisIndex)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
Array < XT_Function * > & dof = faceSources_[thisField][face];
dof(thisIndex) = NULL;
}
}
//-------------------------------------------------------------------------
// fix_robin
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_robin
(const string facesetName,
const FieldName thisField,
const int thisIndex,
const UXT_Function * f)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
// allocate, if necessary
Array < UXT_Function * > & dof = faceSourcesRobin_[thisField][face];
if (dof.size() == 0) {
int ndof = (fieldSizes_.find(thisField))->second;
dof.reset(ndof);
for(int i = 0; i < ndof; i++) dof(i) = NULL;
}
dof(thisIndex) = (UXT_Function*) f;
}
}
//-------------------------------------------------------------------------
// unfix_robin
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_robin
(const string facesetName,
const FieldName thisField,
const int thisIndex)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
Array < UXT_Function * > & dof = faceSourcesRobin_[thisField][face];
dof(thisIndex) = NULL;
}
}
//-------------------------------------------------------------------------
// fix_open
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_open
(const string facesetName,
const FieldName thisField)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
facesOpen_[thisField].insert(face); // uniquely insert this face
}
}
//-------------------------------------------------------------------------
// unfix_open
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_open
(const string facesetName,
const FieldName thisField)
{
const set< pair <int,int> > * fset
= & ( (feEngine_->fe_mesh())->faceset(facesetName));
set< pair<int,int> >::const_iterator iset;
for (iset = fset->begin(); iset != fset->end(); iset++) {
pair<int,int> face = *iset;
facesOpen_[thisField].erase(face);
}
}
//-------------------------------------------------------------------------
// fix_source
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_source
(const string elemsetName,
const FieldName thisField,
const int thisIndex,
const XT_Function *f)
{
set<int> elemSet = (feEngine_->fe_mesh())->elementset(elemsetName);
set<int>::const_iterator iset;
for (iset = elemSet.begin(); iset != elemSet.end(); iset++) {
int ielem = *iset;
// fix source
elementSources_[thisField](ielem,thisIndex) = (XT_Function*) f;
}
}
//-------------------------------------------------------------------------
// fix_source
//-------------------------------------------------------------------------
void PrescribedDataManager::fix_source
(const FieldName thisField,
const int thisIndex,
const set<pair<int,double> > & s)
{
set<pair<int,double> >::const_iterator iset;
DENS_MAT & n(nodalSources_[thisField].set_quantity());
for (iset = s.begin(); iset != s.end(); iset++) {
pair<int,double> p = *iset;
int inode = p.first;
double v = p.second;
n(inode,thisIndex) = v;
}
}
//-------------------------------------------------------------------------
// unfix_source
//-------------------------------------------------------------------------
void PrescribedDataManager::unfix_source
(const string elemsetName,
const FieldName thisField,
const int thisIndex)
{
set<int> elemSet = (feEngine_->fe_mesh())->elementset(elemsetName);
set<int>::const_iterator iset;
for (iset = elemSet.begin(); iset != elemSet.end(); iset++) {
int ielem = *iset;
elementSources_[thisField](ielem,thisIndex) = NULL;
}
}
//-------------------------------------------------------------------------
// set_initial_conditions
//-------------------------------------------------------------------------
void PrescribedDataManager::set_initial_conditions(const double t,
FIELDS &fields,
FIELDS &dot_fields,
FIELDS &ddot_fields,
FIELDS &dddot_fields)
{
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
int thisSize = field->second;
DENS_MAT & myField(fields[thisField].set_quantity());
DENS_MAT & myDotField(dot_fields[thisField].set_quantity());
DENS_MAT & myDDotField(ddot_fields[thisField].set_quantity());
DENS_MAT & myDDDotField(dddot_fields[thisField].set_quantity());
bool warn = false;
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
XT_Function *f = ics_[thisField](inode,thisIndex);
if (!f) f = bcs_[thisField](inode,thisIndex);
if (f)
{
DENS_VEC coords(3);
coords = (feEngine_->fe_mesh())->nodal_coordinates(inode);
double *x = coords.ptr();
myField(inode,thisIndex) = f->f(x,t);
myDotField(inode,thisIndex) = f->dfdt(x,t);
myDDotField(inode,thisIndex) = f->ddfdt(x,t);
myDDDotField(inode,thisIndex) = f->dddfdt(x,t);
}
else {
myField(inode,thisIndex) = 0;
myDotField(inode,thisIndex) = 0;
myDDotField(inode,thisIndex) = 0;
myDDDotField(inode,thisIndex) = 0;
warn = true;
}
}
}
// if (warn && is_dynamic(thisField)) { need access tp physics model or return warn per field
if (warn) {
stringstream ss;
ss << ("WARNING: all initial conditions for " +field_to_string(thisField)+" have not been defined and the undefined are assumed zero");
ATC::LammpsInterface::instance()->print_msg_once(ss.str());
}
}
}
//-------------------------------------------------------------------------
// set_fixed_fields
//-------------------------------------------------------------------------
void PrescribedDataManager::set_fixed_fields(const double t,
FIELDS &fields,
FIELDS &dot_fields,
FIELDS &ddot_fields,
FIELDS &dddot_fields)
{
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
int thisSize = field->second;
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
BC_SET & bcs = (bcValues_[thisField])[thisIndex];
bcs.clear();
for (int inode = 0; inode < nNodes_ ; ++inode) {
XT_Function * f = bcs_[thisField](inode,thisIndex);
if (f) {
DENS_VEC coords(3);
coords = (feEngine_->fe_mesh())->nodal_coordinates(inode);
double * x = coords.ptr();
double val = f->f(x,t);
(fields [thisField].set_quantity())(inode,thisIndex) = val;
(dot_fields [thisField].set_quantity())(inode,thisIndex) = f->dfdt(x,t);
(ddot_fields [thisField].set_quantity())(inode,thisIndex) = f->ddfdt(x,t);
(dddot_fields[thisField].set_quantity())(inode,thisIndex) = f->dddfdt(x,t);
// compact set
pair <int, double > bc = make_pair(inode,val);
bcs.insert(bc);
}
}
}
}
}
//-------------------------------------------------------------------------
// set_fixed_field
//-------------------------------------------------------------------------
void PrescribedDataManager::set_fixed_field(
const double t,
const FieldName & fieldName,
DENS_MAT & fieldMatrix)
{
map<FieldName,int>::iterator fieldSizeIter = fieldSizes_.find(fieldName);
if (fieldSizeIter == fieldSizes_.end()) {
throw ATC_Error( "Unrecognized FieldName in PrescribedDataManager::set_fixed_field()");
}
int thisSize = fieldSizeIter->second;
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
XT_Function * f = bcs_[fieldName](inode,thisIndex);
if (f) {
DENS_VEC coords(3);
coords = (feEngine_->fe_mesh())->nodal_coordinates(inode);
fieldMatrix(inode,thisIndex) = f->f(coords.ptr(),t);
}
}
}
}
//-------------------------------------------------------------------------
// set_fixed_dfield
//-------------------------------------------------------------------------
void PrescribedDataManager::set_fixed_dfield(
const double t,
const FieldName & fieldName,
DENS_MAT & dfieldMatrix)
{
map<FieldName,int>::iterator fieldSizeIter = fieldSizes_.find(fieldName);
if (fieldSizeIter == fieldSizes_.end()) {
throw ATC_Error( "Unrecognized FieldName in PrescribedDataManager::set_fixed_dfield()");
}
int thisSize = fieldSizeIter->second;
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
XT_Function * f = bcs_[fieldName](inode,thisIndex);
if (f) {
DENS_VEC coords(3);
coords = (feEngine_->fe_mesh())->nodal_coordinates(inode);
dfieldMatrix(inode,thisIndex) = f->dfdt(coords.ptr(),t);
}
}
}
}
//-------------------------------------------------------------------------
// set_sources
//-------------------------------------------------------------------------
void PrescribedDataManager::set_sources
(double t,
FIELDS & sources)
{
// zero
Array<bool> fieldMask(NUM_FIELDS);
fieldMask = false;
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
fieldMask(thisField) = true;
int thisSize = field->second;
sources[thisField].reset(nNodes_,thisSize);
}
// compute boundary fluxes
feEngine_->add_fluxes(fieldMask,t,faceSources_,sources);
// compute internal sources
feEngine_->add_sources(fieldMask,t,elementSources_,sources);
feEngine_->add_sources(fieldMask,t,nodalSources_,sources);
// mask out nodes with essential bcs
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
int thisSize = field->second;
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
XT_Function * f = bcs_[thisField](inode,thisIndex);
if (f) {
(sources[thisField].set_quantity())(inode,thisIndex) = 0.0;
}
}
}
}
}
//-------------------------------------------------------------------------
// print
//-------------------------------------------------------------------------
void PrescribedDataManager::print(void)
{
// print and check consistency
enum dataType {FREE=0,FIELD,SOURCE};
Array2D < int > bcTypes;
Array <int> conn;
map<FieldName,int>::const_iterator field;
XT_Function * f;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
int thisFieldSize = field->second;
string fieldName = field_to_string(thisField);
int thisSize = field->second;
bcTypes.reset(nNodes_,thisSize);
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
f = bcs_[thisField](inode,thisIndex);
if (f) { bcTypes(inode,thisIndex) = FIELD; }
else { bcTypes(inode,thisIndex) = FREE; }
}
}
// FIXED has higher precidence than SOURCE
for (int ielem = 0; ielem < nElems_ ; ++ielem) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
f = elementSources_[thisField](ielem,thisIndex);
if (f) {
feEngine_->element_connectivity(ielem,conn);
for (int i = 0; i < conn.size() ; ++i) {
int inode = conn(i);
if (bcTypes(inode,thisIndex) != FIELD)
{ bcTypes(inode,thisIndex) = SOURCE; }
}
}
}
}
map < pair<int,int>, Array < XT_Function * > > & fset
= faceSources_[thisField];
map < pair<int,int>, Array < XT_Function * > > ::const_iterator iset;
for (iset = fset.begin(); iset != fset.end(); iset++) {
pair<int,int> face = iset->first;
Array < XT_Function * > fs = iset->second;
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
f = fs(thisIndex);
if (f) {
feEngine_->face_connectivity(face,conn);
for (int i = 0; i < conn.size() ; ++i) {
int inode = conn(i);
if (bcTypes(inode,thisIndex) != FIELD)
{ bcTypes(inode,thisIndex) = SOURCE; }
}
}
}
}
for (int inode = 0; inode < nNodes_ ; ++inode) {
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
cout << "node: " << inode << " " << fieldName;
if (thisFieldSize > 1) { cout << " " << thisIndex; }
f = ics_[thisField](inode,thisIndex);
if (f) { cout << " IC"; }
if (bcTypes(inode,thisIndex) == FIELD ) {cout << " FIXED"; }
else if (bcTypes(inode,thisIndex) == SOURCE) {cout << " SOURCE"; }
cout << "\n";
}
}
}
}
//-------------------------------------------------------------------------
// get_bcs of a subset of nodes
//-------------------------------------------------------------------------
void PrescribedDataManager::bcs(const FieldName thisField, const set<int> nodeSet, BCS & bcs, bool local) const
{
bcs.clear();
int thisSize = (fieldSizes_.find(thisField))->second;
bcs.resize(thisSize);
for (int thisIndex = 0; thisIndex < thisSize ; ++thisIndex) {
set<int>::const_iterator iset;
int i = 0;
for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
int inode = *iset;
const BC_SET & allBCs
= ((bcValues_.find(thisField))->second)[thisIndex];
BC_SET::const_iterator bset;
for (bset = allBCs.begin(); bset != allBCs.end(); bset++) {
int bnode = (*bset).first;
if (inode == bnode) {
double val = (*bset).second;
if (local) inode = i; // use a local numbering
pair <int, double > bc = make_pair(inode,val);
(bcs[thisIndex]).insert(bc);
}
}
i++;
}
}
}
} // end namespace
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