ATC version 2.0, date: Aug7
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
435
lib/atc/PhysicsModel.cpp
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435
lib/atc/PhysicsModel.cpp
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#include "PhysicsModel.h"
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#include "WeakEquation.h"
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#include "WeakEquationDiffusion.h"
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#include "WeakEquationChargeDiffusion.h"
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#include "WeakEquationMassDiffusion.h"
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#include "WeakEquationElectronContinuity.h"
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#include "WeakEquationElectronMomentum.h"
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#include "WeakEquationElectronTemperature.h"
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#include "WeakEquationMomentum.h"
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#include "WeakEquationPhononTemperature.h"
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#include "WeakEquationPoisson.h"
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#include "WeakEquationSchrodinger.h"
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#include "ATC_Coupling.h" // for tangent operator
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#include <string>
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#include <iostream>
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#include <fstream>
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namespace ATC {
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//---------------------------------------------------------------------
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// PhysicsModel
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//---------------------------------------------------------------------
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PhysicsModel::PhysicsModel(string fileName)
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{
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parse_material_file(fileName);
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}
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PhysicsModel::~PhysicsModel()
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{
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{
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vector< Material* >::iterator iter;
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for (iter = materials_.begin(); iter != materials_.end(); iter++) {
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Material * mat = *iter;
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if (mat) delete mat;
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}
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}
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{
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map<FieldName, WeakEquation* >::iterator iter;
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for (iter = weakEqns_.begin(); iter != weakEqns_.end(); iter++) {
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WeakEquation * weakEq = iter->second;
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if (weakEq) delete weakEq;
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}
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}
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}
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void PhysicsModel::parse_material_file(string fileName)
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{
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vector< Material* >::iterator iter;
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for (iter = materials_.begin(); iter != materials_.end(); iter++) {
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Material * mat = *iter;
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if (mat) delete mat;
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}
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LammpsInterface::UnitsType lammpsUnits = ATC::LammpsInterface::instance()->units_style();
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fstream fileId(fileName.c_str(), std::ios::in);
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if (!fileId.is_open()) throw ATC_Error("cannot open material file");
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vector<string> line;
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int index = 0;
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while(fileId.good()) {
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command_line(fileId, line);
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if (line.size() == 0 || line[0] == "#") continue;
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if (line[0] == "material") {
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string tag = line[1];
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Material * mat = new Material(tag,fileId);
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materials_.push_back(mat);
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materialNameToIndexMap_[tag] = index++;
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if (line.size() > 2) {
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string units = line[2];
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stringstream ss;
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ss << "WARNING: material units " << units << " do not match lammps";
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if (units == "SI") {
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if (lammpsUnits != LammpsInterface::SI)
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ATC::LammpsInterface::instance()->print_msg_once(ss.str());
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}
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else if (units == "real") {
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if (lammpsUnits != LammpsInterface::REAL )
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ATC::LammpsInterface::instance()->print_msg_once(ss.str());
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}
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else if (units == "metal") {
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if (lammpsUnits != LammpsInterface::METAL )
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ATC::LammpsInterface::instance()->print_msg_once(ss.str());
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}
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else {
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throw ATC_Error("unknown units in material file");
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}
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}
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else {
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throw ATC_Error("units need to be specfied in material file");
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}
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}
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}
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if (int(materials_.size()) == 0) {
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throw ATC_Error("No materials were defined"); }
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stringstream ss;
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ss << int(materials_.size()) << " materials defined from " << fileName;
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ATC::LammpsInterface::instance()->print_msg_once(ss.str());
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fileId.close();
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}
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void PhysicsModel::initialize(void)
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{
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// initialize materials
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vector< Material* >::const_iterator iter;
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for (iter = materials_.begin(); iter != materials_.end(); iter++) {
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Material * mat = *iter;
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mat->initialize();
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}
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// set up null (weakEq, material) registry
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null_.reset(ATC::NUM_FIELDS, materials_.size());
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null_ = false;
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// initialize weak equations
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map<FieldName, WeakEquation * >::const_iterator weak;
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for (weak = weakEqns_.begin(); weak!=weakEqns_.end(); weak++) {
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FieldName fieldName = weak->first;
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WeakEquation * weakEq = weak->second;
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set<string> needs= weakEq->needs_material_functions();
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vector< Material* >::iterator iter;
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for (iter = materials_.begin(); iter != materials_.end(); iter++) {
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Material * mat = *iter;
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if (! (mat->check_registry(needs)) ) {
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string tag = mat->label();
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int matId = materialNameToIndexMap_[tag];
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null_(fieldName,matId) = true;
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stringstream ss;
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ss << "WARNING: physics model: [" << type_ << "], material: [" << tag
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<< "] does not provide all interfaces for <"
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<< field_to_string(fieldName)
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<< "> physics and will be treated as null ";
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ATC::LammpsInterface::instance()->print_msg_once(ss.str());
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// if (noNull_)
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//throw ATC_Error("material does not provide all interfaces for physics");
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}
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}
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}
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}
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int PhysicsModel::material_index(const string & name) const
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{
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string tag = name;
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to_lower(tag); // this is an artifact of StringManip parsing
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map<string,int>::const_iterator iter;
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iter = materialNameToIndexMap_.find(tag);
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if (iter == materialNameToIndexMap_.end()) {
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throw ATC_Error("No material named "+name+" found");
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}
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int index = iter->second;
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return index;
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}
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bool PhysicsModel::parameter_value(const string& name, double& value,
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const int imat) const
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{
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// search owned parameters
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value = 0.0;
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map<string,double>::const_iterator it = parameterValues_.find(name);
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if (it != parameterValues_.end()) {
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value = it->second;
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return true;
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}
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// interogate material models
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bool found = materials_[imat]->parameter(name,value);
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return found;
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}
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void PhysicsModel::num_fields(map<FieldName,int> & fieldSizes,
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Array2D<bool> & rhsMask) const
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{
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map<FieldName, WeakEquation * >::const_iterator itr;
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for (itr = weakEqns_.begin(); itr!=weakEqns_.end(); itr++) {
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FieldName field = itr->first;
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WeakEquation * weakEq = itr->second;
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int size = weakEq->field_size();
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fieldSizes[field] = size;
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rhsMask(field,FLUX) = weakEq->has_B_integrand();
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rhsMask(field,SOURCE) = weakEq->has_N_integrand();
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}
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}
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//---------------------------------------------------------------------
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// PhysicsModelThermal
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//---------------------------------------------------------------------
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PhysicsModelThermal::PhysicsModelThermal(string filename):
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PhysicsModel(filename)
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{
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperature();
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}
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//---------------------------------------------------------------------
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// PhysicsModelElastic
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//---------------------------------------------------------------------
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PhysicsModelElastic::PhysicsModelElastic(string filename):
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PhysicsModel(filename)
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{
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weakEqns_[VELOCITY] = new WeakEquationMomentum();
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}
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//---------------------------------------------------------------------
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// PhysicsModelThermoElastic
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//---------------------------------------------------------------------
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PhysicsModelThermoElastic::PhysicsModelThermoElastic(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "thermo-elastic";
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weakEqns_[VELOCITY] = new WeakEquationMomentum();
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperature();
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}
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//---------------------------------------------------------------------
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// PhysicsModelShear
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//---------------------------------------------------------------------
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PhysicsModelShear::PhysicsModelShear(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "shear";
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weakEqns_[VELOCITY] = new WeakEquationMomentumDiffusion();
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}
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//---------------------------------------------------------------------
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// PhysicsModelThermoShear
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//---------------------------------------------------------------------
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PhysicsModelThermoShear::PhysicsModelThermoShear(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "thermo-shear";
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weakEqns_[VELOCITY] = new WeakEquationMomentumDiffusion();
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperature();
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}
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//---------------------------------------------------------------------
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// PhysicsModelSpecies
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//---------------------------------------------------------------------
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PhysicsModelSpecies::PhysicsModelSpecies(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "species";
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weakEqns_[MASS_DENSITY] = new WeakEquationMassDiffusion();
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weakEqns_[SPECIES_CONCENTRATION] = new WeakEquationDiffusion();
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}
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//---------------------------------------------------------------------
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// PhysicsModelSpeciesElectrostatic
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//---------------------------------------------------------------------
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PhysicsModelSpeciesElectrostatic::PhysicsModelSpeciesElectrostatic(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "species electrostatic";
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weakEqns_[MASS_DENSITY] = new WeakEquationMassDiffusion();
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weakEqns_[CHARGE_DENSITY] = new WeakEquationChargeDiffusion();
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weakEqns_[SPECIES_CONCENTRATION]= new WeakEquationDiffusion();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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}
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//---------------------------------------------------------------------
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// PhysicsModelTwoTemperature
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//---------------------------------------------------------------------
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PhysicsModelTwoTemperature::PhysicsModelTwoTemperature(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "two-temperature";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperature();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusion
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusion::PhysicsModelDriftDiffusion(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureJouleHeating();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronContinuity();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionEquilibrium
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionEquilibrium::PhysicsModelDriftDiffusionEquilibrium(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "equilibrium drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureJouleHeating();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoisson();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionSchrodinger
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionSchrodinger::PhysicsModelDriftDiffusionSchrodinger(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "schrodinger drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureJouleHeating();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoisson();
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weakEqns_[ELECTRON_WAVEFUNCTION]= new WeakEquationSchrodinger();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionSchrodingerSlice
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionSchrodingerSlice::PhysicsModelDriftDiffusionSchrodingerSlice(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "schrodinger drift-diffusion slice";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureJouleHeating();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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weakEqns_[ELECTRON_WAVEFUNCTION]= new WeakEquationSchrodinger();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionConvection
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionConvection::PhysicsModelDriftDiffusionConvection(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "convection drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureConvection();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronContinuity();
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weakEqns_[ELECTRON_VELOCITY] = new WeakEquationElectronMomentumDDM();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionConvectionEquilibrium
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionConvectionEquilibrium::PhysicsModelDriftDiffusionConvectionEquilibrium(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "equilibrium convection drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureConvection();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRON_VELOCITY] = new WeakEquationElectronMomentumDDM();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoisson();
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}
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//---------------------------------------------------------------------
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// PhysicsModelDriftDiffusionConvectionSchrodinger
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//---------------------------------------------------------------------
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PhysicsModelDriftDiffusionConvectionSchrodinger::PhysicsModelDriftDiffusionConvectionSchrodinger(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "schrodinger convection drift-diffusion";
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weakEqns_[TEMPERATURE] = new WeakEquationPhononTemperatureExchange();
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weakEqns_[ELECTRON_TEMPERATURE] = new WeakEquationElectronTemperatureConvection();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRON_VELOCITY] = new WeakEquationElectronMomentumDDM();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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weakEqns_[ELECTRON_WAVEFUNCTION] = new WeakEquationSchrodinger();
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}
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//---------------------------------------------------------------------
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// PhysicsModelElectrostatic
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//---------------------------------------------------------------------
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PhysicsModelElectrostatic::PhysicsModelElectrostatic(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "electrostatic";
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weakEqns_[VELOCITY] = new WeakEquationMomentumElectrostatic();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronContinuity();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoissonConstantRHS();
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}
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//---------------------------------------------------------------------
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// PhysicsModelElectrostaticEquilibrium
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//---------------------------------------------------------------------
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PhysicsModelElectrostaticEquilibrium::PhysicsModelElectrostaticEquilibrium(string filename):
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PhysicsModel(filename)
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{
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PhysicsModel::type_ = "equilibrium electrostatic";
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weakEqns_[VELOCITY] = new WeakEquationMomentumElectrostatic();
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weakEqns_[ELECTRON_DENSITY] = new WeakEquationElectronEquilibrium();
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weakEqns_[ELECTRIC_POTENTIAL] = new WeakEquationPoisson();
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}
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//-------------------------------------------------------------------
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// PhysicsModelTangentOperator
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//-------------------------------------------------------------------
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PhysicsModelTangentOperator::PhysicsModelTangentOperator(ATC_Coupling * atc,
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const PhysicsModel * physicsModel,
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Array2D<bool> & rhsMask,
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IntegrationDomainType integrationType,
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FIELDS & rhs,
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FIELDS & fields,
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FieldName fieldName,
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const int dof)
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:TangentOperator(),
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atc_(atc),
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physicsModel_(physicsModel),
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rhsMask_(rhsMask),
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integrationType_(integrationType),
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rhs_(rhs),
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fields_(fields),
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fieldName_(fieldName),
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dof_(dof)
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{
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};
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PhysicsModelTangentOperator::PhysicsModelTangentOperator(ATC_Coupling * atc,
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const PhysicsModel * physicsModel,
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Array2D<bool> & rhsMask,
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IntegrationDomainType integrationType,
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FieldName fieldName,
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const int dof)
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:TangentOperator(),
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atc_(atc),
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physicsModel_(physicsModel),
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rhsMask_(rhsMask),
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integrationType_(integrationType),
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rhs_(atc_->rhs()),
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fields_(atc_->fields()),
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fieldName_(fieldName),
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dof_(dof)
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{
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};
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void PhysicsModelTangentOperator::function(const VECTOR & x, DENS_VEC & r)
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{
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CLON_VEC f = column(fields_[fieldName_].set_quantity(),dof_);
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f = x;
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atc_->compute_rhs_vector(rhsMask_, fields_, rhs_, integrationType_, physicsModel_);
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CLON_VEC rhsv = column(rhs_[fieldName_].quantity(),dof_);
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r = rhsv;
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}
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void PhysicsModelTangentOperator::tangent(const VECTOR & x, DENS_VEC & r,
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MATRIX & K)
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{
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function(x,r);
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pair<FieldName,FieldName> row_col(fieldName_,fieldName_);
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const FIELDS & fields = fields_;
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atc_->compute_rhs_tangent(row_col, rhsMask_, fields , stiffness_, integrationType_, physicsModel_);
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K = stiffness_.dense_copy();
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}
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}; // end namespace
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