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ATC version 2.0, date: Aug28

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10695 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
2013-08-28 22:16:54 +00:00
parent 4df2113a80
commit 8d6d4e9289
29 changed files with 220 additions and 621 deletions
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144
lib/atc/ATC_CouplingMomentumEnergy.cpp
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@ -31,11 +31,6 @@ namespace ATC {
string matParamFile,
ExtrinsicModelType extrinsicModel)
: ATC_Coupling(groupName,perAtomArray,thisFix),
#ifdef OBSOLETE
nodalAtomicMass_(NULL),
nodalAtomicCount_(NULL),
nodalAtomicHeatCapacity_(NULL),
#endif
nodalAtomicKineticTemperature_(NULL),
nodalAtomicConfigurationalTemperature_(NULL),
refPE_(0)
@ -82,9 +77,6 @@ namespace ATC {
extVector_ = 1;
if (extrinsicModel != NO_MODEL)
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
// create PE per atom ccompute
lammpsInterface_->create_compute_pe_peratom();
}
//--------------------------------------------------------
@ -111,88 +103,6 @@ namespace ATC {
// Base class initalizations
ATC_Coupling::initialize();
// resetting precedence:
// time integrator -> kinetostat/thermostat -> time filter
// init_filter uses fieldRateNdFiltered which comes from the time integrator,
// which is why the time integrator is initialized first
// other initializations
#ifdef OBSOLETE
if (reset_methods()) {
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->force_reset();
}
atomicRegulator_->force_reset();
}
#endif
if (reset_methods()) {
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->initialize();
}
atomicRegulator_->initialize();
extrinsicModelManager_.initialize();
}
if (timeFilterManager_.need_reset()) {// reset thermostat power
init_filter();
}
// clears need for reset
timeFilterManager_.initialize();
ghostManager_.initialize();
if (!initialized_) {
// initialize sources based on initial FE temperature
double dt = lammpsInterface_->dt();
prescribedDataMgr_->set_sources(time()+0.5*dt,sources_);
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
atomicRegulator_->compute_boundary_flux(fields_);
compute_atomic_sources(fieldMask_,fields_,atomicSources_);
// read in field data if necessary
if (useRestart_) {
RESTART_LIST data;
read_restart_data(restartFileName_,data);
useRestart_ = false;
}
// set consistent initial conditions, if requested
if (!timeFilterManager_.filter_dynamics()) {
if (consistentInitialization_) {
DENS_MAT & velocity(fields_[VELOCITY].set_quantity());
DENS_MAN * nodalAtomicVelocity(interscaleManager_.dense_matrix("NodalAtomicVelocity"));
const DENS_MAT & atomicVelocity(nodalAtomicVelocity->quantity());
DENS_MAT & temperature(fields_[TEMPERATURE].set_quantity());
DENS_MAN * nodalAtomicTemperature(interscaleManager_.dense_matrix("NodalAtomicTemperature"));
const DENS_MAT & atomicTemperature(nodalAtomicTemperature->quantity());
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
for (int i = 0; i<nNodes_; ++i) {
if (nodeType(i,0)==MD_ONLY) {
for (int j = 0; j < nsd_; j++) {
velocity(i,j) = atomicVelocity(i,j);
}
temperature(i,0) = atomicTemperature(i,0);
}
}
if (trackDisplacement_) {
DENS_MAT & displacement(fields_[DISPLACEMENT].set_quantity());
DENS_MAN * nodalAtomicDisplacement(interscaleManager_.dense_matrix("NodalAtomicDisplacement"));
const DENS_MAT & atomicDisplacement(nodalAtomicDisplacement->quantity());
for (int i = 0; i<nNodes_; ++i) {
if (nodeType(i,0)==MD_ONLY) {
for (int j = 0; j < nsd_; j++) {
displacement(i,j) = atomicDisplacement(i,j);
}
}
}
}
}
}
initialized_ = true;
}
// reset integration field mask
intrinsicMask_.reset(NUM_FIELDS,NUM_FLUX);
@ -368,38 +278,7 @@ namespace ATC {
TEMPERATURE);
interscaleManager_.add_dense_matrix(nodalAtomicTemperature,
"NodalAtomicTemperature");
#ifdef OBSOLETE
if (!useFeMdMassMatrix_) {
// atomic momentum mass matrix
FundamentalAtomQuantity * atomicMass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
nodalAtomicMass_ = new AtfShapeFunctionRestriction(this,
atomicMass,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicMass_,
"AtomicMomentumMassMat");
// atomic dimensionless mass matrix
ConstantQuantity<double> * atomicOnes = new ConstantQuantity<double>(this,1);
interscaleManager_.add_per_atom_quantity(atomicOnes,"AtomicOnes");
nodalAtomicCount_ = new AtfShapeFunctionRestriction(this,
atomicOnes,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicCount_,
"AtomicDimensionlessMassMat");
// classical thermodynamic heat capacity of the atoms
HeatCapacity * heatCapacity = new HeatCapacity(this);
interscaleManager_.add_per_atom_quantity(heatCapacity,
"AtomicHeatCapacity");
// atomic thermal mass matrix
nodalAtomicHeatCapacity_ = new AtfShapeFunctionRestriction(this,
heatCapacity,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicHeatCapacity_,
"NodalAtomicHeatCapacity");
}
#endif
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->construct_transfers();
}
@ -431,28 +310,7 @@ namespace ATC {
atomicRegulator_->reset_lambda_contribution(powerMat,TEMPERATURE);
}
}
#ifdef OBSOLETE
//---------------------------------------------------------
// compute_md_mass_matrix
// compute the mass matrix arising from only atomistic
// quadrature and contributions as a summation
//---------------------------------------------------------
void ATC_CouplingMomentumEnergy::compute_md_mass_matrix(FieldName thisField,
DIAG_MAT & massMat)
{
if (thisField == DISPLACEMENT || thisField == VELOCITY) {
massMat.reset(nodalAtomicMass_->quantity());
}
else if (thisField == MASS_DENSITY) { // dimensionless mass matrix
massMat.reset(nodalAtomicCount_->quantity());
}
else if (thisField == TEMPERATURE) {
massMat.reset(nodalAtomicHeatCapacity_->quantity());
}
}
#endif
//--------------------------------------------------------
// modify
// parses inputs and modifies state of the filter