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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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221
lib/atc/ATC_CouplingMomentum.cpp
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@ -11,6 +11,9 @@
#include <map>
#include <set>
#include <utility>
#include <iostream>
using std::string;
namespace ATC {
@ -32,8 +35,6 @@ namespace ATC {
: ATC_Coupling(groupName,perAtomArray,thisFix),
nodalAtomicMass_(NULL),
nodalAtomicCount_(NULL),
boundaryDynamics_(PRESCRIBED),
gamma_(0),mu_(1),kappa_(1),
refPE_(0)
{
// Allocate PhysicsModel
@ -60,11 +61,13 @@ namespace ATC {
trackDisplacement_ = true;
fieldSizes_[DISPLACEMENT] = fieldSizes_[VELOCITY];
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::VERLET);
ghostManager_.set_boundary_dynamics(GhostManager::PRESCRIBED);
}
else if (intrinsicModel == SHEAR) {
atomToElementMapType_ = EULERIAN;
atomToElementMapFrequency_ = 1;
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::GEAR);
ghostManager_.set_boundary_dynamics(GhostManager::NO_BOUNDARY_DYNAMICS);
}
// output variable vector info:
@ -119,7 +122,9 @@ namespace ATC {
if (timeFilterManager_.need_reset()) { // reset kinetostat power
init_filter();
}
timeFilterManager_.initialize(); // clears need for reset
// clears need for reset
timeFilterManager_.initialize();
ghostManager_.initialize();
if (!initialized_) {
// initialize sources based on initial FE temperature
@ -356,9 +361,11 @@ namespace ATC {
}
// switch for if displacement is tracked or not
/*! \page man_disp_control fix_modify AtC transfer track_displacement
/*! \page man_track_displacement fix_modify AtC track_displacement
\section syntax
fix_modify AtC transfer track_displacement <on/off> \n
fix_modify AtC track_displacement <on/off> \n
\section examples
<TT> fix_modify atc track_displacement on </TT> \n
\section description
Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.
\section restrictions
@ -380,39 +387,10 @@ namespace ATC {
needReset_ = true;
}
}
/*! \page man_boundary_dynamics fix_modify AtC transfer boundary_dynamics
\section syntax
fix_modify AtC transfer boundary_dynamics <type> \n
\section description
\section restrictions
\section default
on
*/
else if (strcmp(arg[argIndex],"boundary_dynamics")==0) {
argIndex++;
gamma_ = 0;
kappa_ = 0;
mu_ = 0;
if (strcmp(arg[argIndex],"damped_harmonic")==0) {
argIndex++;
gamma_ = atof(arg[argIndex++]);
kappa_ = atof(arg[argIndex++]);
mu_ = atof(arg[argIndex++]);
boundaryDynamics_ = DAMPED_HARMONIC;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"prescribed")==0) {
boundaryDynamics_ = PRESCRIBED;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"coupled")==0) {
boundaryDynamics_ = COUPLED;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"none")==0) {
boundaryDynamics_ = NO_BOUNDARY_DYNAMICS;
foundMatch = true;
}
foundMatch = ghostManager_.modify(narg-argIndex,&arg[argIndex]);
}
// no match, call base class parser
@ -474,31 +452,7 @@ namespace ATC {
atomElement_);
}
//--------------------------------------------------------
// pre_init_integrate
// time integration before the lammps atomic
// integration of the Verlet step 1
//--------------------------------------------------------
void ATC_CouplingMomentum::pre_init_integrate()
{
ATC_Coupling::pre_init_integrate();
double dt = lammpsInterface_->dt();
// get any initial data before its modified
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate1(dt);
}
// apply kinetostat force, if needed
atomicRegulator_->apply_pre_predictor(dt,lammpsInterface_->ntimestep());
// predict nodal velocities
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate2(dt);
}
extrinsicModelManager_.pre_init_integrate();
}
#ifdef OBSOLETE
//--------------------------------------------------------
// mid_init_integrate
// time integration between the velocity update and
@ -545,19 +499,13 @@ namespace ATC {
// fixed values, non-group bcs handled through FE
set_fixed_nodes();
// enforce atomic boundary conditions
if (boundaryDynamics_==PRESCRIBED) set_ghost_atoms();
else if (boundaryDynamics_==DAMPED_HARMONIC) initial_integrate_ghost();
else if (boundaryDynamics_==COUPLED) initial_integrate_ghost();
// update time by a half dt
update_time(0.5);
ATC_Coupling::post_init_integrate();
}
#endif
//--------------------------------------------------------
// pre_final_integrate
// integration before the second stage lammps atomic
@ -566,15 +514,6 @@ namespace ATC {
void ATC_CouplingMomentum::pre_final_integrate()
{
ATC_Coupling::pre_final_integrate();
if (boundaryDynamics_==DAMPED_HARMONIC) {
apply_ghost_forces();
final_integrate_ghost();
}
else if (boundaryDynamics_==COUPLED) {
add_ghost_forces();
final_integrate_ghost();
}
}
//--------------------------------------------------------
@ -750,134 +689,6 @@ namespace ATC {
}
}
//--------------------------------------------------------
// set_ghost_atoms
// sets ghost atom positions to finite element
// displacements based on shape functions
//--------------------------------------------------------
void ATC_CouplingMomentum::set_ghost_atoms()
{
// set atomic displacements based on FE displacements
double ** x = lammpsInterface_->xatom();
// prolong
DenseMatrix<double> ghostAtomData(nLocalGhost_,nsd_);
if (nLocalGhost_>0)
ghostAtomData = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
for (int i = 0; i < nLocalGhost_; ++i)
for (int j = 0; j < nsd_; ++j)
x[ghostToAtom_(i)][j] = ghostAtomData(i,j)+xref_[ghostToAtom_(i)][j];
}
//--------------------------------------------------------
// add_ghost_forces
// add forces to dynamic ghosts
//--------------------------------------------------------
void ATC_CouplingMomentum::add_ghost_forces()
{
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
// add forces
DENS_MAT coarseDisp(nLocalGhost_,nsd_);
DENS_MAT coarseVel(nLocalGhost_,nsd_);
if (nLocalGhost_>0) {
coarseDisp = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
coarseVel = (shpFcnGhost_->quantity())*(fields_[VELOCITY].quantity());
}
// dynamics one-way coupled to real atoms in a well tied to coarse scale
for (int i = 0; i < nLocalGhost_; ++i) {
for (int j = 0; j < nsd_; ++j) {
double du = coarseDisp(i,j)+xref_[ghostToAtom_(i)][j]-x[ghostToAtom_(i)][j];
double dv = coarseVel(i,j)-v[ghostToAtom_(i)][j];
f[ghostToAtom_(i)][j] += mu_*du + gamma_*dv;
}
}
}
void ATC_CouplingMomentum::apply_ghost_forces()
{
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
// add forces
DENS_MAT coarseDisp(nLocalGhost_,nsd_);
DENS_MAT coarseVel(nLocalGhost_,nsd_);
if (nLocalGhost_>0) {
coarseDisp = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
coarseVel = (shpFcnGhost_->quantity())*(fields_[VELOCITY].quantity());
}
// dynamics one-way coupled to real atoms in a well tied to coarse scale
for (int i = 0; i < nLocalGhost_; ++i) {
for (int j = 0; j < nsd_; ++j) {
double du = coarseDisp(i,j)+xref_[ghostToAtom_(i)][j]-x[ghostToAtom_(i)][j];
double dv = coarseVel(i,j)-v[ghostToAtom_(i)][j];
f[ghostToAtom_(i)][j] = mu_*du + gamma_*dv;
}
}
}
//--------------------------------------------------------
// initial_integrate_ghost
// does the first step of the Verlet integration for
// ghost atoms, to be used with non-reflecting BCs
//--------------------------------------------------------
void ATC_CouplingMomentum::initial_integrate_ghost()
{
double dtfm;
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
const int *mask = lammpsInterface_->atom_mask();
int nlocal = lammpsInterface_->nlocal();
double dtv = lammpsInterface_->dt();
double dtf = 0.5 * lammpsInterface_->dt() * lammpsInterface_->ftm2v();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbitGhost_) {
dtfm = dtf / mu_;
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
//--------------------------------------------------------
// final_integrate_ghost
// does the second step of the Verlet integration for
// ghost atoms, to be used with non-reflecting BCs
//--------------------------------------------------------
void ATC_CouplingMomentum::final_integrate_ghost()
{
double dtfm;
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
const int *mask = lammpsInterface_->atom_mask();
int nlocal = lammpsInterface_->nlocal();
double dtf = 0.5 * lammpsInterface_->dt() * lammpsInterface_->ftm2v();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbitGhost_) {
dtfm = dtf / mu_;
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
}
//--------------------------------------------------------------------
// compute_scalar : added energy
// this is used in the line search