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ATC version 2.0, date: Aug7

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10557 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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rjones
2013-08-07 21:29:01 +00:00
parent 6d40d7c25d
commit 0e4d1e6b22
87 changed files with 4663 additions and 30479 deletions
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251
lib/atc/ElasticTimeIntegrator.cpp
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@ -1,251 +0,0 @@
// ATC transfer headers
#include "ElasticTimeIntegrator.h"
#include "ATC_Transfer.h"
#include "TimeFilter.h"
#include "ATC_Error.h"
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class ElasticTimeIntegrator
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
ElasticTimeIntegrator::ElasticTimeIntegrator(ATC_Transfer * atcTransfer,
TimeIntegrationType timeIntegrationType) :
TimeIntegrator(atcTransfer, timeIntegrationType)
{
// do nothing
}
//--------------------------------------------------------
// modify
// parses inputs and modifies state of the filter
//--------------------------------------------------------
bool ElasticTimeIntegrator::modify(int narg, char **arg)
{
// currently no parsing for elastic time integration
return false;
}
//--------------------------------------------------------
// initialize
// sets up all the necessary data
//--------------------------------------------------------
void ElasticTimeIntegrator::initialize()
{
if (needReset_ || timeFilterManager_->need_reset()) {
if (timeIntegrationMethod_)
delete timeIntegrationMethod_;
if (timeFilterManager_->need_reset()) {
if (timeFilter_)
delete timeFilter_;
timeFilter_ = timeFilterManager_->construct(TimeFilterManager::IMPLICIT);
}
if (timeFilterManager_->filter_dynamics()) {
timeIntegrationMethod_ = new ElasticTimeIntegratorVerletFiltered(this);
}
else {
timeIntegrationMethod_ = new ElasticTimeIntegratorVerlet(this);
}
}
TimeIntegrator::initialize();
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class ElasticIntegrationMethod
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
ElasticIntegrationMethod::ElasticIntegrationMethod(ElasticTimeIntegrator * elasticTimeIntegrator) :
TimeIntegrationMethod(elasticTimeIntegrator),
timeFilter_(timeIntegrator_->get_time_filter()),
displacement_(atcTransfer_->get_field(DISPLACEMENT)),
velocity_(atcTransfer_->get_field(VELOCITY)),
acceleration_(atcTransfer_->get_field_roc(VELOCITY)),
nodalAtomicDisplacement_(atcTransfer_->get_atomic_field(DISPLACEMENT)),
nodalAtomicVelocity_(atcTransfer_->get_atomic_field(VELOCITY)),
velocityRhs_(atcTransfer_->get_field_rhs(VELOCITY)),
nodalAtomicForce_(atcTransfer_->get_fe_atomic_field_roc(VELOCITY)),
forceFilteringData_(atcTransfer_->get_aux_storage(VELOCITY))
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class ElasticTimeIntegratorVerlet
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ElasticTimeIntegratorVerlet::ElasticTimeIntegratorVerlet(ElasticTimeIntegrator * elasticTimeIntegrator) :
ElasticIntegrationMethod(elasticTimeIntegrator)
{
TimeFilterManager * timeFilterManager = (timeIntegrator_->get_atc_transfer())->get_time_filter_manager();
if (timeFilterManager->need_reset()) {
timeFilter_->initialize(nodalAtomicForce_);
}
// reset filtering data, if needed
if (!(timeFilterManager->end_equilibrate())) {
forceFilteringData_.reset(atcTransfer_->get_nNodes(),atcTransfer_->get_nsd());
}
}
//--------------------------------------------------------
// mid_initial_integrate1
// time integration at the mid-point of Verlet step 1
//--------------------------------------------------------
void ElasticTimeIntegratorVerlet::mid_initial_integrate1(double dt)
{
explicit_1(velocity_,acceleration_,.5*dt);
}
//--------------------------------------------------------
// post_initial_integrate1
// time integration after Verlet step 1
//--------------------------------------------------------
void ElasticTimeIntegratorVerlet::post_initial_integrate1(double dt)
{
// NOTE could use explicit_2 with velocityRhs_ as the 2nd derivative
// for improved accuracy, but this would be inconsistent with
// the atomic integration scheme
explicit_1(displacement_,velocity_,dt);
}
//--------------------------------------------------------
// pre_final_integrate1
// first time integration computations
// before Verlet step 2
//--------------------------------------------------------
void ElasticTimeIntegratorVerlet::pre_final_integrate1(double dt)
{
// Compute MD contribution to FEM equation
DENS_MAT atomicForces;
atcTransfer_->compute_atomic_force(atomicForces,atcTransfer_->get_f());
atcTransfer_->restrict_volumetric_quantity(atomicForces,nodalAtomicForce_);
timeFilter_->apply_post_step2(forceFilteringData_,nodalAtomicForce_,dt);
}
//--------------------------------------------------------
// post_final_integrate1
// second time integration computations
// after Verlet step 2
//--------------------------------------------------------
void ElasticTimeIntegratorVerlet::post_final_integrate1(double dt)
{
atcTransfer_->apply_inverse_mass_matrix(velocityRhs_,
acceleration_,
VELOCITY);
explicit_1(velocity_,acceleration_,.5*dt);
}
//--------------------------------------------------------
// post_process
// post processing of variables before output
//--------------------------------------------------------
void ElasticTimeIntegratorVerlet::post_process(double dt)
{
DENS_MAT atomicQuantity;
atcTransfer_->compute_atomic_momentum(atomicQuantity,atcTransfer_->get_v());
atcTransfer_->project_md_volumetric_quantity(atomicQuantity,nodalAtomicVelocity_,VELOCITY);
atcTransfer_->compute_atomic_centerOfMass_displacement(atomicQuantity,atcTransfer_->get_x());
atcTransfer_->project_md_volumetric_quantity(atomicQuantity,nodalAtomicDisplacement_,VELOCITY);
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class ElasticTimeIntegratorVerletFiltered
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ElasticTimeIntegratorVerletFiltered::ElasticTimeIntegratorVerletFiltered(ElasticTimeIntegrator * elasticTimeIntegrator) :
ElasticTimeIntegratorVerlet(elasticTimeIntegrator),
nodalAtomicAcceleration_(atcTransfer_->get_atomic_field_roc(VELOCITY))
{
// swap filtered and unfiltered forces
if ((timeIntegrator_->get_time_filter_manager())->end_equilibrate()) {
DENS_MAT temp(nodalAtomicForce_);
nodalAtomicForce_ = forceFilteringData_;
forceFilteringData_ = temp;
}
}
//--------------------------------------------------------
// mid_initial_integrate1
// time integration at the mid-point of Verlet step 1
//--------------------------------------------------------
void ElasticTimeIntegratorVerletFiltered::mid_initial_integrate1(double dt)
{
explicit_1(velocity_,acceleration_,.5*dt);
explicit_1(nodalAtomicVelocity_,nodalAtomicAcceleration_,.5*dt);
}
//--------------------------------------------------------
// post_initial_integrate1
// time integration after Verlet step 1
//--------------------------------------------------------
void ElasticTimeIntegratorVerletFiltered::post_initial_integrate1(double dt)
{
// NOTE could use explicit_2 with velocityRhs_ as the 2nd derivative
// for improved accuracy, but this would be inconsistent with
// the atomic integration scheme
explicit_1(displacement_,velocity_,dt);
explicit_1(nodalAtomicDisplacement_,nodalAtomicVelocity_,dt);
}
//--------------------------------------------------------
// pre_final_integrate1
// first time integration computations
// before Verlet step 2
//--------------------------------------------------------
void ElasticTimeIntegratorVerletFiltered::pre_final_integrate1(double dt)
{
// Compute MD contribution to FEM equation
DENS_MAT atomicForces;
atcTransfer_->compute_atomic_force(atomicForces,atcTransfer_->get_f());
// apply time filtering to instantaneous atomic force for FE equation
// NOTE would an explicit-implicit time filter be more accurate?
atcTransfer_->restrict_volumetric_quantity(atomicForces,forceFilteringData_);
timeFilter_->apply_post_step2(nodalAtomicForce_,forceFilteringData_,dt);
}
//--------------------------------------------------------
// post_final_integrate1
// second time integration computations
// after Verlet step 2
//--------------------------------------------------------
void ElasticTimeIntegratorVerletFiltered::post_final_integrate1(double dt)
{
DENS_MAT velocityRoc(velocityRhs_.nRows(),velocityRhs_.nCols());
atcTransfer_->apply_inverse_mass_matrix(velocityRhs_,
acceleration_,
VELOCITY);
explicit_1(velocity_,acceleration_,.5*dt);
atcTransfer_->apply_inverse_md_mass_matrix(nodalAtomicForce_,
nodalAtomicAcceleration_,
VELOCITY);
explicit_1(nodalAtomicVelocity_,nodalAtomicAcceleration_,.5*dt);
}
};