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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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345
lib/atc/TimeFilter.cpp
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// ATC_Transfer headers
#include "ATC_Transfer.h"
#include "TimeFilter.h"
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterManager
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterManager::TimeFilterManager(ATC_Transfer * atcTransfer) :
atcTransfer_(atcTransfer),
filterType_(NO_FILTER),
filterScale_(0.),
useFilter_(false),
equilibrateFilter_(false),
endEquilibrate_(false),
needReset_(true)
{
// do nothing
}
//--------------------------------------------------------
// modify
// parses input commands
//--------------------------------------------------------
bool TimeFilterManager::modify(int narg, char ** arg)
{
bool foundMatch = false;
// filter scale size
/*! \page man_filter_scale fix_modify AtC transfer filter scale
\section syntax
fix_modify AtC transfer filter scale <scale> \n
- scale (real) = characteristic time scale of the filter \n
\section examples
<TT> fix_modify AtC transfer filter scale 10.0 </TT> \n
\section description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
\section restrictions
only for be used with specific transfers:
thermal, two_temperature
\section related
\ref man_time_filter
\section default
0.
*/
if (strcmp(arg[0],"scale")==0) {
filterScale_ = atof(arg[1]);
if (filterScale_<=0.)
throw ATC_Error(0,"Bad filtering time scale");
foundMatch = true;
}
// time filtering activation switch
/*! \page man_time_filter fix_modify AtC transfer filter
\section syntax
fix_modify AtC transfer filter <on | off | equilibrate> \n
- on | off (keyword) = turns filter on or off\n
- equilibrate = runs dynamics without filtering but initializes filtered quantities
\section examples
<TT> fix_modify atc transfer filter on </TT> \n
\section description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
\section restrictions
only for be used with specific transfers:
thermal, two_temperature
\section related
\ref man_filter_scale \n
\ref man_equilibrium_start
\section default
off
*/
else if (strcmp(arg[0],"on")==0) {
if (filterScale_<=0.)
throw ATC_Error(0,"Filtering time scale not initialized");
useFilter_ = true;
if (!equilibrateFilter_) {
needReset_ = true;
endEquilibrate_ = false;
}
else {
endEquilibrate_ = true;
}
equilibrateFilter_ = false;
foundMatch = true;
}
else if (strcmp(arg[0],"off")==0) {
useFilter_ = false;
equilibrateFilter_ = false;
endEquilibrate_ = false;
needReset_ = true;
foundMatch = true;
}
else if (strcmp(arg[0],"equilibrate")==0) {
if (filterScale_<=0.)
throw ATC_Error(0,"Filtering time scale not initialized");
equilibrateFilter_ = true;
endEquilibrate_ = false;
useFilter_ = false;
needReset_ = true;
foundMatch = true;
}
/** Example command for to set time filter scale:
fix_modify atc transfer filter type step*/
else if (strcmp(arg[0],"type")==0) {
if (strcmp(arg[1],"exponential")==0) {
filterType_ = EXPONENTIAL_FILTER;
}
else if (strcmp(arg[1],"no_filter")==0) {
filterType_ = NO_FILTER;
}
else throw ATC_Error(0,"Not a supported time filter type");
foundMatch = true;
}
return foundMatch;
}
//--------------------------------------------------------
// initialize
// filter set up before a run
//--------------------------------------------------------
void TimeFilterManager::initialize()
{
needReset_ = false;
endEquilibrate_ = false;
}
//--------------------------------------------------------
// construct
// instantiates the filter
//--------------------------------------------------------
// NOTE currently the caller is responsible for deletion
TimeFilter * TimeFilterManager::construct(const FilterIntegrationType intType)
{
if (useFilter_ || equilibrateFilter_) {
if (filterType_ == EXPONENTIAL_FILTER) {
if (intType == IMPLICIT_EXPLICIT) {
return new TimeFilterImplicitExplicit(*this);
}
else if (intType == EXPLICIT_IMPLICIT) {
return new TimeFilterExplicitImplicit(*this);
}
else if (intType == EXPLICIT) {
return new TimeFilterExplicit(*this);
}
else if (intType == IMPLICIT) {
return new TimeFilterImplicit(*this);
}
else if (intType == IMPLICIT_UPDATE) {
return new TimeFilterImplicitUpdate(*this);
}
else {
return new TimeFilterCrankNicolson(*this);
}
}
}
// default to return base class
return new TimeFilter(*this);
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilter
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilter::TimeFilter(TimeFilterManager & timeFilterManager) :
atcTransfer_(timeFilterManager.get_atc_transfer()),
filterScale_(timeFilterManager.get_filter_scale())
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterExponential
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterExponential::TimeFilterExponential(TimeFilterManager & timeFilterManager) :
TimeFilter(timeFilterManager)
{
TimeFilter::filterType_ = TimeFilterManager::EXPONENTIAL_FILTER;
}
//--------------------------------------------------------
// initialize
// resets memory as needed
//--------------------------------------------------------
void TimeFilterExponential::initialize(const MATRIX & target)
{
TimeFilter::initialize(target);
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterCrankNicoslon
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterCrankNicolson::TimeFilterCrankNicolson(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
// initialize
// resets memory as needed
//--------------------------------------------------------
void TimeFilterCrankNicolson::initialize(const MATRIX & target)
{
TimeFilterExponential::initialize(target);
unFilteredQuantityOld_.reset(target.nRows(),target.nCols());
unFilteredQuantityOld_ = target;
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterExplicit
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterExplicit::TimeFilterExplicit(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterImplicit
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterImplicit::TimeFilterImplicit(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterImplicitExplicit
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterImplicitExplicit::TimeFilterImplicitExplicit(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterExplicitImplicit
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterExplicitImplicit::TimeFilterExplicitImplicit(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterImplicitUpdate
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterImplicitUpdate::TimeFilterImplicitUpdate(TimeFilterManager & timeFilterManager) :
TimeFilterExponential(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class TimeFilterStep
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
TimeFilterStep::TimeFilterStep(TimeFilterManager & timeFilterManager) :
TimeFilter(timeFilterManager)
{
// do nothing
}
//--------------------------------------------------------
// initialize
// resets memory as needed
//--------------------------------------------------------
void TimeFilterStep::initialize(const MATRIX & target)
{
TimeFilter::initialize(target);
}
};