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lammps/lib/atc/InterscaleOperators.cpp
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InterscaleOperators.cpp
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// ATC transfer headers
#include "InterscaleOperators.h"
#include "PerAtomQuantity.h"
#include "TransferOperator.h"
#include "MoleculeSet.h"
#include "ATC_Method.h"
//#include <typeinfo>
using std::set;
using std::map;
using std::string;
namespace ATC{
//--------------------------------------------------------
//--------------------------------------------------------
// Class InterscaleManager
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
InterscaleManager::InterscaleManager(ATC_Method * atc) :
atc_(atc),
initialized_(false),
prefix_(":fix_atc:")
{
fundamentalAtomQuantities_.resize(NUM_ATOM_TYPES);
for (unsigned int i = 0; i < NUM_ATOM_TYPES; i++) {
fundamentalAtomQuantities_[i].resize(LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES);
for (unsigned int j = 0; j < LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES; j++)
fundamentalAtomQuantities_[i][j] = NULL;
}
}
//----------------------------------------------------
// Set_lammps_data_prefix
//--------------------------------------------------------
void InterscaleManager::set_lammps_data_prefix()
{
prefix_ = (atc_->lammps_interface())->fix_id() + prefix_;
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
InterscaleManager::~InterscaleManager()
{
clear();
}
//--------------------------------------------------------
// clear
//--------------------------------------------------------
void InterscaleManager::clear()
{
// set all memory types to temporary
for (unsigned int i = 0; i < NUM_ATOM_TYPES; i++) {
for (unsigned int j = 0; j < LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES; j++) {
if (fundamentalAtomQuantities_[i][j]) {
fundamentalAtomQuantities_[i][j]->set_memory_type(TEMPORARY);
}
}
}
set_memory_temporary(perAtomQuantities_);
set_memory_temporary(perAtomIntQuantities_);
set_memory_temporary(perAtomDiagonalMatrices_);
set_memory_temporary(perAtomSparseMatrices_);
set_memory_temporary(pairMaps_);
set_memory_temporary(denseMatrices_);
set_memory_temporary(denseMatricesInt_);
set_memory_temporary(denseMatricesBool_);
set_memory_temporary(sparseMatrices_);
set_memory_temporary(diagonalMatrices_);
set_memory_temporary(vectorSparMat_);
set_memory_temporary(setInt_);
set_memory_temporary(smallMoleculeSets_);
// clean up maps and vectors
clear_temporary_data();
}
//--------------------------------------------------------
// clear
//--------------------------------------------------------
void InterscaleManager::clear_temporary_data()
{
deletionList_.clear();
int listSize = fundamentalAtomQuantities_.size()+perAtomQuantities_.size()+perAtomIntQuantities_.size()+perAtomDiagonalMatrices_.size()+perAtomSparseMatrices_.size();
listSize += pairMaps_.size()+denseMatrices_.size()+denseMatricesInt_.size()+denseMatricesBool_.size()+sparseMatrices_.size()+diagonalMatrices_.size()+vectorSparMat_.size()+setInt_.size()+smallMoleculeSets_.size();
deletionList_.reserve(listSize);
create_deletion_list();
for (unsigned int i = 0; i < deletionList_.size(); i++) {
if (deletionList_[i]) {
delete deletionList_[i];
}
}
}
//--------------------------------------------------------
// create_deletion_list
//--------------------------------------------------------
void InterscaleManager::create_deletion_list()
{
// set all quantities to unfound
dfs_prepare_loop(perAtomQuantities_);
dfs_prepare_loop(perAtomIntQuantities_);
dfs_prepare_loop(perAtomDiagonalMatrices_);
dfs_prepare_loop(perAtomSparseMatrices_);
dfs_prepare_loop(perAtomQuantities_);
dfs_prepare_loop(pairMaps_);
dfs_prepare_loop(denseMatrices_);
dfs_prepare_loop(denseMatricesInt_);
dfs_prepare_loop(denseMatricesBool_);
dfs_prepare_loop(sparseMatrices_);
dfs_prepare_loop(diagonalMatrices_);
dfs_prepare_loop(vectorSparMat_);
dfs_prepare_loop(setInt_);
dfs_prepare_loop(smallMoleculeSets_);
// perform dfs, special case for fundamental atom quantities
int index = 0;
for (unsigned int i = 0; i < NUM_ATOM_TYPES; i++) {
for (unsigned int j = 0; j < LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES; j++) {
if (fundamentalAtomQuantities_[i][j]) {
index = dfs_visit(fundamentalAtomQuantities_[i][j],index);
if ((fundamentalAtomQuantities_[i][j])->memory_type()==TEMPORARY) {
fundamentalAtomQuantities_[i][j] = NULL;
}
}
}
}
// dfs for everything else
dfs_visit_loop(perAtomQuantities_,index);
dfs_visit_loop(perAtomIntQuantities_,index);
dfs_visit_loop(perAtomDiagonalMatrices_,index);
dfs_visit_loop(perAtomSparseMatrices_,index);
dfs_visit_loop(pairMaps_,index);
dfs_visit_loop(denseMatrices_,index);
dfs_visit_loop(denseMatricesInt_,index);
dfs_visit_loop(denseMatricesBool_,index);
dfs_visit_loop(sparseMatrices_,index);
dfs_visit_loop(diagonalMatrices_,index);
dfs_visit_loop(vectorSparMat_,index);
dfs_visit_loop(setInt_,index);
dfs_visit_loop(smallMoleculeSets_,index);
}
//--------------------------------------------------------
// dfs_visit
//--------------------------------------------------------
int InterscaleManager::dfs_visit(DependencyManager * quantity, const int index)
{
int myIndex = index;
set<DependencyManager * >::iterator it;
bool isTemporary = (quantity->memory_type()==TEMPORARY);
for (it = (quantity->dependentQuantities_).begin(); it != (quantity->dependentQuantities_).end(); it++) {
// make sure that if quantity isn't persistent, none of it's depedencies are
if ((*it)->memory_type()==PERSISTENT && isTemporary) {
throw ATC_Error("InterscaleManager::dfs_visit - a persistent quantity has a temporary dependency");
}
if (!((*it)->dfsFound_)) {
myIndex = dfs_visit(*it,myIndex);
}
}
quantity->dfsFound_ = true;
if (isTemporary)
deletionList_.push_back(quantity);
return ++myIndex;
}
//--------------------------------------------------------
// initialize
//--------------------------------------------------------
void InterscaleManager::initialize()
{
// force all existing objects to reset
for (unsigned int i = 0; i < NUM_ATOM_TYPES; i++) {
for (unsigned int j = 0; j < LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES; j++) {
if (fundamentalAtomQuantities_[i][j]) {
fundamentalAtomQuantities_[i][j]->force_reset();
}
}
}
force_reset_loop(perAtomQuantities_);
force_reset_loop(perAtomIntQuantities_);
force_reset_loop(perAtomDiagonalMatrices_);
force_reset_loop(perAtomSparseMatrices_);
force_reset_loop(perAtomQuantities_);
force_reset_loop(pairMaps_);
force_reset_loop(denseMatrices_);
force_reset_loop(denseMatricesInt_);
force_reset_loop(denseMatricesBool_);
force_reset_loop(sparseMatrices_);
force_reset_loop(diagonalMatrices_);
force_reset_loop(vectorSparMat_);
force_reset_loop(setInt_);
force_reset_loop(smallMoleculeSets_);
}
// access methods for atomic quantities
//--------------------------------------------------------
// fundamental_atom_quantity
//--------------------------------------------------------
FundamentalAtomQuantity * InterscaleManager::fundamental_atom_quantity(LammpsInterface::FundamentalAtomQuantity id,
AtomType atomType)
{
if (!fundamentalAtomQuantities_[atomType][id]) { // create a new one if it doesn't exist
if (id == LammpsInterface::ATOM_MASS) {
double * mass = LammpsInterface::instance()->atom_mass();
if (mass)
fundamentalAtomQuantities_[atomType][id] = new AtomMass(atc_,atomType);
else
fundamentalAtomQuantities_[atomType][id] = new FundamentalAtomQuantity(atc_,id,atomType);
}
else
fundamentalAtomQuantities_[atomType][id] = new FundamentalAtomQuantity(atc_,id,atomType);
fundamentalAtomQuantities_[atomType][id]->set_memory_type(PERSISTENT);
}
return fundamentalAtomQuantities_[atomType][id];
}
//--------------------------------------------------------
// per_atom_quantity
//--------------------------------------------------------
PerAtomQuantity<double> * InterscaleManager::per_atom_quantity(const string & tag)
{
return return_quantity(perAtomQuantities_,tag);
}
//--------------------------------------------------------
// per_atom_int_quantity
//--------------------------------------------------------
PerAtomQuantity<int> * InterscaleManager::per_atom_int_quantity(const string & tag)
{
return return_quantity(perAtomIntQuantities_,tag);
}
//--------------------------------------------------------
// per_atom_diagonal_matrix
//--------------------------------------------------------
PerAtomDiagonalMatrix<double> * InterscaleManager::per_atom_diagonal_matrix(const string & tag)
{
return return_quantity(perAtomDiagonalMatrices_,tag);
}
//--------------------------------------------------------
// per_atom_sparse_matrix
//--------------------------------------------------------
PerAtomSparseMatrix<double> * InterscaleManager::per_atom_sparse_matrix(const string & tag)
{
return return_quantity(perAtomSparseMatrices_,tag);
}
//--------------------------------------------------------
// pair_map
//--------------------------------------------------------
PairMap * InterscaleManager::pair_map(const string & tag)
{
return return_quantity(pairMaps_,tag);
}
//--------------------------------------------------------
// add_per_atom_quantity
//--------------------------------------------------------
void InterscaleManager::add_per_atom_quantity(PerAtomQuantity<double> * atomQuantity,
const string & tag)
{
add_comm_quantity(perAtomQuantities_,commList_,atomQuantity,tag);
}
//--------------------------------------------------------
// add_per_atom_int_quantity
//--------------------------------------------------------
void InterscaleManager::add_per_atom_int_quantity(PerAtomQuantity<int> * atomQuantity,
const string & tag)
{
add_comm_quantity(perAtomIntQuantities_,commIntList_,atomQuantity,tag);
}
//--------------------------------------------------------
// add_per_atom_diagonal_matrix
//--------------------------------------------------------
void InterscaleManager::add_per_atom_diagonal_matrix(PerAtomDiagonalMatrix<double> * atomQuantity,
const string & tag)
{
add_comm_quantity(perAtomDiagonalMatrices_,commDmList_,atomQuantity,tag);
}
//--------------------------------------------------------
// add_per_atom_sparse_matrix
//--------------------------------------------------------
void InterscaleManager::add_per_atom_sparse_matrix(PerAtomSparseMatrix<double> * atomQuantity,
const string & tag)
{
add_comm_quantity(perAtomSparseMatrices_,commSmList_,atomQuantity,tag);
}
//--------------------------------------------------------
// add_pair_map
//--------------------------------------------------------
void InterscaleManager::add_pair_map(PairMap * pairMap,
const string & tag)
{
add_quantity(pairMaps_,pairMap,tag);
}
//--------------------------------------------------------
// dense_matrix
//--------------------------------------------------------
DENS_MAN * InterscaleManager::dense_matrix(const string & tag)
{
return return_quantity(denseMatrices_,tag);
}
//--------------------------------------------------------
// add_dense_matrix
//--------------------------------------------------------
void InterscaleManager::add_dense_matrix(DENS_MAN * denseMatrix,
const string & tag)
{
add_quantity(denseMatrices_,denseMatrix,tag);
}
//--------------------------------------------------------
// dense_matrix_int
//--------------------------------------------------------
MatrixDependencyManager<DenseMatrix, int> * InterscaleManager::dense_matrix_int(const string & tag)
{
return return_quantity(denseMatricesInt_,tag);
}
//--------------------------------------------------------
// add_dense_matrix_int
//--------------------------------------------------------
void InterscaleManager::add_dense_matrix_int(MatrixDependencyManager<DenseMatrix, int> * denseMatrix,
const string & tag)
{
add_quantity(denseMatricesInt_,denseMatrix,tag);
}
//--------------------------------------------------------
// dense_matrix_bool
//--------------------------------------------------------
MatrixDependencyManager<DenseMatrix, bool> * InterscaleManager::dense_matrix_bool(const string & tag)
{
return return_quantity(denseMatricesBool_,tag);
}
//--------------------------------------------------------
// add_dense_matrix_bool
//--------------------------------------------------------
void InterscaleManager::add_dense_matrix_bool(MatrixDependencyManager<DenseMatrix, bool> * denseMatrix,
const string & tag)
{
add_quantity(denseMatricesBool_,denseMatrix,tag);
}
//--------------------------------------------------------
// sparse_matrix
//--------------------------------------------------------
SPAR_MAN * InterscaleManager::sparse_matrix(const string & tag)
{
return return_quantity(sparseMatrices_,tag);
}
//--------------------------------------------------------
// add_sparse_matrix
//--------------------------------------------------------
void InterscaleManager::add_sparse_matrix(SPAR_MAN * sparseMatrix,
const string & tag)
{
add_quantity(sparseMatrices_,sparseMatrix,tag);
}
//--------------------------------------------------------
// diagonal_matrix
//--------------------------------------------------------
DIAG_MAN * InterscaleManager::diagonal_matrix(const string & tag)
{
return return_quantity(diagonalMatrices_,tag);
}
//--------------------------------------------------------
// add_sparse_matrix
//--------------------------------------------------------
void InterscaleManager::add_diagonal_matrix(DIAG_MAN * diagonalMatrix,
const string & tag)
{
add_quantity(diagonalMatrices_,diagonalMatrix,tag);
}
//--------------------------------------------------------
// vector_spar_mat
//--------------------------------------------------------
VectorDependencyManager<SPAR_MAT * > * InterscaleManager::vector_sparse_matrix(const string & tag)
{
return return_quantity(vectorSparMat_,tag);
}
//--------------------------------------------------------
// add_vector_spar_mat
//--------------------------------------------------------
void InterscaleManager::add_vector_sparse_matrix(VectorDependencyManager<SPAR_MAT * > * vectorSparMat,
const string & tag)
{
add_quantity(vectorSparMat_,vectorSparMat,tag);
}
//--------------------------------------------------------
// set_int
//--------------------------------------------------------
SetDependencyManager<int> * InterscaleManager::set_int(const string & tag)
{
return return_quantity(setInt_,tag);
}
//--------------------------------------------------------
// add_set_int
//--------------------------------------------------------
void InterscaleManager::add_set_int(SetDependencyManager<int> * setInt,
const string & tag)
{
add_quantity(setInt_,setInt,tag);
}
//--------------------------------------------------------
// molecule_set
//--------------------------------------------------------
SmallMoleculeSet * InterscaleManager::small_molecule_set(const string & tag)
{
return return_quantity(smallMoleculeSets_,tag);
}
//--------------------------------------------------------
// add_molecule_set
//--------------------------------------------------------
void InterscaleManager::add_small_molecule_set(SmallMoleculeSet * moleculeSet,
const string & tag)
{
add_quantity(smallMoleculeSets_,moleculeSet,tag);
moleculeSet->initialize();
}
//--------------------------------------------------------
// find_tag
//--------------------------------------------------------
DependencyManager * InterscaleManager::find(const string & tag)
{
// REFACTOR add check for duplicate entries
DependencyManager * quantity = NULL;
quantity = find_in_list(perAtomQuantities_,tag);
if (quantity) return quantity;
quantity = find_in_list(perAtomIntQuantities_,tag);
if (quantity) return quantity;
quantity = find_in_list(perAtomDiagonalMatrices_,tag);
if (quantity) return quantity;
quantity = find_in_list(perAtomSparseMatrices_,tag);
if (quantity) return quantity;
quantity = find_in_list(pairMaps_,tag);
if (quantity) return quantity;
quantity = find_in_list(denseMatrices_,tag);
if (quantity) return quantity;
quantity = find_in_list(denseMatricesInt_,tag);
if (quantity) return quantity;
quantity = find_in_list(denseMatricesBool_,tag);
if (quantity) return quantity;
quantity = find_in_list(sparseMatrices_,tag);
if (quantity) return quantity;
quantity = find_in_list(diagonalMatrices_,tag);
if (quantity) return quantity;
quantity = find_in_list(vectorSparMat_,tag);
if (quantity) return quantity;
quantity = find_in_list(setInt_,tag);
if (quantity) return quantity;
quantity = find_in_list(smallMoleculeSets_,tag);
if (quantity) return quantity;
return NULL;
}
//--------------------------------------------------------
// remove
//--------------------------------------------------------
void InterscaleManager::remove(const string & tag)
{
DependencyManager * toBeDeleted = find(tag);
if (toBeDeleted) {
toBeDeleted->set_memory_type(TEMPORARY);
}
}
//--------------------------------------------------------
// reset_nlocal
//--------------------------------------------------------
void InterscaleManager::reset_nlocal()
{
reset_nlocal_loop(perAtomSparseMatrices_); // this goes in between diagonal matrices and molecule sets above
}
//--------------------------------------------------------
// computes_force_reset
//--------------------------------------------------------
void InterscaleManager::fundamental_force_reset(unsigned quantity)
{
for (unsigned int i = 0; i < NUM_ATOM_TYPES; i++) {
if (fundamentalAtomQuantities_[i][quantity]) {
fundamentalAtomQuantities_[i][quantity]->lammps_force_reset();
}
}
}
//--------------------------------------------------------
// computes_force_reset
//--------------------------------------------------------
void InterscaleManager::lammps_force_reset()
{
for (unsigned int j = 0; j < LammpsInterface::NUM_FUNDAMENTAL_ATOM_QUANTITIES; j++) {
fundamental_force_reset(j);
}
lammps_reset_loop(perAtomQuantities_);
lammps_reset_loop(perAtomIntQuantities_);
lammps_reset_loop(perAtomDiagonalMatrices_);
lammps_reset_loop(perAtomSparseMatrices_);
}
//--------------------------------------------------------
// size_comm_quantities
//--------------------------------------------------------
void InterscaleManager::size_comm_quantities()
{
size_comm_loop(commList_);
size_comm_loop(commIntList_);
size_comm_loop(commDmList_);
size_comm_loop(commSmList_);
}
//--------------------------------------------------------
// prepare_exchange
//--------------------------------------------------------
void InterscaleManager::prepare_exchange()
{
prepare_exchange_loop(perAtomIntQuantities_);
prepare_exchange_loop(perAtomQuantities_);
prepare_exchange_loop(perAtomDiagonalMatrices_);
prepare_exchange_loop(perAtomSparseMatrices_);
}
//--------------------------------------------------------
// post_exchange
//--------------------------------------------------------
void InterscaleManager::post_exchange()
{
post_exchange_loop(perAtomIntQuantities_);
post_exchange_loop(perAtomQuantities_);
post_exchange_loop(perAtomDiagonalMatrices_);
post_exchange_loop(perAtomSparseMatrices_);
post_exchange_loop(smallMoleculeSets_);
post_exchange_loop(pairMaps_);
}
//--------------------------------------------------------
// memory_usage
//--------------------------------------------------------
int InterscaleManager::memory_usage() const
{
int usage = 0;
memory_usage_loop(perAtomQuantities_,usage);
memory_usage_loop(perAtomIntQuantities_,usage);
memory_usage_loop(perAtomDiagonalMatrices_,usage);
memory_usage_loop(perAtomSparseMatrices_,usage);
return usage;
}
//--------------------------------------------------------
// pack_exchange
//--------------------------------------------------------
int InterscaleManager::pack_exchange(int i, double *buffer)
{
int index = 0;
pack_exchange_loop(perAtomQuantities_,index,i,&buffer[index]);
pack_exchange_loop(perAtomIntQuantities_,index,i,&buffer[index]);
pack_exchange_loop(perAtomDiagonalMatrices_,index,i,&buffer[index]);
pack_exchange_loop(perAtomSparseMatrices_,index,i,&buffer[index]);
return index;
}
//--------------------------------------------------------
// unpack_exchange
//--------------------------------------------------------
int InterscaleManager::unpack_exchange(int i, double *buffer)
{
int index = 0;
unpack_exchange_loop(perAtomQuantities_,index,i,&buffer[index]);
unpack_exchange_loop(perAtomIntQuantities_,index,i,&buffer[index]);
unpack_exchange_loop(perAtomDiagonalMatrices_,index,i,&buffer[index]);
unpack_exchange_loop(perAtomSparseMatrices_,index,i,&buffer[index]);
return index;
}
//--------------------------------------------------------
// pack_comm
//--------------------------------------------------------
int InterscaleManager::pack_comm(int index, double *buf,
int pbc_flag, int *pbc)
{
int size = 0;
//pack_comm_loop(commList_,size,index,buf,pbc_flag,pbc);
pack_comm_loop(commIntList_,size,index,buf,pbc_flag,pbc);
//pack_comm_loop(commDmList_,size,index,buf,pbc_flag,pbc);
//pack_comm_loop(commSmList_,size,index,buf,pbc_flag,pbc);
return size;
}
//--------------------------------------------------------
// unpack_comm
//--------------------------------------------------------
int InterscaleManager::unpack_comm(int index, double *buf)
{
int size = 0;
//unpack_comm_loop(commList_,size,index,buf);
unpack_comm_loop(commIntList_,size,index,buf);
//unpack_comm_loop(commDmList_,size,index,buf);
//unpack_comm_loop(commSmList_,size,index,buf);
return size;
}
//--------------------------------------------------------
// grow_array
//--------------------------------------------------------
void InterscaleManager::grow_arrays(int nmax)
{
grow_arrays_loop(perAtomQuantities_,nmax);
grow_arrays_loop(perAtomIntQuantities_,nmax);
grow_arrays_loop(perAtomDiagonalMatrices_,nmax);
grow_arrays_loop(perAtomSparseMatrices_,nmax);
}
//--------------------------------------------------------
// copy_array
//--------------------------------------------------------
void InterscaleManager::copy_arrays(int i, int j)
{
copy_arrays_loop(perAtomQuantities_,i,j);
copy_arrays_loop(perAtomIntQuantities_,i,j);
copy_arrays_loop(perAtomDiagonalMatrices_,i,j);
copy_arrays_loop(perAtomSparseMatrices_,i,j);
}
};
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