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lammps/lib/atc/InterscaleOperators.h
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InterscaleOperators.h
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// An interscale operator class for sharing definitions of atomic quantities, e.g., temperature
// between different parts of the code
#ifndef INTERSCALE_MANAGER_H
#define INTERSCALE_MANAGER_H
#include "MatrixLibrary.h"
#include "ATC_TypeDefs.h"
#include "ATC_Error.h"
#include "LammpsInterface.h"
#include "PerAtomQuantity.h"
#include "PerPairQuantity.h"
#include "FundamentalAtomicQuantity.h"
#include <vector>
#include <map>
#include <set>
#include <string>
#include <utility>
namespace ATC {
// forward declarations
class ATC_Method;
class SmallMoleculeSet;
/**
* @class InterscaleManager
* @brief Handles definitions for atomistic quantities
*/
//--------------------------------------------------------
//--------------------------------------------------------
// Class InterscaleManager
//--------------------------------------------------------
//--------------------------------------------------------
class InterscaleManager {
public:
// constructor
InterscaleManager(ATC_Method * atc);
// destructor
~InterscaleManager();
/** delete all allocated data */
void clear();
/** delete non-persistent data */
void clear_temporary_data();
/** set lammps data prefix */
void set_lammps_data_prefix();
/** parser/modifier */
bool modify(int narg, char **arg);
/** pre time integration */
void initialize();
// access to per atom quantity objects
/** access to fundamental atomic quantities */
FundamentalAtomQuantity * fundamental_atom_quantity(LammpsInterface::FundamentalAtomQuantity id,
AtomType atomType = INTERNAL);
/** access to double per atom quantities */
PerAtomQuantity<double> * per_atom_quantity(const std::string & tag);
/** access to integer per atom quantities */
PerAtomQuantity<int> * per_atom_int_quantity(const std::string & tag);
/** access to double per atom diagonal matrices */
PerAtomDiagonalMatrix<double> * per_atom_diagonal_matrix(const std::string & tag);
/** access to double per atom sparse matrices */
PerAtomSparseMatrix<double> * per_atom_sparse_matrix(const std::string & tag);
/** access to pair maps */
PairMap * pair_map(const std::string & tag);
// addition of new atom quantities, note provider must allocate but the manager will clean-up
/** addition of a double atomic quantity */
void add_per_atom_quantity(PerAtomQuantity<double> * atomQuantity,
const std::string & tag);
/** addition of an integer atomic quantity */
void add_per_atom_int_quantity(PerAtomQuantity<int> * atomQuantity,
const std::string & tag);
/** addition of a double atomic diagonal matrix */
void add_per_atom_diagonal_matrix(PerAtomDiagonalMatrix<double> * atomQuantity,
const std::string & tag);
/** addition of a double atomic sparse matrix */
void add_per_atom_sparse_matrix(PerAtomSparseMatrix<double> * atomQuantity,
const std::string & tag);
/** addition of an pair map */
void add_pair_map(PairMap * pairMap, const std::string & tag);
/** access to dense matrices */
DENS_MAN * dense_matrix(const std::string & tag);
/** addition of dense matrices */
void add_dense_matrix(DENS_MAN * denseMatrix,
const std::string & tag);
/** access integer dense matrices */
MatrixDependencyManager<DenseMatrix, int> * dense_matrix_int(const std::string & tag);
/** addition of integer dense matrices */
void add_dense_matrix_int(MatrixDependencyManager<DenseMatrix, int> * denseMatrix,
const std::string & tag);
/** access boolean dense matrices */
MatrixDependencyManager<DenseMatrix, bool> * dense_matrix_bool(const std::string & tag);
/** addition of boolean dense matrices */
void add_dense_matrix_bool(MatrixDependencyManager<DenseMatrix, bool> * denseMatrix,
const std::string & tag);
/** access to sparse matrices */
SPAR_MAN * sparse_matrix(const std::string & tag);
/** addition of a sparse matrix */
void add_sparse_matrix(SPAR_MAN * sparseMatrix,
const std::string & tag);
/** access to diagonal matrices */
DIAG_MAN * diagonal_matrix(const std::string & tag);
/** addition of a diagonal matrix */
void add_diagonal_matrix(DIAG_MAN * diagonalMatrix,
const std::string & tag);
/** access to vectors of sparse matrices */
VectorDependencyManager<SPAR_MAT * > * vector_sparse_matrix(const std::string & tag);
/** addition of a vector of sparse matrices */
void add_vector_sparse_matrix(VectorDependencyManager<SPAR_MAT * > * sparseMatrix,
const std::string & tag);
/** access to sets of ints */
SetDependencyManager<int> * set_int(const std::string & tag);
/** addition of a set of ints */
void add_set_int(SetDependencyManager<int> * sparseMatrix,
const std::string & tag);
/** access to molecule sets */
SmallMoleculeSet * small_molecule_set(const std::string & tag);
/** addition of a transfer operator */
void add_small_molecule_set(SmallMoleculeSet * moleculeSet,
const std::string & tag);
/** addition of exchange list object */
void add_to_exchange_list(const std::string & tag);
/** searches through all lists to see if a tag is registered */
DependencyManager * find(const std::string & tag);
/** schedules a quantity for deletion, if it exists */
void remove(const std::string & tag);
/** size communicated quantities initially */
void size_comm_quantities();
/** resets nlocal count of managed atomic quantities which do not perform parallel exchange */
void reset_nlocal();
/** resets specific lammps fundamental quantities data, as needed, to account for times when lammps can change quantities */
void fundamental_force_reset(unsigned quantity);
/** resets all lammps data, as needed, to account for times when lammps can change quantities */
void lammps_force_reset();
/** syncs lammps data to managed objects for parallel communication */
void prepare_exchange();
/** syncs managed objects to lammps data after parallel communication */
void post_exchange();
/** returns how much lammps memory is used in this function */
int memory_usage() const;
/** packs up data for parallel transfer, called from pack_exchange */
int pack_exchange(int i, double *buffer);
/** unpacks data after parallel transfer, called from unpack_exchange */
int unpack_exchange(int i, double *buffer);
/** packs up data for parallel transfer to ghost atoms on other processors */
int pack_comm(int index, double *buf,
int pbc_flag, int *pbc);
/** unpacks data after parallel transfer to ghost atoms on other processors */
int unpack_comm(int index, double *buf);
/** changes size of temperary lammps storage data if transfer is being used */
void grow_arrays(int nmax);
/** rearrange memory of temporary lammps storage data, called from copy_array */
void copy_arrays(int i, int j);
protected:
/** pointer to access ATC methods */
ATC_Method * atc_;
/** flag for if first initialization has happened */
bool initialized_;
/** containers for fundamental atom quantities, set on request */
std::vector<std::vector<FundamentalAtomQuantity* > > fundamentalAtomQuantities_;
/** container for per-atom quantities using dense matrices of doubles */
std::map<std::string, PerAtomQuantity<double> * > perAtomQuantities_;
/** container for integer atom quantities, set by AtC classes */
std::map<std::string, PerAtomQuantity<int> * > perAtomIntQuantities_;
/** container for per-atom quantities using diagonal matrices of doubles */
std::map<std::string, PerAtomDiagonalMatrix<double> * > perAtomDiagonalMatrices_;
/** container for per-atom quantities using sparse matrices of doubles */
std::map<std::string, PerAtomSparseMatrix<double> * > perAtomSparseMatrices_;
/** container for pair maps */
std::map<std::string, PairMap * > pairMaps_;
/** container for dense matrices */
std::map<std::string, DENS_MAN * > denseMatrices_;
/** container for dense matrices for integer quantities */
std::map<std::string, MatrixDependencyManager<DenseMatrix, int> * > denseMatricesInt_;
/** container for dense matrces for boolean quantities */
std::map<std::string, MatrixDependencyManager<DenseMatrix, bool> * > denseMatricesBool_;
/** container for sparse matrices */
std::map<std::string, SPAR_MAN * > sparseMatrices_;
/** container for diagonal matrices */
std::map<std::string, DIAG_MAN * > diagonalMatrices_;
/** container for vectors of vectors of sparse matrices */
std::map<std::string, VectorDependencyManager<SPAR_MAT * > * > vectorSparMat_;
/** container for sets of integer quantities */
std::map<std::string, SetDependencyManager<int> * > setInt_;
/** container for molecule sets */
std::map<std::string, SmallMoleculeSet * > smallMoleculeSets_;
/** container for atomic quantities which must be transfered when atoms cross processors */
std::set<PerAtomQuantity<double> *> exchangeList_;
/** container for atomic quantities which must be transfered to ghost atoms on other processors */
std::vector<PerAtomQuantity<double> *> commList_;
/** container for integer atomic quantities which must be transfered to ghost atoms on other processors */
std::vector<PerAtomQuantity<int> *> commIntList_;
/** container for atomic diagonal matrices which must be transfered to ghost atoms on other processors */
std::vector<PerAtomDiagonalMatrix<double> *> commDmList_;
/** container for atomic sparse matrices which must be transfered to ghost atoms on other processors */
std::vector<PerAtomSparseMatrix<double> *> commSmList_;
/** prefix for labeling associated lammps arrays */
std::string prefix_;
/** order of deletion list of managed quantities */
std::vector<DependencyManager * > deletionList_;
/** creates a reverse sorted depth-first search list for deleting managed quantities */
void create_deletion_list();
/** executes a depth-first search visit on a managed quantity */
int dfs_visit(DependencyManager * quantity, const int index);
/** helper function to access a data entry in a list */
template <typename data>
data * return_quantity(std::map<std::string,data * > & list, const std::string & tag)
{
typename std::map<std::string,data * >::iterator it = list.find(tag);
if (it==list.end()) return NULL;
return it->second;
};
/** helper function to add a data entry to a list */
template <typename data>
void add_quantity(std::map<std::string,data * > & list, data * quantity, const std::string & tag)
{
typename std::map<std::string,data * >::iterator it = list.find(tag);
if (it!=list.end())
throw ATC_Error("Tried to add another Quantity with tag "+tag+" in InterscaleManager::add_quantity");
typename std::template pair<std::string,data * > myPair(tag,quantity);
list.insert(myPair);
};
/** helper function to add a data entry to a list when it requires neighbor communication*/
template <typename data>
void add_comm_quantity(std::map<std::string,data * > & list, std::vector<data * > & commList, data * quantity, const std::string & tag)
{
add_quantity(list,quantity,tag);
// allocate data for parallel communication
quantity->grow_lammps_array(LammpsInterface::instance()->nmax(),prefix_+tag);
if (quantity->atom_type() == PROC_GHOST) {
commList.push_back(quantity);
}
};
/** helper function to fina a data entry in a list */
template <typename data>
data * find_in_list(std::map<std::string,data * > & list, const std::string & tag)
{
typename std::map<std::string,data * >::iterator it = list.find(tag);
if (it!=list.end()) return it->second;
return NULL;
};
/** helper function to force the reset of all data in a list */
template <typename data>
void force_reset_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->force_reset();
};
/** helper function to set the memory type to temporary of a list */
template <typename data>
void set_memory_temporary(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->set_memory_type(TEMPORARY);
};
/** helper function to perform intialization for dfs of a list */
template <typename data>
void dfs_prepare_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->dfsFound_ = false;
}
};
/** helper function to start the dfs visit for list */
template <typename data>
void dfs_visit_loop(std::map<std::string,data * > & list,
int & index)
{
typename std::map<std::string,data* >::iterator it = list.begin();
while (it != list.end()) {
if (!((it->second)->dfsFound_)) index = dfs_visit(it->second,index);
if ((it->second)->memory_type()==TEMPORARY) list.erase(it++);
else ++it;
}
};
// PAQ helper functions
/** helper function to adjust local atom count for all data in a list before exchange, only valid with quantities that do that are aware of atom counts */
template <typename data>
void reset_nlocal_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->reset_nlocal();
}
};
/** helper function to indicate lammps data is stale for all data in a list before exchange, only valid with PAQs */
template <typename data>
void lammps_reset_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->lammps_force_reset();
};
/** helper function to size all data in a list, only valid with comm lists */
template <typename data>
void size_comm_loop(std::vector<data * > & list)
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
(*it)->quantity();
};
/** helper function to pack all data in a list before exchange, only valid with quantities that do work before parallel communication */
template <typename data>
void prepare_exchange_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->prepare_exchange();
}
};
/** helper function to extract all data in a list after exchange, only valid with quantities that do work after parallel communication */
template <typename data>
void post_exchange_loop(std::map<std::string,data * > & list)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->post_exchange();
}
};
/** helper function to determine memory usage of all data in a list, only valid with PAQs */
template <typename data>
void memory_usage_loop(const std::map<std::string,data * > & list, int & usage) const
{
for (typename std::map<std::string,data* >::const_iterator it = list.begin(); it != list.end(); ++it)
usage += (it->second)->memory_usage();
};
/** helper function to pack arrays of all data before exchange in a list, only valid with PAQs */
template <typename data>
void pack_exchange_loop(std::map<std::string,data * > & list, int & index, int i, double *buffer)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
index += (it->second)->pack_exchange(i,&buffer[index]);
}
};
/** helper function to unpack arrays of all data after exchange in a list, only valid with PAQs */
template <typename data>
void unpack_exchange_loop(std::map<std::string,data * > & list, int & index, int i, double *buffer)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
index += (it->second)->unpack_exchange(i,&buffer[index]);
};
/** helper function to pack arrays of all data in a list, only valid with comm lists */
template <typename data>
void pack_comm_loop(std::vector<data * > & list, int & size, int index, double *buf,
int pbc_flag, int *pbc)
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
size += (*it)->pack_comm(index,&buf[size],pbc_flag,pbc);
};
/** helper function to unpack arrays of all data in a list, only valid with comm lists */
template <typename data>
void unpack_comm_loop(std::vector<data * > & list, int & size, int index, double *buf)
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
size += (*it)->unpack_comm(index,&buf[size]);
};
/** helper function to grow arrays of all data in a list, only valid with PAQs */
template <typename data>
void grow_arrays_loop(std::map<std::string,data * > & list, int nmax)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->grow_lammps_array(nmax,prefix_+it->first);
};
/** helper function to copy arrays of all data in a list, only valid with PAQs */
template <typename data>
void copy_arrays_loop(std::map<std::string,data * > & list, int i, int j)
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->copy_lammps_array(i,j);
};
private:
InterscaleManager();
};
}
#endif
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