mimic_data_collect

provides routines for interaction with client codes: collection and distribution of data

Uses

- mimic_precision
- mimic_fragments
- mimic_subsystems
- mimic_types
- mcl_requests
- mcl_fortran

Variables

Type	Visibility	Attributes		Name		Initial
character,	public,	parameter	::	delimiter	=	";"

Derived Types

type, public :: mimic_communicator

communicator type providing routines to handle data interactions

Components

Type	Visibility	Attributes		Name		Initial
integer,	public		::	num_clients			number of client codes
type(maps_type),	public,	dimension(:), allocatable	::	overlap_maps			mapping of overlapping atoms

Type-Bound Procedures

procedure, public :: init
procedure, public :: handshake
procedure, public :: send_command
procedure, public :: init_overlaps
procedure, public :: finalize
procedure, public :: destroy_comm
procedure, public :: get_atom_species
procedure, public :: send_coords
procedure, public :: gather_coords
procedure, public :: gather_forces
procedure, public :: gather_energies
procedure, public :: gather_atom_fragment_count
procedure, public :: gather_atom_fragment_ids
procedure, public :: get_multipole_order
procedure, public :: gather_multipoles
procedure, public :: gather_masses
procedure, public :: gather_bonds
procedure, public :: gather_angles
procedure, public :: gather_int
procedure, public :: send_int
procedure, public :: gather_elements
procedure, public :: gather_atom_count
procedure, public :: gather_fragment_count
procedure, public :: gather_bond_count
procedure, public :: gather_angle_count
procedure, public :: gather_type_count
procedure, public :: issue_force_comp

Subroutines

public subroutine init(this, comm)

initialize communication

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(inout)			::	comm	MPI communicator

public subroutine handshake(this, paths)

identify and connect clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
character(len=*),	intent(in),		dimension(:)	::	paths	array of paths to working folders of clients

public subroutine send_command(this, command, dest)

send a command via the CommLib

Arguments

Type	Intent		Name
class(mimic_communicator),	intent(inout)	::	this
integer,	intent(in)	::	command	integer code of the command
integer,	intent(in)	::	dest	destination

public subroutine init_overlaps(this, overlap_maps)

initialize overlap mapping

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
type(maps_type),			dimension(:)	::	overlap_maps	list of overlap_maps

public subroutine get_atom_species(this, atoms_pcode, species, num_atoms, num_species, na, sp_map)

Get the number of atoms per atomic species per code (with overlap treatment)

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:)	::	atoms_pcode
integer,	intent(inout),	dimension(:,:), allocatable, target	::	species	atom species of each atom in the system (-1 for overlapped)
integer,	intent(out)		::	num_atoms
integer,	intent(out)		::	num_species
integer,	intent(inout),	dimension(:)	::	na
integer,	intent(out),	dimension(:,:), allocatable	::	sp_map

public subroutine finalize(this)

routine sending an exit code to each client

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this

public subroutine destroy_comm(this)

destructor for the commlib

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this

public subroutine get_fragment_count(this, frag_count)

get the number of fragment per each of the client code

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(inout),		dimension(:)	::	frag_count	number of fragments per code, return value

public subroutine gather_bonds(this, bonds, bonds_number)

get the bond constraints data - atom indices and lengths

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
type(bond_type),	intent(out),	dimension(:,:), allocatable	::	bonds	list of constrained bonds in the simulation, return value
integer,	intent(inout),	dimension(:)	::	bonds_number	number of bond constraints in the system. WARNING!!! this routine updates this value

public subroutine gather_angles(this, angles, angle_number)

get the angle constraints data - atom indices and equilibrium values

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
type(angle_type),	intent(out),	dimension(:,:), allocatable	::	angles	list of angle constraints, return value
integer,	intent(in),	dimension(:)	::	angle_number	number of angle constraints

public subroutine gather_elements(this, elements_pcode, elements, species_map)

gather element number associated to MM atom types

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:)	::	elements_pcode	number of elements to expect per code
integer,	intent(out),	dimension(:)	::	elements	element numbers per code
integer,	intent(in),	dimension(:,:)	::	species_map

public subroutine gather_atom_fragment_count(this, fragment_count, fragment_data)

get the number of atoms per each fragment in the system

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:)	::	fragment_count	number of fragments per each code
integer,	intent(inout),	dimension(:, :)	::	fragment_data	number of atoms per fragment per code

public subroutine gather_atom_fragment_ids(this, atoms_pcode, fragment_data, fragment_ids)

get IDs of atoms per each fragment in the system

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:)	::	atoms_pcode	number of fragments per each code
integer,	intent(in),	dimension(:, :)	::	fragment_data	number of atoms per fragment per code
integer,	intent(inout),	dimension(:, :, :)	::	fragment_ids	ids of atoms belonging to a fragment

public subroutine gather_masses(this, masses, species_pcode, species_map)

get the data about atoms in the system

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
real(kind=dp),	intent(out),	dimension(:)	::	masses	mass of each atom in the system
integer,	intent(in),	dimension(:)	::	species_pcode	number of atoms per client code
integer,	intent(in),	dimension(:,:)	::	species_map	mapping of MM species to CPMD species

public subroutine gather_multipoles(this, species, multipoles, atoms_pcode, multipoles_patom)

get the data about atoms in the system

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:,:), target	::	species	atom species of each atom in the system (-1 for overlapped)
real(kind=dp),	intent(inout),	dimension(:,:,:), target	::	multipoles	multipoles of each atom in the system (0 charge for overlapped)
integer,	intent(in),	dimension(:)	::	atoms_pcode	number of atoms per client code
integer,	intent(in),	dimension(:)	::	multipoles_patom	amount of multipoles per atom per code

public subroutine gather_coords(this, frag_code)

gather coordinates of atoms within the system (dealing with overlaps) and store result in the tau matrix through pointers

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
type(subsystem_type),	intent(in),		dimension(:)	::	frag_code	subsystem_type belonging to each code

public subroutine gather_forces(this, frag_code)

gather forces acting on atoms within the system and store result in the forces matrix through pointers

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
type(subsystem_type),	intent(in),		dimension(:)	::	frag_code	subsystem_type belonging to each code

public subroutine gather_energies(this, energy, frag_code)

gather MM energies from clients

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
real(kind=dp),	intent(out)		::	energy	resulting total MM energy
type(subsystem_type),	intent(in),	dimension(:)	::	frag_code	mapping of fragments per code

public subroutine get_multipole_order(this, multipoles_orders)

get the orders of multipoles used in each client code

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	multipoles_orders	multipoles_orders array of orders

public subroutine send_coords(this, subsystems)

send coordinates of atoms to client codes (sends a flattened array)

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
type(subsystem_type),	intent(in),		dimension(:)	::	subsystems	subsystem_type belonging to each code

public subroutine gather_int(this, data, command)

gather integer parameter from client codes

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(out),	dimension(:), target	::	data	Integer data to gather
integer,	intent(in)		::	command	MCL command to execute

public subroutine issue_force_comp(this)

issue a command to compute forces and energies

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this

public subroutine send_int(this, data, command)

gather integer parameter from client codes

Arguments

Type	Intent	Attributes		Name
class(mimic_communicator),	intent(inout)		::	this
integer,	intent(in),	dimension(:), target	::	data	Integer data to gather
integer,	intent(in)		::	command	MCL command to execute

public subroutine gather_atom_count(this, atoms_pcode)

gather atom count from all clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	atoms_pcode	Integer data to gather

public subroutine gather_fragment_count(this, frags_pcode)

gather fragment count from all clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	frags_pcode	Integer data to gather

public subroutine gather_bond_count(this, bonds_pcode)

gather bond count from all clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	bonds_pcode	Integer data to gather

public subroutine gather_angle_count(this, angles_pcode)

gather angle count from all clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	angles_pcode	Integer data to gather

public subroutine gather_type_count(this, types_pcode)

gather atom types count from all clients

Arguments

Type	Intent	Optional	Attributes		Name
class(mimic_communicator),	intent(inout)			::	this
integer,	intent(out),		dimension(:), target	::	types_pcode	Integer data to gather

public subroutine unique_entries(input, output)

search for unique occurences in the array

Arguments

Type	Intent	Optional	Attributes		Name
integer,	intent(in),		dimension(:,:)	::	input	original array
integer,	intent(out),		dimension(:,:), allocatable	::	output	resulting array, containing unique entries from the original one

public subroutine move_alloc_str(source, dest)

Arguments

Type	Intent	Optional	Attributes		Name
character(len=:),	intent(inout),		dimension(:, :), allocatable	::	source
character(len=:),	intent(inout),		dimension(:, :), allocatable	::	dest

mimic_data_collect Module

Contents

Variables

Derived Types

Subroutines

Uses

Contents

Variables

Derived Types

Subroutines

Variables

Derived Types

type, public :: mimic_communicator

Components

Type-Bound Procedures

Subroutines

public subroutine init(this, comm)

Arguments

public subroutine handshake(this, paths)

Arguments

public subroutine send_command(this, command, dest)

Arguments

public subroutine init_overlaps(this, overlap_maps)

Arguments

public subroutine get_atom_species(this, atoms_pcode, species, num_atoms, num_species, na, sp_map)

Arguments

public subroutine finalize(this)

Arguments

public subroutine destroy_comm(this)

Arguments

public subroutine get_fragment_count(this, frag_count)

Arguments

public subroutine gather_bonds(this, bonds, bonds_number)

Arguments

public subroutine gather_angles(this, angles, angle_number)

Arguments

public subroutine gather_elements(this, elements_pcode, elements, species_map)

Arguments

public subroutine gather_atom_fragment_count(this, fragment_count, fragment_data)

Arguments

public subroutine gather_atom_fragment_ids(this, atoms_pcode, fragment_data, fragment_ids)

Arguments

public subroutine gather_masses(this, masses, species_pcode, species_map)

Arguments

public subroutine gather_multipoles(this, species, multipoles, atoms_pcode, multipoles_patom)

Arguments

public subroutine gather_coords(this, frag_code)

Arguments

public subroutine gather_forces(this, frag_code)

Arguments

public subroutine gather_energies(this, energy, frag_code)

Arguments

public subroutine get_multipole_order(this, multipoles_orders)

Arguments

public subroutine send_coords(this, subsystems)

Arguments

public subroutine gather_int(this, data, command)

Arguments

public subroutine issue_force_comp(this)

Arguments

public subroutine send_int(this, data, command)

Arguments

public subroutine gather_atom_count(this, atoms_pcode)

Arguments

public subroutine gather_fragment_count(this, frags_pcode)

Arguments

public subroutine gather_bond_count(this, bonds_pcode)

Arguments

public subroutine gather_angle_count(this, angles_pcode)

Arguments

public subroutine gather_type_count(this, types_pcode)

Arguments

public subroutine unique_entries(input, output)

Arguments

public subroutine move_alloc_str(source, dest)

Arguments