mimic_main – MiMiC

MiMiC main contains all API calls

Uses

Variables

communicator CENTROID CENTER_OF_MASS CENTER_OF_CHARGE MINIMUM_DISTANCE ATOM_WISE

Variables

Type	Visibility	Attributes		Name		Initial
type(mimic_communicator),	public		::	communicator			communicator handling data collection
integer,	public,	parameter	::	CENTROID	=	1	sort fragments according to distance between centroids
integer,	public,	parameter	::	CENTER_OF_MASS	=	2	sort fragments according to distance between center-of-mass
integer,	public,	parameter	::	CENTER_OF_CHARGE	=	3	sort fragments according to distance between center-of-charge for charged fragments and center-of-mass for neutral fragments
integer,	public,	parameter	::	MINIMUM_DISTANCE	=	4	sort fragments according to minimum distance
integer,	public,	parameter	::	ATOM_WISE	=	5	sort atoms according to distance from quantum fragment centroid

Subroutines

public subroutine mimic_init(comm)

initialize MiMiC

Arguments

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

public subroutine mimic_init_error_handler(process_id, error_handler)

initialize error handling

Arguments

Type	Intent	Optional	Attributes		Name
integer,	intent(in)			::	process_id	process id (preferrably MPI rank)
procedure(handle),		optional	pointer	::	error_handler	optional external error handler

public subroutine mimic_handshake(paths)

MiMiC initialization routine

Arguments

Type	Intent	Optional	Attributes		Name
character(len=*),	intent(in),		dimension(:)	::	paths	paths to client codes

public subroutine mimic_set_num_clients(num)

set the number of clients (needed for non-root processes)

Arguments

Type	Intent	Optional	Attributes		Name
integer,	intent(in)			::	num	number of clients

public subroutine mimic_init_overlaps(overlaps)

initialize overlap maps using the input file data

Arguments

Type	Intent	Optional	Attributes		Name
integer,	intent(in),		dimension(:,:)	::	overlaps	overlaps in the format: code_id : atom_id => code_id : atom_id (e.g. code_one : atom_three => code_two : atom_one)

public subroutine mimic_finalize()

Arguments

None

public subroutine mimic_destroy()

MiMiC destruction routine - deallocates all arrays and shuts down communicator

Arguments

None

public subroutine mimic_request_sizes(sizes, system_data)

wrapper to request sizes of MM parts (number of atoms/species/fragments)

Arguments

Type	Intent	Optional	Attributes		Name
type(sizes_type),	intent(out)			::	sizes	sizes data Todo check if it can be made intent(out)
type(system_type),	intent(out)			::	system_data	atom species of each atom in the system are stored here (-1 for overlapped) Todo check if it can be made intent(out)

public subroutine mimic_request_system_data(sizes, system_data)

return data about atomic species, masses and multipoles in the MM part

Arguments

Type	Intent	Optional	Attributes		Name
type(sizes_type),	intent(inout)			::	sizes	sizes data of the MM part
type(system_type),	intent(inout)			::	system_data	system data Todo intent(out)?

public subroutine mimic_allocate_mm_struct(subsystems, factors, tau, force, num_qm_atoms, total_species, cov_radii, sizes, system_data)

allocates fragments for MM part

Arguments

Type	Intent	Attributes		Name
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	array of subsystems associated with client codes
real(kind=dp),	intent(in),	dimension(:)	::	factors	factors applied to forces contribution (by code) Todo clarify if this is also for energies, potential, etc.
real(kind=dp),	intent(in),	dimension(:,:,:)	::	tau	coordinate matrix of CPMD
real(kind=dp),	intent(in),	dimension(:,:,:)	::	force	force matrix of CPMD
integer,		dimension(:)	::	num_qm_atoms	number of quantum atoms per species
integer,	intent(in)		::	total_species	total number of species
real(kind=dp),	intent(in),	dimension(:)	::	cov_radii	covalent radius of each species
type(sizes_type),	intent(in)		::	sizes	sizes data
type(system_type),	intent(inout)		::	system_data	system data

public subroutine mimic_allocate_qm_struct(quantum_fragment, n_sp_atoms, charges, origin, box, n_points, n_points_r, rho, extf, tau, force)

allocates quantum fragment (at the moment one per simulation)

Arguments

Type	Intent	Attributes		Name
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment	quantum subsystem
integer,	intent(in),	dimension(:)	::	n_sp_atoms	number of atoms per quantum species
real(kind=dp),	intent(in),	dimension(:)	::	charges	ionic charges
real(kind=dp),	intent(in),	dimension(3)	::	origin	point of origin of quantum box
real(kind=dp),	intent(in),	dimension(3,3)	::	box	quantum box vectors
integer,	intent(in),	dimension(3)	::	n_points	number of points in the electronic grid in each direction
integer,	intent(in),	dimension(3)	::	n_points_r	real number of points in the electronic grid in each direction
real(kind=dp),	intent(in),	dimension(:,:,:)	::	rho	electronic density matrix
real(kind=dp),	intent(in),	dimension(:,:,:)	::	extf	external field on the electronic grid
real(kind=dp),	intent(in),	dimension(:,:,:)	::	tau	coordinate matrix of CPMD
real(kind=dp),	intent(in),	dimension(:,:,:)	::	force	force matrix of CPMD

public subroutine mimic_collect_coordinates(subsystems)

wrapper to request coordinates of MM part

Arguments

Type	Intent	Optional	Attributes		Name
type(subsystem_type),			dimension(:)	::	subsystems	array of subsystems associated with client codes

public subroutine mimic_send_coords(subsystems)

Arguments

Type	Intent	Optional	Attributes		Name
type(subsystem_type),			dimension(:)	::	subsystems	array of subsystems associated with client codes

public subroutine mimic_collect_forces(subsystems)

wrapper to request MM forces

Arguments

Type	Intent	Optional	Attributes		Name
type(subsystem_type),	intent(inout),		dimension(:)	::	subsystems	array of subsystems associated with client codes

public subroutine mimic_collect_energies(subsystems, energy)

wrapper to request MM energies

Arguments

Type	Intent	Optional	Attributes		Name
type(subsystem_type),	intent(inout),		dimension(:)	::	subsystems	array of subsystems associated with client codes
real(kind=dp),	intent(out)			::	energy	energy from external programs

public subroutine mimic_sort_fragments(subsystem, quantum_fragment, cutoff_distance, sorting_method)

sort fragments into short- and long-range according to distance criterion

Arguments

Type	Intent		Name
type(subsystem_type),	intent(inout)	::	subsystem	array of subsystems associated with client codes
type(quantum_fragment_type),	intent(in)	::	quantum_fragment	the quantum fragment
real(kind=dp),	intent(in)	::	cutoff_distance	distance cutoff
integer,	intent(in)	::	sorting_method	sorting method (centroid, center_of_mass, center_of_charge, minimum_distance)

public subroutine mimic_compute_tensors(subsystems, quantum_fragment, tensors, tensor_sums, atom_start, atom_end)

compute folded tensors for long-range electrostatics

Arguments

Type	Intent	Attributes		Name
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	array of subsystems associated with client codes
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment	quantum subsystem
real(kind=dp),	intent(out),	dimension(:,:), allocatable	::	tensors	array with tensors
real(kind=dp),	intent(out),	dimension(:,:), allocatable	::	tensor_sums	array with tensor sums
integer,	intent(in),	dimension(:)	::	atom_start	first atom id in the chunk
integer,	intent(in),	dimension(:)	::	atom_end	last atom id in the chunk

public subroutine mimic_compute_energy(subsystems, quantum_fragment, energy, sr_atom_start, sr_atom_end, tensor_sums)

compute interaction energy

Arguments

Type	Intent	Attributes		Name
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	array of subsystems associated with client codes
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment	quantum subsystem
real(kind=dp),	intent(out)		::	energy	interaction energy
integer,	intent(in),	dimension(:)	::	sr_atom_start	index of the first short-range atom for this process
integer,	intent(in),	dimension(:)	::	sr_atom_end	index of the last short-range atom for this process
real(kind=dp),	intent(in),	dimension(:,:), allocatable	::	tensor_sums	Array stroing tensor sums

public subroutine mimic_compute_forces(subsystems, quantum_fragment, x_start, x_end, gr_sr_atom_start, gr_sr_atom_end, gr_lr_atom_start, gr_lr_atom_end, pr_sr_atom_start, pr_sr_atom_end, pr_lr_atom_start, pr_lr_atom_end, root)

compute forces from electrostatic interactions

Arguments

Type	Intent	Attributes		Name
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	array of subsystems associated with client codes
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment	quantum subsystem
integer,	intent(in)		::	x_start	index of the first yz-plane for this process
integer,	intent(in)		::	x_end	index of the last yz-plane for this process
integer,	intent(in),	dimension(:)	::	gr_sr_atom_start	index of the first short-range atom for this process group
integer,	intent(in),	dimension(:)	::	gr_sr_atom_end	index of the last short-range atom for this process group
integer,	intent(in),	dimension(:)	::	gr_lr_atom_start	index of the first long-ange atom for this process group
integer,	intent(in),	dimension(:)	::	gr_lr_atom_end	index of the last long-range atom for this process group
integer,	intent(in),	dimension(:)	::	pr_sr_atom_start	index of the first short-range atom for this process
integer,	intent(in),	dimension(:)	::	pr_sr_atom_end	index of the last short-range atom for this process
integer,	intent(in),	dimension(:)	::	pr_lr_atom_start	index of the first long-ange atom for this process
integer,	intent(in),	dimension(:)	::	pr_lr_atom_end	index of the last long-range atom for this process
logical,	intent(in)		::	root	logical for root process

public subroutine mimic_compute_potential(subsystems, quantum_fragment, x_start, x_end, sr_atom_start, sr_atom_end, tensor_sums)

compute electrostatic potential

Arguments

Type	Intent	Attributes		Name
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	array of subsystems associated with client codes
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment	quantum subsystem
integer,	intent(in)		::	x_start	index of the first yz-plane for this process
integer,	intent(in)		::	x_end	index of the last yz-plane for this process
integer,	intent(in),	dimension(:)	::	sr_atom_start	index of the first short-range atom for this process
integer,	intent(in),	dimension(:)	::	sr_atom_end	index of the last short-range atom for this process
real(kind=dp),	intent(inout),	dimension(:,:), allocatable	::	tensor_sums	Array stroing tensor sums

public subroutine mimic_compute_multipoles(quantum_fragment, order, x_start, x_end)

compute multipoles of the quantum fragment

Arguments

Type	Intent		Name
type(quantum_fragment_type),	intent(inout)	::	quantum_fragment	quantum subsystem
integer,	intent(in)	::	order	order of the multipole expansion
integer,	intent(in)	::	x_start	index of the first yz-plane for this process
integer,	intent(in)	::	x_end	index of the last yz-plane for this process

public subroutine mimic_min_image(box, pivot, subsystems)

apply MIC to the whole system with respect to a pivot point

Arguments

Type	Intent	Attributes		Name
real(kind=dp),	intent(in),	dimension(3,3)	::	box	vectors of the encompassing box
real(kind=dp),	intent(in),	dimension(3)	::	pivot	pivot point
class(subsystem_type),	intent(inout),	dimension(:)	::	subsystems	classical fragments

public subroutine mimic_center_qm(r_diff, subsystem, quantum_fragment)

re-center the quantum box

Arguments

Type	Intent	Attributes		Name
real(kind=dp),	intent(out),	dimension(3)	::	r_diff	resulting translation vector
class(subsystem_type),	intent(in),	dimension(:)	::	subsystem	classical subsystem
class(quantum_fragment_type),	intent(in)		::	quantum_fragment	quantum fragment

public subroutine mimic_count_trcnst(nconn, conn_map, bonds, bonds_pcode)

Routine to count the number of interdependent constraints amoung bonds

Arguments

Type	Intent	Attributes		Name
integer,	intent(out),	dimension(:), allocatable	::	nconn	number of dependencies per bond
integer,	intent(out),	dimension(:, :), allocatable	::	conn_map	dependency map
type(bond_type),	intent(in),	dimension(:,:)	::	bonds	list of bond constraints
integer,	intent(in),	dimension(:)	::	bonds_pcode	number of bonds per code

public subroutine mimic_translate(quantum_fragment, subsystems, shift)

Routine that does translation of the whole system with a given vector

Arguments

Type	Intent	Attributes		Name
type(quantum_fragment_type),	intent(inout)		::	quantum_fragment
type(subsystem_type),	intent(inout),	dimension(:)	::	subsystems
real(kind=dp),		dimension(3)	::	shift	Vector of translation to apply

public subroutine mimic_print_timings()

Routine that prints timings accumulated during the current run of MiMiC

Arguments

None

mimic_main Module

Contents

Variables

Subroutines

Uses

Contents

Variables

Subroutines

Variables

Subroutines

public subroutine mimic_init(comm)

Arguments

public subroutine mimic_init_error_handler(process_id, error_handler)

Arguments

public subroutine mimic_handshake(paths)

Arguments

public subroutine mimic_set_num_clients(num)

Arguments

public subroutine mimic_init_overlaps(overlaps)

Arguments

public subroutine mimic_finalize()

Arguments

public subroutine mimic_destroy()

Arguments

public subroutine mimic_request_sizes(sizes, system_data)

Arguments

Todo

Todo

public subroutine mimic_request_system_data(sizes, system_data)

Arguments

Todo

public subroutine mimic_allocate_mm_struct(subsystems, factors, tau, force, num_qm_atoms, total_species, cov_radii, sizes, system_data)

Arguments

Todo

public subroutine mimic_allocate_qm_struct(quantum_fragment, n_sp_atoms, charges, origin, box, n_points, n_points_r, rho, extf, tau, force)

Arguments

public subroutine mimic_collect_coordinates(subsystems)

Arguments

public subroutine mimic_send_coords(subsystems)

Arguments

public subroutine mimic_collect_forces(subsystems)

Arguments

public subroutine mimic_collect_energies(subsystems, energy)

Arguments

public subroutine mimic_sort_fragments(subsystem, quantum_fragment, cutoff_distance, sorting_method)

Arguments

public subroutine mimic_compute_tensors(subsystems, quantum_fragment, tensors, tensor_sums, atom_start, atom_end)

Arguments

public subroutine mimic_compute_energy(subsystems, quantum_fragment, energy, sr_atom_start, sr_atom_end, tensor_sums)

Arguments

public subroutine mimic_compute_forces(subsystems, quantum_fragment, x_start, x_end, gr_sr_atom_start, gr_sr_atom_end, gr_lr_atom_start, gr_lr_atom_end, pr_sr_atom_start, pr_sr_atom_end, pr_lr_atom_start, pr_lr_atom_end, root)

Arguments

public subroutine mimic_compute_potential(subsystems, quantum_fragment, x_start, x_end, sr_atom_start, sr_atom_end, tensor_sums)

Arguments

public subroutine mimic_compute_multipoles(quantum_fragment, order, x_start, x_end)

Arguments

public subroutine mimic_min_image(box, pivot, subsystems)

Arguments

public subroutine mimic_center_qm(r_diff, subsystem, quantum_fragment)

Arguments

public subroutine mimic_count_trcnst(nconn, conn_map, bonds, bonds_pcode)

Arguments

public subroutine mimic_translate(quantum_fragment, subsystems, shift)

Arguments

public subroutine mimic_print_timings()

Arguments