Handles all functions related to the CELL. More...

Functions/Subroutines
subroutine, public	cell_create (cell, hmat, periodic, tag)
	allocates and initializes a cell

subroutine, public	init_cell (cell, hmat, periodic)
	Initialise/readjust a simulation cell after hmat has been changed.

recursive subroutine, public	read_cell (cell, cell_ref, use_ref_cell, cell_section, topology_section, check_for_ref, para_env)
	...

subroutine, public	set_cell_param (cell, cell_length, cell_angle, periodic, do_init_cell)
	Sets the cell using the internal parameters (a,b,c) (alpha,beta,gamma) using the convention: a parallel to the x axis, b in the x-y plane and and c univoquely determined; gamma is the angle between a and b; beta is the angle between c and a and alpha is the angle between c and b.

subroutine, public	read_cell_cif (cif_file_name, cell, para_env)
	Reads cell information from CIF file.

subroutine, public	read_cell_extxyz (extxyz_file_name, cell, para_env)
	Reads cell information from comment line of extended xyz file.

subroutine, public	read_cell_pdb (pdb_file_name, cell, para_env)
	Reads cell information from CRYST1 record of PDB file.

subroutine, public	read_cell_cp2k (cp2k_file_name, cell, para_env)
	Reads cell information from cp2k file.

subroutine, public	read_cell_xsc (xsc_file_name, cell, para_env)
	Reads cell information from xsc file.

subroutine, public	write_cell (cell, subsys_section, tag)
	Write the cell parameters to the output unit.

subroutine, public	write_cell_low (cell, unit_str, output_unit, label)
	Write the cell parameters to the output unit.

Detailed Description

Handles all functions related to the CELL.

History: 11.2008 Teodoro Laino [tlaino] - deeply cleaning cell_type from units 10.2014 Moved many routines to cell_types.F.

Author: Matthias KracK (16.01.2002, based on a earlier version of CJM, JGH)

Function/Subroutine Documentation

◆ cell_create()

subroutine, public cell_methods::cell_create	(	type(cell_type), pointer	cell,
		real(kind=dp), dimension(3, 3), intent(in), optional	hmat,
		integer, dimension(3), intent(in), optional	periodic,
		character(len=*), intent(in), optional	tag
	)

allocates and initializes a cell

Parameters

cell	the cell to initialize
hmat	the h matrix that defines the cell
periodic	periodicity of the cell
tag	...

History: 09.2003 created [fawzi]

Author: Fawzi Mohamed

Definition at line 90 of file cell_methods.F.

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◆ init_cell()

subroutine, public cell_methods::init_cell	(	type(cell_type), pointer	cell,
		real(kind=dp), dimension(3, 3), intent(in), optional	hmat,
		integer, dimension(3), intent(in), optional	periodic
	)

Initialise/readjust a simulation cell after hmat has been changed.

Parameters

cell	...
hmat	...
periodic	...

Date: 16.01.2002

Author: Matthias Krack

Version: 1.0

Definition at line 122 of file cell_methods.F.

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◆ read_cell()

recursive subroutine, public cell_methods::read_cell	(	type(cell_type), pointer	cell,
		type(cell_type), pointer	cell_ref,
		logical, intent(inout), optional	use_ref_cell,
		type(section_vals_type), optional, pointer	cell_section,
		type(section_vals_type), optional, pointer	topology_section,
		logical, intent(in), optional	check_for_ref,
		type(mp_para_env_type), pointer	para_env
	)

...

Parameters

cell	...
cell_ref	...
use_ref_cell	...
cell_section	...
topology_section	...
check_for_ref	...
para_env	...

History: 03.2005 created [teo] 03.2026 revamped logic with pdb and extxyz parsers

Author: Teodoro Laino

Definition at line 278 of file cell_methods.F.

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◆ set_cell_param()

subroutine, public cell_methods::set_cell_param	(	type(cell_type), pointer	cell,
		real(kind=dp), dimension(3), intent(in)	cell_length,
		real(kind=dp), dimension(3), intent(in)	cell_angle,
		integer, dimension(3), intent(in), optional	periodic,
		logical, intent(in)	do_init_cell
	)

Sets the cell using the internal parameters (a,b,c) (alpha,beta,gamma) using the convention: a parallel to the x axis, b in the x-y plane and and c univoquely determined; gamma is the angle between a and b; beta is the angle between c and a and alpha is the angle between c and b.

Parameters

cell	...
cell_length	...
cell_angle	...
periodic	...
do_init_cell	...

Date: 03.2008

Author: Teodoro Laino

Definition at line 581 of file cell_methods.F.

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◆ read_cell_cif()

subroutine, public cell_methods::read_cell_cif	(	character(len=*)	cif_file_name,
		type(cell_type), pointer	cell,
		type(mp_para_env_type), pointer	para_env
	)

Reads cell information from CIF file.

Parameters

cif_file_name	...
cell	...
para_env	...

Date: 12.2008

Format Information implemented:: _cell_length_a (_cell.length_a) _cell_length_b (_cell.length_b) _cell_length_c (_cell.length_c) _cell_angle_alpha (_cell.length_alpha) _cell_angle_beta (_cell.length_beta) _cell_angle_gamma (_cell.length_gamma)

Author: Teodoro Laino [tlaino] moved from topology_cif (1/2019 JHU)

Definition at line 668 of file cell_methods.F.

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◆ read_cell_extxyz()

subroutine, public cell_methods::read_cell_extxyz	(	character(len=*)	extxyz_file_name,
		type(cell_type), pointer	cell,
		type(mp_para_env_type), pointer	para_env
	)

Reads cell information from comment line of extended xyz file.

Parameters

extxyz_file_name	...
cell	...
para_env	...

Date: 03.2026

Extended xyz format has comment on the second line in the form as: Lattice="Ax Ay Az Bx By Bz Cx Cy Cz" where Ax, Ay, Az are three Cartesian components of cell vector A, Bx, By, Bz are components of B, Cx, Cy, Cz are components of C, all in the unit of angstrom.

Definition at line 806 of file cell_methods.F.

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◆ read_cell_pdb()

subroutine, public cell_methods::read_cell_pdb	(	character(len=*)	pdb_file_name,
		type(cell_type), pointer	cell,
		type(mp_para_env_type), pointer	para_env
	)

Reads cell information from CRYST1 record of PDB file.

Parameters

pdb_file_name	...
cell	...
para_env	...

Date: 03.2026

CRYST1 record may contain space group and Z value at the end,: but here only the first entries are read:

COLUMNS DATA TYPE FIELD DEFINITION

1 - 6 Record name "CRYST1" 7 - 15 Real(9.3) a a (Angstroms). 16 - 24 Real(9.3) b b (Angstroms). 25 - 33 Real(9.3) c c (Angstroms). 34 - 40 Real(7.2) alpha alpha (degrees). 41 - 47 Real(7.2) beta beta (degrees). 48 - 54 Real(7.2) gamma gamma (degrees).

Definition at line 865 of file cell_methods.F.

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◆ read_cell_cp2k()

subroutine, public cell_methods::read_cell_cp2k	(	character(len=*)	cp2k_file_name,
		type(cell_type), pointer	cell,
		type(mp_para_env_type), pointer	para_env
	)

Reads cell information from cp2k file.

Parameters

cp2k_file_name	...
cell	...
para_env	...

Date: 03.2026

Isolated from former read_cell_from_external_file

Definition at line 913 of file cell_methods.F.

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◆ read_cell_xsc()

subroutine, public cell_methods::read_cell_xsc	(	character(len=*)	xsc_file_name,
		type(cell_type), pointer	cell,
		type(mp_para_env_type), pointer	para_env
	)

Reads cell information from xsc file.

Parameters

xsc_file_name	...
cell	...
para_env	...

Date: 03.2026

Isolated from former read_cell_from_external_file

Definition at line 958 of file cell_methods.F.

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◆ write_cell()

subroutine, public cell_methods::write_cell	(	type(cell_type), pointer	cell,
		type(section_vals_type), pointer	subsys_section,
		character(len=*), intent(in), optional	tag
	)

Write the cell parameters to the output unit.

Parameters

cell	...
subsys_section	...
tag	...

Date: 02.06.2000

History

11.2008 Teodoro Laino [tlaino] - rewrite and enabling user driven units

Author: Matthias Krack

Version: 1.0

Definition at line 1034 of file cell_methods.F.

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◆ write_cell_low()

subroutine, public cell_methods::write_cell_low	(	type(cell_type), pointer	cell,
		character(len=*), intent(in)	unit_str,
		integer, intent(in)	output_unit,
		character(len=*), intent(in), optional	label
	)

Write the cell parameters to the output unit.

Parameters

cell	...
unit_str	...
output_unit	...
label	...

Date: 17.05.2023

History

Extracted from write_cell (17.05.2023, MK)

Version: 1.0

Definition at line 1070 of file cell_methods.F.

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Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ cell_create()

◆ init_cell()

◆ read_cell()

◆ set_cell_param()

◆ read_cell_cif()

◆ read_cell_extxyz()

◆ read_cell_pdb()

COLUMNS DATA TYPE FIELD DEFINITION

◆ read_cell_cp2k()

◆ read_cell_xsc()

◆ write_cell()

◆ write_cell_low()