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	cell_finalize_canonical_input (cell, hmat_input, hmat_canonical)
	Store the transform between the user input cell and the canonical 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_xyz (xyz_file_name, cell, para_env)
	Reads xyz file and pass comments on the second line to get cell information.

subroutine, public	read_xyz_comment (line, cell, has_cell, step, time, ener)
	Reads comment line of XYZ files to get cell, step, time and energy info.

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 93 of file cell_methods.F.

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◆ cell_finalize_canonical_input()

subroutine, public cell_methods::cell_finalize_canonical_input	(	type(cell_type), pointer	cell,
		real(kind=dp), dimension(3, 3), intent(in)	hmat_input,
		real(kind=dp), dimension(3, 3), intent(in)	hmat_canonical
	)

Store the transform between the user input cell and the canonical cell.

Parameters

cell	...
hmat_input	...
hmat_canonical	...

Definition at line 126 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 183 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 339 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 667 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 754 of file cell_methods.F.

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◆ read_cell_xyz()

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

Reads xyz file and pass comments on the second line to get cell information.

Parameters

xyz_file_name	...
cell	...
para_env	...

History: 03.2026 - Created as read_cell_extxyz with extended XYZ parser 06.2026 - Refactored the parser to allow for reftraj use

Author: HE Zilong

Definition at line 890 of file cell_methods.F.

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◆ read_xyz_comment()

subroutine, public cell_methods::read_xyz_comment	(	character(len=*), intent(in)	line,
		type(cell_type), intent(inout), pointer	cell,
		logical, intent(out)	has_cell,
		integer, intent(out), optional	step,
		real(kind=dp), intent(out), optional	time,
		real(kind=dp), intent(out), optional	ener
	)

Reads comment line of XYZ files to get cell, step, time and energy info.

Parameters

line	the single comment line of an XYZ file
cell	the pointer to which cell is written
has_cell	a flag for presence of cell information
step	an integer value for step number, if requested; HUGE(0) if not available
time	a real value for time, if requested; HUGE(0.0_dp) if not available
ener	a real value for energy, if requested; HUGE(0.0_dp) if not available

Intended for both the FORCE_EVAL/SUBSYS/CELL and MOTION/MD/REFTRAJ.: At minimum, should work with outputs from write_trajectory() in src/motion_utils.F, around line 879 of src/motion/dumpdcd.F and write_final_structure() in src/particle_methods.F (for cell only). Recognized formats (case insensitive, no hard restriction on data width): (1) Extended xyz format, whose comment on the second line contains fields: 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, and must occur; Step=S where S is the integer step number; Time=T where T is the time in femtoseconds; Energy=E where E is the energy. No whitespace around the = sign is present; the whitespace is used as the delimiter between fields; apart from lattice= at the front, other fields are optional and do not have a fixed order. (2) dumpdcd format, whose comment on the second line contains fields: a = A, b = B, c = C, alpha = ALPHA, beta = BETA, gamma = GAMMA where A, B, C are three lengths of cell vectors in angstrom, ALPHA, BETA, GAMMA are three angles between cell vectors in degrees; i = I, where I is the integer step number; time = T, where T is the time in femtoseconds; E = ENER, where ENER is the energy. There is one whitespace before and after each equal sign; the comma is used as the delimiter between fields; the cell information is optional.

History 06.2026 - Created by combining the extxyz parser from former read_cell_extxyz and the parser for reftraj in src/motion/integrator.F

Author: HE Zilong

Definition at line 965 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 1173 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 1226 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 1271 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 1347 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 1383 of file cell_methods.F.

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Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ cell_create()

◆ cell_finalize_canonical_input()

◆ init_cell()

◆ read_cell()

◆ set_cell_param()

◆ read_cell_cif()

◆ read_cell_xyz()

◆ read_xyz_comment()

◆ read_cell_pdb()

COLUMNS DATA TYPE FIELD DEFINITION

◆ read_cell_cp2k()

◆ read_cell_xsc()

◆ write_cell()

◆ write_cell_low()