Utility routines. More...

Data Types
type	alist_t
	Appendable lists of double precision data. More...

type	args_t
	Container for the standard command-line arguments to RMPCDMD. More...

type	enzyme_kinetics_t
	Container for the list of times for enzymatic kinetics. More...

type	histogram_t
	Container for a histogram, e.g. p(x) More...

type	profile_t
	Container for a profile, e.g. v(x) More...

interface	switch

type	timer_list_t

type	timer_pointer_t

type	timer_t

Functions/Subroutines
pure double precision function, dimension(3), public	rel_pos (x, y, L)
	Return x-y distance with minimum image convention. More...

subroutine	profile_init (this, xmin, xmax, n)

subroutine	profile_bin (this, x, value)

subroutine	profile_reset (this)

subroutine	profile_norm (this)

subroutine	histogram_init (this, xmin, xmax, n, n_species)

subroutine	histogram_bin (this, x, s)

subroutine	switch_d2 (p1, p2)

subroutine	switch_i1 (p1, p2)

subroutine	switch_i2 (p1, p2)

character(len=max_path_length) function, public	get_input_filename ()

type(args_t) function, public	get_input_args ()

subroutine	timer_init (this, name, system_name)

subroutine	tic (this)

subroutine	tac (this)

subroutine	timer_list_init (this, n)

subroutine	timer_list_append (this, timer_target)

subroutine	timer_list_write (this, group, total_out)

pure double precision function, dimension(3), public	cross (x1, x2)

subroutine	alist_init (this, block_size)

subroutine	alist_append (this, value)

character(len=:) function, allocatable, public	numbered_string (base_string, index, length)

Variables
integer, parameter	max_path_length = 255

double precision, parameter, public	pi = 4*atan(1.d0)

integer, parameter, public	reac_bit = 1

integer, parameter, public	md_bit = 2

integer, parameter, public	wall_bit = 3

integer, parameter, public	past_md_bit = 4

integer, parameter, public	outbound_bit = 5

integer, parameter, public	catalyzed_bit = 6

integer, parameter, public	enzyme_region_bit = 7

integer, parameter, public	reac_mask = ibset(0, REAC_BIT)

integer, parameter, public	md_mask = ibset(0, MD_BIT)

integer, parameter, public	wall_mask = ibset(0, WALL_BIT)

integer, parameter, public	catalyzed_mask = ibset(0, CATALYZED_BIT)

integer, parameter, public	enzyme_region_mask = ibset(0, ENZYME_REGION_BIT)

Detailed Description

Utility routines.

This module contains routines of general use for RMPCDMD: minimum distance convention routine, histogramming, command-line options processing, timers.

A parameter constant for pi is also defined.

Function/Subroutine Documentation

◆ alist_append()

subroutine common::alist_append	(	class(alist_t), intent(inout)	this,
		double precision, intent(in)	value
	)

private

Definition at line 425 of file common.f90.

◆ alist_init()

subroutine common::alist_init	(	class(alist_t), intent(out)	this,
		integer, intent(in)	block_size
	)

private

Definition at line 415 of file common.f90.

◆ cross()

pure double precision function, dimension(3), public common::cross	(	double precision, dimension(3), intent(in)	x1,
		double precision, dimension(3), intent(in)	x2
	)

Definition at line 405 of file common.f90.

◆ get_input_args()

type(args_t) function, public common::get_input_args ( )

Definition at line 309 of file common.f90.

◆ get_input_filename()

character(len=max_path_length) function, public common::get_input_filename ( )

Definition at line 299 of file common.f90.

◆ histogram_bin()

subroutine common::histogram_bin	(	class(histogram_t), intent(inout)	this,
		double precision, intent(in)	x,
		integer, intent(in), optional	s
	)

private

Definition at line 249 of file common.f90.

◆ histogram_init()

subroutine common::histogram_init	(	class(histogram_t), intent(out)	this,
		double precision, intent(in)	xmin,
		double precision, intent(in)	xmax,
		integer, intent(in)	n,
		integer, intent(in), optional	n_species
	)

private

Definition at line 228 of file common.f90.

◆ numbered_string()

character(len=:) function, allocatable, public common::numbered_string	(	character(len=*), intent(in)	base_string,
		integer, intent(in)	index,
		integer, intent(in)	length
	)

Definition at line 448 of file common.f90.

◆ profile_bin()

subroutine common::profile_bin	(	class(profile_t), intent(inout)	this,
		double precision, intent(in)	x,
		double precision, intent(in)	value
	)

private

Definition at line 197 of file common.f90.

◆ profile_init()

subroutine common::profile_init	(	class(profile_t), intent(out)	this,
		double precision, intent(in)	xmin,
		double precision, intent(in)	xmax,
		integer, intent(in)	n
	)

private

Definition at line 181 of file common.f90.

◆ profile_norm()

subroutine common::profile_norm ( class(profile_t), intent(inout) this )

private

Definition at line 219 of file common.f90.

◆ profile_reset()

subroutine common::profile_reset ( class(profile_t), intent(inout) this )

private

Definition at line 211 of file common.f90.

◆ rel_pos()

pure double precision function, dimension(3), public common::rel_pos	(	double precision, dimension(3), intent(in)	x,
		double precision, dimension(3), intent(in)	y,
		double precision, dimension(3), intent(in)	L
	)

Return x-y distance with minimum image convention.

Definition at line 163 of file common.f90.

◆ switch_d2()

subroutine common::switch_d2	(	double precision, dimension(:,:), intent(inout), pointer	p1,
		double precision, dimension(:,:), intent(inout), pointer	p2
	)

private

Definition at line 269 of file common.f90.

◆ switch_i1()

subroutine common::switch_i1	(	integer, dimension(:), intent(inout), pointer	p1,
		integer, dimension(:), intent(inout), pointer	p2
	)

private

Definition at line 279 of file common.f90.

◆ switch_i2()

subroutine common::switch_i2	(	integer, dimension(:,:), intent(inout), pointer	p1,
		integer, dimension(:,:), intent(inout), pointer	p2
	)

private

Definition at line 289 of file common.f90.

◆ tac()

subroutine common::tac ( class(timer_t), intent(inout) this )

Definition at line 360 of file common.f90.

◆ tic()

subroutine common::tic ( class(timer_t), intent(inout) this )

private

Definition at line 354 of file common.f90.

◆ timer_init()

subroutine common::timer_init	(	class(timer_t), intent(out)	this,
		character(len=*), intent(in)	name,
		character(len=*), intent(in), optional	system_name
	)

private

Definition at line 336 of file common.f90.

◆ timer_list_append()

subroutine common::timer_list_append	(	class(timer_list_t), intent(inout)	this,
		type(timer_t), intent(in), target	timer_target
	)

private

Definition at line 375 of file common.f90.

◆ timer_list_init()

subroutine common::timer_list_init	(	class(timer_list_t), intent(out)	this,
		integer, intent(in)	n
	)

Definition at line 366 of file common.f90.

◆ timer_list_write()

subroutine common::timer_list_write	(	class(timer_list_t), intent(inout)	this,
		integer(hid_t), intent(inout)	group,
		double precision, intent(out), optional	total_out
	)

private

Definition at line 385 of file common.f90.

Variable Documentation

◆ catalyzed_bit

integer, parameter, public common::catalyzed_bit = 6

Definition at line 54 of file common.f90.

◆ catalyzed_mask

integer, parameter, public common::catalyzed_mask = ibset(0, CATALYZED_BIT)

Definition at line 60 of file common.f90.

◆ enzyme_region_bit

integer, parameter, public common::enzyme_region_bit = 7

Definition at line 55 of file common.f90.

◆ enzyme_region_mask

integer, parameter, public common::enzyme_region_mask = ibset(0, ENZYME_REGION_BIT)

Definition at line 61 of file common.f90.

◆ max_path_length

integer, parameter common::max_path_length = 255

private

Definition at line 46 of file common.f90.

◆ md_bit

integer, parameter, public common::md_bit = 2

Definition at line 50 of file common.f90.

◆ md_mask

integer, parameter, public common::md_mask = ibset(0, MD_BIT)

Definition at line 58 of file common.f90.

◆ outbound_bit

integer, parameter, public common::outbound_bit = 5

Definition at line 53 of file common.f90.

◆ past_md_bit

integer, parameter, public common::past_md_bit = 4

Definition at line 52 of file common.f90.

◆ pi

double precision, parameter, public common::pi = 4*atan(1.d0)

Definition at line 47 of file common.f90.

◆ reac_bit

integer, parameter, public common::reac_bit = 1

Definition at line 49 of file common.f90.

◆ reac_mask

integer, parameter, public common::reac_mask = ibset(0, REAC_BIT)

Definition at line 57 of file common.f90.

◆ wall_bit

integer, parameter, public common::wall_bit = 3

Definition at line 51 of file common.f90.

◆ wall_mask

integer, parameter, public common::wall_mask = ibset(0, WALL_BIT)

Definition at line 59 of file common.f90.

Data Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ alist_append()

◆ alist_init()

◆ cross()

◆ get_input_args()

◆ get_input_filename()

◆ histogram_bin()

◆ histogram_init()

◆ numbered_string()

◆ profile_bin()

◆ profile_init()

◆ profile_norm()

◆ profile_reset()

◆ rel_pos()

◆ switch_d2()

◆ switch_i1()

◆ switch_i2()

◆ tac()

◆ tic()

◆ timer_init()

◆ timer_list_append()

◆ timer_list_init()

◆ timer_list_write()

Variable Documentation

◆ catalyzed_bit

◆ catalyzed_mask

◆ enzyme_region_bit

◆ enzyme_region_mask

◆ max_path_length

◆ md_bit

◆ md_mask

◆ outbound_bit

◆ past_md_bit

◆ pi

◆ reac_bit

◆ reac_mask

◆ wall_bit

◆ wall_mask