mod_input_parameter::param_list Type Reference

Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after. More...

Collaboration diagram for mod_input_parameter::param_list:

Public Attributes
character(128)	computation
	assign to the type type_computation: association/dissociation rate or docking or electron transfert More...
real(kind=8)	dseed
	Variables not associated to a group. More...
real(kind=8)	timemax
integer	nrun
integer	novers
integer	napt1
integer	napt2
integer	nrec
integer	save_exclusion
real(kind=4)	probep
real(kind=4)	probew
real(kind=4)	hexcl
real(kind=4)	thresold
real(kind=4)	rboost
logical	save_access
logical	account_occurency
integer	desolv_img_chg
real(kind=8)	epsilon_scale
logical	ignore_exclusion
logical	record_startpos
type(type_calculation)	t_calc
	For group type calculation. More...
integer	total_solutes
integer	total_grids
real(kind=4)	win0
	For rate claculation. More...
real(kind=4)	dwin
integer	nwin
integer	nb_contact
logical	ibootstrap
logical	ifpt
logical	stop_traj
logical	anal_corr
real(kind=8)	rmsd_min
	For complexes and trajectories. More...
integer	ncmx
integer	ntraj_rec
integer	max_array_traj
integer	freq_print
integer	mem_traj_frames
logical	ionerun
character(128)	fcomplexes
character(128)	ftrajectories
logical	format_ascii_complexe
logical	format_ascii_trajectory
logical	traj_sum_nrj
logical	compl_sum_nrj
logical	rst_complex
integer	merge_step
integer	size_thread
character(128)	rxna12f
	For reaction criteria. More...
character(128)	et1f
character(128)	et2f
real(kind=4)	dind
integer	nnnons
integer	nwrec
logical	itimestep
	For timestep. More...
logical	height_dependent_dt
real(kind=8)	dt1
real(kind=8)	swd1
real(kind=8)	dt2
real(kind=8)	swd2
real(kind=4)	c
	For geometry. More...
real(kind=4)	xmin
real(kind=4)	xmax
real(kind=4)	ymin
real(kind=4)	ymax
real(kind=4)	zmin
real(kind=4)	zmax
real(kind=4)	start_pos
real(kind=4)	min_height
logical	escape
logical	pbc
logical	surf_geom
logical	half_sphere
integer	type_geom
real(kind=8)	epfct
	global parameter, apply to all solutes More...
real(kind=8)	edfct
real(kind=8)	hdfct
real(kind=8)	ljrepfct
real(kind=8)	ljfct
real(kind=4)	ionic
	analytic group, only HI and DH now, crowder later More...
real(kind=4)	h_analytic
real(kind=4)	lvol_rcut
logical	ianalytic
logical	debyeh
logical	hydro
logical	ionic_read
character(128)	pdb_filename
	For solute group. More...
character(128)	qef
character(128)	epf
character(128)	edf
character(128)	hdf
character(128)	lj_repf
character(128), dimension(:), allocatable	ljf
character(2), dimension(:), allocatable	atom_type_lj
real(kind=8)	dm
real(kind=8)	dr
real(kind=8)	stoke_rad
real(kind=8)	real_net_charge
integer	nb_solute
integer	nb_lenjones
logical	irot
logical	isurf
logical	iflex
logical	iimg_chg
logical	vert_excl
logical	charge_read
logical	radius_read
real(kind=8)	xcent
real(kind=8)	ycent
real(kind=8)	zcent
integer	total_conf
	For flexibility. More...
integer	initial_conf
logical	nearest_ngb
real(kind=4)	frequence
real(kind=4)	std_freq
character(128)	list_conf_name
character(128)	flex_method
character(128)	restart_filename
	For restart. More...
logical	irestart
integer	fixe_bin_size
	For residence_time. More...
character(128)	enum_str_residtime
real(kind=4)	size_cell_x
real(kind=4)	size_cell_y
real(kind=4)	size_cell_z
real(kind=4)	shift_rt_x
real(kind=4)	shift_rt_y
real(kind=4)	shift_rt_z
integer	nb_cell_x
integer	nb_cell_y
integer	nb_cell_z
integer	format_rt3d
logical	pair_proteins
logical	imetaldesolv
	Special group for MetalDesolvation, distance_to_surface, energy_per_water, radius_patch, radius_water. More...
real(kind=4)	zadw
real(kind=4)	eadw
real(kind=4)	radw
real(kind=4)	aadw
logical	ipmf
	Group for PMF calculations. More...
integer	mentth
integer	mentfi
integer	mentom
integer	mentx
integer	menty
real(kind=8)	pstart
real(kind=8)	pfinish
real(kind=8)	dz

Detailed Description

Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after.

Member Data Documentation

aadw

real(kind=4) mod_input_parameter::param_list::aadw

account_occurency

logical mod_input_parameter::param_list::account_occurency

anal_corr

logical mod_input_parameter::param_list::anal_corr

atom_type_lj

character ( 2 ), dimension(:), allocatable mod_input_parameter::param_list::atom_type_lj

c

real ( kind=4 ) mod_input_parameter::param_list::c

For geometry.

charge_read

logical mod_input_parameter::param_list::charge_read

compl_sum_nrj

logical mod_input_parameter::param_list::compl_sum_nrj

computation

character ( 128 ) mod_input_parameter::param_list::computation

assign to the type type_computation: association/dissociation rate or docking or electron transfert

debyeh

logical mod_input_parameter::param_list::debyeh

desolv_img_chg

integer mod_input_parameter::param_list::desolv_img_chg

dind

real ( kind=4 ) mod_input_parameter::param_list::dind

dm

real ( kind=8 ) mod_input_parameter::param_list::dm

dr

real ( kind=8 ) mod_input_parameter::param_list::dr

dseed

real ( kind=8 ) mod_input_parameter::param_list::dseed

Variables not associated to a group.

dt1

real ( kind=8 ) mod_input_parameter::param_list::dt1

dt2

real ( kind=8 ) mod_input_parameter::param_list::dt2

dwin

real ( kind=4 ) mod_input_parameter::param_list::dwin

dz

real(kind=8) mod_input_parameter::param_list::dz

eadw

real(kind=4) mod_input_parameter::param_list::eadw

edf

character ( 128 ) mod_input_parameter::param_list::edf

edfct

real ( kind=8 ) mod_input_parameter::param_list::edfct

enum_str_residtime

character ( 128 ) mod_input_parameter::param_list::enum_str_residtime

epf

character ( 128 ) mod_input_parameter::param_list::epf

epfct

real ( kind=8 ) mod_input_parameter::param_list::epfct

global parameter, apply to all solutes

epsilon_scale

real ( kind=8 ) mod_input_parameter::param_list::epsilon_scale

escape

logical mod_input_parameter::param_list::escape

et1f

character ( 128 ) mod_input_parameter::param_list::et1f

et2f

character ( 128 ) mod_input_parameter::param_list::et2f

fcomplexes

character ( 128 ) mod_input_parameter::param_list::fcomplexes

fixe_bin_size

integer mod_input_parameter::param_list::fixe_bin_size

For residence_time.

flex_method

character ( 128 ) mod_input_parameter::param_list::flex_method

format_ascii_complexe

logical mod_input_parameter::param_list::format_ascii_complexe

format_ascii_trajectory

logical mod_input_parameter::param_list::format_ascii_trajectory

format_rt3d

integer mod_input_parameter::param_list::format_rt3d

freq_print

integer mod_input_parameter::param_list::freq_print

frequence

real ( kind=4 ) mod_input_parameter::param_list::frequence

ftrajectories

character ( 128 ) mod_input_parameter::param_list::ftrajectories

h_analytic

real (kind=4) mod_input_parameter::param_list::h_analytic

half_sphere

logical mod_input_parameter::param_list::half_sphere

hdf

character ( 128 ) mod_input_parameter::param_list::hdf

hdfct

real ( kind=8 ) mod_input_parameter::param_list::hdfct

height_dependent_dt

logical mod_input_parameter::param_list::height_dependent_dt

hexcl

real ( kind=4 ) mod_input_parameter::param_list::hexcl

hydro

logical mod_input_parameter::param_list::hydro

ianalytic

logical mod_input_parameter::param_list::ianalytic

ibootstrap

logical mod_input_parameter::param_list::ibootstrap

iflex

logical mod_input_parameter::param_list::iflex

ifpt

logical mod_input_parameter::param_list::ifpt

ignore_exclusion

logical mod_input_parameter::param_list::ignore_exclusion

iimg_chg

logical mod_input_parameter::param_list::iimg_chg

imetaldesolv

logical mod_input_parameter::param_list::imetaldesolv

Special group for MetalDesolvation, distance_to_surface, energy_per_water, radius_patch, radius_water.

initial_conf

integer mod_input_parameter::param_list::initial_conf

ionerun

logical mod_input_parameter::param_list::ionerun

ionic

real (kind=4) mod_input_parameter::param_list::ionic

analytic group, only HI and DH now, crowder later

ionic_read

logical mod_input_parameter::param_list::ionic_read

ipmf

logical mod_input_parameter::param_list::ipmf

Group for PMF calculations.

irestart

logical mod_input_parameter::param_list::irestart

irot

logical mod_input_parameter::param_list::irot

isurf

logical mod_input_parameter::param_list::isurf

itimestep

logical mod_input_parameter::param_list::itimestep

For timestep.

list_conf_name

character ( 128 ) mod_input_parameter::param_list::list_conf_name

lj_repf

character ( 128 ) mod_input_parameter::param_list::lj_repf

ljf

character ( 128 ), dimension(:), allocatable mod_input_parameter::param_list::ljf

ljfct

real ( kind=8 ) mod_input_parameter::param_list::ljfct

ljrepfct

real ( kind=8 ) mod_input_parameter::param_list::ljrepfct

lvol_rcut

real (kind=4) mod_input_parameter::param_list::lvol_rcut

max_array_traj

integer mod_input_parameter::param_list::max_array_traj

mem_traj_frames

integer mod_input_parameter::param_list::mem_traj_frames

mentfi

integer mod_input_parameter::param_list::mentfi

mentom

integer mod_input_parameter::param_list::mentom

mentth

integer mod_input_parameter::param_list::mentth

mentx

integer mod_input_parameter::param_list::mentx

menty

integer mod_input_parameter::param_list::menty

merge_step

integer mod_input_parameter::param_list::merge_step

min_height

real ( kind=4 ) mod_input_parameter::param_list::min_height

napt1

integer mod_input_parameter::param_list::napt1

napt2

integer mod_input_parameter::param_list::napt2

nb_cell_x

integer mod_input_parameter::param_list::nb_cell_x

nb_cell_y

integer mod_input_parameter::param_list::nb_cell_y

nb_cell_z

integer mod_input_parameter::param_list::nb_cell_z

nb_contact

integer mod_input_parameter::param_list::nb_contact

nb_lenjones

integer mod_input_parameter::param_list::nb_lenjones

nb_solute

integer mod_input_parameter::param_list::nb_solute

ncmx

integer mod_input_parameter::param_list::ncmx

nearest_ngb

logical mod_input_parameter::param_list::nearest_ngb

nnnons

integer mod_input_parameter::param_list::nnnons

novers

integer mod_input_parameter::param_list::novers

nrec

integer mod_input_parameter::param_list::nrec

nrun

integer mod_input_parameter::param_list::nrun

ntraj_rec

integer mod_input_parameter::param_list::ntraj_rec

nwin

integer mod_input_parameter::param_list::nwin

nwrec

integer mod_input_parameter::param_list::nwrec

pair_proteins

logical mod_input_parameter::param_list::pair_proteins

pbc

logical mod_input_parameter::param_list::pbc

pdb_filename

character ( 128 ) mod_input_parameter::param_list::pdb_filename

For solute group.

pfinish

real(kind=8) mod_input_parameter::param_list::pfinish

probep

real ( kind=4 ) mod_input_parameter::param_list::probep

probew

real ( kind=4 ) mod_input_parameter::param_list::probew

pstart

real(kind=8) mod_input_parameter::param_list::pstart

qef

character ( 128 ) mod_input_parameter::param_list::qef

radius_read

logical mod_input_parameter::param_list::radius_read

radw

real(kind=4) mod_input_parameter::param_list::radw

rboost

real ( kind=4 ) mod_input_parameter::param_list::rboost

real_net_charge

real ( kind=8 ) mod_input_parameter::param_list::real_net_charge

record_startpos

logical mod_input_parameter::param_list::record_startpos

restart_filename

character ( 128 ) mod_input_parameter::param_list::restart_filename

For restart.

rmsd_min

real ( kind=8 ) mod_input_parameter::param_list::rmsd_min

For complexes and trajectories.

rst_complex

logical mod_input_parameter::param_list::rst_complex

rxna12f

character ( 128 ) mod_input_parameter::param_list::rxna12f

For reaction criteria.

save_access

logical mod_input_parameter::param_list::save_access

save_exclusion

integer mod_input_parameter::param_list::save_exclusion

shift_rt_x

real ( kind=4) mod_input_parameter::param_list::shift_rt_x

shift_rt_y

real ( kind=4) mod_input_parameter::param_list::shift_rt_y

shift_rt_z

real ( kind=4) mod_input_parameter::param_list::shift_rt_z

size_cell_x

real ( kind=4) mod_input_parameter::param_list::size_cell_x

size_cell_y

real ( kind=4) mod_input_parameter::param_list::size_cell_y

size_cell_z

real ( kind=4) mod_input_parameter::param_list::size_cell_z

size_thread

integer mod_input_parameter::param_list::size_thread

start_pos

real ( kind=4 ) mod_input_parameter::param_list::start_pos

std_freq

real ( kind=4 ) mod_input_parameter::param_list::std_freq

stoke_rad

real ( kind=8 ) mod_input_parameter::param_list::stoke_rad

stop_traj

logical mod_input_parameter::param_list::stop_traj

surf_geom

logical mod_input_parameter::param_list::surf_geom

swd1

real ( kind=8 ) mod_input_parameter::param_list::swd1

swd2

real ( kind=8 ) mod_input_parameter::param_list::swd2

t_calc

type ( type_calculation ) mod_input_parameter::param_list::t_calc

For group type calculation.

thresold

real ( kind=4 ) mod_input_parameter::param_list::thresold

timemax

real ( kind=8 ) mod_input_parameter::param_list::timemax

total_conf

integer mod_input_parameter::param_list::total_conf

For flexibility.

total_grids

integer mod_input_parameter::param_list::total_grids

total_solutes

integer mod_input_parameter::param_list::total_solutes

traj_sum_nrj

logical mod_input_parameter::param_list::traj_sum_nrj

type_geom

integer mod_input_parameter::param_list::type_geom

vert_excl

logical mod_input_parameter::param_list::vert_excl

win0

real ( kind=4 ) mod_input_parameter::param_list::win0

For rate claculation.

xcent

real ( kind=8 ) mod_input_parameter::param_list::xcent

xmax

real ( kind=4 ) mod_input_parameter::param_list::xmax

xmin

real ( kind=4 ) mod_input_parameter::param_list::xmin

ycent

real ( kind=8 ) mod_input_parameter::param_list::ycent

ymax

real ( kind=4 ) mod_input_parameter::param_list::ymax

ymin

real ( kind=4 ) mod_input_parameter::param_list::ymin

zadw

real(kind=4) mod_input_parameter::param_list::zadw

zcent

real ( kind=8 ) mod_input_parameter::param_list::zcent

zmax

real ( kind=4 ) mod_input_parameter::param_list::zmax

zmin

real ( kind=4 ) mod_input_parameter::param_list::zmin

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The documentation for this type was generated from the following file:

• mod_input_parameter.f90