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


real(kind=8)	dseed
	Variables not associated to a group.

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

logical	oneway_surf_chg

logical	old_rotation


type(type_calculation)	t_calc
	For group type calculation.

integer	total_solutes

integer	total_grids

real(kind=4)	win0
	For rate claculation.

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.

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.

character(128)	et1f

character(128)	et2f

real(kind=4)	dind

integer	nnnons

integer	nwrec

integer	sdamd


logical	itimestep
	For timestep.

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.

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

real(kind=8)	edfct

real(kind=8)	hdfct

real(kind=8)	ljrepfct

real(kind=8)	ljfct

real(kind=8)	epfct_oneway_surf

real(kind=4)	ionic
	analytic group, only HI and DH now, crowder later

real(kind=4)	h_analytic

real(kind=4)	lvol_rcut

real(kind=4)	surface_height

real(kind=4)	surface_prefct

real(kind=4)	rep_bfct

logical	ianalytic

logical	debyeh

logical	hydro

logical	dh_imgchg

logical	dh_only

logical	ihom_charged_surf

logical	gouy_chapman

logical	no_normal_hi

logical	no_image_hi

logical	no_height_hi

logical	ionic_read

character(128)	pdb_filename
	For solute group.

character(128)	qef

character(128)	epf

character(128)	edf

character(128)	hdf

character(128)	lj_repf

character(128)	sasa_filename

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

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

real(kind=8)	dm

real(kind=8)	dr

real(kind=8)	real_net_charge

real(kind=8)	surface_charge_dens

real(kind=8)	dh_rad

real(kind=8)	rep_rad

real(kind=8)	vol_rad

integer	nb_solute

integer	nb_lenjones

logical	irot

logical	isurf

logical	iflex

logical	iimg_chg

logical	vert_excl

logical	charge_read

logical	radius_read

logical	rep_rad_read

logical	dh_rad_read

real(kind=8)	xcent

real(kind=8)	ycent

real(kind=8)	zcent

logical	ishape_crowd

logical	isphere_crowd


integer	total_conf
	For flexibility.

integer	initial_conf

logical	nearest_ngb

real(kind=4)	frequence

real(kind=4)	std_freq

character(128)	list_conf_name

character(128)	flex_method

logical	internal
	For internal energy calculation.

logical	imarkov

real(kind=8)	conf_weight

character(128)	transition_matrix_file

character(128)	restart_filename
	For restart.

logical	irestart


integer	fixe_bin_size
	For residence_time.

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.

real(kind=4)	zadw

real(kind=4)	eadw

real(kind=4)	radw

real(kind=4)	aadw


logical	ipmf
	Group for PMF calculations.

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

◆ conf_weight

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

◆ debyeh

logical mod_input_parameter::param_list::debyeh

◆ desolv_img_chg

integer mod_input_parameter::param_list::desolv_img_chg

◆ dh_imgchg

logical mod_input_parameter::param_list::dh_imgchg

◆ dh_only

logical mod_input_parameter::param_list::dh_only

◆ dh_rad

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

◆ dh_rad_read

logical mod_input_parameter::param_list::dh_rad_read

◆ 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

◆ epfct_oneway_surf

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

◆ 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

◆ gouy_chapman

logical mod_input_parameter::param_list::gouy_chapman

◆ 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

◆ ihom_charged_surf

logical mod_input_parameter::param_list::ihom_charged_surf

◆ iimg_chg

logical mod_input_parameter::param_list::iimg_chg

◆ imarkov

logical mod_input_parameter::param_list::imarkov

◆ 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

◆ internal

logical mod_input_parameter::param_list::internal

For internal energy calculation.

◆ 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

◆ ishape_crowd

logical mod_input_parameter::param_list::ishape_crowd

◆ isphere_crowd

logical mod_input_parameter::param_list::isphere_crowd

◆ 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

◆ no_height_hi

logical mod_input_parameter::param_list::no_height_hi

◆ no_image_hi

logical mod_input_parameter::param_list::no_image_hi

◆ no_normal_hi

logical mod_input_parameter::param_list::no_normal_hi

◆ 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

◆ old_rotation

logical mod_input_parameter::param_list::old_rotation

◆ oneway_surf_chg

logical mod_input_parameter::param_list::oneway_surf_chg

◆ 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

◆ rep_bfct

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

◆ rep_rad

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

◆ rep_rad_read

logical mod_input_parameter::param_list::rep_rad_read

◆ 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.

◆ sasa_filename

character ( 128 ) mod_input_parameter::param_list::sasa_filename

◆ save_access

logical mod_input_parameter::param_list::save_access

◆ save_exclusion

integer mod_input_parameter::param_list::save_exclusion

◆ sdamd

integer mod_input_parameter::param_list::sdamd

◆ 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

◆ stop_traj

logical mod_input_parameter::param_list::stop_traj

◆ surf_geom

logical mod_input_parameter::param_list::surf_geom

◆ surface_charge_dens

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

◆ surface_height

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

◆ surface_prefct

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

◆ 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

◆ transition_matrix_file

character ( 128 ) mod_input_parameter::param_list::transition_matrix_file

◆ type_geom

integer mod_input_parameter::param_list::type_geom

◆ vert_excl

logical mod_input_parameter::param_list::vert_excl

◆ vol_rad

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

◆ 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

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

mod_input_parameter.f90

Public Attributes