Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after.
More...
|
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 |
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logical | save_access |
|
logical | account_occurency |
|
integer | desolv_img_chg |
|
real(kind=8) | epsilon_scale |
|
logical | ignore_exclusion |
|
logical | record_startpos |
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logical | oneway_surf_chg |
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logical | old_rotation |
|
|
type(type_calculation) | t_calc |
| For group type calculation. More...
|
|
integer | total_solutes |
|
integer | total_grids |
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real(kind=4) | win0 |
| For rate claculation. More...
|
|
real(kind=4) | dwin |
|
integer | nwin |
|
integer | nb_contact |
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logical | ibootstrap |
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logical | ifpt |
|
logical | stop_traj |
|
logical | anal_corr |
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real(kind=8) | rmsd_min |
| For complexes and trajectories. More...
|
|
integer | ncmx |
|
integer | ntraj_rec |
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integer | max_array_traj |
|
integer | freq_print |
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integer | mem_traj_frames |
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logical | ionerun |
|
character(128) | fcomplexes |
|
character(128) | ftrajectories |
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logical | format_ascii_complexe |
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logical | format_ascii_trajectory |
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logical | traj_sum_nrj |
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logical | compl_sum_nrj |
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logical | rst_complex |
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integer | merge_step |
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integer | size_thread |
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|
character(128) | rxna12f |
| For reaction criteria. More...
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|
character(128) | et1f |
|
character(128) | et2f |
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real(kind=4) | dind |
|
integer | nnnons |
|
integer | nwrec |
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integer | sdamd |
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|
logical | itimestep |
| For timestep. More...
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logical | height_dependent_dt |
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real(kind=8) | dt1 |
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real(kind=8) | swd1 |
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real(kind=8) | dt2 |
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real(kind=8) | swd2 |
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real(kind=4) | c |
| For geometry. More...
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real(kind=4) | xmin |
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real(kind=4) | xmax |
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real(kind=4) | ymin |
|
real(kind=4) | ymax |
|
real(kind=4) | zmin |
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real(kind=4) | zmax |
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real(kind=4) | start_pos |
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real(kind=4) | min_height |
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logical | escape |
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logical | pbc |
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logical | surf_geom |
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logical | half_sphere |
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integer | type_geom |
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real(kind=8) | epfct |
| global parameter, apply to all solutes More...
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real(kind=8) | edfct |
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real(kind=8) | hdfct |
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real(kind=8) | ljrepfct |
|
real(kind=8) | ljfct |
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real(kind=8) | epfct_oneway_surf |
|
real(kind=4) | ionic |
| analytic group, only HI and DH now, crowder later More...
|
|
real(kind=4) | h_analytic |
|
real(kind=4) | lvol_rcut |
|
real(kind=4) | surface_height |
|
real(kind=4) | surface_prefct |
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logical | ianalytic |
|
logical | debyeh |
|
logical | hydro |
|
logical | dh_imgchg |
|
logical | dh_only |
|
logical | ihom_charged_surf |
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logical | gouy_chapman |
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logical | no_normal_hi |
|
logical | no_image_hi |
|
logical | no_height_hi |
|
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 |
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real(kind=8) | dm |
|
real(kind=8) | dr |
|
real(kind=8) | real_net_charge |
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real(kind=8) | surface_charge_dens |
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real(kind=8) | dh_rad |
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real(kind=8) | rep_rad |
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real(kind=8) | vol_rad |
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integer | nb_solute |
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integer | nb_lenjones |
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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 |
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real(kind=4) | size_cell_x |
|
real(kind=4) | size_cell_y |
|
real(kind=4) | size_cell_z |
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real(kind=4) | shift_rt_x |
|
real(kind=4) | shift_rt_y |
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real(kind=4) | shift_rt_z |
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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...
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|
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 |
|
Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after.
◆ 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 |
real ( kind=4 ) mod_input_parameter::param_list::c |
◆ 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 |
◆ 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 |
◆ 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 |
◆ 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 |
◆ 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 |
◆ 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 |
◆ 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_rad
real ( kind=8 ) mod_input_parameter::param_list::rep_rad |
◆ restart_filename
character ( 128 ) mod_input_parameter::param_list::restart_filename |
◆ 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 |
◆ 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
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 |
◆ 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 |
◆ vol_rad
real ( kind=8 ) mod_input_parameter::param_list::vol_rad |
◆ win0
real ( kind=4 ) mod_input_parameter::param_list::win0 |
◆ 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: