Analytical expressions, store energy and force in precomputed array.
More...
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type | analytic |
| Define tyoe analytic interactions (Debye-Huckel/crowders) More...
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subroutine | fill_array_dh (this, list_dh_radius) |
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subroutine | set_zeroes (this, cutoff) |
| Specific to Debye-Huckel set zero for at distance where the grid is available Allow to call normal electrostatic and debye-huckel without taking care (hopefully) More...
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subroutine | allocate_analytic (this) |
| Allocate the object with default values, arrays filled by param_force_energy:init_analytic when all data (cutoff,..) are known. More...
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subroutine | deallocate_analytic (this) |
| Deallocate all analytic arrays.
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subroutine | set_analytic_params (this, h, max_size, epfct, dh_radius, vol_radius, rep_radius, surface_charge_dens, surf_prefct, gouy_chapman) |
| fill the arrays, here need to setup dimension More...
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subroutine | set_dh_params (this, opt_ionic) |
| Initialize debye-huckel parameters. More...
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real(kind=8) function | get_energy_analytic (this, bin, type_nb) |
| Return precomputed energy values. More...
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real(kind=8) function | get_force_analytic (this, bin, type_nb) |
| Return precomputed force values. More...
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real(kind=8) function | get_force_analytic_hom_charged_surf (this, bin, type_nb) |
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subroutine | print_analytic (this) |
| Print values of array force and energy.
Called by info_analytic. More...
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subroutine | info_analytic (this, opt_print) |
| Print info about analytical grids. More...
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subroutine | print_analytic_external (this) |
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subroutine | print_analytic_external_hom_charged_surf (this) |
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Analytical expressions, store energy and force in precomputed array.
- Todo:
- Extend to the case of a surface
◆ allocate_analytic()
subroutine mod_analytic::allocate_analytic |
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type ( analytic ) |
this | ) |
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Allocate the object with default values, arrays filled by param_force_energy:init_analytic when all data (cutoff,..) are known.
- Parameters
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◆ deallocate_analytic()
subroutine mod_analytic::deallocate_analytic |
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type ( analytic ) |
this | ) |
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Deallocate all analytic arrays.
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- Parameters
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◆ fill_array_dh()
subroutine mod_analytic::fill_array_dh |
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type ( analytic ) |
this, |
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real (kind=8), dimension(:) |
list_dh_radius |
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◆ get_energy_analytic()
real(kind=8) function mod_analytic::get_energy_analytic |
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type ( analytic ) |
this, |
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integer |
bin, |
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integer |
type_nb |
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Return precomputed energy values.
- Parameters
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this | : instance of mod_analytic |
bin | : integer bin number |
type_nb | : integer number corresponding to the type of protein |
◆ get_force_analytic()
real(kind=8) function mod_analytic::get_force_analytic |
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type ( analytic ) |
this, |
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integer |
bin, |
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integer |
type_nb |
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) |
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Return precomputed force values.
- Parameters
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this | : instance of mod_analytic |
bin | : integer bin number |
type_nb | : integer number corresponding to the type of protein |
◆ get_force_analytic_hom_charged_surf()
real(kind=8) function mod_analytic::get_force_analytic_hom_charged_surf |
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type ( analytic ) |
this, |
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integer |
bin, |
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integer |
type_nb |
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) |
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◆ info_analytic()
subroutine mod_analytic::info_analytic |
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type ( analytic ) |
this, |
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logical, optional |
opt_print |
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Print info about analytical grids.
Should apply to all, not only D-H
- Parameters
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this | : instance of mod_analytic |
opt_print | : optional, print full arrays |
◆ print_analytic()
subroutine mod_analytic::print_analytic |
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type ( analytic ) |
this | ) |
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Print values of array force and energy.
Called by info_analytic.
- Parameters
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◆ print_analytic_external()
subroutine mod_analytic::print_analytic_external |
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type ( analytic ) |
this | ) |
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◆ print_analytic_external_hom_charged_surf()
subroutine mod_analytic::print_analytic_external_hom_charged_surf |
( |
type ( analytic ) |
this | ) |
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◆ set_analytic_params()
subroutine mod_analytic::set_analytic_params |
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type ( analytic ) |
this, |
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real(kind=8), intent(in) |
h, |
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real(kind=4) |
max_size, |
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real(kind=8), intent(in) |
epfct, |
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real(kind=8), intent(in) |
dh_radius, |
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real(kind=8), intent(in) |
vol_radius, |
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real(kind=8), intent(in) |
rep_radius, |
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real(kind=8), intent(in) |
surface_charge_dens, |
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real(kind=8), intent(in) |
surf_prefct, |
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logical |
gouy_chapman |
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) |
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fill the arrays, here need to setup dimension
- Parameters
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this | : instance of mod_analytic |
h | : bin size of the precomputed arrays |
max_size | : extensiom of DH, half the box for sdamm, c-surface for sda_2proteins |
epfct | : scaling factor for DH electrostatics. Like grid calcs, usually 0.5 to stop double counting |
dh_radius | : radius of this solute used for dh cavity |
vol_radius | : radius of this solute used for volume occupancy |
rep_radius | : radius of this solute used for repulsive crowder interactions |
surface_charge_dens | : charge density for DH charged surface routine. |
◆ set_dh_params()
subroutine mod_analytic::set_dh_params |
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type ( analytic ) |
this, |
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real(kind=4), optional |
opt_ionic |
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) |
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Initialize debye-huckel parameters.
- Parameters
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this | : instance of mod_analytic |
opt_ionic | : optional, if present set the ionic strength |
◆ set_zeroes()
subroutine mod_analytic::set_zeroes |
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type ( analytic ) |
this, |
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real ( kind=4 ) |
cutoff |
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) |
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Specific to Debye-Huckel set zero for at distance where the grid is available Allow to call normal electrostatic and debye-huckel without taking care (hopefully)
- Parameters
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this | : instance of mod_analytic |
cutoff | : max distance to which the value is set to 0 |