Todo List

Subprogram compute_distance (prot1, prot2, dist)

See if some function should be moved into mod_geometry.

Subprogram compute_distance_test (geom, rtry, prot1_pos, dist)

prot_pos1, always 0 (only call by 2proteins) ?? prot1_pos to delete ?

Subprogram create_filename_flex (input_filename, counter)

Merge this three functions.

Subprogram init_time (param_timestep, geom, dist, rhit, dm30, dtnow, hit)

full check of dthet modifications with sda6

Subprogram initialize_bits (o_record, tab_prot)

to move to mod_record ?

Module mod_analytic

Extend to the case of a surface

Module mod_compute_energy_flex

maybe need to add the versions fast (really necessary ?)

Module mod_compute_image_charge

implement a cutoff for image charge

Subprogram mod_flexibility::list_flex_type::max_size_movable_charge

need to add max_atom_lj or already included ? to check

Subprogram mod_input_parameter::reset_default_solutegrid (this)

add flexibility to reset_default_values ??

Subprogram mod_onecomplexe::one_complexe::sum_square_energy

check if used, in main array now

Subprogram mod_onecomplexe::return_compatible_array (this, array_int, array_real, other_real, size_other_real, bit_integer, bit_energy, opt_sum, nb_to_sum)

add box information

Subprogram mod_protein::protein::box

check if still needed

Subprogram mod_reactioncriteria::allocate_react_criter (this, type_reaction_string, filename, et1f, et2f, nnons, nwrec, sdamd)

check initialization of dind

Subprogram mod_reactioncriteria::make_independent (this, dind)

Need to think about independent pairs in case of flexible/multi-proteins

Subprogram mod_record::fill_listcomplexe (this, basecl, position, orient_x, orient_y, array_energy, array_integer, dist_max, opt_other_real)

Check the logic, tested but could make simpler ( maybe faster )

Subprogram mod_record::get_max_bit_energy (this)

combine with get_nbterms_X, easier to use.

Subprogram mod_record::read_string_complexe (this, basecl, rebuild_sum_square, io_err)

combine with read_string_trajectory if possible, check why io_err !
Check if line is not empty, and really read some data

Type mod_residencetime::residence_time

correct the normalisation of rdf with different types of solutes

check if resid 3d / 2d with sdamm is possible

Subprogram rdf

At present calculation not parallelised

Could add option to skip certain number of trajectory frames

Virial

Subprogram trajectory2dcd

check possible bug, in allocating list_all_filename, when calling with explicit argument -pdb1/2