File List

Here is a list of all files with brief descriptions:

[detail level 1234]

► test_module
measure_time_force_energy.f90
setup_sda.f90
test_analytic.f90
test_force_energy2.f90
► test_signal
test_signal.f90
► tools
► DT-Grid
► datastructures
ArrayPrs.hpp	Define the array for storing pairs of indices
ArrayPtr.hpp	Define the array for storing pointers into ArrayPrs
ArrayReg.hpp	Define arrays of regular type used in any of the DT-Grid layers
DTGrid1D.hpp	Define the 1D DT-Grid class and group its functions
DTGrid2D.hpp	Define 2D DT-Grid class and group its functions
DTGrid3D.hpp	Main DT-Grid class to create a complete 3D grid structure with a user-defined data type
DTGrid3Dex.hpp	Main DT-Grid class to create a boolean-type 3D grid structure
► tools
compareUHBD.cpp
DTgrd.hpp	Group functions related to create a DT-Grid format file.
dtgrid2UHBD.cpp	Main program to convert a DT-Grid file into a UHBD format file
PDBstructure.cpp	Group functions to read-write PDB files and describe the molecular structures inside
PDBstructure.hpp	Group functions to read-write PDB files and describe the molecular structures inside (Header)
UHBD2dtgrid.cpp	Main program to convert a UHBD grid file into DT-Grid format file
UHBDgrd.hpp	Define a 3D UHBD grid and functions to read-write its format files
► ECM
diagonalisation_ecm.f90
ecm_all.f90	Program ecm_all
ecm_expand.f90	Program ecm_expand
ecm_mainsubroutine.f90
ecm_mkreglev.f90	Program ecm_mkreglev
ecm_mksites.f90	Program ecm_mksites
ecm_regularize.f90	Program ecm_regularize
linear_solver_ecm.f90
linear_solver_ecm_new.f90
mod_parameters_ecm.f90	Define all input parameters used by ECM calculation
utils_ecm.f90
analyze_subroutines.f90
calc_solvaccess.f90
cluster_sdamm.f90
contacts_sdamm.f90
convert_grid.f90
convert_traj_sdamm.f90	Tool to convert SDA 7 many molecules trajectory to old SDAMM fort.55 format
dcc.f90
diffusion_calc.f90
energy_analyze.f90
gen_init_box.f90
genbox_subroutines.f90
get_clusters_per_frame.f90
make_edhdlj_grid.f90
mod_histogram.f90
mod_pdb_type.f90
mod_sda_input_tools.f90
nos2rates.f90
rdf.f90	Compute the radial distribution function
read_record.f90
rot_diffusion.f90
surf_trans_diffusion.f90
trajectory2dcd.f90
trans_diffusion.f90	Compute the autocorrelation function and translational diffusion coefficients
utils_diffusion.f90
alltimer.f90
bd_move.f90	Implement functions for BD translation and rotation, boost
change_conformation.f90	Functions used for the change of conformation
check_exclusion.f90	Check if protein 2 overlaps with protein 1
check_reaction_pair.f90
compute_distance.f90
dtgrid_wrapper.cpp	Wrapper for linking C++ and Fortran functions
eschk.f90
footer.html
genbox_subroutines.f90
header.html
init_time.f90
main.f90
MainLoop_sda_2proteins.f90
MainLoop_sda_2proteins_omp.f90
MainLoop_sda_energy.f90
MainLoop_sda_pmf.f90
MainLoop_sdamm.f90
make_bd_move_2prot.f90
make_bd_move_2prot_timer_excl.f90	Same as make_bd_move_2prot, but use timer_excl as input ( could be optional )
make_bd_move_sdamm.f90
make_exclusion_grid.f90	Compute the exclusion grid, only for sda_2proteins and solute 1
maths.f
maths_thread_safe.f90	Implement thread-safe mathematical subroutines which deals with RGN
mod_analytic.f90
mod_array_protein.f90	Define an array where all proteins are stored
mod_compute_analytic_2proteins.f90
mod_compute_analytic_sdamm.f90
mod_compute_crowder_sdamm.f90
mod_compute_energy.f90
mod_compute_energy_flex.f90
mod_compute_energy_sdamm.f90
mod_compute_force.f90
mod_compute_force_sdamm.f90
mod_compute_image_charge.f90
mod_compute_metaldesolv.f90
mod_compute_pmf.f90
mod_crowder.f90
mod_dqagi.f90
mod_exclusion_grid.f90	Define the exclusion grid
mod_flexibility.f90
mod_force_energy.f90
mod_geometry.f90	Define geometric properties of the simulation box
mod_gouy_chapman.f90
mod_grid.f90
mod_gridtype.f90	Enumeration and function of the different grids and charges and array used in sda
mod_hydrodynamics.f90
mod_info_printing.f90
mod_init_position.f90
mod_input_parameter.f90
mod_interface.f90	Define the equivalent of overloading functions. Only read_value() at this point
mod_ljgrid.f90
mod_onecomplexe.f90
mod_par_zig.f90	Thread-safe random generator with the ziggurat method
mod_protein.f90
mod_rate_calculation.f90
mod_rate_constant_calculation.f90
mod_rate_constant_calculation_quadpack.f90
mod_ReactionCriteria.f90
mod_record.f90
mod_ResidenceTime.f90
mod_sda_new_common.f90
mod_set_parameters.f90
mod_setofgrid.f90
mod_type_calculation.f90	Define the type of the calculation : sda_2proteins, sda_energy, sdamm,..
mod_van.f90
prepare_atom_protein.f90
prepare_grid.f90
randgen.f	Random generator number
read_eff_charges.f90
read_group_file.f90
read_input_file.f90
read_pdb.f90
restart.f90
solva.f90
solva_naccess.f90
solva_SDA.f90
utils.f90