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QCaml/examples/ex_localization.ml

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2021-02-03 10:47:34 +01:00
(* ./run_Localisation.native -b basis -x xyz -c charge -o name.mos -i EZFIOdirectory > name.out *)
(*
#.mos contains the localised orbitales
#.out contains the localization convergence and the analysis of the spatial extent of the orbitales
*)
open Qcaml
module Command_line = Common.Command_line
module Util = Common.Util
module Range = Common.Range
module Electrons = Particles.Electrons
open Linear_algebra
let read_qp_mo dirname =
let ic = Unix.open_process_in ("zcat "^dirname^"/mo_basis/mo_coef.gz") in
let check = String.trim (input_line ic) in
assert (check = "2");
let int_list =
input_line ic
|> String.split_on_char ' '
|> List.filter (fun x -> x <> "")
|> List.map int_of_string
in
let n_ao, n_mo =
match int_list with
| [ x ; y ] -> x, y
| _ -> assert false
in
let result =
Matrix.init_cols n_ao n_mo (fun _ _ ->
let s = input_line ic in
Scanf.sscanf s " %f " (fun x -> x)
)
in
let exit_code = Unix.close_process_in ic in
assert (exit_code = Unix.WEXITED 0);
result
let () =
let open Command_line in
begin
set_header_doc (Sys.argv.(0) ^ " - QCaml command");
set_description_doc "Localizes MOs";
set_specs
[ { short='b' ; long="basis" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the basis set"; } ;
{ short='x' ; long="xyz" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
{ short='m' ; long="multiplicity" ; opt=Optional;
arg=With_arg "<int>";
doc="Spin multiplicity (2S+1). Default is singlet"; } ;
{ short='c' ; long="charge" ; opt=Optional;
arg=With_arg "<int>";
doc="Total charge of the molecule. Default is 0"; } ;
{ short='o' ; long="output" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the localized MOs"; } ;
{ short='i' ; long="import" ; opt=Optional;
arg=With_arg "<string>";
doc="Name of the EZFIO directory containing MOs"; } ;
{ short='r' ; long="range" ; opt=Mandatory;
arg=With_arg "<range>";
doc="Range of orbitals to include in localization"; } ;
]
end;
(* II : Hartree-Fock *)
(* 1. Def pour HF *)
let basis_file = Util.of_some @@ Command_line.get "basis" in
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
let charge =
match Command_line.get "charge" with
| Some x -> ( if x.[0] = 'm' then
~- (int_of_string (String.sub x 1 (String.length x - 1)))
else
int_of_string x )
| None -> 0
in
let multiplicity =
match Command_line.get "multiplicity" with
| Some x -> int_of_string x
| None -> 1
in
let range =
Command_line.get "range"
|> Util.of_some
|> Range.of_string
|> Range.to_int_list
in
let ezfio_file = Command_line.get "import" in
let output_filename = Util.of_some @@ Command_line.get "output" in
(* Interpretation:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:1]] *)
let nuclei =
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
in
(* Computation:1 ends here *)
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:2]] *)
let ao_basis =
Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
in
(* Computation:2 ends here *)
let simulation =
Simulation.make ~charge ~multiplicity ~nuclei ao_basis
in
(* 2. Calcul de Hartree-Fock*)
let mo_basis =
match ezfio_file with
| Some ezfio_file ->
let mo_coef = read_qp_mo ezfio_file in
let mo_type = Mo.Basis.Localized "Boys" in
let elec = Simulation.electrons simulation in
let n_mo = Matrix.dim2 mo_coef in
let mo_occupation = Vector.init n_mo (fun i ->
if i <= Electrons.n_beta elec then 2.
else if i <= Electrons.n_alfa elec then 1.
else 0.) in
Mo.Basis.make ~simulation ~mo_type ~mo_occupation ~mo_coef ()
| None -> Mo.Hartree_fock.make simulation
|> Mo.Basis.of_hartree_fock
in
let localization =
Mo.Localization.make ~kind:Mo.Localization.Boys mo_basis range
in
Format.printf "@[%a@]" (Mo.Localization.pp) localization;
let local_mo_basis =
Mo.Localization.to_basis localization
in
let local_mos =
Mo.Basis.mo_coef local_mo_basis
in
let oc = open_out output_filename in
Printf.fprintf oc "[\n";
Matrix.as_vec local_mos
|> Vector.iter (fun x -> Printf.fprintf oc "%20.15e,\n" x);
Printf.fprintf oc "]\n";
close_out oc