mirror of
https://github.com/pfloos/quack
synced 2024-11-03 20:53:53 +01:00
134 lines
4.0 KiB
OCaml
134 lines
4.0 KiB
OCaml
let quack_dir =
|
|
try Sys.getenv "QUACK_ROOT" with
|
|
Not_found -> "."
|
|
|
|
let quack_basis_filename = quack_dir ^ "/input/basis"
|
|
let quack_molecule_filename = quack_dir ^ "/input/molecule"
|
|
|
|
module Command_line = Qcaml.Common.Command_line
|
|
module Util = Qcaml.Common.Util
|
|
|
|
let () =
|
|
let open Command_line in
|
|
begin
|
|
set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
|
|
set_description_doc "Prepares the input data for QuAcK.
|
|
Writes $QUACK_ROOT/input/basis and $QUACK_ROOT/input/molecule.
|
|
If $QUACK_ROOT is not set, $QUACK_ROOT is replaces by the current
|
|
directory.";
|
|
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. Specify negative charges with 'm' instead of the minus sign, for example m1 instead of -1. Default is 0"; } ;
|
|
|
|
{ short='f' ; long="frozen-core" ; opt=Optional;
|
|
arg=Without_arg ;
|
|
doc="Freeze core MOs. Default is false"; } ;
|
|
|
|
{ short='r' ; long="rydberg" ; opt=Optional;
|
|
arg=With_arg "<int>" ;
|
|
doc="Number of Rydberg electrons. Default is 0"; } ;
|
|
]
|
|
end;
|
|
|
|
(* Handle options *)
|
|
let basis_file = Util.of_some @@ Command_line.get "basis" in
|
|
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
|
|
let frozen_core = Command_line.get_bool "frozen-core" 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 rydberg =
|
|
match Command_line.get "rydberg" with
|
|
| Some x -> int_of_string x
|
|
| None -> 0
|
|
in
|
|
|
|
|
|
let nuclei =
|
|
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
|
|
in
|
|
|
|
let electrons =
|
|
Qcaml.Particles.Electrons.of_atoms ~multiplicity ~charge nuclei
|
|
in
|
|
|
|
let basis =
|
|
Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
|
|
in
|
|
|
|
|
|
let print_basis nuclei basis =
|
|
let oc = open_out quack_basis_filename in
|
|
let ocf = Format.formatter_of_out_channel oc in
|
|
let g_basis = Qcaml.Gaussian.Basis.general_basis basis in
|
|
let dict =
|
|
Array.to_list nuclei
|
|
|> List.mapi (fun i (e, _) ->
|
|
(i+1), List.assoc e g_basis
|
|
)
|
|
in
|
|
List.iter (fun (i,b) ->
|
|
Format.fprintf ocf "%d %d\n" i (Array.length b);
|
|
Array.iter (fun x ->
|
|
Format.fprintf ocf "%a" Qcaml.Gaussian.General_basis.pp_gcs x) b
|
|
) dict;
|
|
close_out oc
|
|
in
|
|
print_basis nuclei basis;
|
|
|
|
|
|
let print_molecule nuclei electrons =
|
|
let oc = open_out quack_molecule_filename in
|
|
let nat = Array.length nuclei in
|
|
let nela = Qcaml.Particles.Electrons.n_alfa electrons in
|
|
let nelb = Qcaml.Particles.Electrons.n_beta electrons in
|
|
let ncore =
|
|
if frozen_core then
|
|
Qcaml.Particles.Nuclei.small_core nuclei
|
|
else 0
|
|
in
|
|
let nryd = rydberg in
|
|
Printf.fprintf oc "# nAt nEla nElb nCore nRyd\n";
|
|
Printf.fprintf oc " %4d %4d %4d %5d %4d\n" nat nela nelb ncore nryd;
|
|
Printf.fprintf oc "# Znuc x y z\n";
|
|
let open Qcaml.Common.Coordinate in
|
|
Array.iter (fun (element, coord) ->
|
|
Printf.fprintf oc "%3s %16.10f %16.10f %16.10f\n"
|
|
(Qcaml.Particles.Element.to_string element)
|
|
coord.x coord.y coord.z
|
|
) nuclei;
|
|
close_out oc
|
|
in
|
|
print_molecule nuclei electrons;
|
|
|
|
()
|
|
|
|
|
|
|