mirror of
https://github.com/pfloos/quack
synced 2024-12-22 20:34:46 +01:00
134 lines
4.0 KiB
OCaml
134 lines
4.0 KiB
OCaml
let quack_dir =
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try Sys.getenv "QUACK_ROOT" with
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Not_found -> "."
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let quack_basis_filename = quack_dir ^ "/input/basis"
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let quack_molecule_filename = quack_dir ^ "/input/molecule"
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module Command_line = Qcaml.Common.Command_line
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module Util = Qcaml.Common.Util
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let () =
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let open Command_line in
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begin
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set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
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set_description_doc "Prepares the input data for QuAcK.
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Writes $QUACK_ROOT/input/basis and $QUACK_ROOT/input/molecule.
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If $QUACK_ROOT is not set, $QUACK_ROOT is replaces by the current
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directory.";
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set_specs
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[ { short='b' ; long="basis" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the basis set"; } ;
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{ short='x' ; long="xyz" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
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{ short='m' ; long="multiplicity" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Spin multiplicity (2S+1). Default is singlet"; } ;
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{ short='c' ; long="charge" ; opt=Optional;
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arg=With_arg "<int>";
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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"; } ;
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{ short='f' ; long="frozen-core" ; opt=Optional;
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arg=Without_arg ;
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doc="Freeze core MOs. Default is false"; } ;
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{ short='r' ; long="rydberg" ; opt=Optional;
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arg=With_arg "<int>" ;
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doc="Number of Rydberg electrons. Default is 0"; } ;
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]
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end;
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(* Handle options *)
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let basis_file = Util.of_some @@ Command_line.get "basis" in
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let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
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let frozen_core = Command_line.get_bool "frozen-core" in
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let charge =
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match Command_line.get "charge" with
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| Some x -> ( if x.[0] = 'm' then
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~- (int_of_string (String.sub x 1 (String.length x - 1)))
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else
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int_of_string x )
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| None -> 0
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in
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let multiplicity =
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match Command_line.get "multiplicity" with
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| Some x -> int_of_string x
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| None -> 1
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in
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let rydberg =
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match Command_line.get "rydberg" with
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| Some x -> int_of_string x
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| None -> 0
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in
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let nuclei =
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Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
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in
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let electrons =
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Qcaml.Particles.Electrons.of_atoms ~multiplicity ~charge nuclei
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in
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let basis =
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Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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let print_basis nuclei basis =
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let oc = open_out quack_basis_filename in
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let ocf = Format.formatter_of_out_channel oc in
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let g_basis = Qcaml.Gaussian.Basis.general_basis basis in
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let dict =
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Array.to_list nuclei
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|> List.mapi (fun i (e, _) ->
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(i+1), List.assoc e g_basis
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)
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in
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List.iter (fun (i,b) ->
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Format.fprintf ocf "%d %d\n" i (Array.length b);
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Array.iter (fun x ->
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Format.fprintf ocf "%a" Qcaml.Gaussian.General_basis.pp_gcs x) b
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) dict;
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close_out oc
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in
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print_basis nuclei basis;
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let print_molecule nuclei electrons =
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let oc = open_out quack_molecule_filename in
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let nat = Array.length nuclei in
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let nela = Qcaml.Particles.Electrons.n_alfa electrons in
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let nelb = Qcaml.Particles.Electrons.n_beta electrons in
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let ncore =
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if frozen_core then
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Qcaml.Particles.Nuclei.small_core nuclei
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else 0
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in
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let nryd = rydberg in
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Printf.fprintf oc "# nAt nEla nElb nCore nRyd\n";
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Printf.fprintf oc " %4d %4d %4d %5d %4d\n" nat nela nelb ncore nryd;
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Printf.fprintf oc "# Znuc x y z\n";
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let open Qcaml.Common.Coordinate in
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Array.iter (fun (element, coord) ->
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Printf.fprintf oc "%3s %16.10f %16.10f %16.10f\n"
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(Qcaml.Particles.Element.to_string element)
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coord.x coord.y coord.z
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) nuclei;
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close_out oc
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in
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print_molecule nuclei electrons;
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()
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