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https://github.com/pfloos/quack
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Better CLI
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@ -4,7 +4,6 @@
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quack_integrals
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)
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(libraries
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qcaml.common
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qcaml
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)
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)
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@ -5,84 +5,71 @@ let quack_dir =
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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 basis_file : string option ref = ref None
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let nuclei_file : string option ref = ref None
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let charge : int option ref = ref None
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let multiplicity : int option ref = ref None
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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_DIR/input/basis and $QUACK_DIR/input/molecule.
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If $QUACK_DIR is not set, $QUACK_DIR 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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let speclist = [
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( "-b" , Arg.String (fun x -> basis_file := Some x),
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"File containing the atomic basis set") ;
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( "-c" , Arg.Int (fun x -> charge := Some x),
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"Total charge of the system") ;
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( "-m" , Arg.Int (fun x -> multiplicity := Some x),
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"Multiplicity of the system") ;
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( "-x" , Arg.String (fun x -> nuclei_file := Some x),
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"File containing the nuclear coordinates") ;
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]
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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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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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{ 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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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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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 = Qcaml.Particles.Nuclei.small_core nuclei in
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let nryd = 0 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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let run () =
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let basis_file =
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match !basis_file with
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| None -> raise (Invalid_argument "Basis set file should be specified with -b")
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| Some x -> x
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and nuclei_file =
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match !nuclei_file with
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| None -> raise (Invalid_argument "Coordinate file should be specified with -x")
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| Some x -> x
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and charge =
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match !charge with
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| None -> 0
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| Some c -> c
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and multiplicity =
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match !multiplicity with
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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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| Some m -> m
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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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@ -95,14 +82,52 @@ let run () =
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Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
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in
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(* Print basis *)
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print_molecule nuclei electrons;
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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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let () =
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let usage_msg = "Available options:" in
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Arg.parse speclist (fun _ -> ()) usage_msg;
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run ()
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@ -1,30 +1,32 @@
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let out_file : string option ref = ref None
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let basis_file : string option ref = ref None
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let nuclei_file : string option ref = ref None
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let charge : int option ref = ref None
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let multiplicity : int option ref = ref None
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let range_separation : float option ref = ref None
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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 "Computes the one- and two-electron integrals on the Gaussian atomic basis set.";
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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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let speclist = [
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( "-b" , Arg.String (fun x -> basis_file := Some x),
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"File containing the atomic basis set") ;
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( "-x" , Arg.String (fun x -> nuclei_file := Some x),
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"File containing the nuclear coordinates") ;
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( "-u" , Arg.Float (fun x -> range_separation := Some x),
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"Value of mu, the range separation factor") ;
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]
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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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let run () =
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let basis_file =
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match !basis_file with
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| None -> raise (Invalid_argument "Basis set file should be specified with -b")
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| Some x -> x
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and nuclei_file =
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match !nuclei_file with
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| None -> raise (Invalid_argument "Coordinate file should be specified with -x")
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| Some x -> x
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and range_separation = !range_separation
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{ short='u' ; long="range-separation" ; opt=Optional;
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arg=With_arg "<float>";
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doc="Range-separation parameter."; } ;
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]
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end;
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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 range_separation =
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match Command_line.get "range-separation" with
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| None -> None
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| Some mu -> Some (float_of_string mu)
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in
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let nuclei =
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@ -56,8 +58,4 @@ let run () =
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| None -> ()
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let () =
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let usage_msg = "Available options:" in
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Arg.parse speclist (fun _ -> ()) usage_msg;
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run ()
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