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Better CLI

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This commit is contained in:
Anthony Scemama 2020-10-11 22:26:37 +02:00
parent ade70d4062
commit ba958ff550
3 changed files with 125 additions and 103 deletions
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1
qcaml-tools/dune
View File

@ -4,7 +4,6 @@
quack_integrals
)
(libraries
qcaml.common
qcaml
)
)

173
qcaml-tools/quack_input.ml
View File

@ -5,84 +5,71 @@ let quack_dir =
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 basis_file : string option ref = ref None
let nuclei_file : string option ref = ref None
let charge : int option ref = ref None
let multiplicity : int option ref = ref None
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_DIR/input/basis and $QUACK_DIR/input/molecule.
If $QUACK_DIR is not set, $QUACK_DIR 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"; } ;
let speclist = [
( "-b" , Arg.String (fun x -> basis_file := Some x),
"File containing the atomic basis set") ;
( "-c" , Arg.Int (fun x -> charge := Some x),
"Total charge of the system") ;
( "-m" , Arg.Int (fun x -> multiplicity := Some x),
"Multiplicity of the system") ;
( "-x" , Arg.String (fun x -> nuclei_file := Some x),
"File containing the nuclear coordinates") ;
]
{ 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"; } ;
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
)
{ 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
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
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 = Qcaml.Particles.Nuclei.small_core nuclei in
let nryd = 0 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
let run () =
let basis_file =
match !basis_file with
| None -> raise (Invalid_argument "Basis set file should be specified with -b")
| Some x -> x
and nuclei_file =
match !nuclei_file with
| None -> raise (Invalid_argument "Coordinate file should be specified with -x")
| Some x -> x
and charge =
match !charge with
| None -> 0
| Some c -> c
and multiplicity =
match !multiplicity with
let multiplicity =
match Command_line.get "multiplicity" with
| Some x -> int_of_string x
| None -> 1
| Some m -> m
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
@ -95,14 +82,52 @@ let run () =
Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
in
(* Print basis *)
print_molecule nuclei electrons;
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;
()
let () =
let usage_msg = "Available options:" in
Arg.parse speclist (fun _ -> ()) usage_msg;
run ()

54
qcaml-tools/quack_integrals.ml
View File

@ -1,30 +1,32 @@
let out_file : string option ref = ref None
let basis_file : string option ref = ref None
let nuclei_file : string option ref = ref None
let charge : int option ref = ref None
let multiplicity : int option ref = ref None
let range_separation : float option ref = ref None
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 "Computes the one- and two-electron integrals on the Gaussian atomic basis set.";
set_specs
[ { short='b' ; long="basis" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the basis set"; } ;
let speclist = [
( "-b" , Arg.String (fun x -> basis_file := Some x),
"File containing the atomic basis set") ;
( "-x" , Arg.String (fun x -> nuclei_file := Some x),
"File containing the nuclear coordinates") ;
( "-u" , Arg.Float (fun x -> range_separation := Some x),
"Value of mu, the range separation factor") ;
]
{ short='x' ; long="xyz" ; opt=Mandatory;
arg=With_arg "<string>";
doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
let run () =
let basis_file =
match !basis_file with
| None -> raise (Invalid_argument "Basis set file should be specified with -b")
| Some x -> x
and nuclei_file =
match !nuclei_file with
| None -> raise (Invalid_argument "Coordinate file should be specified with -x")
| Some x -> x
and range_separation = !range_separation
{ short='u' ; long="range-separation" ; opt=Optional;
arg=With_arg "<float>";
doc="Range-separation parameter."; } ;
]
end;
let basis_file = Util.of_some @@ Command_line.get "basis" in
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
let range_separation =
match Command_line.get "range-separation" with
| None -> None
| Some mu -> Some (float_of_string mu)
in
let nuclei =
@ -56,8 +58,4 @@ let run () =
| None -> ()
let () =
let usage_msg = "Available options:" in
Arg.parse speclist (fun _ -> ()) usage_msg;
run ()