Fixed options
This commit is contained in:
parent
316fb508d5
commit
cd7d0280d7
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@ -15,12 +15,12 @@ Usage
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.. code:: bash
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qp_convert_output_to_ezfio <file.out> [-o EZFIO_DIR]
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qp_convert_output_to_ezfio [-o EZFIO_DIR] FILE
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.. option:: -o, --output=EZFIO_DIR
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Renames the |EZFIO| directory. If this option is not present, the default
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name fill be :file:`<FILE.out>.ezfio`
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name fill be :file:`FILE.ezfio`
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.. note::
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All the parameters of the wave functgion need to be presente in the output
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@ -13,14 +13,9 @@ Usage
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.. code:: bash
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qp_create_ezfio_from_xyz [FLAGS] (<xyz_file> | <zmt_file>)
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qp_create_ezfio_from_xyz [-a] -b <string> [-c <int>] [-d <float>]
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[-h] [-m <int>] [-o EZFIO_DIR] [-p <string>] [-x] [--] FILE
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Flags :
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[-a|--au] [-b string|--basis=string]
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[-c int|--charge=int] [-d float|--dummy=float] [-h|--help]
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[-m int|--multiplicity=int] [-o file|--output=file]
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[-p string|--pseudo=string] [-x|--cartesian]
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.. option:: -a, --au
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@ -37,6 +32,10 @@ Usage
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-b "cc-pvtz | 1,H:sto-3g | 3,H:6-31g"
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By default, the basis set is obtained from the local database of the |qp|.
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This option is mandatory.
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If ``<string>`` is set to ``show``, the list of all available basis sets is
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displayed.
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.. option:: -c, --charge=<int>
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@ -27,8 +27,7 @@ Usage
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.. code:: bash
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qp_edit [-c|--check] [-h|--help] [-n <int>|--ndet=<int>]
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[-s <range>|--state=<range>] [--] EZFIO_DIR
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qp_edit [-c] [-h] [-n <int>] [-s <range>] [--] EZFIO_DIR
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.. option:: -c, --check
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@ -24,7 +24,7 @@ Usage
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Prints the help message
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.. note::
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There can be conflicts due to the version of Glibc. The machine on which |QP| is
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There can be conflicts due to the version of glibc. The machine on which |QP| is
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compiled should be the oldest one.
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@ -15,11 +15,11 @@ Usage
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.. code:: bash
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qp_plugins list [ -i, --installed | -u, --uninstalled | -q, --repositories ]
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qp_plugins list [-i] [-u] [-q]
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qp_plugins download <url>
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qp_plugins install <name>...
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qp_plugins uninstall <name>
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qp_plugins create -n <name> [-r, --repository=<repo>] [<needed_modules>...]
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qp_plugins create -n <name> [-r <repo>] [<needed_modules>...]
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.. option:: list
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@ -37,7 +37,7 @@ Usage
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List all the downloaded repositories.
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.. option:: download URL
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.. option:: download <url>
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Download an external repository. The URL points to a tar.gz file or a
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git repository, for example:
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@ -15,8 +15,7 @@ Usage
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.. code:: bash
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qp_run [-h|--help] [-p <string>|--prefix=<string>] [-s|--slave] [--]
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PROGRAM EZFIO_DIR
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qp_run [-h] [-p <string>] [-s] [--] PROGRAM EZFIO_DIR
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``PROGRAM`` is the name of the |QP| program to be run, and ``EZFIO_DIR`` is
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the name of the |EZFIO| directory containing the data.
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@ -21,7 +21,7 @@ Usage
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.. code:: bash
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qp_set_frozen_core [-q] <EZFIO_DIRECTORY>
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qp_set_frozen_core [-q] EZFIO_DIR
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.. option:: -q
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@ -38,38 +38,32 @@ Usage
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.. code:: bash
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qp_set_mo_class [FLAGS] <EZFIO_DIRECTORY>
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Flags:
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[-act range] [-core range] [-del range]
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[-inact range] [-q] [-virt range]
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[-help]
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qp_set_mo_class [-a <range>] [-c <range>] [-d <range>] [-h] [-i <range>]
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[-q] [-v <range>] [--] EZFIO_DIR
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.. option:: -act <range>
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.. option:: -a, --act=<range>
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Range of active orbitals
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.. option:: -core <range>
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.. option:: -c, --core=<range>
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Range of core orbitals
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.. option:: -del <range>
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.. option:: -d, --del=<range>
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Range of deleted orbitals
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.. option:: -inact <range>
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.. option:: -i, --inact=<range>
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Range of inactive orbitals
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.. option:: -q
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.. option:: -q, --query
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Query: print the current masks
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Print the |MO| classes
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.. option:: -virt <range>
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.. option:: -v, --virt=<range>
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Range of virtual orbitals
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.. option:: -help, -?
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@ -1,161 +1,199 @@
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type argument = With_arg | Without_arg | With_opt_arg
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type short_opt = char
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type long_opt = string
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type optional = Mandatory | Optional
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type documentation = string
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type argument = With_arg of string | Without_arg | With_opt_arg of string
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let anon_args = ref []
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type description = {
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short: short_opt ;
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long : long_opt ;
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opt : optional ;
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doc : documentation ;
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arg : argument ;
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}
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let anon_args = ref []
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and header_doc = ref ""
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and description_doc = ref ""
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and footer_doc = ref ""
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and specs = ref []
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and specs = ref []
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let set_header_doc s = header_doc := s
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let set_description_doc s = description_doc := s
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let set_footer_doc s = footer_doc := s
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let dict =
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let d = Hashtbl.create 67 in
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d
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(* Hash table containing all the options *)
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let dict = Hashtbl.create 67
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let get_bool x = Hashtbl.mem dict x
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let show_help () = get_bool "help"
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let get x =
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try Some (Hashtbl.find dict x)
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with Not_found -> None
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try Some (Hashtbl.find dict x)
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with Not_found -> None
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let get_bool x =
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Hashtbl.mem dict x
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let anonymous name opt doc =
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{ short=' ' ; long=name; opt; doc; arg=Without_arg; }
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let show_help () =
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get_bool "help"
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let output_text t =
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Format.printf "@[<v 0>";
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begin
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match Str.split (Str.regexp "\n") t with
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| x :: [] -> Format.printf "@[<hov 0>";
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Str.split (Str.regexp " ") x
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|> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
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Format.printf "@]"
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| t -> List.iter (fun x ->
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Format.printf "@[<hov 0>";
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Str.split (Str.regexp " ") x
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|> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
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Format.printf "@]@;") t
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end;
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Format.printf "@]"
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;;
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let output_short x =
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match x.short, x.opt, x.arg with
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| ' ', Mandatory, _ -> Format.printf "@[%s@]" x.long
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| ' ', Optional , _ -> Format.printf "@[[%s]@]" x.long
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| _ , Mandatory, Without_arg -> Format.printf "@[-%c@]" x.short
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| _ , Optional , Without_arg -> Format.printf "@[[-%c]@]" x.short
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| _ , Mandatory, With_arg arg -> Format.printf "@[-%c %s@]" x.short arg
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| _ , Optional , With_arg arg -> Format.printf "@[[-%c %s]@]" x.short arg
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| _ , Mandatory, With_opt_arg arg -> Format.printf "@[-%c [%s]@]" x.short arg
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| _ , Optional , With_opt_arg arg -> Format.printf "@[[-%c [%s]]@]" x.short arg
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let output_long max_width x =
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let arg =
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match x.short, x.arg with
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| ' ' , _ -> x.long
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| _ , Without_arg -> x.long
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| _ , With_arg arg -> Printf.sprintf "%s=%s" x.long arg
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| _ , With_opt_arg arg -> Printf.sprintf "%s[=%s]" x.long arg
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in
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let long =
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let l = String.length arg in
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arg^(String.make (max_width-l) ' ')
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in
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Format.printf "@[<v 0>";
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begin
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match x.short with
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| ' ' -> Format.printf "@[%s @]" long
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| short -> Format.printf "@[-%c --%s @]" short long
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end;
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Format.printf "@]";
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output_text x.doc
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let anonymous ?(optional=false) name doc =
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( ' ', name, doc,
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if optional then With_opt_arg else Without_arg
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)
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let help () =
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Format.printf "@[%s@]@.@." !header_doc;
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let get_param_from_doc doc =
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match Str.split (Str.regexp "[ \n\r\x0c\t]+") doc with
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| param :: doc -> param, (String.concat " " doc)
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| _ -> failwith "Bad format for documentation"
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in
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(* Print the header *)
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output_text !header_doc;
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Format.printf "@.@.";
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let anon =
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List.filter (fun (x,_,_,_) -> x = ' ') !specs
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|> List.map (fun x ->
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match x with
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| (_,name,doc,Without_arg) -> (name,doc,false)
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| (_,name,doc,_) -> (name,doc,true)
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)
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in
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(* Find the anonymous arguments *)
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let anon =
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List.filter (fun x -> x.short = ' ') !specs
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in
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let options =
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List.filter (fun (x,_,_,_) -> x <> ' ') !specs
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|> List.sort (fun (x,_,_,_) (y,_,_,_) -> Char.compare x y)
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|> List.map (fun x ->
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match x with
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| (short,long,doc,With_arg) -> (* with arg *)
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let param, doc = get_param_from_doc doc in
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(Printf.sprintf "-%c %s" short param,
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Printf.sprintf "--%s=%s" long param,
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doc)
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| (short,long,doc,Without_arg) -> (* without arg *)
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(Printf.sprintf "-%c" short,
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Printf.sprintf "--%s" long,
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doc)
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| (short,long,doc,With_opt_arg) -> (* with or without arg *)
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let param, doc = get_param_from_doc doc in
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(Printf.sprintf "-%c [%s]" short param,
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Printf.sprintf "--%s[=%s]" long param,
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doc)
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)
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in
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(* Find the options *)
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let options =
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List.filter (fun x -> x.short <> ' ') !specs
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|> List.sort (fun x y -> Char.compare x.short y.short)
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in
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let max_short =
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List.map (fun (x,_,_) -> String.length x) options
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|> List.fold_left max 0
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in
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let max_long =
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List.map (fun (_,x,_) -> String.length x) options
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|> List.fold_left max 0
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in
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let fmt_opt max_w o =
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let l = String.length o in
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o^(String.make (max_w-l) ' ')
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in
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(* Find column lengths *)
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let max_width =
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List.map (fun x ->
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( match x.arg with
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| Without_arg -> String.length x.long
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| With_arg arg -> String.length x.long + String.length arg
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| With_opt_arg arg -> String.length x.long + String.length arg + 2
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)
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+ ( if x.opt = Optional then 2 else 0)
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) !specs
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|> List.fold_left max 0
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in
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let output_option ?(fixed_width=false) (short, long, doc) =
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if fixed_width then
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Format.printf "@[%s %s@]"
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(fmt_opt max_short short) (fmt_opt max_long long)
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else
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Format.printf "@[%s|%s@]" short long
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in
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(* Print usage *)
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Format.printf "@[<v>@[<v 2>Usage:@,@,@[<hov 4>@[%s@]" Sys.argv.(0);
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List.iter (fun x -> Format.printf "@ "; output_short x) options;
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Format.printf "@ @[[--]@]";
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List.iter (fun x -> Format.printf "@ "; output_short x;) anon;
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Format.printf "@]@,@]@,";
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let output_anon ?(fixed_width=false) (name, doc, optional) =
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if optional then
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Format.printf "@[[%s]@]" name
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else
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Format.printf "@[%s@]" name
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in
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Format.printf "@[<v>@[<v 2>Usage:@,@,@[<hov 4>@[%s@]" Sys.argv.(0);
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List.iter (fun x ->
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Format.printf "@ @[[";
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output_option ~fixed_width:false x;
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Format.printf "]@]"
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) options;
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Format.printf "@ @[[--]@]";
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List.iter (fun x ->
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Format.printf "@ @[";
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output_anon ~fixed_width:false x;
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Format.printf "@]"
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) anon;
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Format.printf "@]@]@,@,";
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(* Print arguments and doc *)
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Format.printf "@[<v 2>Arguments:@,";
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Format.printf "@[<v 0>" ;
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List.iter (fun x -> Format.printf "@ "; output_long max_width x) anon;
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Format.printf "@]@,@]@,";
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Format.printf "@[<v>Arguments:@,";
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Format.printf "@[<v 2>@," ;
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List.iter (fun (name,doc,optional) ->
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Format.printf "@[<h>";
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output_anon ~fixed_width:true (name,doc,optional);
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Format.printf "@ @[<v 0>%s@]@]@," doc
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) anon;
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Format.printf "@]@;";
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(* Print options and doc *)
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Format.printf "@[<v 2>Options:@,";
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Format.printf "@[<v>Options:@,";
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Format.printf "@[<v 0>" ;
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List.iter (fun x -> Format.printf "@ "; output_long max_width x) options;
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Format.printf "@]@,@]@,";
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(* Print footer *)
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||||
if !description_doc <> "" then
|
||||
begin
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Format.printf "@[<v 2>Description:@,@,";
|
||||
output_text !description_doc;
|
||||
Format.printf "@,"
|
||||
end;
|
||||
|
||||
(* Print footer *)
|
||||
output_text !footer_doc;
|
||||
Format.printf "@."
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||||
|
||||
Format.printf "@[<v 2>@," ;
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List.iter (fun (short,long,doc) ->
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Format.printf "@[<h>";
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||||
output_option ~fixed_width:true (short,long,doc);
|
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Format.printf "@ @[<v 0>%s@]@]@," doc
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) options;
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Format.printf "@]@;";
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||||
|
||||
Format.printf "@[%s@]@." !footer_doc
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||||
|
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let set_specs specs_in =
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specs := ( 'h', "help", "Prints the help message", Without_arg) :: specs_in;
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specs := { short='h' ;
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long ="help" ;
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doc ="Prints the help message." ;
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arg =Without_arg ;
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opt =Optional ;
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} :: specs_in;
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let specs =
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List.filter (fun (x,_,_,_) -> x != ' ') !specs
|
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|> List.map (fun x ->
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match x with
|
||||
| (short, long, doc, With_arg) ->
|
||||
(short, long, None, Some (fun x -> Hashtbl.replace dict long x) )
|
||||
| (short, long, doc, Without_arg) ->
|
||||
(short, long, Some (fun () -> Hashtbl.replace dict long ""), None)
|
||||
| (short, long, doc, With_opt_arg) ->
|
||||
(short, long, Some (fun () -> Hashtbl.replace dict long ""),
|
||||
Some (fun x -> Hashtbl.replace dict long x) )
|
||||
)
|
||||
in
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let cmd_specs =
|
||||
List.filter (fun x -> x.short != ' ') !specs
|
||||
|> List.map (fun { short ; long ; opt ; doc ; arg } ->
|
||||
match arg with
|
||||
| With_arg _ ->
|
||||
(short, long, None, Some (fun x -> Hashtbl.replace dict long x) )
|
||||
| Without_arg ->
|
||||
(short, long, Some (fun () -> Hashtbl.replace dict long ""), None)
|
||||
| With_opt_arg _ ->
|
||||
(short, long, Some (fun () -> Hashtbl.replace dict long ""),
|
||||
Some (fun x -> Hashtbl.replace dict long x) )
|
||||
)
|
||||
in
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|
||||
Getopt.parse_cmdline specs (fun x -> anon_args := !anon_args @ [x]);
|
||||
Getopt.parse_cmdline cmd_specs (fun x -> anon_args := !anon_args @ [x]);
|
||||
|
||||
if show_help () then
|
||||
(help () ; exit 0);
|
||||
|
||||
(* Check that all mandatory arguments are set *)
|
||||
List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
|
||||
|> List.iter (fun x ->
|
||||
match get x.long with
|
||||
| Some _ -> ()
|
||||
| None -> failwith ("Error: --"^x.long^" option is missing.")
|
||||
)
|
||||
;;
|
||||
|
||||
if show_help () then
|
||||
(help () ; exit 0)
|
||||
|
||||
let anon_args () = !anon_args
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,126 @@
|
|||
(** Handles command-line arguments, using getopt.
|
||||
|
||||
Example:
|
||||
|
||||
let () =
|
||||
|
||||
(* Command-line specs *)
|
||||
let open Command_line in
|
||||
begin
|
||||
set_header_doc (Sys.argv.(0) ^ " - quantum_package command");
|
||||
|
||||
[ { short='c'; long="check"; opt=Optional;
|
||||
doc="Checks the input data";
|
||||
arg=Without_arg; };
|
||||
|
||||
{ short='n'; long="ndet"; opt=Optional;
|
||||
doc="Truncate the wavefunction to the target number of determinants";
|
||||
arg=With_arg "<int>"; };
|
||||
|
||||
{ short='s'; long="state"; opt=Optional;
|
||||
doc="Extract selected states, for example \"[1,3-5]\"";
|
||||
arg=With_arg "<range>"; };
|
||||
|
||||
anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
|
||||
]
|
||||
|> set_specs ;
|
||||
|
||||
set_description_doc
|
||||
"Opens a text editor to edit the parameters of a EZFIO directory.";
|
||||
end;
|
||||
|
||||
|
||||
(* Handle options *)
|
||||
let ndet =
|
||||
match Command_line.get "ndet" with
|
||||
| None -> None
|
||||
| Some s -> (try Some (int_of_string s)
|
||||
with _ -> failwith "[-n|--ndet] expects an integer")
|
||||
in
|
||||
let state =
|
||||
match Command_line.get "state" with
|
||||
| None -> None
|
||||
| Some s -> (try Some (Range.of_string s)
|
||||
with _ -> failwith "[-s|--state] expects a range")
|
||||
in
|
||||
|
||||
let c = Command_line.get_bool "check" in
|
||||
|
||||
let filename =
|
||||
match Command_line.anon_args () with
|
||||
| [x] -> x
|
||||
| _ -> (Command_line.help () ; failwith "EZFIO_DIR is missing")
|
||||
in
|
||||
|
||||
(* Run the program *)
|
||||
run c ?ndet ?state filename
|
||||
|
||||
|
||||
*)
|
||||
|
||||
|
||||
type short_opt = char
|
||||
|
||||
type long_opt = string
|
||||
|
||||
type optional = Mandatory
|
||||
| Optional
|
||||
|
||||
type documentation = string
|
||||
|
||||
type argument = With_arg of string
|
||||
| Without_arg
|
||||
| With_opt_arg of string
|
||||
|
||||
|
||||
type description =
|
||||
{
|
||||
short : short_opt;
|
||||
long : long_opt;
|
||||
opt : optional;
|
||||
doc : documentation;
|
||||
arg : argument;
|
||||
}
|
||||
|
||||
|
||||
(** Sets the header of the help message. *)
|
||||
val set_header_doc : string -> unit
|
||||
|
||||
|
||||
(** Sets the description of the help message. *)
|
||||
val set_description_doc : string -> unit
|
||||
|
||||
(** Sets the footer of the help message. *)
|
||||
val set_footer_doc : string -> unit
|
||||
|
||||
|
||||
(** Gets the value of an option. If the option is not set, returns [None]. If
|
||||
the option is set, returns Some <string>. *)
|
||||
val get : string -> string option
|
||||
|
||||
|
||||
(** Gets the value of an option with no argument. If the option is set, returns [true]. *)
|
||||
val get_bool : string -> bool
|
||||
|
||||
|
||||
(** True if the '-h' or "--help" option was found. *)
|
||||
val show_help : unit -> bool
|
||||
|
||||
|
||||
(** Creates a specification of an anonymous argument. *)
|
||||
val anonymous : long_opt -> optional -> documentation -> description
|
||||
|
||||
|
||||
(** Prints the help message *)
|
||||
val help : unit -> unit
|
||||
|
||||
|
||||
(** Sets the specification list as a list of tuples:
|
||||
( short option, long option, documentation, argument ) *)
|
||||
val set_specs : description list -> unit
|
||||
|
||||
|
||||
(** Returns the list of anonymous arguments *)
|
||||
val anon_args : unit -> string list
|
||||
|
||||
|
||||
|
|
@ -69,7 +69,6 @@ let list_basis () =
|
|||
)
|
||||
in
|
||||
List.sort basis_list ~compare:String.ascending
|
||||
|> String.concat ~sep:"\n"
|
||||
|
||||
|
||||
(** Run the program *)
|
||||
|
|
@ -648,36 +647,54 @@ let run ?o b au c d m p cart xyz_file =
|
|||
|
||||
let () =
|
||||
|
||||
"=== Available basis sets ===
|
||||
|
||||
" ^ (list_basis ()) ^ "
|
||||
let open Command_line in
|
||||
begin
|
||||
"Creates an EZFIO directory from a standard xyz file or from a z-matrix file in Gaussian format. The basis set is defined as a single string if all the atoms are taken from the same basis set, otherwise specific elements can be defined as follows:
|
||||
|
||||
============================
|
||||
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
|
||||
-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
|
||||
|
||||
Creates an EZFIO directory from a standard xyz file or from a z-matrix file
|
||||
in Gaussian format. The basis set is defined as a single string if all the
|
||||
atoms are taken from the same basis set, otherwise specific elements can be
|
||||
defined as follows:
|
||||
If a file with the same name as the basis set exists, this file will be read. Otherwise, the basis set is obtained from the database.
|
||||
" |> set_description_doc ;
|
||||
set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
|
||||
|
||||
-b \"cc-pcvdz | H:cc-pvdz | C:6-31g\"
|
||||
-b \"cc-pvtz | 1,H:sto-3g | 3,H:6-31g\"
|
||||
[ { opt=Optional ; short='o'; long="output";
|
||||
arg=With_arg "EZFIO_DIR";
|
||||
doc="Name of the created EZFIO directory."} ;
|
||||
|
||||
If a file with the same name as the basis set exists, this file will be read.
|
||||
Otherwise, the basis set is obtained from the database.
|
||||
{ opt=Mandatory; short='b'; long="basis";
|
||||
arg=With_arg "<string>";
|
||||
doc="Name of basis set. If <string>=show, the list of all basis sets is displayed."} ;
|
||||
|
||||
" |> Command_line.set_header_doc ;
|
||||
{ opt=Optional ; short='a'; long="au";
|
||||
arg=Without_arg;
|
||||
doc="Input geometry is in atomic units."} ;
|
||||
|
||||
[ ( 'o', "output", "<file> Name of the created EZFIO file.", Command_line.With_arg) ;
|
||||
( 'b', "basis", "<string> Name of basis set.", Command_line.With_arg) ;
|
||||
( 'a', "au", "Input geometry is in atomic units.", Command_line.Without_arg) ;
|
||||
( 'c', "charge", "<int> Total charge of the molecule. Default is 0.", Command_line.With_arg) ;
|
||||
( 'd', "dummy", "<float> Add dummy atoms. x * (covalent radii of the atoms)", Command_line.With_arg);
|
||||
( 'm', "multiplicity", "<int> Spin multiplicity (2S+1) of the molecule. Default is 1.", Command_line.With_arg);
|
||||
( 'p', "pseudo", "<string> Name of the pseudopotential.", Command_line.With_arg);
|
||||
( 'x', "cartesian", "Compute AOs in the Cartesian basis set (6d, 10f, ...)", Command_line.Without_arg);
|
||||
Command_line.anonymous "(xyz_file|zmt_file)" "input file in xyz format or z-matrix."
|
||||
]
|
||||
|> Command_line.set_specs ;
|
||||
{ opt=Optional ; short='c'; long="charge";
|
||||
arg=With_arg "<int>";
|
||||
doc="Total charge of the molecule. Default is 0."} ;
|
||||
|
||||
{ opt=Optional ; short='d'; long="dummy";
|
||||
arg=With_arg "<float>";
|
||||
doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
|
||||
|
||||
{ opt=Optional ; short='m'; long="multiplicity";
|
||||
arg=With_arg "<int>";
|
||||
doc="Spin multiplicity (2S+1) of the molecule. Default is 1."} ;
|
||||
|
||||
{ opt=Optional ; short='p'; long="pseudo";
|
||||
arg=With_arg "<string>";
|
||||
doc="Name of the pseudopotential."} ;
|
||||
|
||||
{ opt=Optional ; short='x'; long="cartesian";
|
||||
arg=Without_arg;
|
||||
doc="Compute AOs in the Cartesian basis set (6d, 10f, ...)."} ;
|
||||
|
||||
anonymous "FILE" Mandatory "Input file in xyz format or z-matrix.";
|
||||
]
|
||||
|> set_specs
|
||||
end;
|
||||
|
||||
|
||||
(* Handle options *)
|
||||
|
|
@ -687,7 +704,7 @@ Otherwise, the basis set is obtained from the database.
|
|||
|
||||
let basis =
|
||||
match Command_line.get "basis" with
|
||||
| None -> (Command_line.help () ; failwith "Error: [-b|--basis] option is missing.")
|
||||
| None -> assert false
|
||||
| Some x -> x
|
||||
in
|
||||
|
||||
|
|
@ -721,6 +738,13 @@ Otherwise, the basis set is obtained from the database.
|
|||
Command_line.get_bool "cartesian"
|
||||
in
|
||||
|
||||
if basis = "show" then
|
||||
begin
|
||||
list_basis ()
|
||||
|> List.iter ~f:print_endline;
|
||||
exit 0
|
||||
end;
|
||||
|
||||
let xyz_filename =
|
||||
match Command_line.anon_args () with
|
||||
| [x] -> x
|
||||
|
|
|
|||
|
|
@ -141,34 +141,32 @@ let run slave ?prefix exe ezfio_file =
|
|||
|
||||
let () =
|
||||
(* Command-line specs *)
|
||||
"Executes a Quantum Package binary file among these:\n\n"
|
||||
^ (Lazy.force Qpackage.executables
|
||||
|> List.map (fun (x,_) -> Printf.sprintf " * %s" x )
|
||||
|> String.concat "\n"
|
||||
) |> Command_line.set_header_doc;
|
||||
let open Command_line in
|
||||
begin
|
||||
set_header_doc (Sys.argv.(0) ^ " - Quantum Package command");
|
||||
"Executes a Quantum Package binary file among these:\n\n"
|
||||
^ (Lazy.force Qpackage.executables
|
||||
|> List.map (fun (x,_) -> Printf.sprintf " * %s" x )
|
||||
|> String.concat "\n")
|
||||
|> set_description_doc;
|
||||
|
||||
[ ( 's', "slave", "Required to run slave tasks in distributed environments",
|
||||
Command_line.Without_arg);
|
||||
( 'p', "prefix", "<string> Prefix before running the program, like gdb or valgrind",
|
||||
Command_line.With_arg );
|
||||
Command_line.anonymous "PROGRAM" "Name of the QP program to be run";
|
||||
Command_line.anonymous "EZFIO_DIR" "EZFIO directory";
|
||||
[ { short='s'; long="slave"; opt=Optional;
|
||||
doc="Required to run slave tasks in distributed environments.";
|
||||
arg=Without_arg; };
|
||||
|
||||
{ short='p'; long="prefix"; opt=Optional;
|
||||
doc="Prefix before running the program, like gdb or valgrind.";
|
||||
arg=With_arg "<string>"; };
|
||||
|
||||
anonymous "PROGRAM" Mandatory "Name of the QP program to be run";
|
||||
anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
|
||||
]
|
||||
|> Command_line.set_specs ;
|
||||
|
||||
|> set_specs ;
|
||||
end;
|
||||
|
||||
(* Handle options *)
|
||||
if Command_line.show_help () then
|
||||
exit 0;
|
||||
|
||||
let slave =
|
||||
match Command_line.get "slave" with
|
||||
| None -> false
|
||||
| _ -> true
|
||||
in
|
||||
|
||||
let prefix =
|
||||
Command_line.get "prefix"
|
||||
let slave = Command_line.get_bool "slave"
|
||||
and prefix = Command_line.get "prefix"
|
||||
in
|
||||
|
||||
(* Run the program *)
|
||||
|
|
|
|||
|
|
@ -314,30 +314,50 @@ let default range =
|
|||
|
||||
|
||||
let () =
|
||||
"Set the orbital classes in an EZFIO directory.
|
||||
The range of MOs has the form : \"[36-53,72-107,126-131]\"." |> Command_line.set_header_doc ;
|
||||
let open Command_line in
|
||||
begin
|
||||
"Set the orbital classes in an EZFIO directory. The range of MOs has the form : \"[36-53,72-107,126-131]\"."
|
||||
|> set_footer_doc ;
|
||||
|
||||
[ ( 'c', "core", "range Range of core MOs", Command_line.With_opt_arg);
|
||||
( 'i', "inact", "range Range of inactive MOs", Command_line.With_opt_arg);
|
||||
( 'a', "act", "range Range of active MOs", Command_line.With_opt_arg);
|
||||
( 'v', "virt", "range Range of virtual MOs", Command_line.With_opt_arg);
|
||||
( 'd', "del", "range Range of deleted MOs", Command_line.With_opt_arg);
|
||||
( 'q', "query", "Print the current MOs classes", Command_line.Without_arg);
|
||||
Command_line.anonymous "<EZFIO_FILE>" "EZFIO directory";
|
||||
] |> Command_line.set_specs ;
|
||||
[ { opt=Optional ; short='c'; long="core";
|
||||
arg=With_arg "<range>";
|
||||
doc="Range of core MOs." };
|
||||
|
||||
{ opt=Optional ; short='i'; long="inact";
|
||||
arg=With_arg "<range>";
|
||||
doc="Range of inactive MOs." };
|
||||
|
||||
{ opt=Optional ; short='a'; long="act";
|
||||
arg=With_arg "<range>";
|
||||
doc="Range of active MOs." };
|
||||
|
||||
{ opt=Optional ; short='v'; long="virt";
|
||||
arg=With_arg "<range>";
|
||||
doc="Range of virtual MOs." };
|
||||
|
||||
{ opt=Optional ; short='d'; long="del";
|
||||
arg=With_arg "<range>";
|
||||
doc="Range of deleted MOs." };
|
||||
|
||||
{ opt=Optional ; short='q'; long="query";
|
||||
arg=Without_arg;
|
||||
doc="Print the current MO classes." };
|
||||
|
||||
anonymous "EZFIO_DIR" Mandatory "EZFIO directory.";
|
||||
] |> set_specs
|
||||
end;
|
||||
|
||||
(* Handle options *)
|
||||
if Command_line.show_help () then
|
||||
exit 0;
|
||||
|
||||
let core = Command_line.get "core"
|
||||
and inact = Command_line.get "inact"
|
||||
and act = Command_line.get "act"
|
||||
and virt = Command_line.get "virt"
|
||||
and del = Command_line.get "del"
|
||||
and q = Command_line.get_bool "q"
|
||||
and q = Command_line.get_bool "query"
|
||||
in
|
||||
|
||||
|
||||
let ezfio_filename =
|
||||
match Command_line.anon_args () with
|
||||
| [x] -> x
|
||||
|
|
|
|||
|
|
@ -39,10 +39,10 @@ do
|
|||
done
|
||||
|
||||
if [[ $? -ne 0 ]] ; then
|
||||
echo "==================================================" 1>& 2
|
||||
echo "Unable to create temporary file $tmpfile" 1>& 2
|
||||
echo "==================================================" 1>& 2
|
||||
echo "ERROR"
|
||||
>&2 echo "=================================================="
|
||||
>&2 echo "Unable to create temporary file $tmpfile"
|
||||
>&2 echo "=================================================="
|
||||
>&2 echo "ERROR"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
|
|
|||
|
|
@ -3,11 +3,11 @@
|
|||
convert output of GAMESS/GAU$$IAN to ezfio
|
||||
|
||||
Usage:
|
||||
qp_convert_output_to_ezfio [-o EZFIO_DIR|--output=EZFIO_DIR] <file.out>
|
||||
qp_convert_output_to_ezfio [-o EZFIO_DIR] FILE
|
||||
|
||||
Options:
|
||||
-o EZFIO_DIR --output=EZFIO_DIR Produced directory
|
||||
by default is file.out.ezfio
|
||||
-o --output=EZFIO_DIR Produced directory
|
||||
by default is FILE.ezfio
|
||||
|
||||
"""
|
||||
|
||||
|
|
@ -342,7 +342,7 @@ def get_full_path(file_path):
|
|||
if __name__ == '__main__':
|
||||
ARGUMENTS = docopt(__doc__)
|
||||
|
||||
FILE = get_full_path(ARGUMENTS['<file.out>'])
|
||||
FILE = get_full_path(ARGUMENTS['FILE'])
|
||||
|
||||
if ARGUMENTS["--output"]:
|
||||
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
file=$1
|
||||
|
||||
if [[ -z ${QP_ROOT} ]] ; then
|
||||
2>& echo "please source quantum_package.rc"
|
||||
>&2 echo "please source quantum_package.rc"
|
||||
exit 1
|
||||
fi
|
||||
source ${QP_ROOT}/quantum_package.rc
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ zero.
|
|||
|
||||
|
||||
Usage:
|
||||
qp_set_frozen_core [-q|--query] <EZFIO_DIRECTORY>
|
||||
qp_set_frozen_core [-q|--query] EZFIO_DIR
|
||||
|
||||
Options:
|
||||
-q --query Prints in the standard output the number of frozen MOs
|
||||
|
|
@ -37,7 +37,7 @@ from ezfio import ezfio
|
|||
def main(arguments):
|
||||
"""Main function"""
|
||||
|
||||
filename = arguments["<EZFIO_DIRECTORY>"]
|
||||
filename = arguments["EZFIO_DIR"]
|
||||
ezfio.set_filename(filename)
|
||||
|
||||
n_frozen = 0
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@
|
|||
if [[ -n $1 ]] ; then
|
||||
exec sed --in-place 's| *$||' $1
|
||||
else
|
||||
2>& echo "Usage: $0 FILE"
|
||||
>&2 echo "Usage: $0 FILE"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue