mirror of
https://gitlab.com/scemama/QCaml.git
synced 2024-12-22 12:23:31 +01:00
Remove org-mode
This commit is contained in:
parent
d53c0e6ea3
commit
c4b022aeee
@ -12,6 +12,7 @@
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qcaml.gaussian_integrals
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qcaml.operators
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)
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(instrumentation (backend landmarks))
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(modules_without_implementation ao_dim)
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)
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@ -1,96 +0,0 @@
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#+begin_src elisp tangle: no :results none :exports none
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(setq pwd (file-name-directory buffer-file-name))
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(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
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(setq lib (concat pwd "lib/"))
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(setq testdir (concat pwd "test/"))
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(setq mli (concat lib name ".mli"))
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(setq ml (concat lib name ".ml"))
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(setq test-ml (concat testdir name ".ml"))
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(org-babel-tangle)
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#+end_src
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* Charge
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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** Type
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<<<~Charge.t~>>>
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#+begin_src ocaml :tangle (eval mli)
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type t
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#+end_src
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This type should be used for all charges in the program (electrons, nuclei,...).
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#+begin_src ocaml :tangle (eval ml) :exports none
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type t = float
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#+end_src
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** Conversions
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#+begin_src ocaml :tangle (eval mli)
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val of_float : float -> t
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val to_float : t -> float
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val of_int : int -> t
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val to_int : t -> int
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val of_string: string -> t
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val to_string: t -> string
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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external of_float : float -> t = "%identity"
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external to_float : t -> float = "%identity"
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let of_int = float_of_int
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let to_int = int_of_float
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let of_string = float_of_string
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let to_string x =
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if x > 0. then
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Printf.sprintf "+%f" x
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else if x < 0. then
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Printf.sprintf "%f" x
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else
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"0.0"
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#+end_src
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** Simple operations
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#+begin_src ocaml :tangle (eval mli)
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val ( + ) : t -> t -> t
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val ( - ) : t -> t -> t
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val ( * ) : t -> float -> t
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val ( / ) : t -> float -> t
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val is_null : t -> bool
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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let gen_op op =
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fun a b ->
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op (to_float a) (to_float b)
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|> of_float
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let ( + ) = gen_op ( +. )
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let ( - ) = gen_op ( -. )
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let ( * ) = gen_op ( *. )
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let ( / ) = gen_op ( /. )
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let is_null t = t == 0.
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#+end_src
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** Printers
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#+begin_src ocaml :tangle (eval mli)
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val pp : Format.formatter -> t -> unit
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#+end_src
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#+begin_src ocaml :tangle (eval ml) :exports none
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let pp ppf x =
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Format.fprintf ppf "@[%s@]" (to_string x)
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#+end_src
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@ -1,354 +0,0 @@
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#+begin_src elisp tangle: no :results none :exports none
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(setq pwd (file-name-directory buffer-file-name))
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(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
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(setq lib (concat pwd "lib/"))
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(setq testdir (concat pwd "test/"))
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(setq mli (concat lib name ".mli"))
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(setq ml (concat lib name ".ml"))
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(setq test-ml (concat testdir name ".ml"))
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(org-babel-tangle)
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#+end_src
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* Command line
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:PROPERTIES:
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:header-args: :noweb yes :comments both
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:END:
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This module is a wrapper around the ~Getopt~ library and helps to
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define command-line arguments.
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Here is an example of how to use this module.
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First, define the specification:
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#+begin_src ocaml :tangle no
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let open Command_line in
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begin
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set_header_doc (Sys.argv.(0) ^ " - One-line description");
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set_description_doc "Long description of the command.";
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set_specs
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[ { short='c'; long="check"; opt=Optional;
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doc="Checks the input data";
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arg=Without_arg; };
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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='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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]
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end;
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#+end_src
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Then, define what to do with the arguments:
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#+begin_src ocaml :tangle no
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let c =
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Command_line.get_bool "check"
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in
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let basis =
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match Command_line.get "basis" with
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| Some x -> x
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| None -> assert false
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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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| None -> 1
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| Some n -> int_of_string n
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in
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#+end_src
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** Types
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#+NAME:type
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#+begin_src ocaml :tangle (eval mli)
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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
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| Without_arg
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| With_opt_arg of string
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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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#+end_src
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- <<<Short option>>>: in the command line, a dash with a single character
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(ex: =ls -l=)
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- <<<Long option>>>: in the command line, two dashes with a word
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(ex: =ls --directory=)
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- Command-line options can be ~Mandatory~ or ~Optional~
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- Documentation of the option is used in the help function
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- Some options require an argument (~ls --ignore="*.ml"~ ), some
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don't (~ls -l~) and for some arguments the argument is optional
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(~git --log[=<n>]~)
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#+begin_src ocaml :tangle (eval ml) :exports none
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<<type>>
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#+end_src
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** Mutable attributes
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All the options are stored in the hash table ~dict~ where the key
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is the long option and the value is a value of type ~description~.
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#+begin_src ocaml :tangle (eval ml) :exports none
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let header_doc = ref ""
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let description_doc = ref ""
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let footer_doc = ref ""
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let anon_args_ref = ref []
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let specs = ref []
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let dict = Hashtbl.create 67
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#+end_src
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#+begin_src ocaml :tangle (eval mli)
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val set_header_doc : string -> unit
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val set_description_doc : string -> unit
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val set_footer_doc : string -> unit
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#+end_src
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Functions to set the header, footer and main description of the
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documentation provided by the ~help~ function:
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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#+end_src
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#+begin_src ocaml :tangle (eval mli)
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val anonymous : long_opt -> optional -> documentation -> description
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#+end_src
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Function to create an anonymous argument.
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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#+end_src
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** Text formatting functions :noexport:
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Function to print some text such that it fits on the screen
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#+begin_src ocaml :tangle (eval ml) :exports none
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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 :: [] ->
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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 "@]"
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| t ->
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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 "@]@;"
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) t
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end;
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Format.printf "@]"
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#+end_src
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Function to build the short description of the command-line
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arguments, such as
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Example:
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#+begin_example
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my_program -b <string> [-h] [-u <float>] -x <string> [--]
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#+end_example
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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#+end_src
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Function to build the long description of the command-line
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arguments, such as
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Example:
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#+begin_example
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-x --xyz=<string> Name of the file containing the nuclear
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coordinates in xyz format
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#+end_example
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#+begin_src ocaml :tangle (eval ml) :exports none
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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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#+end_src
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** Query functions
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#+begin_src ocaml :tangle (eval mli)
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val get : long_opt -> string option
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val get_bool : long_opt -> bool
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val anon_args : unit -> string list
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#+end_src
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| ~get~ | Returns the argument associated with a long option |
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| ~get_bool~ | True if the ~Optional~ argument is present in the command-line |
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| ~anon_args~ | Returns the list of anonymous arguments |
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#+begin_src ocaml :tangle (eval ml) :exports none
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let anon_args () = !anon_args_ref
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let help () =
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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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(* 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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(* 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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(* 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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||||
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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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||||
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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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||||
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||||
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||||
(* Print options and doc *)
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||||
Format.printf "@[<v 2>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;
|
||||
Format.printf "@]@,@]@,";
|
||||
|
||||
|
||||
(* Print footer *)
|
||||
if !description_doc <> "" then
|
||||
begin
|
||||
Format.printf "@[<v 2>Description:@,@,";
|
||||
output_text !description_doc;
|
||||
Format.printf "@,"
|
||||
end;
|
||||
|
||||
(* Print footer *)
|
||||
output_text !footer_doc;
|
||||
Format.printf "@."
|
||||
|
||||
|
||||
let get x =
|
||||
try Some (Hashtbl.find dict x)
|
||||
with Not_found -> None
|
||||
|
||||
|
||||
let get_bool x = Hashtbl.mem dict x
|
||||
#+end_src
|
||||
|
||||
** Specification
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val set_specs : description list -> unit
|
||||
#+end_src
|
||||
|
||||
Sets the specifications of the current program from a list of
|
||||
~descrption~ variables.
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let set_specs specs_in =
|
||||
specs := { short = 'h' ;
|
||||
long = "help" ;
|
||||
doc = "Prints the help message." ;
|
||||
arg = Without_arg ;
|
||||
opt = Optional ;
|
||||
} :: specs_in;
|
||||
|
||||
let cmd_specs =
|
||||
List.filter (fun x -> x.short != ' ') !specs
|
||||
|> List.map (fun { short ; long ; 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
|
||||
|
||||
Getopt.parse_cmdline cmd_specs (fun x -> anon_args_ref := !anon_args_ref @ [x]);
|
||||
|
||||
if (get_bool "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.")
|
||||
)
|
||||
#+end_src
|
||||
@ -1,79 +0,0 @@
|
||||
#+begin_src elisp tangle: no :results none :exports none
|
||||
(setq pwd (file-name-directory buffer-file-name))
|
||||
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
||||
(setq lib (concat pwd "lib/"))
|
||||
(setq testdir (concat pwd "test/"))
|
||||
(setq mli (concat lib name ".mli"))
|
||||
(setq ml (concat lib name ".ml"))
|
||||
(setq test-ml (concat testdir name ".ml"))
|
||||
(org-babel-tangle)
|
||||
#+end_src
|
||||
|
||||
* Constants
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
All constants used in the program.
|
||||
|
||||
** Thresholds
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val epsilon : float
|
||||
val integrals_cutoff : float
|
||||
#+end_src
|
||||
|
||||
| ~epsilon~ | Value below which a float is considered null. Default is \epsilon = 2.10^{-15} |
|
||||
| ~integrals_cutoff~ | Cutoff value for integrals. Default is \epsilon |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let epsilon = 2.e-15
|
||||
let integrals_cutoff = epsilon
|
||||
#+end_src
|
||||
|
||||
** Mathematical constants
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val pi : float
|
||||
val two_pi : float
|
||||
val sq_pi : float
|
||||
val sq_pi_over_two : float
|
||||
val pi_inv : float
|
||||
val two_over_sq_pi : float
|
||||
#+end_src
|
||||
|
||||
| ~pi~ | $\pi = 3.141~592~653~589~793~12$ |
|
||||
| ~two_pi~ | $2 \pi$ |
|
||||
| ~sq_pi~ | $\sqrt{\pi}$ |
|
||||
| ~sq_pi_over_two~ | $\sqrt{\pi} / 2$ |
|
||||
| ~pi_inv~ | $1 / \pi$ |
|
||||
| ~two_over_sq_pi~ | $2 / \sqrt{\pi}$ |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let pi = acos (-1.)
|
||||
let two_pi = 2. *. pi
|
||||
let sq_pi = sqrt pi
|
||||
let sq_pi_over_two = sq_pi *. 0.5
|
||||
let pi_inv = 1. /. pi
|
||||
let two_over_sq_pi = 2. /. sq_pi
|
||||
#+end_src
|
||||
|
||||
** Physical constants
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val a0 : float
|
||||
val a0_inv : float
|
||||
val ha_to_ev : float
|
||||
val ev_to_ha : float
|
||||
#+end_src
|
||||
|
||||
| ~a0~ | Bohr's radius : $a_0 = 0.529~177~210~67(23)$ angstrom |
|
||||
| ~a0_inv~ | $1 / a_0$ |
|
||||
| ~ha_to_ev~ | Hartree to eV conversion factor : $27.211~386~02(17)$ |
|
||||
| ~ev_to_ha~ | eV to Hartree conversion factor : 1 / ~ha_to_ev~ |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let a0 = 0.529_177_210_67
|
||||
let a0_inv = 1. /. a0
|
||||
let ha_to_ev = 27.211_386_02
|
||||
let ev_to_ha = 1. /. ha_to_ev
|
||||
#+end_src
|
||||
@ -1,218 +0,0 @@
|
||||
#+begin_src elisp tangle: no :results none :exports none
|
||||
(setq pwd (file-name-directory buffer-file-name))
|
||||
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
||||
(setq lib (concat pwd "lib/"))
|
||||
(setq testdir (concat pwd "test/"))
|
||||
(setq mli (concat lib name ".mli"))
|
||||
(setq ml (concat lib name ".ml"))
|
||||
(setq test-ml (concat testdir name ".ml"))
|
||||
(org-babel-tangle)
|
||||
#+end_src
|
||||
|
||||
* Coordinate
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
|
||||
Coordinates in 3D space.
|
||||
|
||||
All operations on points are done in atomic units. Therefore,
|
||||
all coordinates are given in bohr and manipulated with this
|
||||
module.
|
||||
|
||||
** Type
|
||||
|
||||
<<<~Coordinate.t~>>>
|
||||
#+NAME: types
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
type bohr
|
||||
type angstrom
|
||||
|
||||
type xyz = {
|
||||
x : float ;
|
||||
y : float ;
|
||||
z : float ;
|
||||
}
|
||||
|
||||
type 'a point = xyz
|
||||
|
||||
type t = bohr point
|
||||
|
||||
type axis = X | Y | Z
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
type bohr
|
||||
type angstrom
|
||||
|
||||
type xyz = {
|
||||
x : float ;
|
||||
y : float ;
|
||||
z : float ;
|
||||
}
|
||||
|
||||
type 'a point = xyz
|
||||
|
||||
type t = bohr point
|
||||
|
||||
type axis = X | Y | Z
|
||||
#+end_src
|
||||
|
||||
** Creation
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val make : 'a point -> t
|
||||
val make_angstrom : 'a point -> angstrom point
|
||||
val zero : bohr point
|
||||
#+end_src
|
||||
|
||||
| ~make~ | Creates a point in atomic units |
|
||||
| ~make_angstrom~ | Creates a point in angstrom |
|
||||
| ~zero~ | $(0., 0., 0.)$ |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external make : 'a point -> t = "%identity"
|
||||
external make_angstrom : 'a point -> angstrom point = "%identity"
|
||||
|
||||
let zero =
|
||||
make { x = 0. ; y = 0. ; z = 0. }
|
||||
#+end_src
|
||||
|
||||
** Conversion
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val bohr_to_angstrom : bohr point -> angstrom point
|
||||
val angstrom_to_bohr : angstrom point -> bohr point
|
||||
#+end_src
|
||||
|
||||
| ~bohr_to_angstrom~ | Converts a point in bohr to angstrom |
|
||||
| ~angstrom_to_bohr~ | Converts a point in angstrom to bohr |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let b_to_a b = Constants.a0 *. b
|
||||
let bohr_to_angstrom { x ; y ; z } =
|
||||
make { x = b_to_a x ;
|
||||
y = b_to_a y ;
|
||||
z = b_to_a z ; }
|
||||
|
||||
|
||||
let a_to_b a = Constants.a0_inv *. a
|
||||
let angstrom_to_bohr { x ; y ; z } =
|
||||
make { x = a_to_b x ;
|
||||
y = a_to_b y ;
|
||||
z = a_to_b z ; }
|
||||
#+end_src
|
||||
|
||||
** Vector operations
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val neg : t -> t
|
||||
val get : axis -> bohr point -> float
|
||||
val dot : t -> t -> float
|
||||
val norm : t -> float
|
||||
val ( |. ) : float -> t -> t
|
||||
val ( |+ ) : t -> t -> t
|
||||
val ( |- ) : t -> t -> t
|
||||
#+end_src
|
||||
|
||||
| ~neg~ | Negative of a point |
|
||||
| ~get~ | Extracts the projection of the coordinate on an axis |
|
||||
| ~dot~ | Dot product |
|
||||
| ~norm~ | $\ell{^2}$ norm of the vector |
|
||||
| $\vert .$ | Scales the vector by a constant |
|
||||
| $\vert +$ | Adds two vectors |
|
||||
| $\vert -$ | Subtracts two vectors |
|
||||
|
||||
Example:
|
||||
#+begin_example
|
||||
Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
|
||||
- : Coordinate.t = -1.0000 -2.0000 -3.0000
|
||||
|
||||
Coordinate.(get Y { x=1. ; y=2. ; z=3. }) ;;
|
||||
- : float = 2.
|
||||
|
||||
Coordinate.(
|
||||
2. |. { x=1. ; y=2. ; z=3. }
|
||||
) ;;
|
||||
- : Coordinate.t = 2.0000 4.0000 6.0000
|
||||
|
||||
Coordinate.(
|
||||
{ x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. }
|
||||
);;
|
||||
- : Coordinate.t = 3.0000 5.0000 4.0000
|
||||
|
||||
Coordinate.(
|
||||
{ x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. }
|
||||
);;
|
||||
- : Coordinate.t = -1.0000 -1.0000 2.0000
|
||||
#+end_example
|
||||
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let get axis { x ; y ; z } =
|
||||
match axis with
|
||||
| X -> x
|
||||
| Y -> y
|
||||
| Z -> z
|
||||
|
||||
|
||||
let ( |. ) s { x ; y ; z } =
|
||||
make { x = s *. x ;
|
||||
y = s *. y ;
|
||||
z = s *. z ; }
|
||||
|
||||
|
||||
let ( |+ )
|
||||
{ x = x1 ; y = y1 ; z = z1 }
|
||||
{ x = x2 ; y = y2 ; z = z2 } =
|
||||
make { x = x1 +. x2 ;
|
||||
y = y1 +. y2 ;
|
||||
z = z1 +. z2 ; }
|
||||
|
||||
|
||||
let ( |- )
|
||||
{ x = x1 ; y = y1 ; z = z1 }
|
||||
{ x = x2 ; y = y2 ; z = z2 } =
|
||||
make { x = x1 -. x2 ;
|
||||
y = y1 -. y2 ;
|
||||
z = z1 -. z2 ; }
|
||||
|
||||
|
||||
let neg a = -1. |. a
|
||||
|
||||
|
||||
let dot
|
||||
{ x = x1 ; y = y1 ; z = z1 }
|
||||
{ x = x2 ; y = y2 ; z = z2 } =
|
||||
x1 *. x2 +.
|
||||
y1 *. y2 +.
|
||||
z1 *. z2
|
||||
|
||||
|
||||
let norm u =
|
||||
sqrt ( dot u u )
|
||||
#+end_src
|
||||
|
||||
** Printers
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val pp : Format.formatter -> t -> unit
|
||||
val pp_bohr: Format.formatter -> t -> unit
|
||||
val pp_angstrom : Format.formatter -> t -> unit
|
||||
#+end_src
|
||||
|
||||
Coordinates can be printed in bohr or angstrom.
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
open Format
|
||||
let pp ppf c =
|
||||
fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
|
||||
|
||||
let pp_bohr ppf c =
|
||||
fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Bohr)@]" c.x c.y c.z
|
||||
|
||||
let pp_angstrom ppf c =
|
||||
let c = bohr_to_angstrom c in
|
||||
fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z
|
||||
#+end_src
|
||||
|
||||
@ -1,13 +1,7 @@
|
||||
|
||||
|
||||
(* This type should be used for all charges in the program (electrons, nuclei,...). *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Type][Type:2]] *)
|
||||
type t = float
|
||||
(* Type:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:2]] *)
|
||||
(** Conversions *)
|
||||
external of_float : float -> t = "%identity"
|
||||
external to_float : t -> float = "%identity"
|
||||
|
||||
@ -23,9 +17,8 @@ let to_string x =
|
||||
Printf.sprintf "%f" x
|
||||
else
|
||||
"0.0"
|
||||
(* Conversions:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Simple operations][Simple operations:2]] *)
|
||||
(** Simple operations *)
|
||||
let gen_op op =
|
||||
fun a b ->
|
||||
op (to_float a) (to_float b)
|
||||
@ -37,9 +30,7 @@ let ( * ) = gen_op ( *. )
|
||||
let ( / ) = gen_op ( /. )
|
||||
|
||||
let is_null t = t == 0.
|
||||
(* Simple operations:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Printers][Printers:2]] *)
|
||||
(** Printers *)
|
||||
let pp ppf x =
|
||||
Format.fprintf ppf "@[%s@]" (to_string x)
|
||||
(* Printers:2 ends here *)
|
||||
|
||||
@ -1,15 +1,10 @@
|
||||
(* Type
|
||||
*
|
||||
* <<<~Charge.t~>>> *)
|
||||
(** Type *)
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
|
||||
type t
|
||||
(* Type:1 ends here *)
|
||||
|
||||
(* Conversions *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:1]] *)
|
||||
(** Conversions *)
|
||||
|
||||
val of_float : float -> t
|
||||
val to_float : t -> float
|
||||
|
||||
@ -18,22 +13,18 @@ val to_int : t -> int
|
||||
|
||||
val of_string: string -> t
|
||||
val to_string: t -> string
|
||||
(* Conversions:1 ends here *)
|
||||
|
||||
(* Simple operations *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Simple operations][Simple operations:1]] *)
|
||||
(** Simple operations *)
|
||||
|
||||
val ( + ) : t -> t -> t
|
||||
val ( - ) : t -> t -> t
|
||||
val ( * ) : t -> float -> t
|
||||
val ( / ) : t -> float -> t
|
||||
val is_null : t -> bool
|
||||
(* Simple operations:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/charge.org::*Printers][Printers:1]] *)
|
||||
(** Printers *)
|
||||
|
||||
val pp : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
||||
|
||||
@ -1,17 +1,4 @@
|
||||
|
||||
|
||||
(* - <<<Short option>>>: in the command line, a dash with a single character
|
||||
* (ex: =ls -l=)
|
||||
* - <<<Long option>>>: in the command line, two dashes with a word
|
||||
* (ex: =ls --directory=)
|
||||
* - Command-line options can be ~Mandatory~ or ~Optional~
|
||||
* - Documentation of the option is used in the help function
|
||||
* - Some options require an argument (~ls --ignore="*.ml"~ ), some
|
||||
* don't (~ls -l~) and for some arguments the argument is optional
|
||||
* (~git --log[=<n>]~) *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Types][Types:2]] *)
|
||||
(** Types *)
|
||||
type short_opt = char
|
||||
type long_opt = string
|
||||
type optional = Mandatory | Optional
|
||||
@ -27,51 +14,34 @@ type description = {
|
||||
doc : documentation ;
|
||||
arg : argument ;
|
||||
}
|
||||
(* Types:2 ends here *)
|
||||
|
||||
(* Mutable attributes
|
||||
(** Mutable attributes
|
||||
*
|
||||
* All the options are stored in the hash table ~dict~ where the key
|
||||
* is the long option and the value is a value of type ~description~. *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:1]] *)
|
||||
let header_doc = ref ""
|
||||
let description_doc = ref ""
|
||||
let footer_doc = ref ""
|
||||
let anon_args_ref = ref []
|
||||
let specs = ref []
|
||||
let dict = Hashtbl.create 67
|
||||
(* Mutable attributes:1 ends here *)
|
||||
|
||||
|
||||
|
||||
(* Functions to set the header, footer and main description of the
|
||||
* documentation provided by the ~help~ function: *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:3]] *)
|
||||
let set_header_doc s = header_doc := s
|
||||
let set_description_doc s = description_doc := s
|
||||
let set_footer_doc s = footer_doc := s
|
||||
(* Mutable attributes:3 ends here *)
|
||||
|
||||
|
||||
|
||||
(* Function to create an anonymous argument. *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:5]] *)
|
||||
let anonymous name opt doc =
|
||||
{ short=' ' ; long=name; opt; doc; arg=Without_arg; }
|
||||
(* Mutable attributes:5 ends here *)
|
||||
|
||||
(* Text formatting functions :noexport:
|
||||
|
||||
(* Text formatting functions
|
||||
*
|
||||
* Function to print some text such that it fits on the screen *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Text formatting functions][Text formatting functions:1]] *)
|
||||
let output_text t =
|
||||
Format.printf "@[<v 0>";
|
||||
begin
|
||||
@ -90,8 +60,6 @@ let output_text t =
|
||||
) t
|
||||
end;
|
||||
Format.printf "@]"
|
||||
(* Text formatting functions:1 ends here *)
|
||||
|
||||
|
||||
|
||||
|
||||
@ -99,12 +67,11 @@ let output_text t =
|
||||
* arguments, such as
|
||||
*
|
||||
* Example:
|
||||
* #+begin_example
|
||||
|
||||
* my_program -b <string> [-h] [-u <float>] -x <string> [--]
|
||||
* #+end_example *)
|
||||
*)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Text formatting functions][Text formatting functions:2]] *)
|
||||
let output_short x =
|
||||
match x.short, x.opt, x.arg with
|
||||
| ' ', Mandatory, _ -> Format.printf "@[%s@]" x.long
|
||||
@ -115,8 +82,6 @@ let output_short x =
|
||||
| _ , Optional , With_arg arg -> Format.printf "@[[-%c %s]@]" x.short arg
|
||||
| _ , Mandatory, With_opt_arg arg -> Format.printf "@[-%c [%s]@]" x.short arg
|
||||
| _ , Optional , With_opt_arg arg -> Format.printf "@[[-%c [%s]]@]" x.short arg
|
||||
(* Text formatting functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
|
||||
@ -124,13 +89,12 @@ let output_short x =
|
||||
* arguments, such as
|
||||
*
|
||||
* Example:
|
||||
* #+begin_example
|
||||
*
|
||||
* -x --xyz=<string> Name of the file containing the nuclear
|
||||
* coordinates in xyz format
|
||||
* #+end_example *)
|
||||
*)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Text formatting functions][Text formatting functions:3]] *)
|
||||
let output_long max_width x =
|
||||
let arg =
|
||||
match x.short, x.arg with
|
||||
@ -151,17 +115,9 @@ let output_long max_width x =
|
||||
end;
|
||||
Format.printf "@]";
|
||||
output_text x.doc
|
||||
(* Text formatting functions:3 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~get~ | Returns the argument associated with a long option |
|
||||
* | ~get_bool~ | True if the ~Optional~ argument is present in the command-line |
|
||||
* | ~anon_args~ | Returns the list of anonymous arguments | *)
|
||||
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Query functions][Query functions:2]] *)
|
||||
let anon_args () = !anon_args_ref
|
||||
|
||||
let help () =
|
||||
@ -237,15 +193,8 @@ let get x =
|
||||
|
||||
|
||||
let get_bool x = Hashtbl.mem dict x
|
||||
(* Query functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* Sets the specifications of the current program from a list of
|
||||
* ~descrption~ variables. *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Specification][Specification:2]] *)
|
||||
let set_specs specs_in =
|
||||
specs := { short = 'h' ;
|
||||
long = "help" ;
|
||||
@ -280,4 +229,4 @@ let set_specs specs_in =
|
||||
| Some _ -> ()
|
||||
| None -> failwith ("Error: --"^x.long^" option is missing.")
|
||||
)
|
||||
(* Specification:2 ends here *)
|
||||
|
||||
|
||||
@ -1,8 +1,64 @@
|
||||
(* Types
|
||||
*
|
||||
* #+NAME:type *)
|
||||
(** Command line *)
|
||||
|
||||
(* This module is a wrapper around the ~Getopt~ library and helps to
|
||||
* define command-line arguments.
|
||||
*
|
||||
* Here is an example of how to use this module.
|
||||
* First, define the specification:
|
||||
*
|
||||
* let open Command_line in
|
||||
* begin
|
||||
* set_header_doc (Sys.argv.(0) ^ " - One-line description");
|
||||
* set_description_doc "Long description of the command.";
|
||||
* set_specs
|
||||
* [ { short='c'; long="check"; opt=Optional;
|
||||
* doc="Checks the input data";
|
||||
* arg=Without_arg; };
|
||||
*
|
||||
* { short='b' ; long="basis" ; opt=Mandatory;
|
||||
* arg=With_arg "<string>";
|
||||
* doc="Name of the file containing the basis set"; } ;
|
||||
*
|
||||
* { short='m' ; long="multiplicity" ; opt=Optional;
|
||||
* arg=With_arg "<int>";
|
||||
* doc="Spin multiplicity (2S+1). Default is singlet"; } ;
|
||||
* ]
|
||||
* end;
|
||||
*
|
||||
* Then, define what to do with the arguments:
|
||||
*
|
||||
* let c =
|
||||
* Command_line.get_bool "check"
|
||||
* in
|
||||
*
|
||||
* let basis =
|
||||
* match Command_line.get "basis" with
|
||||
* | Some x -> x
|
||||
* | None -> assert false
|
||||
* in
|
||||
*
|
||||
* let multiplicity =
|
||||
* match Command_line.get "multiplicity" with
|
||||
* | None -> 1
|
||||
* | Some n -> int_of_string n
|
||||
* in
|
||||
* ...
|
||||
*)
|
||||
|
||||
|
||||
(* - <<<Short option>>>: in the command line, a dash with a single character
|
||||
* (ex: =ls -l=)
|
||||
* - <<<Long option>>>: in the command line, two dashes with a word
|
||||
* (ex: =ls --directory=)
|
||||
* - Command-line options can be `Mandatory` or `Optional`
|
||||
* - Documentation of the option is used in the help function
|
||||
* - Some options require an argument (`ls --ignore="*.ml"`), some
|
||||
* don't (`ls -l`) and for some arguments the argument is optional
|
||||
* (`git --log[=<n>]`) *)
|
||||
|
||||
|
||||
(** Types *)
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::type][type]] *)
|
||||
type short_opt = char
|
||||
type long_opt = string
|
||||
type optional = Mandatory | Optional
|
||||
@ -18,30 +74,38 @@ type description = {
|
||||
doc : documentation ;
|
||||
arg : argument ;
|
||||
}
|
||||
(* type ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:2]] *)
|
||||
|
||||
(** Mutable attributes *)
|
||||
|
||||
val set_header_doc : string -> unit
|
||||
(** Sets the header of the documentation provided by the ~help~ function: *)
|
||||
|
||||
val set_description_doc : string -> unit
|
||||
(** Sets the description of the documentation provided by the ~help~ function: *)
|
||||
|
||||
val set_footer_doc : string -> unit
|
||||
(* Mutable attributes:2 ends here *)
|
||||
(** Sets the footer of the documentation provided by the ~help~ function: *)
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:4]] *)
|
||||
val anonymous : long_opt -> optional -> documentation -> description
|
||||
(* Mutable attributes:4 ends here *)
|
||||
|
||||
(* Query functions *)
|
||||
(** Creates an anonymous argument. *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Query functions][Query functions:1]] *)
|
||||
(** Query functions *)
|
||||
|
||||
val get : long_opt -> string option
|
||||
(** Returns the argument associated with a long option *)
|
||||
|
||||
val get_bool : long_opt -> bool
|
||||
(** True if the ~Optional~ argument is present in the command-line *)
|
||||
|
||||
val anon_args : unit -> string list
|
||||
(* Query functions:1 ends here *)
|
||||
|
||||
(* Specification *)
|
||||
(** Returns the list of anonymous arguments *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/command_line.org::*Specification][Specification:1]] *)
|
||||
(** Specification *)
|
||||
|
||||
val set_specs : description list -> unit
|
||||
(* Specification:1 ends here *)
|
||||
(** Sets the specifications of the current program from a list of
|
||||
* ~descrption~ variables. *)
|
||||
|
||||
|
||||
@ -1,44 +1,21 @@
|
||||
|
||||
|
||||
(* | ~epsilon~ | Value below which a float is considered null. Default is \epsilon = 2.10^{-15} |
|
||||
* | ~integrals_cutoff~ | Cutoff value for integrals. Default is \epsilon | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Thresholds][Thresholds:2]] *)
|
||||
(** Thresholds *)
|
||||
let epsilon = 2.e-15
|
||||
let integrals_cutoff = epsilon
|
||||
(* Thresholds:2 ends here *)
|
||||
|
||||
|
||||
(** Mathematical constants *)
|
||||
|
||||
(* | ~pi~ | $\pi = 3.141~592~653~589~793~12$ |
|
||||
* | ~two_pi~ | $2 \pi$ |
|
||||
* | ~sq_pi~ | $\sqrt{\pi}$ |
|
||||
* | ~sq_pi_over_two~ | $\sqrt{\pi} / 2$ |
|
||||
* | ~pi_inv~ | $1 / \pi$ |
|
||||
* | ~two_over_sq_pi~ | $2 / \sqrt{\pi}$ | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Mathematical constants][Mathematical constants:2]] *)
|
||||
let pi = acos (-1.)
|
||||
let two_pi = 2. *. pi
|
||||
let sq_pi = sqrt pi
|
||||
let sq_pi_over_two = sq_pi *. 0.5
|
||||
let pi_inv = 1. /. pi
|
||||
let two_over_sq_pi = 2. /. sq_pi
|
||||
(* Mathematical constants:2 ends here *)
|
||||
|
||||
|
||||
(** Physical constants *)
|
||||
|
||||
(* | ~a0~ | Bohr's radius : $a_0 = 0.529~177~210~67(23)$ angstrom |
|
||||
* | ~a0_inv~ | $1 / a_0$ |
|
||||
* | ~ha_to_ev~ | Hartree to eV conversion factor : $27.211~386~02(17)$ |
|
||||
* | ~ev_to_ha~ | eV to Hartree conversion factor : 1 / ~ha_to_ev~ | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Physical constants][Physical constants:2]] *)
|
||||
let a0 = 0.529_177_210_67
|
||||
let a0_inv = 1. /. a0
|
||||
let ha_to_ev = 27.211_386_02
|
||||
let ev_to_ha = 1. /. ha_to_ev
|
||||
(* Physical constants:2 ends here *)
|
||||
|
||||
@ -1,29 +1,43 @@
|
||||
(* Thresholds *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Thresholds][Thresholds:1]] *)
|
||||
val epsilon : float
|
||||
(** Value below which a float is considered null. Default is \epsilon = 2.10^{-15}. *)
|
||||
|
||||
val integrals_cutoff : float
|
||||
(* Thresholds:1 ends here *)
|
||||
|
||||
(* Mathematical constants *)
|
||||
(** Cutoff value for integrals. Default is \epsilon. *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Mathematical constants][Mathematical constants:1]] *)
|
||||
(** Mathematical constants *)
|
||||
val pi : float
|
||||
(** $\pi = 3.141~592~653~589~793~12$ *)
|
||||
|
||||
val two_pi : float
|
||||
(** $2 \pi$ *)
|
||||
|
||||
val sq_pi : float
|
||||
(** $\sqrt{\pi}$ *)
|
||||
|
||||
val sq_pi_over_two : float
|
||||
(** $\sqrt{\pi} / 2$ *)
|
||||
|
||||
val pi_inv : float
|
||||
(** $1 / \pi$ *)
|
||||
|
||||
val two_over_sq_pi : float
|
||||
(* Mathematical constants:1 ends here *)
|
||||
|
||||
(* Physical constants *)
|
||||
(** $2 / \sqrt{\pi}$ *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/constants.org::*Physical constants][Physical constants:1]] *)
|
||||
(** Physical constants *)
|
||||
|
||||
val a0 : float
|
||||
(** Bohr's radius : $a_0 = 0.529~177~210~67(23)$ angstrom. *)
|
||||
|
||||
val a0_inv : float
|
||||
(** $1 / a_0$ *)
|
||||
|
||||
val ha_to_ev : float
|
||||
(** Hartree to eV conversion factor : $27.211~386~02(17)$ *)
|
||||
|
||||
val ev_to_ha : float
|
||||
(* Physical constants:1 ends here *)
|
||||
(** eV to Hartree conversion factor : 1 / ~ha_to_ev~ *)
|
||||
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Type][Type:2]] *)
|
||||
(** Types *)
|
||||
|
||||
type bohr
|
||||
type angstrom
|
||||
|
||||
@ -13,30 +14,22 @@ type 'a point = xyz
|
||||
type t = bohr point
|
||||
|
||||
type axis = X | Y | Z
|
||||
(* Type:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~make~ | Creates a point in atomic units |
|
||||
* | ~make_angstrom~ | Creates a point in angstrom |
|
||||
* | ~zero~ | $(0., 0., 0.)$ | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Creation][Creation:2]] *)
|
||||
(** Creation *)
|
||||
external make : 'a point -> t = "%identity"
|
||||
external make_angstrom : 'a point -> angstrom point = "%identity"
|
||||
|
||||
let zero =
|
||||
make { x = 0. ; y = 0. ; z = 0. }
|
||||
(* Creation:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~bohr_to_angstrom~ | Converts a point in bohr to angstrom |
|
||||
* | ~angstrom_to_bohr~ | Converts a point in angstrom to bohr | *)
|
||||
(** Conversion *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Conversion][Conversion:2]] *)
|
||||
let b_to_a b = Constants.a0 *. b
|
||||
let bohr_to_angstrom { x ; y ; z } =
|
||||
make { x = b_to_a x ;
|
||||
@ -49,45 +42,9 @@ let angstrom_to_bohr { x ; y ; z } =
|
||||
make { x = a_to_b x ;
|
||||
y = a_to_b y ;
|
||||
z = a_to_b z ; }
|
||||
(* Conversion:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~neg~ | Negative of a point |
|
||||
* | ~get~ | Extracts the projection of the coordinate on an axis |
|
||||
* | ~dot~ | Dot product |
|
||||
* | ~norm~ | $\ell{^2}$ norm of the vector |
|
||||
* | $\vert .$ | Scales the vector by a constant |
|
||||
* | $\vert +$ | Adds two vectors |
|
||||
* | $\vert -$ | Subtracts two vectors |
|
||||
*
|
||||
* Example:
|
||||
* #+begin_example
|
||||
* Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
|
||||
* - : Coordinate.t = -1.0000 -2.0000 -3.0000
|
||||
*
|
||||
* Coordinate.(get Y { x=1. ; y=2. ; z=3. }) ;;
|
||||
* - : float = 2.
|
||||
*
|
||||
* Coordinate.(
|
||||
* 2. |. { x=1. ; y=2. ; z=3. }
|
||||
* ) ;;
|
||||
* - : Coordinate.t = 2.0000 4.0000 6.0000
|
||||
*
|
||||
* Coordinate.(
|
||||
* { x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. }
|
||||
* );;
|
||||
* - : Coordinate.t = 3.0000 5.0000 4.0000
|
||||
*
|
||||
* Coordinate.(
|
||||
* { x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. }
|
||||
* );;
|
||||
* - : Coordinate.t = -1.0000 -1.0000 2.0000
|
||||
* #+end_example *)
|
||||
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Vector operations][Vector operations:2]] *)
|
||||
let get axis { x ; y ; z } =
|
||||
match axis with
|
||||
| X -> x
|
||||
@ -130,14 +87,12 @@ let dot
|
||||
|
||||
let norm u =
|
||||
sqrt ( dot u u )
|
||||
(* Vector operations:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* Coordinates can be printed in bohr or angstrom. *)
|
||||
|
||||
(** Printers *)
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Printers][Printers:2]] *)
|
||||
open Format
|
||||
let pp ppf c =
|
||||
fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
|
||||
@ -148,4 +103,3 @@ let pp_bohr ppf c =
|
||||
let pp_angstrom ppf c =
|
||||
let c = bohr_to_angstrom c in
|
||||
fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z
|
||||
(* Printers:2 ends here *)
|
||||
|
||||
@ -1,9 +1,14 @@
|
||||
(* Type
|
||||
(** Coordinates
|
||||
*
|
||||
* <<<~Coordinate.t~>>>
|
||||
* #+NAME: types *)
|
||||
* Coordinates in 3D space.
|
||||
*
|
||||
* All operations on points are done in atomic units.
|
||||
* Therefore, all coordinates are given in bohr and
|
||||
* manipulated with this module.
|
||||
*)
|
||||
|
||||
(** Types *)
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::types][types]] *)
|
||||
type bohr
|
||||
type angstrom
|
||||
|
||||
@ -18,43 +23,85 @@ type 'a point = xyz
|
||||
type t = bohr point
|
||||
|
||||
type axis = X | Y | Z
|
||||
(* types ends here *)
|
||||
|
||||
(* Creation *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Creation][Creation:1]] *)
|
||||
(** Creation *)
|
||||
|
||||
val make : 'a point -> t
|
||||
(** Creates a point in atomic units *)
|
||||
|
||||
val make_angstrom : 'a point -> angstrom point
|
||||
(** Creates a point in angstrom *)
|
||||
|
||||
val zero : bohr point
|
||||
(* Creation:1 ends here *)
|
||||
|
||||
(* Conversion *)
|
||||
(** (0., 0., 0.) *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Conversion][Conversion:1]] *)
|
||||
(** Conversion *)
|
||||
|
||||
val bohr_to_angstrom : bohr point -> angstrom point
|
||||
(** Converts a point in bohr to angstrom *)
|
||||
|
||||
val angstrom_to_bohr : angstrom point -> bohr point
|
||||
(* Conversion:1 ends here *)
|
||||
(** Converts a point in angstrom to bohr *)
|
||||
|
||||
(* Vector operations *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Vector operations][Vector operations:1]] *)
|
||||
(** Vector operations *)
|
||||
|
||||
val neg : t -> t
|
||||
(** Negative of a point *)
|
||||
|
||||
val get : axis -> bohr point -> float
|
||||
(** Extracts the projection of the coordinate on an axis *)
|
||||
|
||||
val dot : t -> t -> float
|
||||
(** Dot product *)
|
||||
|
||||
val norm : t -> float
|
||||
(** $\ell{^2}$ norm of the vector *)
|
||||
|
||||
val ( |. ) : float -> t -> t
|
||||
(** Scales the vector by a constant *)
|
||||
|
||||
val ( |+ ) : t -> t -> t
|
||||
(** Adds two vectors *)
|
||||
|
||||
val ( |- ) : t -> t -> t
|
||||
(* Vector operations:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
(** Subtracts two vectors *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/coordinate.org::*Printers][Printers:1]] *)
|
||||
(** Example
|
||||
|
||||
* Coordinate.neg { x=1. ; y=2. ; z=3. } ;;
|
||||
* - : Coordinate.t = -1.0000 -2.0000 -3.0000
|
||||
*
|
||||
* Coordinate.(get Y { x=1. ; y=2. ; z=3. }) ;;
|
||||
* - : float = 2.
|
||||
*
|
||||
* Coordinate.(
|
||||
* 2. |. { x=1. ; y=2. ; z=3. }
|
||||
* ) ;;
|
||||
* - : Coordinate.t = 2.0000 4.0000 6.0000
|
||||
*
|
||||
* Coordinate.(
|
||||
* { x=1. ; y=2. ; z=3. } |+ { x=2. ; y=3. ; z=1. }
|
||||
* );;
|
||||
* - : Coordinate.t = 3.0000 5.0000 4.0000
|
||||
*
|
||||
* Coordinate.(
|
||||
* { x=1. ; y=2. ; z=3. } |- { x=2. ; y=3. ; z=1. }
|
||||
* );;
|
||||
* - : Coordinate.t = -1.0000 -1.0000 2.0000
|
||||
*)
|
||||
|
||||
|
||||
|
||||
(** Printers *)
|
||||
|
||||
(* Coordinates can be printed in bohr or angstrom. *)
|
||||
|
||||
val pp : Format.formatter -> t -> unit
|
||||
val pp_bohr: Format.formatter -> t -> unit
|
||||
val pp_angstrom : Format.formatter -> t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
||||
@ -1,51 +1,31 @@
|
||||
(* [[file:~/QCaml/common/util.org::*Erf][Erf:3]] *)
|
||||
(** Utility functions *)
|
||||
|
||||
external erf_float : float -> float
|
||||
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
|
||||
(* Erf:3 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Erfc][Erfc:3]] *)
|
||||
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
|
||||
(* Erfc:3 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Gamma][Gamma:3]] *)
|
||||
external gamma_float : float -> float
|
||||
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
|
||||
(* Gamma:3 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Popcnt][Popcnt:3]] *)
|
||||
external popcnt : int64 -> int32 = "popcnt_bytecode" "popcnt"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let popcnt i = (popcnt [@inlined] ) i |> Int32.to_int
|
||||
(* Popcnt:3 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Trailz][Trailz:3]] *)
|
||||
external trailz : int64 -> int32 = "trailz_bytecode" "trailz" "int"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let trailz i = trailz i |> Int32.to_int
|
||||
(* Trailz:3 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Leadz][Leadz:3]] *)
|
||||
external leadz : int64 -> int32 = "leadz_bytecode" "leadz" "int"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let leadz i = leadz i |> Int32.to_int
|
||||
(* Leadz:3 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~fact~ | Factorial function. |
|
||||
* | ~binom~ | Binomial coefficient. ~binom n k~ = $C_n^k$ |
|
||||
* | ~binom_float~ | float variant of ~binom~ |
|
||||
* | ~pow~ | Fast implementation of the power function for small integer powers |
|
||||
* | ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
|
||||
* | ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
|
||||
* | ~not_implemented~ | Fails if some functionality is not implemented |
|
||||
* | ~of_some~ | Extracts the value of an option | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*General functions][General functions:2]] *)
|
||||
let memo_float_of_int =
|
||||
Array.init 64 float_of_int
|
||||
|
||||
@ -133,26 +113,11 @@ let not_implemented string =
|
||||
let of_some = function
|
||||
| Some a -> a
|
||||
| None -> assert false
|
||||
(* General functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* The lower [[https://en.wikipedia.org/wiki/Incomplete_gamma_function][Incomplete Gamma function]] is implemented :
|
||||
* \[
|
||||
* \gamma(\alpha,x) = \int_0^x e^{-t} t^{\alpha-1} dt
|
||||
* \]
|
||||
*
|
||||
* p: $\frac{1}{\Gamma(\alpha)} \int_0^x e^{-t} t^{\alpha-1} dt$
|
||||
*
|
||||
* q: $\frac{1}{\Gamma(\alpha)} \int_x^\infty e^{-t} t^{\alpha-1} dt$
|
||||
*
|
||||
* Reference : Haruhiko Okumura: C-gengo niyoru saishin algorithm jiten
|
||||
* (New Algorithm handbook in C language) (Gijyutsu hyouron sha,
|
||||
* Tokyo, 1991) p.227 [in Japanese] *)
|
||||
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Functions related to the Boys function][Functions related to the Boys function:2]] *)
|
||||
let incomplete_gamma ~alpha x =
|
||||
assert (alpha >= 0.);
|
||||
assert (x >= 0.);
|
||||
@ -195,26 +160,8 @@ let incomplete_gamma ~alpha x =
|
||||
qg_loop min_float (w /. lb) 1. lb w 2.0
|
||||
in
|
||||
gf *. p_gamma x
|
||||
(* Functions related to the Boys function:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* The [[https://link.springer.com/article/10.1007/s10910-005-9023-3][Generalized Boys function]] is implemented,
|
||||
* ~maxm~ is the maximum total angular momentum.
|
||||
*
|
||||
* \[
|
||||
* F_m(x) = \frac{\gamma(m+1/2,x)}{2x^{m+1/2}}
|
||||
* \]
|
||||
* where $\gamma$ is the incomplete gamma function.
|
||||
*
|
||||
* - $F_0(0.) = 1$
|
||||
* - $F_0(t) = \frac{\sqrt{\pi}}{2\sqrt{t}} \text{erf} ( \sqrt{t} )$
|
||||
* - $F_m(0.) = \frac{1}{2m+1}$
|
||||
* - $F_m(t) = \frac{\gamma{m+1/2,t}}{2t^{m+1/2}}$
|
||||
* - $F_m(t) = \frac{ 2t\, F_{m+1}(t) + e^{-t} }{2m+1}$ *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Functions related to the Boys function][Functions related to the Boys function:4]] *)
|
||||
let boys_function ~maxm t =
|
||||
assert (t >= 0.);
|
||||
match maxm with
|
||||
@ -251,16 +198,8 @@ let boys_function ~maxm t =
|
||||
result
|
||||
with Exit -> result
|
||||
end
|
||||
(* Functions related to the Boys function:4 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~list_some~ | Filters out all ~None~ elements of the list, and returns the elements without the ~Some~ |
|
||||
* | ~list_range~ | Creates a list of consecutive integers |
|
||||
* | ~list_pack~ | ~list_pack n l~ Creates a list of ~n~-elements lists | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*List functions][List functions:2]] *)
|
||||
let list_some l =
|
||||
List.filter (function None -> false | _ -> true) l
|
||||
|> List.rev_map (function Some x -> x | _ -> assert false)
|
||||
@ -289,16 +228,9 @@ let list_pack n l =
|
||||
| _ -> (aux [@tailcall]) (i-1) (a::accu1) accu2 rest
|
||||
in
|
||||
aux (n-1) [] [] l
|
||||
(* List functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~array_range~ | Creates an array of consecutive integers |
|
||||
* | ~array_sum~ | Returns the sum of all the elements of the array |
|
||||
* | ~array_product~ | Returns the product of all the elements of the array | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Array functions][Array functions:2]] *)
|
||||
let array_range first last =
|
||||
if last < first then [| |] else
|
||||
Array.init (last-first+1) (fun i -> i+first)
|
||||
@ -310,16 +242,8 @@ let array_sum a =
|
||||
|
||||
let array_product a =
|
||||
Array.fold_left ( *. ) 1. a
|
||||
(* Array functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~seq_range~ | Creates a sequence returning consecutive integers |
|
||||
* | ~seq_to_list~ | Read a sequence and put items in a list |
|
||||
* | ~seq_fold~ | Apply a fold to the elements of the sequence | *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Seq functions][Seq functions:2]] *)
|
||||
let seq_range first last =
|
||||
Seq.init (last-first) (fun i -> i+first)
|
||||
|
||||
@ -334,39 +258,8 @@ let seq_to_list seq =
|
||||
|
||||
let seq_fold f init seq =
|
||||
Seq.fold_left f init seq
|
||||
(* Seq functions:2 ends here *)
|
||||
|
||||
|
||||
|
||||
(* | ~pp_float_array~ | Printer for float arrays |
|
||||
* | ~pp_float_array_size~ | Printer for float arrays with size |
|
||||
* | ~pp_float_2darray~ | Printer for matrices |
|
||||
* | ~pp_float_2darray_size~ | Printer for matrices with size |
|
||||
* | ~pp_bitstring~ | Printer for bit strings (used by ~Bitstring~ module) |
|
||||
*
|
||||
* Example:
|
||||
* #+begin_example
|
||||
* pp_float_array_size:
|
||||
* [ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
*
|
||||
* pp_float_array:
|
||||
* [ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
*
|
||||
* pp_float_2darray_size
|
||||
* [
|
||||
* 2:[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
* [ 4: 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
*
|
||||
* pp_float_2darray:
|
||||
* [ [ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
* [ 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
*
|
||||
* pp_bitstring 14:
|
||||
* +++++------+--
|
||||
* #+end_example *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Printers][Printers:2]] *)
|
||||
let pp_float_array ppf a =
|
||||
Format.fprintf ppf "@[<2>[@ ";
|
||||
Array.iter (fun f -> Format.fprintf ppf "@[%10f@]@ " f) a;
|
||||
@ -390,4 +283,3 @@ let pp_float_2darray_size ppf a =
|
||||
let pp_bitstring n ppf bs =
|
||||
String.init n (fun i -> if (Z.testbit bs i) then '+' else '-')
|
||||
|> Format.fprintf ppf "@[<h>%s@]"
|
||||
(* Printers:2 ends here *)
|
||||
|
||||
@ -1,96 +1,157 @@
|
||||
(* [[file:~/QCaml/common/util.org::*Erf][Erf:2]] *)
|
||||
(** Error function *)
|
||||
external erf_float : float -> float
|
||||
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
|
||||
(* Erf:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Erfc][Erfc:2]] *)
|
||||
external erfc_float : float -> float
|
||||
= "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
|
||||
(* Erfc:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Gamma][Gamma:2]] *)
|
||||
external gamma_float : float -> float
|
||||
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
|
||||
(* Gamma:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Popcnt][Popcnt:2]] *)
|
||||
|
||||
(** Bit manipulation functions *)
|
||||
val popcnt : int64 -> int
|
||||
(* Popcnt:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Trailz][Trailz:2]] *)
|
||||
val trailz : int64 -> int
|
||||
(* Trailz:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Leadz][Leadz:2]] *)
|
||||
val leadz : int64 -> int
|
||||
(* Leadz:2 ends here *)
|
||||
|
||||
(* General functions *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*General functions][General functions:1]] *)
|
||||
(** General functions *)
|
||||
|
||||
val fact : int -> float
|
||||
(* @raise Invalid_argument for negative arguments or arguments >100. *)
|
||||
(** Factorial function.
|
||||
* @raise Invalid_argument for negative arguments or arguments >100. *)
|
||||
|
||||
val binom : int -> int -> int
|
||||
(** Binomial coefficient. ~binom n k~ = $C_n^k$ *)
|
||||
|
||||
val binom_float : int -> int -> float
|
||||
(** Binomial coefficient (float). ~binom n k~ = $C_n^k$ *)
|
||||
|
||||
val chop : float -> (unit -> float) -> float
|
||||
(** In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. *)
|
||||
|
||||
val pow : float -> int -> float
|
||||
(** Fast implementation of the power function for small integer powers *)
|
||||
|
||||
val float_of_int_fast : int -> float
|
||||
(** Faster implementation of float_of_int for small positive ints *)
|
||||
|
||||
val of_some : 'a option -> 'a
|
||||
(** Extracts the value of an option *)
|
||||
|
||||
exception Not_implemented of string
|
||||
val not_implemented : string -> 'a
|
||||
(* @raise Not_implemented. *)
|
||||
(* General functions:1 ends here *)
|
||||
|
||||
(* Functions related to the Boys function *)
|
||||
(** Fails if some functionality is not implemented
|
||||
* @raise Not_implemented. *)
|
||||
|
||||
|
||||
(** Functions related to the Boys function *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Functions related to the Boys function][Functions related to the Boys function:1]] *)
|
||||
val incomplete_gamma : alpha:float -> float -> float
|
||||
(* @raise Failure when the calculation doesn't converge. *)
|
||||
(* Functions related to the Boys function:1 ends here *)
|
||||
(** The lower [[https://en.wikipedia.org/wiki/Incomplete_gamma_function][Incomplete Gamma function]] is implemented :
|
||||
* \[
|
||||
* \gamma(\alpha,x) = \int_0^x e^{-t} t^{\alpha-1} dt
|
||||
* \]
|
||||
*
|
||||
* p: $\frac{1}{\Gamma(\alpha)} \int_0^x e^{-t} t^{\alpha-1} dt$
|
||||
*
|
||||
* q: $\frac{1}{\Gamma(\alpha)} \int_x^\infty e^{-t} t^{\alpha-1} dt$
|
||||
*
|
||||
* Reference : Haruhiko Okumura: C-gengo niyoru saishin algorithm jiten
|
||||
* (New Algorithm handbook in C language) (Gijyutsu hyouron sha,
|
||||
* Tokyo, 1991) p.227 [in Japanese].
|
||||
*
|
||||
* @raise Failure when the calculation doesn't converge. *)
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Functions related to the Boys function][Functions related to the Boys function:3]] *)
|
||||
val boys_function : maxm:int -> float -> float array
|
||||
(* Functions related to the Boys function:3 ends here *)
|
||||
(** Functions related to the Boys function:3 ends here
|
||||
|
||||
(* List functions *)
|
||||
The [[https://link.springer.com/article/10.1007/s10910-005-9023-3][Generalized Boys function]] is implemented,
|
||||
~maxm~ is the maximum total angular momentum.
|
||||
|
||||
\[
|
||||
F_m(x) = \frac{\gamma(m+1/2,x)}{2x^{m+1/2}}
|
||||
\]
|
||||
where $\gamma$ is the incomplete gamma function.
|
||||
|
||||
- $F_0(0.) = 1$
|
||||
- $F_0(t) = \frac{\sqrt{\pi}}{2\sqrt{t}} \text{erf} ( \sqrt{t} )$
|
||||
- $F_m(0.) = \frac{1}{2m+1}$
|
||||
- $F_m(t) = \frac{\gamma{m+1/2,t}}{2t^{m+1/2}}$
|
||||
- $F_m(t) = \frac{ 2t\, F_{m+1}(t) + e^{-t} }{2m+1}$
|
||||
*)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*List functions][List functions:1]] *)
|
||||
(** List functions *)
|
||||
|
||||
val list_some : 'a option list -> 'a list
|
||||
(** Filters out all ~None~ elements of the list, and returns the elements without the ~Some~ *)
|
||||
|
||||
val list_range : int -> int -> int list
|
||||
(** Creates a list of consecutive integers *)
|
||||
|
||||
val list_pack : int -> 'a list -> 'a list list
|
||||
(* List functions:1 ends here *)
|
||||
|
||||
(* Array functions *)
|
||||
(** ~list_pack n l~ Creates a list of ~n~-elements lists *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Array functions][Array functions:1]] *)
|
||||
(** Array functions *)
|
||||
|
||||
val array_range : int -> int -> int array
|
||||
(** Creates an array of consecutive integers *)
|
||||
|
||||
val array_sum : float array -> float
|
||||
(** Returns the sum of all the elements of the array *)
|
||||
|
||||
val array_product : float array -> float
|
||||
(* Array functions:1 ends here *)
|
||||
|
||||
(* Seq functions *)
|
||||
(** Returns the product of all the elements of the array *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Seq functions][Seq functions:1]] *)
|
||||
(** Seq functions *)
|
||||
|
||||
val seq_range : int -> int -> int Seq.t
|
||||
(** Creates a sequence returning consecutive integers *)
|
||||
|
||||
val seq_to_list : 'a Seq.t -> 'a list
|
||||
(** Read a sequence and put items in a list *)
|
||||
|
||||
val seq_fold : ('a -> 'b -> 'a) -> 'a -> 'b Seq.t -> 'a
|
||||
(* Seq functions:1 ends here *)
|
||||
|
||||
(* Printers *)
|
||||
(** Apply a fold to the elements of the sequence *)
|
||||
|
||||
|
||||
(* [[file:~/QCaml/common/util.org::*Printers][Printers:1]] *)
|
||||
(** Printers *)
|
||||
|
||||
(**
|
||||
| ~pp_float_array~ | Printer for float arrays |
|
||||
| ~pp_float_array_size~ | Printer for float arrays with size |
|
||||
| ~pp_float_2darray~ | Printer for matrices |
|
||||
| ~pp_float_2darray_size~ | Printer for matrices with size |
|
||||
| ~pp_bitstring~ | Printer for bit strings (used by ~Bitstring~ module) |
|
||||
|
||||
Example:
|
||||
#+begin_example
|
||||
pp_float_array_size:
|
||||
[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
|
||||
pp_float_array:
|
||||
[ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
|
||||
pp_float_2darray_size
|
||||
[
|
||||
2:[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
[ 4: 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
|
||||
pp_float_2darray:
|
||||
[ [ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
[ 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
|
||||
pp_bitstring 14:
|
||||
+++++------+--
|
||||
#+end_example
|
||||
*)
|
||||
|
||||
val pp_float_array_size : Format.formatter -> float array -> unit
|
||||
val pp_float_array : Format.formatter -> float array -> unit
|
||||
val pp_float_2darray_size : Format.formatter -> float array array -> unit
|
||||
val pp_float_2darray : Format.formatter -> float array array -> unit
|
||||
val pp_bitstring : int -> Format.formatter -> Z.t -> unit
|
||||
(* Printers:1 ends here *)
|
||||
|
||||
672
common/util.org
672
common/util.org
@ -1,672 +0,0 @@
|
||||
#+begin_src elisp tangle: no :results none :exports none
|
||||
(setq pwd (file-name-directory buffer-file-name))
|
||||
(setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
|
||||
(setq lib (concat pwd "lib/"))
|
||||
(setq testdir (concat pwd "test/"))
|
||||
(setq mli (concat lib name ".mli"))
|
||||
(setq ml (concat lib name ".ml"))
|
||||
(setq c (concat lib name ".c"))
|
||||
(setq test-ml (concat testdir name ".ml"))
|
||||
(org-babel-tangle)
|
||||
#+end_src
|
||||
|
||||
* Util
|
||||
:PROPERTIES:
|
||||
:header-args: :noweb yes :comments both
|
||||
:END:
|
||||
|
||||
Utility functions.
|
||||
|
||||
|
||||
** Test header :noexport:
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
open Common.Util
|
||||
open Alcotest
|
||||
#+end_src
|
||||
|
||||
** External C functions
|
||||
|
||||
| ~erf_float~ | Error function ~erf~ from =libm= |
|
||||
| ~erfc_float~ | Complementary error function ~erfc~ from =libm= |
|
||||
| ~gamma_float~ | Gamma function ~gamma~ from =libm= |
|
||||
| ~popcnt~ | ~popcnt~ instruction |
|
||||
| ~trailz~ | ~ctz~ instruction |
|
||||
| ~leadz~ | ~bsf~ instruction |
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
#include <math.h>
|
||||
#include <caml/mlvalues.h>
|
||||
#include <caml/alloc.h>
|
||||
#+end_src
|
||||
|
||||
*** Erf
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim value erf_float_bytecode(value x) {
|
||||
return caml_copy_double(erf(Double_val(x)));
|
||||
}
|
||||
|
||||
CAMLprim double erf_float(double x) {
|
||||
return erf(x);
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
external erf_float : float -> float
|
||||
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external erf_float : float -> float
|
||||
= "erf_float_bytecode" "erf_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
*** Erfc
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim value erfc_float_bytecode(value x) {
|
||||
return caml_copy_double(erfc(Double_val(x)));
|
||||
}
|
||||
|
||||
CAMLprim double erfc_float(double x) {
|
||||
return erfc(x);
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
external erfc_float : float -> float
|
||||
= "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external erfc_float : float -> float = "erfc_float_bytecode" "erfc_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
*** Gamma
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim value gamma_float_bytecode(value x) {
|
||||
return caml_copy_double(tgamma(Double_val(x)));
|
||||
}
|
||||
|
||||
|
||||
CAMLprim double gamma_float(double x) {
|
||||
return tgamma(x);
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
external gamma_float : float -> float
|
||||
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external gamma_float : float -> float
|
||||
= "gamma_float_bytecode" "gamma_float" [@@unboxed] [@@noalloc]
|
||||
#+end_src
|
||||
|
||||
*** Popcnt
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim int32_t popcnt(int64_t i) {
|
||||
return __builtin_popcountll (i);
|
||||
}
|
||||
|
||||
|
||||
CAMLprim value popcnt_bytecode(value i) {
|
||||
return caml_copy_int32(__builtin_popcountll (Int64_val(i)));
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val popcnt : int64 -> int
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external popcnt : int64 -> int32 = "popcnt_bytecode" "popcnt"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let popcnt i = (popcnt [@inlined] ) i |> Int32.to_int
|
||||
#+end_src
|
||||
|
||||
*** Trailz
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim int32_t trailz(int64_t i) {
|
||||
return i == 0L ? 64 : __builtin_ctzll (i);
|
||||
}
|
||||
|
||||
|
||||
CAMLprim value trailz_bytecode(value i) {
|
||||
return caml_copy_int32(i == 0L ? 64 : __builtin_ctzll (Int64_val(i)));
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val trailz : int64 -> int
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external trailz : int64 -> int32 = "trailz_bytecode" "trailz" "int"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let trailz i = trailz i |> Int32.to_int
|
||||
#+end_src
|
||||
|
||||
*** Leadz
|
||||
|
||||
#+begin_src c :tangle (eval c) :exports none
|
||||
CAMLprim int32_t leadz(int64_t i) {
|
||||
return i == 0L ? 64 : __builtin_clzll(i);
|
||||
}
|
||||
|
||||
|
||||
CAMLprim value leadz_bytecode(value i) {
|
||||
return caml_copy_int32(i == 0L ? 64 : __builtin_clzll (Int64_val(i)));
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val leadz : int64 -> int
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
external leadz : int64 -> int32 = "leadz_bytecode" "leadz" "int"
|
||||
[@@unboxed] [@@noalloc]
|
||||
|
||||
let leadz i = leadz i |> Int32.to_int
|
||||
#+end_src
|
||||
|
||||
*** Test
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let test_external () =
|
||||
check (float 1.e-15) "erf" 0.842700792949715 (erf_float 1.0);
|
||||
check (float 1.e-15) "erf" 0.112462916018285 (erf_float 0.1);
|
||||
check (float 1.e-15) "erf" (-0.112462916018285) (erf_float (-0.1));
|
||||
check (float 1.e-15) "erfc" 0.157299207050285 (erfc_float 1.0);
|
||||
check (float 1.e-15) "erfc" 0.887537083981715 (erfc_float 0.1);
|
||||
check (float 1.e-15) "erfc" (1.112462916018285) (erfc_float (-0.1));
|
||||
check (float 1.e-14) "gamma" (1.77245385090552) (gamma_float 0.5);
|
||||
check (float 1.e-14) "gamma" (9.51350769866873) (gamma_float (0.1));
|
||||
check (float 1.e-14) "gamma" (-3.54490770181103) (gamma_float (-0.5));
|
||||
check int "popcnt" 6 (popcnt @@ Int64.of_int 63);
|
||||
check int "popcnt" 8 (popcnt @@ Int64.of_int 299605);
|
||||
check int "popcnt" 1 (popcnt @@ Int64.of_int 65536);
|
||||
check int "popcnt" 0 (popcnt @@ Int64.of_int 0);
|
||||
check int "trailz" 3 (trailz @@ Int64.of_int 8);
|
||||
check int "trailz" 2 (trailz @@ Int64.of_int 12);
|
||||
check int "trailz" 0 (trailz @@ Int64.of_int 1);
|
||||
check int "trailz" 64 (trailz @@ Int64.of_int 0);
|
||||
check int "leadz" 60 (leadz @@ Int64.of_int 8);
|
||||
check int "leadz" 60 (leadz @@ Int64.of_int 12);
|
||||
check int "leadz" 63 (leadz @@ Int64.of_int 1);
|
||||
check int "leadz" 64 (leadz @@ Int64.of_int 0);
|
||||
()
|
||||
#+end_src
|
||||
|
||||
** General functions
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val fact : int -> float
|
||||
(* @raise Invalid_argument for negative arguments or arguments >100. *)
|
||||
val binom : int -> int -> int
|
||||
val binom_float : int -> int -> float
|
||||
|
||||
val chop : float -> (unit -> float) -> float
|
||||
val pow : float -> int -> float
|
||||
val float_of_int_fast : int -> float
|
||||
|
||||
val of_some : 'a option -> 'a
|
||||
|
||||
exception Not_implemented of string
|
||||
val not_implemented : string -> 'a
|
||||
(* @raise Not_implemented. *)
|
||||
#+end_src
|
||||
|
||||
| ~fact~ | Factorial function. |
|
||||
| ~binom~ | Binomial coefficient. ~binom n k~ = $C_n^k$ |
|
||||
| ~binom_float~ | float variant of ~binom~ |
|
||||
| ~pow~ | Fast implementation of the power function for small integer powers |
|
||||
| ~chop~ | In ~chop a f~, evaluate ~f~ only if the absolute value of ~a~ is larger than ~Constants.epsilon~, and return ~a *. f ()~. |
|
||||
| ~float_of_int_fast~ | Faster implementation of float_of_int for small positive ints |
|
||||
| ~not_implemented~ | Fails if some functionality is not implemented |
|
||||
| ~of_some~ | Extracts the value of an option |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let memo_float_of_int =
|
||||
Array.init 64 float_of_int
|
||||
|
||||
let float_of_int_fast i =
|
||||
if Int.logand i 63 = i then
|
||||
memo_float_of_int.(i)
|
||||
else
|
||||
float_of_int i
|
||||
|
||||
|
||||
let factmax = 150
|
||||
|
||||
let fact_memo =
|
||||
let rec aux accu_l accu = function
|
||||
| 0 -> (aux [@tailcall]) [1.] 1. 1
|
||||
| i when (i = factmax) ->
|
||||
let x = (float_of_int factmax) *. accu in
|
||||
List.rev (x::accu_l)
|
||||
| i -> let x = (float_of_int i) *. accu in
|
||||
(aux [@tailcall]) (x::accu_l) x (i+1)
|
||||
in
|
||||
aux [] 0. 0
|
||||
|> Array.of_list
|
||||
|
||||
let fact = function
|
||||
| i when (i < 0) ->
|
||||
raise (Invalid_argument "Argument of factorial should be non-negative")
|
||||
| i when (i > 150) ->
|
||||
raise (Invalid_argument "Result of factorial is infinite")
|
||||
| i -> fact_memo.(i)
|
||||
|
||||
|
||||
let binom =
|
||||
let memo =
|
||||
let m = Array.make_matrix 64 64 0 in
|
||||
for n=0 to Array.length m - 1 do
|
||||
m.(n).(0) <- 1;
|
||||
m.(n).(n) <- 1;
|
||||
for k=1 to (n - 1) do
|
||||
m.(n).(k) <- m.(n-1).(k-1) + m.(n-1).(k)
|
||||
done
|
||||
done;
|
||||
m
|
||||
in
|
||||
let rec f n k =
|
||||
assert (k >= 0);
|
||||
assert (n >= k);
|
||||
if k = 0 || k = n then
|
||||
1
|
||||
else if n < 64 then
|
||||
memo.(n).(k)
|
||||
else
|
||||
f (n-1) (k-1) + f (n-1) k
|
||||
in f
|
||||
|
||||
|
||||
let binom_float n k =
|
||||
binom n k
|
||||
|> float_of_int_fast
|
||||
|
||||
|
||||
let rec pow a = function
|
||||
| 0 -> 1.
|
||||
| 1 -> a
|
||||
| 2 -> a *. a
|
||||
| 3 -> a *. a *. a
|
||||
| -1 -> 1. /. a
|
||||
| n when n > 0 ->
|
||||
let b = pow a (n / 2) in
|
||||
b *. b *. (if n mod 2 = 0 then 1. else a)
|
||||
| n when n < 0 -> (pow [@tailcall]) (1./.a) (-n)
|
||||
| _ -> assert false
|
||||
|
||||
|
||||
let chop f g =
|
||||
if (abs_float f) < Constants.epsilon then 0.
|
||||
else f *. (g ())
|
||||
|
||||
|
||||
exception Not_implemented of string
|
||||
let not_implemented string =
|
||||
raise (Not_implemented string)
|
||||
|
||||
|
||||
let of_some = function
|
||||
| Some a -> a
|
||||
| None -> assert false
|
||||
|
||||
#+end_src
|
||||
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let test_general () =
|
||||
check int "of_some_of_int_fast" 1 (of_some (Some 1)) ;
|
||||
check int "binom" 35 (binom 7 4);
|
||||
check (float 1.e-15) "fact" 5040. (fact 7);
|
||||
check (float 1.e-15) "binom_float" 35.0 (binom_float 7 4);
|
||||
check (float 1.e-15) "pow" 729.0 (pow 3.0 6);
|
||||
check (float 1.e-15) "float_of_int_fast" 10.0 (float_of_int_fast 10);
|
||||
()
|
||||
#+end_src
|
||||
|
||||
** Functions related to the Boys function
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val incomplete_gamma : alpha:float -> float -> float
|
||||
(* @raise Failure when the calculation doesn't converge. *)
|
||||
#+end_src
|
||||
|
||||
The lower [[https://en.wikipedia.org/wiki/Incomplete_gamma_function][Incomplete Gamma function]] is implemented :
|
||||
\[
|
||||
\gamma(\alpha,x) = \int_0^x e^{-t} t^{\alpha-1} dt
|
||||
\]
|
||||
|
||||
p: $\frac{1}{\Gamma(\alpha)} \int_0^x e^{-t} t^{\alpha-1} dt$
|
||||
|
||||
q: $\frac{1}{\Gamma(\alpha)} \int_x^\infty e^{-t} t^{\alpha-1} dt$
|
||||
|
||||
Reference : Haruhiko Okumura: C-gengo niyoru saishin algorithm jiten
|
||||
(New Algorithm handbook in C language) (Gijyutsu hyouron sha,
|
||||
Tokyo, 1991) p.227 [in Japanese]
|
||||
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let incomplete_gamma ~alpha x =
|
||||
assert (alpha >= 0.);
|
||||
assert (x >= 0.);
|
||||
let a = alpha in
|
||||
let a_inv = 1./. a in
|
||||
let gf = gamma_float alpha in
|
||||
let loggamma_a = log gf in
|
||||
let rec p_gamma x =
|
||||
if x >= 1. +. a then 1. -. q_gamma x
|
||||
else if x = 0. then 0.
|
||||
else
|
||||
let rec pg_loop prev res term k =
|
||||
if k > 1000. then failwith "p_gamma did not converge."
|
||||
else if prev = res then res
|
||||
else
|
||||
let term = term *. x /. (a +. k) in
|
||||
(pg_loop [@tailcall]) res (res +. term) term (k +. 1.)
|
||||
in
|
||||
let r0 = exp (a *. log x -. x -. loggamma_a) *. a_inv in
|
||||
pg_loop min_float r0 r0 1.
|
||||
|
||||
and q_gamma x =
|
||||
if x < 1. +. a then 1. -. p_gamma x
|
||||
else
|
||||
let rec qg_loop prev res la lb w k =
|
||||
if k > 1000. then failwith "q_gamma did not converge."
|
||||
else if prev = res then res
|
||||
else
|
||||
let k_inv = 1. /. k in
|
||||
let kma = (k -. 1. -. a) *. k_inv in
|
||||
let la, lb =
|
||||
lb, kma *. (lb -. la) +. (k +. x) *. lb *. k_inv
|
||||
in
|
||||
let w = w *. kma in
|
||||
let prev, res = res, res +. w /. (la *. lb) in
|
||||
(qg_loop [@tailcall]) prev res la lb w (k +. 1.)
|
||||
in
|
||||
let w = exp (a *. log x -. x -. loggamma_a) in
|
||||
let lb = (1. +. x -. a) in
|
||||
qg_loop min_float (w /. lb) 1. lb w 2.0
|
||||
in
|
||||
gf *. p_gamma x
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val boys_function : maxm:int -> float -> float array
|
||||
#+end_src
|
||||
|
||||
The [[https://link.springer.com/article/10.1007/s10910-005-9023-3][Generalized Boys function]] is implemented,
|
||||
~maxm~ is the maximum total angular momentum.
|
||||
|
||||
\[
|
||||
F_m(x) = \frac{\gamma(m+1/2,x)}{2x^{m+1/2}}
|
||||
\]
|
||||
where $\gamma$ is the incomplete gamma function.
|
||||
|
||||
- $F_0(0.) = 1$
|
||||
- $F_0(t) = \frac{\sqrt{\pi}}{2\sqrt{t}} \text{erf} ( \sqrt{t} )$
|
||||
- $F_m(0.) = \frac{1}{2m+1}$
|
||||
- $F_m(t) = \frac{\gamma{m+1/2,t}}{2t^{m+1/2}}$
|
||||
- $F_m(t) = \frac{ 2t\, F_{m+1}(t) + e^{-t} }{2m+1}$
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let boys_function ~maxm t =
|
||||
assert (t >= 0.);
|
||||
match maxm with
|
||||
| 0 ->
|
||||
begin
|
||||
if t = 0. then [| 1. |] else
|
||||
let sq_t = sqrt t in
|
||||
[| (Constants.sq_pi_over_two /. sq_t) *. erf_float sq_t |]
|
||||
end
|
||||
| _ ->
|
||||
begin
|
||||
assert (maxm > 0);
|
||||
let result =
|
||||
Array.init (maxm+1) (fun m -> 1. /. float_of_int (2*m+1))
|
||||
in
|
||||
let power_t_inv = (maxm+maxm+1) in
|
||||
try
|
||||
let fmax =
|
||||
let t_inv = sqrt (1. /. t) in
|
||||
let n = float_of_int maxm in
|
||||
let dm = 0.5 +. n in
|
||||
let f = (pow t_inv power_t_inv ) in
|
||||
match classify_float f with
|
||||
| FP_normal -> (incomplete_gamma ~alpha:dm t) *. 0.5 *. f
|
||||
| FP_zero
|
||||
| FP_subnormal -> 0.
|
||||
| _ -> raise Exit
|
||||
in
|
||||
let emt = exp (-. t) in
|
||||
result.(maxm) <- fmax;
|
||||
for n=maxm-1 downto 0 do
|
||||
result.(n) <- ( (t+.t) *. result.(n+1) +. emt) *. result.(n)
|
||||
done;
|
||||
result
|
||||
with Exit -> result
|
||||
end
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let test_boys () =
|
||||
check (float 1.e-15) "incomplete_gamma" 0.0 (incomplete_gamma ~alpha:0.5 0.);
|
||||
check (float 1.e-15) "incomplete_gamma" 1.114707979049507 (incomplete_gamma ~alpha:0.5 0.4);
|
||||
check (float 1.e-15) "incomplete_gamma" 1.4936482656248544 (incomplete_gamma ~alpha:0.5 1.);
|
||||
check (float 1.e-15) "incomplete_gamma" 1.7724401246392805 (incomplete_gamma ~alpha:0.5 10.);
|
||||
check (float 1.e-15) "incomplete_gamma" 1.7724538509055159 (incomplete_gamma ~alpha:0.5 100.);
|
||||
|
||||
check (float 1.e-15) "boys" 1.0 (boys_function ~maxm:0 0.).(0);
|
||||
check (float 1.e-15) "boys" 0.2 (boys_function ~maxm:2 0.).(2);
|
||||
check (float 1.e-15) "boys" (1./.3.) (boys_function ~maxm:2 0.).(1);
|
||||
check (float 1.e-15) "boys" 0.8556243918921488 (boys_function ~maxm:0 0.5).(0);
|
||||
check (float 1.e-15) "boys" 0.14075053682591263 (boys_function ~maxm:2 0.5).(2);
|
||||
check (float 1.e-15) "boys" 0.00012711171070276764 (boys_function ~maxm:3 15.).(3);
|
||||
()
|
||||
#+end_src
|
||||
|
||||
** List functions
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val list_some : 'a option list -> 'a list
|
||||
val list_range : int -> int -> int list
|
||||
val list_pack : int -> 'a list -> 'a list list
|
||||
#+end_src
|
||||
|
||||
| ~list_some~ | Filters out all ~None~ elements of the list, and returns the elements without the ~Some~ |
|
||||
| ~list_range~ | Creates a list of consecutive integers |
|
||||
| ~list_pack~ | ~list_pack n l~ Creates a list of ~n~-elements lists |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let list_some l =
|
||||
List.filter (function None -> false | _ -> true) l
|
||||
|> List.rev_map (function Some x -> x | _ -> assert false)
|
||||
|> List.rev
|
||||
|
||||
|
||||
let list_range first last =
|
||||
if last < first then [] else
|
||||
let rec aux accu = function
|
||||
| 0 -> first :: accu
|
||||
| i -> (aux [@tailcall]) ( (first+i)::accu ) (i-1)
|
||||
in
|
||||
aux [] (last-first)
|
||||
|
||||
|
||||
let list_pack n l =
|
||||
assert (n>=0);
|
||||
let rec aux i accu1 accu2 = function
|
||||
| [] -> if accu1 = [] then
|
||||
List.rev accu2
|
||||
else
|
||||
List.rev ((List.rev accu1) :: accu2)
|
||||
| a :: rest ->
|
||||
match i with
|
||||
| 0 -> (aux [@tailcall]) (n-1) [] ((List.rev (a::accu1)) :: accu2) rest
|
||||
| _ -> (aux [@tailcall]) (i-1) (a::accu1) accu2 rest
|
||||
in
|
||||
aux (n-1) [] [] l
|
||||
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let test_list () =
|
||||
check bool "list_range" true ([ 2; 3; 4 ] = list_range 2 4);
|
||||
check bool "list_some" true ([ 2; 3; 4 ] =
|
||||
list_some ([ None ; Some 2 ; None ; Some 3 ; None ; None ; Some 4]) );
|
||||
check bool "list_pack" true (list_pack 3 (list_range 1 20) =
|
||||
[[1; 2; 3]; [4; 5; 6]; [7; 8; 9]; [10; 11; 12]; [13; 14; 15];
|
||||
[16; 17; 18]; [19; 20]]);
|
||||
()
|
||||
#+end_src
|
||||
|
||||
** Array functions
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val array_range : int -> int -> int array
|
||||
val array_sum : float array -> float
|
||||
val array_product : float array -> float
|
||||
#+end_src
|
||||
|
||||
| ~array_range~ | Creates an array of consecutive integers |
|
||||
| ~array_sum~ | Returns the sum of all the elements of the array |
|
||||
| ~array_product~ | Returns the product of all the elements of the array |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let array_range first last =
|
||||
if last < first then [| |] else
|
||||
Array.init (last-first+1) (fun i -> i+first)
|
||||
|
||||
|
||||
let array_sum a =
|
||||
Array.fold_left ( +. ) 0. a
|
||||
|
||||
|
||||
let array_product a =
|
||||
Array.fold_left ( *. ) 1. a
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let test_array () =
|
||||
check bool "array_range" true ([| 2; 3; 4 |] = array_range 2 4);
|
||||
check (float 1.e-15) "array_sum" 9. (array_sum [| 2.; 3.; 4. |]);
|
||||
check (float 1.e-15) "array_product" 24. (array_product [| 2.; 3.; 4. |]);
|
||||
()
|
||||
#+end_src
|
||||
|
||||
** Seq functions
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val seq_range : int -> int -> int Seq.t
|
||||
val seq_to_list : 'a Seq.t -> 'a list
|
||||
val seq_fold : ('a -> 'b -> 'a) -> 'a -> 'b Seq.t -> 'a
|
||||
#+end_src
|
||||
|
||||
| ~seq_range~ | Creates a sequence returning consecutive integers |
|
||||
| ~seq_to_list~ | Read a sequence and put items in a list |
|
||||
| ~seq_fold~ | Apply a fold to the elements of the sequence |
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let seq_range first last =
|
||||
Seq.init (last-first) (fun i -> i+first)
|
||||
|
||||
let seq_to_list seq =
|
||||
let rec aux accu xs =
|
||||
match Seq.uncons xs with
|
||||
| Some (x, xs) -> aux (x::accu) xs
|
||||
| None -> List.rev accu
|
||||
in
|
||||
aux [] seq
|
||||
|
||||
|
||||
let seq_fold f init seq =
|
||||
Seq.fold_left f init seq
|
||||
#+end_src
|
||||
|
||||
** Printers
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
val pp_float_array_size : Format.formatter -> float array -> unit
|
||||
val pp_float_array : Format.formatter -> float array -> unit
|
||||
val pp_float_2darray_size : Format.formatter -> float array array -> unit
|
||||
val pp_float_2darray : Format.formatter -> float array array -> unit
|
||||
val pp_bitstring : int -> Format.formatter -> Z.t -> unit
|
||||
#+end_src
|
||||
|
||||
| ~pp_float_array~ | Printer for float arrays |
|
||||
| ~pp_float_array_size~ | Printer for float arrays with size |
|
||||
| ~pp_float_2darray~ | Printer for matrices |
|
||||
| ~pp_float_2darray_size~ | Printer for matrices with size |
|
||||
| ~pp_bitstring~ | Printer for bit strings (used by ~Bitstring~ module) |
|
||||
|
||||
Example:
|
||||
#+begin_example
|
||||
pp_float_array_size:
|
||||
[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
|
||||
pp_float_array:
|
||||
[ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
|
||||
pp_float_2darray_size
|
||||
[
|
||||
2:[ 6: 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
[ 4: 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
|
||||
pp_float_2darray:
|
||||
[ [ 1.000000 1.732051 1.732051 1.000000 1.732051 1.000000 ]
|
||||
[ 1.000000 2.000000 3.000000 4.000000 ] ]
|
||||
|
||||
pp_bitstring 14:
|
||||
+++++------+--
|
||||
#+end_example
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let pp_float_array ppf a =
|
||||
Format.fprintf ppf "@[<2>[@ ";
|
||||
Array.iter (fun f -> Format.fprintf ppf "@[%10f@]@ " f) a;
|
||||
Format.fprintf ppf "]@]"
|
||||
|
||||
let pp_float_array_size ppf a =
|
||||
Format.fprintf ppf "@[<2>@[ %d:@[<2>" (Array.length a);
|
||||
Array.iter (fun f -> Format.fprintf ppf "@[%10f@]@ " f) a;
|
||||
Format.fprintf ppf "]@]@]"
|
||||
|
||||
let pp_float_2darray ppf a =
|
||||
Format.fprintf ppf "@[<2>[@ ";
|
||||
Array.iter (fun f -> Format.fprintf ppf "@[%a@]@ " pp_float_array f) a;
|
||||
Format.fprintf ppf "]@]"
|
||||
|
||||
let pp_float_2darray_size ppf a =
|
||||
Format.fprintf ppf "@[<2>@[ %d:@[" (Array.length a);
|
||||
Array.iter (fun f -> Format.fprintf ppf "@[%a@]@ " pp_float_array_size f) a;
|
||||
Format.fprintf ppf "]@]@]"
|
||||
|
||||
let pp_bitstring n ppf bs =
|
||||
String.init n (fun i -> if (Z.testbit bs i) then '+' else '-')
|
||||
|> Format.fprintf ppf "@[<h>%s@]"
|
||||
#+end_src
|
||||
|
||||
|
||||
** Test footer :noexport:
|
||||
|
||||
#+begin_src ocaml :tangle (eval test-ml) :exports none
|
||||
let tests = [
|
||||
"External", `Quick, test_external;
|
||||
"General" , `Quick, test_general;
|
||||
"Boys" , `Quick, test_boys;
|
||||
"List" , `Quick, test_list;
|
||||
"Array" , `Quick, test_array;
|
||||
]
|
||||
#+end_src
|
||||
@ -1,3 +1,5 @@
|
||||
[@@@landmark "auto-off"]
|
||||
|
||||
open Common
|
||||
|
||||
type t = {
|
||||
@ -16,7 +18,7 @@ module Co = Coordinate
|
||||
module Ps = Primitive_shell
|
||||
|
||||
|
||||
let make ?(index=0) lc =
|
||||
let[@landmark] make ?(index=0) lc =
|
||||
assert (Array.length lc > 0);
|
||||
|
||||
let coef = Array.map fst lc
|
||||
@ -76,7 +78,7 @@ let primitives x = x.prim
|
||||
|
||||
let zkey_array x = Ps.zkey_array x.prim.(0)
|
||||
|
||||
let values t point =
|
||||
let[@landmark] values t point =
|
||||
(* Radial part *)
|
||||
let r = Co.( point |- t.center ) in
|
||||
let r2 = Co.dot r r in
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
[@@@landmark "auto-off"]
|
||||
open Common
|
||||
|
||||
type t =
|
||||
@ -18,7 +19,7 @@ module Psp = Primitive_shell_pair
|
||||
A contracted shell with N functions combined with a contracted
|
||||
shell with M functions generates a NxM array of shell pairs.
|
||||
*)
|
||||
let make ?(cutoff=Constants.epsilon) s_a s_b =
|
||||
let[@landmark] make ?(cutoff=Constants.epsilon) s_a s_b =
|
||||
|
||||
let make = Psp.create_make_of (Cs.primitives s_a).(0) (Cs.primitives s_b).(0) in
|
||||
|
||||
@ -49,15 +50,15 @@ let shell_a x = x.shell_a
|
||||
let shell_b x = x.shell_b
|
||||
let coefs_and_shell_pairs x = x.coefs_and_shell_pairs
|
||||
|
||||
let shell_pairs x =
|
||||
let[@landmark] shell_pairs x =
|
||||
List.map snd x.coefs_and_shell_pairs
|
||||
|> Array.of_list
|
||||
|
||||
let coefficients x =
|
||||
let[@landmark] coefficients x =
|
||||
List.map fst x.coefs_and_shell_pairs
|
||||
|> Array.of_list
|
||||
|
||||
let exponents_inv x =
|
||||
let[@landmark] exponents_inv x =
|
||||
List.map (fun (_,sp) -> Psp.exponent_inv sp) x.coefs_and_shell_pairs
|
||||
|> Array.of_list
|
||||
|
||||
@ -89,12 +90,12 @@ let monocentric x =
|
||||
|
||||
|
||||
(** Returns an integer characteristic of a contracted shell pair *)
|
||||
let hash a =
|
||||
let[@landmark] hash a =
|
||||
List.rev_map Hashtbl.hash a
|
||||
|> Array.of_list
|
||||
|
||||
(** Comparison function, used for sorting *)
|
||||
let compare t t' =
|
||||
let[@landmark] compare t t' =
|
||||
let a = hash t.coefs_and_shell_pairs in
|
||||
let b = hash t'.coefs_and_shell_pairs in
|
||||
if a = b then 0
|
||||
@ -118,7 +119,7 @@ let compare t t' =
|
||||
(** The array of all shell pairs with their correspondance in the list
|
||||
of contracted shells.
|
||||
*)
|
||||
let of_contracted_shell_array ?(cutoff=Constants.epsilon) basis =
|
||||
let[@landmark] of_contracted_shell_array ?(cutoff=Constants.epsilon) basis =
|
||||
let rec loop accu = function
|
||||
| [] -> accu
|
||||
| (s_a :: rest) as l ->
|
||||
@ -165,7 +166,7 @@ let unique sp =
|
||||
*)
|
||||
|
||||
|
||||
let zkey_array x =
|
||||
let[@landmark] zkey_array x =
|
||||
Am.zkey_array (Am.Doublet
|
||||
Cs.(ang_mom x.shell_a, ang_mom x.shell_b)
|
||||
)
|
||||
|
||||
@ -1,3 +1,5 @@
|
||||
[@@@landmark "auto-off"]
|
||||
|
||||
open Common
|
||||
|
||||
type t =
|
||||
@ -18,7 +20,7 @@ module Cs = Contracted_shell
|
||||
module Csp = Contracted_shell_pair
|
||||
module Pspc = Primitive_shell_pair_couple
|
||||
|
||||
let make ?(cutoff=Constants.epsilon) shell_pair_p shell_pair_q =
|
||||
let[@landmark] make ?(cutoff=Constants.epsilon) shell_pair_p shell_pair_q =
|
||||
let ang_mom =
|
||||
Am.(Csp.ang_mom shell_pair_p + Csp.ang_mom shell_pair_q)
|
||||
in
|
||||
|
||||
@ -1,3 +1,5 @@
|
||||
[@@@landmark "auto-off"]
|
||||
|
||||
open Common
|
||||
open Constants
|
||||
|
||||
@ -21,6 +23,24 @@ module Am = Angular_momentum
|
||||
module Co = Coordinate
|
||||
module Ps = Primitive_shell
|
||||
|
||||
let ang_mom x = x.ang_mom
|
||||
|
||||
let a_minus_b x = x.a_minus_b
|
||||
|
||||
let a_minus_b_sq x = x.a_minus_b_sq
|
||||
|
||||
let center_minus_a x = x.center_minus_a
|
||||
|
||||
let normalization x = x.normalization
|
||||
|
||||
let exponent x = x.exponent
|
||||
|
||||
let center x = x.center
|
||||
|
||||
let shell_a x = x.shell_a
|
||||
|
||||
let shell_b x = x.shell_b
|
||||
|
||||
|
||||
let hash a =
|
||||
Hashtbl.hash a
|
||||
@ -39,14 +59,14 @@ let cmp a b =
|
||||
hash a - hash b
|
||||
|
||||
|
||||
let compute_norm_scales p_a p_b =
|
||||
let[@landmark] compute_norm_scales p_a p_b =
|
||||
Array.map (fun v1 ->
|
||||
Array.map (fun v2 -> v1 *. v2) (Ps.norm_scales p_b)
|
||||
) (Ps.norm_scales p_a)
|
||||
|> Array.to_list
|
||||
|> Array.concat
|
||||
|
||||
let create_make_of p_a p_b =
|
||||
let[@landmark] create_make_of p_a p_b =
|
||||
|
||||
let a_minus_b =
|
||||
Co.( Ps.center p_a |- Ps.center p_b )
|
||||
@ -119,7 +139,7 @@ let create_make_of p_a p_b =
|
||||
else None
|
||||
|
||||
|
||||
let make p_a p_b =
|
||||
let[@landmark] make p_a p_b =
|
||||
let f =
|
||||
create_make_of p_a p_b
|
||||
in
|
||||
@ -128,7 +148,7 @@ let make p_a p_b =
|
||||
| None -> assert false
|
||||
|
||||
|
||||
let norm_scales x =
|
||||
let[@landmark] norm_scales x =
|
||||
try
|
||||
Lazy.force x.norm_scales
|
||||
with Lazy.Undefined -> compute_norm_scales x.shell_a x.shell_b
|
||||
@ -139,26 +159,8 @@ let monocentric x =
|
||||
Ps.center x.shell_a = Ps.center x.shell_b
|
||||
|
||||
|
||||
let ang_mom x = x.ang_mom
|
||||
|
||||
let a_minus_b x = x.a_minus_b
|
||||
|
||||
let a_minus_b_sq x = x.a_minus_b_sq
|
||||
|
||||
let center_minus_a x = x.center_minus_a
|
||||
|
||||
let normalization x = x.normalization
|
||||
|
||||
let exponent x = x.exponent
|
||||
|
||||
let center x = x.center
|
||||
|
||||
let shell_a x = x.shell_a
|
||||
|
||||
let shell_b x = x.shell_b
|
||||
|
||||
|
||||
let zkey_array x =
|
||||
let[@landmark] zkey_array x =
|
||||
Am.zkey_array (Am.Doublet
|
||||
Ps.(ang_mom x.shell_a, ang_mom x.shell_b)
|
||||
)
|
||||
|
||||
@ -1,3 +1,5 @@
|
||||
[@@@landmark "auto-off"]
|
||||
|
||||
open Common
|
||||
|
||||
type t =
|
||||
@ -17,7 +19,7 @@ module Co = Coordinate
|
||||
module Ps = Primitive_shell
|
||||
module Psp = Primitive_shell_pair
|
||||
|
||||
let make shell_pair_p shell_pair_q =
|
||||
let[@landmark] make shell_pair_p shell_pair_q =
|
||||
let ang_mom =
|
||||
Am.(Psp.ang_mom shell_pair_p + Psp.ang_mom shell_pair_q)
|
||||
in
|
||||
@ -27,9 +29,10 @@ let make shell_pair_p shell_pair_q =
|
||||
and shell_d = Psp.shell_b shell_pair_q
|
||||
in
|
||||
let zkey_array = lazy (
|
||||
let open Ps in
|
||||
Am.zkey_array (Am.Quartet
|
||||
Ps.(ang_mom shell_a, ang_mom shell_b,
|
||||
ang_mom shell_c, ang_mom shell_d)
|
||||
(ang_mom shell_a, ang_mom shell_b,
|
||||
ang_mom shell_c, ang_mom shell_d)
|
||||
)
|
||||
)
|
||||
in
|
||||
@ -62,7 +65,7 @@ let p_minus_q t =
|
||||
|
||||
let zkey_array t = Lazy.force t.zkey_array
|
||||
|
||||
let norm_scales t =
|
||||
let[@landmark] norm_scales t =
|
||||
let norm_coef_scale_p_list = Array.to_list (Psp.norm_scales t.shell_pair_p) in
|
||||
let norm_coef_scale_q = Psp.norm_scales t.shell_pair_q in
|
||||
List.map (fun v1 -> Array.map (fun v2 -> v1 *. v2) norm_coef_scale_q)
|
||||
|
||||
@ -1,5 +1,7 @@
|
||||
(** Electron-electron repulsion integrals *)
|
||||
|
||||
[@@@landmark "auto-off"]
|
||||
|
||||
open Common
|
||||
open Gaussian
|
||||
|
||||
@ -12,7 +14,16 @@ module T = struct
|
||||
|
||||
open Zero_m_parameters
|
||||
|
||||
let zero_m z =
|
||||
let rec aux_zero_m result expo_pq accu k = function
|
||||
| 0 -> result.(k) <- result.(k) *. accu
|
||||
| l ->
|
||||
begin
|
||||
result.(k) <- result.(k) *. accu;
|
||||
let new_accu = -. accu *. expo_pq in
|
||||
(aux_zero_m [@tailcall]) result expo_pq new_accu (k+1) (l-1)
|
||||
end
|
||||
|
||||
let[@landmark] zero_m z =
|
||||
let expo_pq_inv = z.expo_p_inv +. z.expo_q_inv in
|
||||
assert (expo_pq_inv <> 0.);
|
||||
let expo_pq = 1. /. expo_pq_inv in
|
||||
@ -23,20 +34,11 @@ module T = struct
|
||||
in
|
||||
let maxm = z.maxm in
|
||||
let result = Util.boys_function ~maxm t in
|
||||
let rec aux accu k = function
|
||||
| 0 -> result.(k) <- result.(k) *. accu
|
||||
| l ->
|
||||
begin
|
||||
result.(k) <- result.(k) *. accu;
|
||||
let new_accu = -. accu *. expo_pq in
|
||||
(aux [@tailcall]) new_accu (k+1) (l-1)
|
||||
end
|
||||
in
|
||||
let f = Constants.two_over_sq_pi *. (sqrt expo_pq) in
|
||||
aux f 0 maxm;
|
||||
aux_zero_m result expo_pq f 0 maxm;
|
||||
result
|
||||
|
||||
let class_of_contracted_shell_pair_couple ?operator shell_pair_couple =
|
||||
let[@landmark] class_of_contracted_shell_pair_couple ?operator shell_pair_couple =
|
||||
assert (operator = None);
|
||||
let shell_p = Cspc.shell_pair_p shell_pair_couple
|
||||
and shell_q = Cspc.shell_pair_q shell_pair_couple
|
||||
|
||||
@ -96,8 +96,9 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
end;
|
||||
let amxyz = Po.get xyz am in
|
||||
if amxyz < 1 then
|
||||
let center_pq_xyz = center_pq xyz in
|
||||
Array.iteri (fun l expo_inv_p_l ->
|
||||
let center_pq_xyz_l = (center_pq xyz).(l) in
|
||||
let center_pq_xyz_l = center_pq_xyz.(l) in
|
||||
Array.iteri (fun m result_m ->
|
||||
let result_ml = result_m.(l) in
|
||||
let p0 = v_am.(m+1) in
|
||||
@ -114,10 +115,10 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
let amm = Po.decr xyz am in
|
||||
let amxyz = Util.float_of_int_fast amxyz in
|
||||
let v_amm = vrr0_v amm in
|
||||
let center_pq_xyz = center_pq xyz in
|
||||
Array.iteri (fun l expo_inv_p_l ->
|
||||
let f = amxyz *. expo_p_inv.(l) *. 0.5
|
||||
and center_pq_xyz_l = (center_pq xyz).(l)
|
||||
in
|
||||
and center_pq_xyz_l = center_pq_xyz.(l) in
|
||||
Array.iteri (fun m result_m ->
|
||||
let v1 = v_amm.(m) in
|
||||
let v1_l = v1.(l) in
|
||||
@ -182,8 +183,9 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
|
||||
let v2 =
|
||||
let f2 =
|
||||
let center_pq_xyz = center_pq xyz in
|
||||
Array.init np (fun l ->
|
||||
let cpq_l = (center_pq xyz).(l) in
|
||||
let cpq_l = center_pq_xyz.(l) in
|
||||
Array.init nq (fun k ->
|
||||
let x = expo_q_inv.(k) *. cpq_l.(k) in
|
||||
if (!do_compute) then x
|
||||
@ -197,8 +199,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
begin
|
||||
for l=0 to np-1 do
|
||||
let f2_l = f2.(l)
|
||||
and v2_l = v2.(l)
|
||||
in
|
||||
and v2_l = v2.(l) in
|
||||
for k=0 to nq-1 do
|
||||
f2_l.(k) <- -. v2_l.(k) *. f2_l.(k)
|
||||
done
|
||||
@ -217,8 +218,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
begin
|
||||
for l=0 to np-1 do
|
||||
let v1_l = v1.(l)
|
||||
and v2_l = v2.(l)
|
||||
in
|
||||
and v2_l = v2.(l) in
|
||||
for k=0 to nq-1 do
|
||||
v2_l.(k) <- v2_l.(k) +. v1_l.(k)
|
||||
done
|
||||
@ -248,8 +248,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
let result = Array.make_matrix np nq 0. in
|
||||
for l=0 to np-1 do
|
||||
let v1_l = v1.(l)
|
||||
and result_l = result.(l)
|
||||
in
|
||||
and result_l = result.(l) in
|
||||
for k=0 to nq-1 do
|
||||
result_l.(k) <- v1_l.(k) *. f1.(k)
|
||||
done;
|
||||
@ -295,8 +294,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
for l=0 to np-1 do
|
||||
let v3_l = v3.(l)
|
||||
and v1_l = v1.(l)
|
||||
and p1_l = p1.(l)
|
||||
in
|
||||
and p1_l = p1.(l) in
|
||||
for k=0 to nq-1 do
|
||||
v3_l.(k) <- p1_l.(k) +. v1_l.(k) +. v3_l.(k)
|
||||
done
|
||||
@ -307,8 +305,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
begin
|
||||
for l=0 to np-1 do
|
||||
let v1_l = v1.(l)
|
||||
and p1_l = p1.(l)
|
||||
in
|
||||
and p1_l = p1.(l) in
|
||||
for k=0 to nq-1 do
|
||||
p1_l.(k) <- v1_l.(k) +. p1_l.(k)
|
||||
done
|
||||
@ -319,8 +316,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
begin
|
||||
for l=0 to np-1 do
|
||||
let v3_l = v3.(l)
|
||||
and p1_l = p1.(l)
|
||||
in
|
||||
and p1_l = p1.(l) in
|
||||
for k=0 to nq-1 do
|
||||
p1_l.(k) <- p1_l.(k) +. v3_l.(k)
|
||||
done
|
||||
@ -331,8 +327,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
|
||||
begin
|
||||
for l=0 to np-1 do
|
||||
let v3_l = v3.(l)
|
||||
and v1_l = v1.(l)
|
||||
in
|
||||
and v1_l = v1.(l) in
|
||||
for k=0 to nq-1 do
|
||||
v3_l.(k) <- v1_l.(k) +. v3_l.(k)
|
||||
done
|
||||
@ -637,10 +632,8 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
|
||||
if (abs_float coefx.{j,i} ) < 1.e-3*.cutoff then
|
||||
raise NullQuartet;
|
||||
|
||||
let expo_p_inv, expo_q_inv =
|
||||
(expo_p_inv%.(i)),
|
||||
(expo_q_inv%.(j))
|
||||
in
|
||||
let expo_p_inv = expo_p_inv%.(i) in
|
||||
let expo_q_inv = expo_q_inv%.(j) in
|
||||
|
||||
let center_pq =
|
||||
Co.(Psp.center sp.(i-1) |- Psp.center sq.(j-1))
|
||||
@ -671,7 +664,10 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
|
||||
| _ ->
|
||||
|
||||
let coef =
|
||||
Array.init np (fun l -> Array.init nq (fun k -> cq.(k) *. cp.(l)) )
|
||||
Array.init np (fun l ->
|
||||
let cpl = cp.(l) in
|
||||
Array.map (fun cqk -> cqk *. cpl) cq
|
||||
)
|
||||
in
|
||||
|
||||
let norm = Cspc.norm_scales shell_pair_couple in
|
||||
@ -688,99 +684,98 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
|
||||
Array.map (fun shell_cd -> Ps.exponent (Psp.shell_b shell_cd) ) sq
|
||||
in
|
||||
|
||||
let center_pq =
|
||||
let result =
|
||||
Array.init 3 (fun xyz ->
|
||||
Array.init np (fun ab ->
|
||||
let shell_ab = sp.(ab) in
|
||||
Array.init nq (fun cd ->
|
||||
let shell_cd = sq.(cd)
|
||||
in
|
||||
let cpq =
|
||||
Co.(Psp.center shell_ab |- Psp.center shell_cd)
|
||||
in
|
||||
match xyz with
|
||||
| 0 -> Co.get X cpq;
|
||||
| 1 -> Co.get Y cpq;
|
||||
| _ -> Co.get Z cpq;
|
||||
)
|
||||
)
|
||||
)
|
||||
in function
|
||||
| Co.X -> result.(0)
|
||||
| Co.Y -> result.(1)
|
||||
| Co.Z -> result.(2)
|
||||
in
|
||||
let center_pa =
|
||||
let result =
|
||||
Array.init 3 (fun xyz ->
|
||||
Array.init np (fun ab ->
|
||||
let shell_ab = sp.(ab) in
|
||||
let cpa =
|
||||
Co.(Psp.center shell_ab |- Cs.center shell_a)
|
||||
in
|
||||
match xyz with
|
||||
| 0 -> Co.(get X cpa);
|
||||
| 1 -> Co.(get Y cpa);
|
||||
| _ -> Co.(get Z cpa);
|
||||
)
|
||||
)
|
||||
in function
|
||||
| Co.X -> result.(0)
|
||||
| Co.Y -> result.(1)
|
||||
| Co.Z -> result.(2)
|
||||
in
|
||||
let center_qc =
|
||||
let center_pq_x, center_pq_y, center_pq_z =
|
||||
let result =
|
||||
Array.init 3 (fun xyz ->
|
||||
let xyz = match xyz with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
Array.init np (fun ab ->
|
||||
let shell_ab = sp.(ab) in
|
||||
Array.init nq (fun cd ->
|
||||
let shell_cd = sq.(cd) in
|
||||
let cqc =
|
||||
Co.(Psp.center shell_cd |- Cs.center shell_c)
|
||||
in
|
||||
match xyz with
|
||||
| 0 -> Co.(get X cqc);
|
||||
| 1 -> Co.(get Y cqc);
|
||||
| _ -> Co.(get Z cqc);
|
||||
)
|
||||
let shell_cd = sq.(cd) in
|
||||
let cpq =
|
||||
Co.(Psp.center shell_ab |- Psp.center shell_cd)
|
||||
in
|
||||
Co.get xyz cpq;
|
||||
)
|
||||
)
|
||||
in function
|
||||
| Co.X -> result.(0)
|
||||
| Co.Y -> result.(1)
|
||||
| Co.Z -> result.(2)
|
||||
)
|
||||
in
|
||||
result.(0), result.(1), result.(2)
|
||||
in
|
||||
let center_pa_x, center_pa_y, center_pa_z =
|
||||
let result =
|
||||
Array.init 3 (fun xyz ->
|
||||
let xyz = match xyz with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
Array.init np (fun ab ->
|
||||
let shell_ab = sp.(ab) in
|
||||
let cpa =
|
||||
Co.(Psp.center shell_ab |- Cs.center shell_a)
|
||||
in
|
||||
Co.get xyz cpa;
|
||||
)
|
||||
)
|
||||
in result.(0), result.(1), result.(2)
|
||||
in
|
||||
let center_qc_x, center_qc_y, center_qc_z =
|
||||
let result =
|
||||
Array.init 3 (fun xyz ->
|
||||
let xyz = match xyz with
|
||||
| 0 -> Co.X
|
||||
| 1 -> Co.Y
|
||||
| _ -> Co.Z
|
||||
in
|
||||
Array.init nq (fun cd ->
|
||||
let shell_cd = sq.(cd) in
|
||||
let cqc =
|
||||
Co.(Psp.center shell_cd |- Cs.center shell_c)
|
||||
in
|
||||
Co.get xyz cqc;
|
||||
)
|
||||
)
|
||||
in result.(0), result.(1), result.(2)
|
||||
in
|
||||
let zero_m_array =
|
||||
let result =
|
||||
Array.init (maxm+1) (fun _ ->
|
||||
Array.init np (fun _ -> Array.make nq 0. ) )
|
||||
Array.make_matrix np nq 0. )
|
||||
in
|
||||
let empty = Array.make (maxm+1) 0. in
|
||||
let center_qc_tmp = Array.init nq (fun cd ->
|
||||
Coordinate.make { Coordinate.
|
||||
x = (center_qc Co.X).(cd) ;
|
||||
y = (center_qc Co.Y).(cd) ;
|
||||
z = (center_qc Co.Z).(cd) ;
|
||||
x = center_qc_x.(cd) ;
|
||||
y = center_qc_y.(cd) ;
|
||||
z = center_qc_z.(cd) ;
|
||||
})
|
||||
in
|
||||
Array.iteri (fun ab _shell_ab ->
|
||||
let center_pa = Coordinate.make { Coordinate.
|
||||
x = (center_pa Co.X).(ab) ;
|
||||
y = (center_pa Co.Y).(ab) ;
|
||||
z = (center_pa Co.Z).(ab) ;
|
||||
x = center_pa_x.(ab) ;
|
||||
y = center_pa_y.(ab) ;
|
||||
z = center_pa_z.(ab) ;
|
||||
}
|
||||
in
|
||||
let coef_ab = coef.(ab) in
|
||||
let expo_p_inv = expo_p_inv.(ab) in
|
||||
let zero_m_array_tmp =
|
||||
let xab = center_pq_x.(ab)
|
||||
and yab = center_pq_y.(ab)
|
||||
and zab = center_pq_z.(ab) in
|
||||
Array.mapi (fun cd _shell_cd ->
|
||||
if (abs_float coef.(ab).(cd) < cutoff) then
|
||||
if (abs_float coef_ab.(cd) < cutoff) then
|
||||
empty
|
||||
else
|
||||
let expo_p_inv, expo_q_inv =
|
||||
expo_p_inv.(ab), expo_q_inv.(cd)
|
||||
in
|
||||
let x = (center_pq X).(ab).(cd)
|
||||
and y = (center_pq Y).(ab).(cd)
|
||||
and z = (center_pq Z).(ab).(cd)
|
||||
in
|
||||
let expo_q_inv = expo_q_inv.(cd) in
|
||||
let x = xab.(cd)
|
||||
and y = yab.(cd)
|
||||
and z = zab.(cd) in
|
||||
let norm_pq_sq =
|
||||
x *. x +. y *. y +. z *. z
|
||||
in
|
||||
@ -795,8 +790,7 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
|
||||
(* Transpose result *)
|
||||
let coef_ab = coef.(ab) in
|
||||
for m=0 to maxm do
|
||||
let result_m_ab = result.(m).(ab)
|
||||
in
|
||||
let result_m_ab = result.(m).(ab) in
|
||||
for cd=0 to nq-1 do
|
||||
result_m_ab.(cd) <- zero_m_array_tmp.(cd).(m) *. coef_ab.(cd)
|
||||
done
|
||||
@ -848,6 +842,21 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
|
||||
if schwartz_p *. schwartz_q < cutoff2 then raise NullQuartet;
|
||||
);
|
||||
|
||||
let center_pq = function
|
||||
| Co.X -> center_pq_x
|
||||
| Co.Y -> center_pq_y
|
||||
| Co.Z -> center_pq_z
|
||||
in
|
||||
let center_pa = function
|
||||
| Co.X -> center_pa_x
|
||||
| Co.Y -> center_pa_y
|
||||
| Co.Z -> center_pa_z
|
||||
in
|
||||
let center_qc = function
|
||||
| Co.X -> center_qc_x
|
||||
| Co.Y -> center_qc_y
|
||||
| Co.Z -> center_qc_z
|
||||
in
|
||||
let abcd =
|
||||
{ expo_b ; expo_d ; expo_p_inv ; expo_q_inv ;
|
||||
center_ab = Csp.a_minus_b shell_p;
|
||||
|
||||
Loading…
Reference in New Issue
Block a user