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Anthony Scemama 2023-06-28 16:22:56 +02:00
parent ca727440db
commit ff872e9479
13 changed files with 344 additions and 828 deletions
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96
common/charge.org
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@ -1,96 +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
* Charge
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
** Type
<<<~Charge.t~>>>
#+begin_src ocaml :tangle (eval mli)
type t
#+end_src
This type should be used for all charges in the program (electrons, nuclei,...).
#+begin_src ocaml :tangle (eval ml) :exports none
type t = float
#+end_src
** Conversions
#+begin_src ocaml :tangle (eval mli)
val of_float : float -> t
val to_float : t -> float
val of_int : int -> t
val to_int : t -> int
val of_string: string -> t
val to_string: t -> string
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
external of_float : float -> t = "%identity"
external to_float : t -> float = "%identity"
let of_int = float_of_int
let to_int = int_of_float
let of_string = float_of_string
let to_string x =
if x > 0. then
Printf.sprintf "+%f" x
else if x < 0. then
Printf.sprintf "%f" x
else
"0.0"
#+end_src
** Simple operations
#+begin_src ocaml :tangle (eval mli)
val ( + ) : t -> t -> t
val ( - ) : t -> t -> t
val ( * ) : t -> float -> t
val ( / ) : t -> float -> t
val is_null : t -> bool
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let gen_op op =
fun a b ->
op (to_float a) (to_float b)
|> of_float
let ( + ) = gen_op ( +. )
let ( - ) = gen_op ( -. )
let ( * ) = gen_op ( *. )
let ( / ) = gen_op ( /. )
let is_null t = t == 0.
#+end_src
** Printers
#+begin_src ocaml :tangle (eval mli)
val pp : Format.formatter -> t -> unit
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let pp ppf x =
Format.fprintf ppf "@[%s@]" (to_string x)
#+end_src

354
common/command_line.org
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@ -1,354 +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
* Command line
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
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:
#+begin_src ocaml :tangle no
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;
#+end_src
Then, define what to do with the arguments:
#+begin_src ocaml :tangle no
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
#+end_src
** Types
#+NAME:type
#+begin_src ocaml :tangle (eval mli)
type short_opt = char
type long_opt = string
type optional = Mandatory | Optional
type documentation = string
type argument = | With_arg of string
| Without_arg
| With_opt_arg of string
type description = {
short: short_opt ;
long : long_opt ;
opt : optional ;
doc : documentation ;
arg : argument ;
}
#+end_src
- <<<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>]~)
#+begin_src ocaml :tangle (eval ml) :exports none
<<type>>
#+end_src
** 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~.
#+begin_src ocaml :tangle (eval ml) :exports none
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
#+end_src
#+begin_src ocaml :tangle (eval mli)
val set_header_doc : string -> unit
val set_description_doc : string -> unit
val set_footer_doc : string -> unit
#+end_src
Functions to set the header, footer and main description of the
documentation provided by the ~help~ function:
#+begin_src ocaml :tangle (eval ml) :exports none
let set_header_doc s = header_doc := s
let set_description_doc s = description_doc := s
let set_footer_doc s = footer_doc := s
#+end_src
#+begin_src ocaml :tangle (eval mli)
val anonymous : long_opt -> optional -> documentation -> description
#+end_src
Function to create an anonymous argument.
#+begin_src ocaml :tangle (eval ml) :exports none
let anonymous name opt doc =
{ short=' ' ; long=name; opt; doc; arg=Without_arg; }
#+end_src
** Text formatting functions :noexport:
Function to print some text such that it fits on the screen
#+begin_src ocaml :tangle (eval ml) :exports none
let output_text t =
Format.printf "@[<v 0>";
begin
match Str.split (Str.regexp "\n") t with
| x :: [] ->
Format.printf "@[<hov 0>";
Str.split (Str.regexp " ") x
|> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
Format.printf "@]"
| t ->
List.iter (fun x ->
Format.printf "@[<hov 0>";
Str.split (Str.regexp " ") x
|> List.iter (fun y -> Format.printf "@[%s@]@ " y) ;
Format.printf "@]@;"
) t
end;
Format.printf "@]"
#+end_src
Function to build the short description of the command-line
arguments, such as
Example:
#+begin_example
my_program -b <string> [-h] [-u <float>] -x <string> [--]
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let output_short x =
match x.short, x.opt, x.arg with
| ' ', Mandatory, _ -> Format.printf "@[%s@]" x.long
| ' ', Optional , _ -> Format.printf "@[[%s]@]" x.long
| _ , Mandatory, Without_arg -> Format.printf "@[-%c@]" x.short
| _ , Optional , Without_arg -> Format.printf "@[[-%c]@]" x.short
| _ , Mandatory, With_arg arg -> Format.printf "@[-%c %s@]" x.short arg
| _ , 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
#+end_src
Function to build the long description of the command-line
arguments, such as
Example:
#+begin_example
-x --xyz=<string> Name of the file containing the nuclear
coordinates in xyz format
#+end_example
#+begin_src ocaml :tangle (eval ml) :exports none
let output_long max_width x =
let arg =
match x.short, x.arg with
| ' ' , _ -> x.long
| _ , Without_arg -> x.long
| _ , With_arg arg -> Printf.sprintf "%s=%s" x.long arg
| _ , With_opt_arg arg -> Printf.sprintf "%s[=%s]" x.long arg
in
let long =
let l = String.length arg in
arg^(String.make (max_width-l) ' ')
in
Format.printf "@[<v 0>";
begin
match x.short with
| ' ' -> Format.printf "@[%s @]" long
| short -> Format.printf "@[-%c --%s @]" short long
end;
Format.printf "@]";
output_text x.doc
#+end_src
** Query functions
#+begin_src ocaml :tangle (eval mli)
val get : long_opt -> string option
val get_bool : long_opt -> bool
val anon_args : unit -> string list
#+end_src
| ~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 |
#+begin_src ocaml :tangle (eval ml) :exports none
let anon_args () = !anon_args_ref
let help () =
(* Print the header *)
output_text !header_doc;
Format.printf "@.@.";
(* Find the anonymous arguments *)
let anon =
List.filter (fun x -> x.short = ' ') !specs
in
(* Find the options *)
let options =
List.filter (fun x -> x.short <> ' ') !specs
|> List.sort (fun x y -> Char.compare x.short y.short)
in
(* Find column lengths *)
let max_width =
List.map (fun x ->
( match x.arg with
| Without_arg -> String.length x.long
| With_arg arg -> String.length x.long + String.length arg
| With_opt_arg arg -> String.length x.long + String.length arg + 2
)
+ ( if x.opt = Optional then 2 else 0)
) !specs
|> List.fold_left max 0
in
(* Print usage *)
Format.printf "@[<v>@[<v 2>Usage:@,@,@[<hov 4>@[%s@]" Sys.argv.(0);
List.iter (fun x -> Format.printf "@ "; output_short x) options;
Format.printf "@ @[[--]@]";
List.iter (fun x -> Format.printf "@ "; output_short x;) anon;
Format.printf "@]@,@]@,";
(* Print arguments and doc *)
Format.printf "@[<v 2>Arguments:@,";
Format.printf "@[<v 0>" ;
List.iter (fun x -> Format.printf "@ "; output_long max_width x) anon;
Format.printf "@]@,@]@,";
(* Print options and doc *)
Format.printf "@[<v 2>Options:@,";
Format.printf "@[<v 0>" ;
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

79
common/constants.org
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@ -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

13
common/lib/charge.ml
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@ -1,13 +1,5 @@
(* 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]] *)
external of_float : float -> t = "%identity"
external to_float : t -> float = "%identity"
@ -23,9 +15,7 @@ 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]] *)
let gen_op op =
fun a b ->
op (to_float a) (to_float b)
@ -37,9 +27,6 @@ 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]] *)
let pp ppf x =
Format.fprintf ppf "@[%s@]" (to_string x)
(* Printers:2 ends here *)

22
common/lib/charge.mli
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@ -1,15 +1,9 @@
(* Type
*
* <<<~Charge.t~>>> *)
(** This type should be used for all charges in the program (electrons, nuclei,...). *)
(* [[file:~/QCaml/common/charge.org::*Type][Type:1]] *)
type t
(* Type:1 ends here *)
(* Conversions *)
(** Conversions *)
(* [[file:~/QCaml/common/charge.org::*Conversions][Conversions:1]] *)
val of_float : float -> t
val to_float : t -> float
@ -18,22 +12,16 @@ val to_int : t -> int
val of_string: string -> t
val to_string: t -> string
(* Conversions:1 ends here *)
(* Simple operations *)
(** Simple operations *)
(* [[file:~/QCaml/common/charge.org::*Simple operations][Simple operations:1]] *)
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 *)

100
common/lib/command_line.ml
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@ -1,17 +1,5 @@
(** Types *)
(* - <<<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]] *)
type short_opt = char
type long_opt = string
type optional = Mandatory | Optional
@ -27,51 +15,32 @@ type description = {
doc : documentation ;
arg : argument ;
}
(* Types:2 ends here *)
(* 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]] *)
(** 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~. *)
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:
*
* Function to print some text such that it fits on the screen *)
(** Text formatting functions *)
(* [[file:~/QCaml/common/command_line.org::*Text formatting functions][Text formatting functions:1]] *)
(** Function to print some text such that it fits on the screen *)
let output_text t =
Format.printf "@[<v 0>";
begin
@ -90,21 +59,15 @@ let output_text t =
) t
end;
Format.printf "@]"
(* Text formatting functions:1 ends here *)
(** Function to build the short description of the command-line arguments, such as
(* Function to build the short description of the command-line
* 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]] *)
#+begin_example
my_program -b <string> [-h] [-u <float>] -x <string> [--]
#+end_example
*)
let output_short x =
match x.short, x.opt, x.arg with
| ' ', Mandatory, _ -> Format.printf "@[%s@]" x.long
@ -115,22 +78,15 @@ 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 *)
(** Function to build the long description of the command-line arguments, such as
(* Function to build the long description of the command-line
* 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]] *)
#+begin_example
-x --xyz=<string> Name of the file containing the nuclear
coordinates in xyz format
#+end_example
*)
let output_long max_width x =
let arg =
match x.short, x.arg with
@ -151,17 +107,9 @@ 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 +185,8 @@ 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 +221,3 @@ let set_specs specs_in =
| Some _ -> ()
| None -> failwith ("Error: --"^x.long^" option is missing.")
)
(* Specification:2 ends here *)

94
common/lib/command_line.mli
View File

@ -1,15 +1,71 @@
(* Types
*
* #+NAME:type *)
(** 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:
#+begin_src ocaml :tangle no
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;
#+end_src
Then, define what to do with the arguments:
#+begin_src ocaml :tangle no
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
#+end_src
*)
(** Types *)
(* [[file:~/QCaml/common/command_line.org::type][type]] *)
type short_opt = char
(** In the command line, a dash with a single character (ex: =ls -l=) *)
type long_opt = string
(** In the command line, two dashes with a word (ex: =ls --directory=) *)
type optional = Mandatory | Optional
(** Command-line options can be ~Mandatory~ or ~Optional~ *)
type documentation = string
(** Documentation of the option is used in the help function *)
type argument = | With_arg of string
| Without_arg
| With_opt_arg of string
(** Some options require an argument (~ls --ignore="*.ml"~ ), some
don't (~ls -l~) and for some arguments the argument is optional
(~git --log[=<n>]~) *)
type description = {
short: short_opt ;
@ -18,30 +74,34 @@ type description = {
doc : documentation ;
arg : argument ;
}
(* type ends here *)
(* [[file:~/QCaml/common/command_line.org::*Mutable attributes][Mutable attributes:2]] *)
(** Functions to set the header, footer and main description of the
documentation provided by the ~help~ function: *)
val set_header_doc : string -> unit
val set_description_doc : string -> unit
val set_footer_doc : string -> unit
(* Mutable attributes:2 ends here *)
(* [[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 *)
(** Function to create an anonymous argument. *)
(** Query functions *)
(* [[file:~/QCaml/common/command_line.org::*Query functions][Query functions:1]] *)
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. *)

28
common/lib/constants.ml
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@ -1,44 +1,22 @@
(** Thresholds *)
(* | ~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]] *)
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 *)

41
common/lib/constants.mli
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@ -1,29 +1,46 @@
(* Thresholds *)
(** Thresholds *)
(* [[file:~/QCaml/common/constants.org::*Thresholds][Thresholds:1]] *)
val epsilon : float
(** Value below which a float is considered null. Default is \epsilon = 2.e-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~ *)

103
common/lib/smallarray.ml Normal file
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@ -0,0 +1,103 @@
type t = { dim1 : int;
dim2 : int;
dim3 : int;
data : float array;
}
let dim1 t = t.dim1
let dim2 t = t.dim2
let dim3 t = t.dim3
let data t = t.data
let at t i j k =
k + t.dim3*(j + t.dim2*i)
let from t l =
let i = l / (t.dim3*t.dim2) in
let l' = l - i*t.dim3*t.dim2 in
let j = l' / t.dim3 in
let k = l' - j * t.dim3
in (i,j,k)
let init dim1 dim2 dim3 f =
let t = { dim1 ; dim2 ; dim3 ; data = Array.create_float (dim1 * dim2 * dim3) } in
let l = ref 0 in
for i=0 to dim1-1 do
for j=0 to dim2-1 do
for k=0 to dim3-1 do
t.data.(!l) <- f i j k;
incr l
done
done
done;
t
let make dim1 dim2 dim3 v =
{ dim1 ; dim2 ; dim3 ;
data = Array.make (dim1 * dim2 * dim3) v
}
let get t i j k =
Array.get t.data (at t i j k)
let unsafe_get t i j k =
Array.unsafe_get t.data (at t i j k)
let set t i j k v =
Array.set t.data (at t i j k) v
let unsafe_set t i j k v =
Array.unsafe_set t.data (at t i j k) v
let iter3 i j f t =
assert (0 <= i && i < t.dim1);
assert (0 <= j && j < t.dim2);
let start = t.dim3*(j+i*t.dim2) in
for k=0 to t.dim3-1 do
f (Array.unsafe_get t.data (k+start))
done
let iteri3 i j f t =
assert (0 <= i && i < t.dim1);
assert (0 <= j && j < t.dim2);
let start = t.dim3*(j+i*t.dim2) in
for k=0 to t.dim3-1 do
f k (Array.unsafe_get t.data (k+start))
done
let to_array t =
Array.init t.dim1 (fun i ->
Array.init t.dim2 (fun j ->
Array.init t.dim3 (fun k ->
unsafe_get t i j k)))
let of_array a =
init (Array.length a) (Array.length a.(0)) (Array.length a.(0).(0))
(fun i j k -> a.(i).(j).(k) )
let sub1 i t =
let n = t.dim2 * t.dim3 in
let shift = i * n in
{ dim1 = 1 ; dim2 = t.dim2 ; dim3 = t.dim3 ;
data = Array.init n (fun k -> Array.unsafe_get t.data (shift+k)) }
let sum t =
Array.fold_left (+.) 0. t.data
let sum_sub1 k t =
let n = t.dim2 * t.dim3 in
let shift = k * n in
let accu = ref 0. in
for i=shift to shift+n-1 do
accu := !accu +. Array.unsafe_get t.data i
done;
!accu
let scale f t =
{ dim1 = t.dim1 ; dim2 = t.dim2 ; dim3 = t.dim3 ;
data = Array.map (fun x -> f *. x) t.data }
let ( .@() ) t (i,j,k) = get t i j k
let ( .@() <- ) t (i,j,k) v = set t i j k v

24
common/lib/smallarray.mli Normal file
View File

@ -0,0 +1,24 @@
type t = { dim1 : int; dim2 : int; dim3 : int; data : float array; }
val dim1 : t -> int
val dim2 : t -> int
val dim3 : t -> int
val data : t -> float array
val at : t -> int -> int -> int -> int
val from : t -> int -> int * int * int
val init : int -> int -> int -> (int -> int -> int -> float) -> t
val make : int -> int -> int -> float -> t
val get : t -> int -> int -> int -> float
val unsafe_get : t -> int -> int -> int -> float
val set : t -> int -> int -> int -> float -> unit
val unsafe_set : t -> int -> int -> int -> float -> unit
val iter3 : int -> int -> (float -> unit) -> t -> unit
val iteri3 : int -> int -> (int -> float -> unit) -> t -> unit
val to_array : t -> float array array array
val of_array : float array array array -> t
val sub1 : int -> t -> t
val sum : t -> float
val sum_sub1 : int -> t -> float
val scale : float -> t -> t
val ( .@() ) : t -> int * int * int -> float
val ( .@()<- ) : t -> int * int * int -> float -> unit

217
gaussian_integrals/lib/two_electron_rr_vectorized.ml
View File

@ -10,6 +10,7 @@ module Cspc = Contracted_shell_pair_couple
module Po = Powers
module Psp = Primitive_shell_pair
module Ps = Primitive_shell
module Sa = Smallarray
module Zp = Zero_m_parameters
exception NullQuartet
@ -35,7 +36,7 @@ type four_idx_intermediate =
center_pq : Co.axis -> float array array;
center_pa : Co.axis -> float array;
center_qc : Co.axis -> float array;
zero_m_array : float array array array;
zero_m_array : Sa.t;
}
@ -54,7 +55,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let zero_m_array = abcd.zero_m_array in
let maxm = Array.length zero_m_array - 1 in
let maxm = Sa.dim1 zero_m_array - 1 in
let get_xyz angMom =
match angMom with
@ -77,62 +78,48 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
let xyz = get_xyz angMom_a in
let am = Po.decr xyz angMom_a in
let cab = Co.get xyz center_ab in
let result = Array.init (maxm+1-angMom_a.Po.tot) (fun _ -> Array.make_matrix np nq 0.) in
let result = Sa.make (maxm+1-angMom_a.Po.tot) np nq 0. in
let v_am= vrr0_v am in
begin
if abs_float cab >= cutoff then
let expo_b = abcd.expo_b in
Array.iteri (fun m result_m ->
let v0 = v_am.(m) in
Array.iteri (fun l result_ml ->
let f0 = -. expo_b.(l) *. expo_p_inv.(l) *. cab
and v0_l = v0.(l)
in
Array.iteri (fun k v0_lk ->
result_ml.(k) <- v0_lk *. f0) v0_l
) result_m
) result
let expo_b = abcd.expo_b in
for m=0 to Sa.dim1 result - 1 do
for l=0 to Sa.dim2 result - 1 do
let f0 = -. expo_b.(l) *. expo_p_inv.(l) *. cab in
Sa.iteri3 m l (fun k _ ->
Sa.(result.@(m,l,k) <- v_am.@(m,l,k) *. f0)) result
done
done
end;
let amxyz = Po.get xyz am in
if amxyz < 1 then
Array.iteri (fun l expo_inv_p_l ->
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
let p0_l = p0.(l)
in
Array.iteri (fun k p0_lk ->
result_ml.(k) <- result_ml.(k)
+. expo_inv_p_l *. center_pq_xyz_l.(k) *. p0_lk
) p0_l
) result
) expo_p_inv
Array.iteri (fun l expo_inv_p_l ->
let center_pq_xyz_l = (center_pq xyz).(l) in
for m=0 to Sa.dim1 result - 1 do
Sa.iteri3 m l (fun k result_mlk ->
Sa.(result.@(m,l,k) <- result_mlk
+. expo_inv_p_l *. center_pq_xyz_l.(k) *. v_am.@(m+1,l,k))
) result
done
) expo_p_inv
else
begin
let amm = Po.decr xyz am in
let amxyz = Util.float_of_int_fast amxyz in
let v_amm = vrr0_v amm 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
Array.iteri (fun m result_m ->
let v1 = v_amm.(m) in
let v1_l = v1.(l) in
let result_ml = result_m.(l) in
let v2 = v_amm.(m+1) in
let p0 = v_am.(m+1) in
let v2_l = v2.(l)
in
Array.iteri (fun k p0_lk ->
result_ml.(k) <- result_ml.(k) +.
expo_inv_p_l *. center_pq_xyz_l.(k) *. p0_lk +.
f *. (v1_l.(k) +. v2_l.(k) *. expo_inv_p_l)
) p0.(l)
) result
) expo_p_inv
begin
let amm = Po.decr xyz am in
let amxyz = Util.float_of_int_fast amxyz in
let v_amm = vrr0_v amm 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
for m=0 to Sa.dim1 result - 1 do
Sa.iteri3 m l (fun k result_mlk ->
Sa.(result.@(m,l,k) <- result_mlk +.
expo_inv_p_l *. center_pq_xyz_l.(k) *. v_am.@(m+1,l,k) +.
f *. (v_amm.@(m,l,k) +. v_amm.@(m+1,l,k) *. expo_inv_p_l) )
) result
done
) expo_p_inv
end;
result
in
@ -142,7 +129,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
and vrr_v m angMom_a angMom_c =
match (angMom_a.Po.tot, angMom_c.Po.tot) with
| (_,0) -> Some (vrr0_v angMom_a).(m)
| (_,0) -> Some (vrr0_v angMom_a |> Sa.sub1 m)
| (_,_) ->
let key = Zkey.of_powers_six angMom_a angMom_c in
@ -171,38 +158,36 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
match vrr_v m angMom_a cm with
| None -> None
| Some v1 ->
Some (Sa.init 1 np nq (fun _ l k ->
Sa.(v1.@(0,l,k)) *. f1.(k) ))
(*
begin
Some (Array.init np (fun l ->
let v1_l = v1.(l) in
Array.mapi (fun k f1k -> v1_l.(k) *. f1k) f1
) )
end
*)
else None
in
let v2 =
let f2 =
Array.init np (fun l ->
Sa.init 1 np nq (fun _ l k ->
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
else (if abs_float x > cutoff then do_compute := true ; x)
) )
let x = expo_q_inv.(k) *. cpq_l.(k) in
if (!do_compute) then x
else (if abs_float x > cutoff then do_compute := true ; x)
)
in
if (!do_compute) then
match vrr_v (m+1) angMom_a cm with
| None -> None
| Some v2 ->
begin
for l=0 to np-1 do
let f2_l = f2.(l)
and v2_l = v2.(l)
in
for k=0 to nq-1 do
f2_l.(k) <- -. v2_l.(k) *. f2_l.(k)
done
done;
let data_f2 = Sa.data f2
and data_v2 = Sa.data v2 in
Array.iteri (fun i x -> data_f2.(i) <- -. x *. data_f2.(i)) data_v2;
Some f2
end
else None
@ -215,14 +200,9 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| Some v1, None -> Some v1
| Some v1, Some v2 ->
begin
for l=0 to np-1 do
let v1_l = v1.(l)
and v2_l = v2.(l)
in
for k=0 to nq-1 do
v2_l.(k) <- v2_l.(k) +. v1_l.(k)
done
done;
let v1_data = Sa.data v1
and v2_data = Sa.data v2 in
Array.iteri (fun i x -> v2_data.(i) <- v2_data.(i) +. x) v1_data;
Some v2
end
in
@ -245,14 +225,10 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| None -> None
| Some v1 ->
begin
let result = Array.make_matrix np nq 0. in
let result = Sa.make 1 np nq 0. in
for l=0 to np-1 do
let v1_l = v1.(l)
and result_l = result.(l)
in
for k=0 to nq-1 do
result_l.(k) <- v1_l.(k) *. f1.(k)
done;
Sa.iteri3 0 l (fun k v1_0lk ->
Sa.(result.@(0,l,k) <- v1_0lk *. f1.(k))) v1
done;
Some result
end
@ -272,14 +248,10 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| None -> None
| Some v3 ->
begin
let result = Array.make_matrix np nq 0. in
let result = Sa.make 1 np nq 0. in
for l=0 to np-1 do
let v3_l = v3.(l)
and result_l = result.(l)
in
for k=0 to nq-1 do
result_l.(k) <- v3_l.(k) *. f2.(k)
done
Sa.iteri3 0 l (fun k v1_0lk ->
Sa.(result.@(0,l,k) <- v1_0lk *. f2.(k))) v3
done;
Some result
end
@ -292,51 +264,40 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| None, None, Some v3 -> Some v3
| Some p1, Some v1, Some v3 ->
begin
for l=0 to np-1 do
let v3_l = v3.(l)
and v1_l = v1.(l)
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
done;
let v3_data = Sa.data v3
and p1_data = Sa.data p1
and v1_data = Sa.data v1 in
Array.iteri (fun i p ->
v3_data.(i) <- p +. v1_data.(i) +. v3_data.(i) ) p1_data;
Some v3
end
| Some p1, Some v1, None ->
begin
for l=0 to np-1 do
let v1_l = v1.(l)
and p1_l = p1.(l)
in
for k=0 to nq-1 do
p1_l.(k) <- v1_l.(k) +. p1_l.(k)
done
done;
let p1_data = Sa.data p1
and v1_data = Sa.data v1 in
Array.iteri (fun i p ->
p1_data.(i) <- v1_data.(i) +. p ) p1_data;
Some p1
end
| Some p1, None, Some v3 ->
begin
for l=0 to np-1 do
let v3_l = v3.(l)
and p1_l = p1.(l)
in
for k=0 to nq-1 do
p1_l.(k) <- p1_l.(k) +. v3_l.(k)
Sa.(p1.@(0,l,k) <- p1.@(0,l,k) +. v3.@(0,l,k))
done
done;
let v3_data = Sa.data v3
and p1_data = Sa.data p1 in
Array.iteri (fun i v ->
p1_data.(i) <- v +. p1_data.(i) ) v3_data;
Some p1
end
| None , Some v1, Some v3 ->
begin
for l=0 to np-1 do
let v3_l = v3.(l)
and v1_l = v1.(l)
in
for k=0 to nq-1 do
v3_l.(k) <- v1_l.(k) +. v3_l.(k)
done
done;
let v3_data = Sa.data v3
and v1_data = Sa.data v1 in
Array.iteri (fun i v ->
v3_data.(i) <- v +. v3_data.(i) ) v1_data;
Some v3
end
in
@ -352,16 +313,13 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
begin
let p2 =
match p2 with
| None -> Array.make_matrix np nq 0.
| None -> Sa.make 1 np nq 0.
| Some p2 -> p2
in
for l=0 to np-1 do
let fa = (Util.float_of_int_fast axyz) *. expo_p_inv.(l) *. 0.5 in
let p2_l = p2.(l)
and v_l = v.(l)
in
for k=0 to nq-1 do
p2_l.(k) <- p2_l.(k) -. fa *. expo_q_inv.(k) *. v_l.(k)
Sa.(p2.@(0,l,k) <- p2.@(0,l,k) -. fa *. expo_q_inv.(k) *. v.@(0,l,k));
done
done;
Some p2
@ -498,10 +456,6 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
*)
in
let sum matrix =
Array.fold_left (fun accu c -> accu +. Array.fold_left (+.) 0. c) 0. matrix
in
let vrr_v a c =
let v =
(*
@ -512,7 +466,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
vrr_v 0 a c
in
match v with
| Some matrix -> sum matrix
| Some matrix -> Sa.sum matrix
| None -> 0.
in
@ -524,7 +478,7 @@ let hvrr_two_e_vector (angMom_a, angMom_b, angMom_c, angMom_d)
| 0 ->
begin
match (angMom_a.Po.tot, angMom_c.Po.tot) with
| (0,0) -> sum zero_m_array.(0)
| (0,0) -> Sa.sum zero_m_array
| (_,_) -> vrr_v angMom_a angMom_c
end
| 1 ->
@ -750,10 +704,7 @@ let contracted_class_shell_pairs ?operator ~zero_m ?schwartz_p ?schwartz_q shell
| Co.Z -> result.(2)
in
let zero_m_array =
let result =
Array.init (maxm+1) (fun _ ->
Array.init np (fun _ -> Array.make nq 0. ) )
in
let result = Sa.make (maxm+1) np nq 0. in
let empty = Array.make (maxm+1) 0. in
let center_qc_tmp = Array.init nq (fun cd ->
Coordinate.make { Coordinate.
@ -795,10 +746,8 @@ 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
for cd=0 to nq-1 do
result_m_ab.(cd) <- zero_m_array_tmp.(cd).(m) *. coef_ab.(cd)
Sa.(result.@(m,ab,cd) <- zero_m_array_tmp.(cd).(m) *. coef_ab.(cd))
done
done
) sp;

1
top/lib/install_printers.ml
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@ -1,7 +1,6 @@
(* [[file:~/QCaml/top/install_printers.org::*Intall printers][Intall printers:3]] *)
let printers =
[
"Common.Charge.pp" ;
"Common.Coordinate.pp" ;
"Common.Powers.pp" ;
"Common.Range.pp" ;