Documentation and printing

Basis/Basis.ml

@@ -56,8 +56,8 @@ let to_string b =
 -----------------------------------------------------------------------
 "
   ^
-  ( Array.map (fun i -> 
+  ( Array.map (fun p -> Format.(fprintf str_formatter "%a" Cs.pp p;
-        Cs.to_string i) b
+    flush_str_formatter ())) b
     |> Array.to_list
     |> String.concat line
   )

Basis/Basis.mli

@@ -14,9 +14,9 @@ val to_string : t -> string
 val of_nuclei_and_general_basis : Nuclei.t -> GeneralBasis.t -> t
 (** Takes an array of {!Nuclei.t}, and a {!GeneralBasis.t} (such as cc-pVDZ
   for instance) and creates the corresponding atomic basis set.
-  All the {!Element.t}s of the array of {!Nuclei.t} are searched in 
+  All the {!Element.t}'s of the array of {!Nuclei.t} are searched in 
   the {!GeneralBasis.t}, and the basis is built by creating
-  {!ContractedShell.t}s centered on the nuclei with the exponents
+  {!ContractedShell.t}'s centered on the nuclei with the exponents
   and contraction coefficients given by the {!GeneralBasis.t}.
 *)
 

Basis/ContractedShell.ml

@@ -56,20 +56,6 @@ let with_index a i =
   { a with index = i }
 
 
-let to_string s =
-  let coord = s.center in
-  let open Printf in
-  (match s.totAngMom with
-   | Am.S -> sprintf "%3d    " (s.index+1)
-   | _                  -> sprintf "%3d-%-3d" (s.index+1) (s.index+(Array.length s.norm_coef_scale))
-  ) ^
-  ( sprintf "%1s %8.3f %8.3f %8.3f " (Am.to_string s.totAngMom)
-      (get X coord) (get Y coord) (get Z coord) ) ^
-  (Array.map2 (fun e c -> sprintf "%16.8e  %16.8e" e c) s.expo s.coef
-   |> Array.to_list |> String.concat (sprintf "\n%36s" " ") ) 
-
-
-
 let expo x = x.expo
 
 let coef x = x.coef
@@ -93,8 +79,9 @@ let prim x = x.prim
 
 (** {2 Printers} *)
 
-let pp ppf x =
+open Format
-  let open Format in
+
+let pp_debug ppf x =
   fprintf ppf "@[<2>{@ ";
   fprintf ppf "@[<2>expo =@ %a ;@]@ " pp_float_array_size x.expo;
   fprintf ppf "@[<2>coef =@ %a ;@]@ " pp_float_array_size x.coef;
@@ -105,3 +92,14 @@ let pp ppf x =
   fprintf ppf "@[<2>index =@ %d ;@]@ " x.index;
   fprintf ppf "}@,@]"
 
+let pp ppf s =
+  (match s.totAngMom with
+   | Am.S -> fprintf ppf "@[%3d@]    " (s.index+1)
+   | _    -> fprintf ppf "@[%3d-%-3d@]" (s.index+1) (s.index+(Array.length s.norm_coef_scale))
+  );
+  fprintf ppf "@[%a@ %a@]@[" Am.pp_string s.totAngMom Co.pp s.center;
+  Array.iter2 (fun e c -> fprintf ppf "@[%16.8e  %16.8e@]@;" e c) s.expo s.coef;
+  fprintf ppf "@]"
+
+
+

Basis/ContractedShell.mli

@@ -28,9 +28,6 @@ where:
 
 type t 
 
-val to_string : t -> string
-(** Pretty-printing of the contracted shell in a string. *)
-
 val make : ?index:int -> (float * PrimitiveShell.t) array -> t 
 (** Creates a contracted shell from a list of coefficients and primitives.  *)
 

Makefile

@@ -6,7 +6,7 @@ PKGS=
 OCAMLCFLAGS="-g -warn-error A"
 OCAMLOPTFLAGS="opt -O3 -nodynlink -remove-unused-arguments -rounds 16 -inline 100 -inline-max-unroll 100"
 #ODOC_LTXHTML_DIR=qpackage.docdir/ltx
-ODOCFLAGS=-docflags "-g ltxhtml.cma -sort"
+ODOCFLAGS=-docflags "-g ltxhtml.cma -sort -css-style $(PWD)/style.css -colorize-code"
 OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) $(ODOCFLAGS) -Is $(INCLUDE_DIRS) -ocamlopt $(OCAMLOPTFLAGS)
 MLLFILES=$(wildcard */*.mll) $(wildcard *.mll) Utils/math_functions.c
 MLYFILES=$(wildcard */*.mly) $(wildcard *.mly) 

Utils/AngularMomentum.mli

@@ -8,24 +8,31 @@ exception AngularMomentumError of string
 (** Raised when the {!AngularMomentum.t} element can't be created.
   *)
 
+
 val of_char : char -> t
 (** Returns an {!AngularMomentum.t} when a shell is given as a character (case
   insensitive).
 
   Example:
 
-  [AngularMomentum.of_char 'p' -> AngularMomentum.P]
+{[
+  AngularMomentum.of_char 'p' -> AngularMomentum.P
+]}
  *)
 
 val to_string : t -> string
 (** 
-  [AngularMomentum.(to_string D) -> "D"]
+{[
+  AngularMomentum.(to_string D) -> "D"
+]}
  *)
 
 
 val to_char : t -> char
 (** 
-  [AngularMomentum.(to_char D) -> 'D']
+{[
+  AngularMomentum.(to_char D) -> 'D'
+]}
  *)
 
 
@@ -35,7 +42,9 @@ val to_int : t -> int
 
   Example:
 
-  [AngularMomentum.of_int 3 -> AngularMomentum.F]
+{[
+  AngularMomentum.of_int 3 -> AngularMomentum.F
+]}
  *)
 
 val of_int : int -> t
@@ -44,7 +53,9 @@ val of_int : int -> t
 
   Example:
 
-  [AngularMomentum.of_int 3 -> AngularMomentum.F]
+{[
+  AngularMomentum.of_int 3 -> AngularMomentum.F
+]}
  *)
 
 type kind =
@@ -59,7 +70,9 @@ val n_functions : t -> int
 
   Example:
 
-  [AngularMomentum.n_functions D -> 6]
+{[
+  AngularMomentum.n_functions D -> 6
+]}
   *)
 
 
@@ -69,7 +82,7 @@ val zkey_array : kind -> Zkey.t array
 
   Example:
 
-  {[
+{[
   AngularMomentum.( zkey_array Doublet (P,S) ) ->
     [| {Zkey.left = 0; right = 1125899906842624} ;
        {Zkey.left = 0; right = 1099511627776}    ;
@@ -84,9 +97,9 @@ val zkey_array : kind -> Zkey.t array
   in
   Array.map (fun (a,b) -> {!Zkey.of_powers_six} a b)
       [| (x,s) ; (y,s) ; (z,s) |]
-  ]}
+]}
 
-  *)
+*)
 
 val ( + ) : t -> t -> t
 val ( - ) : t -> t -> t

Utils/Bohr.mli

@@ -8,6 +8,5 @@ type t = private {
 
 
 val make : Point.t -> t
-(** Create from a {!Point.t}. *)
 
 

Utils/Charge.ml

@@ -1,10 +1,11 @@
 type t = float
 
-let of_float x = x
+external of_float : float -> t = "%identity"
+external to_float : t -> float = "%identity"
+
 let of_int i = float_of_int i
 let of_string s = float_of_string s
 
-let to_float x = x
 let to_int   x = int_of_float x
 let to_string x = 
   if x >= 0. then
@@ -23,3 +24,9 @@ let ( * ) a b =
 
 let ( / ) a b =
   (to_float a) /. b |> of_float
+
+let pp ppf x = 
+  if x > 0. then
+    Format.fprintf ppf "@[+%f@]" (to_float x)
+  else
+    Format.fprintf ppf "@[%f@]" (to_float x)

Utils/Charge.mli

@@ -1,18 +1,25 @@
 (** This type should be used for all charges in the program (electrons, nuclei,...). *)
 
-type t = private float
+type t 
+
+(** {2 Conversions} *)
+
+val of_float : float -> t
+val of_int   : int -> t
+val of_string: string -> t
 
 val to_float : t -> float
-val of_float : float -> t
-
 val to_int   : t -> int
-val of_int   : int -> t
-
 val to_string: t -> string 
-val of_string: string -> t
+
+(** {2 Operations} *)
 
 val ( + ) : t -> t -> t
 val ( - ) : t -> t -> t
 val ( * ) : t -> float -> t
 val ( / ) : t -> float -> t 
 
+(** {2 Printers } *)
+
+val pp : Format.formatter -> t -> unit
+

Utils/Constants.mli

@@ -1,6 +1,7 @@
 (** All constants used in the program.
  *)
 
+(** {2 Thresholds } *)
 
 val epsilon : float
 (** Value below which a float is considered null. Default is {% $\epsilon$ %} = 10{^-20}. *)
@@ -8,6 +9,8 @@ val epsilon : float
 val integrals_cutoff : float
 (** Cutoff value for integrals. Default is 10{^-15}. *)
 
+(** {2 Mathematical constants } *)
+
 val pi : float
 (** {% $\pi$ %} = 3.141_592_653_589_793_12 *)
 
@@ -23,8 +26,11 @@ val pi_inv : float
 val two_over_sq_pi : float
 (** {% $\frac{2}{\sqrt{\pi}}$ %} *)
 
+(** {2 Physical constants} *)
+
 val a0 : float
 (** Bohr radius : {% $a_0$ %} = 0.529_177_210_671_2 Angstrom *)
 
 val a0_inv : float
 (** {% $\frac{1}{a_0}$ %} *)
+

Utils/Coordinate.ml

@@ -77,11 +77,16 @@ let get axis { Bohr.x ; y ; z } =
   | Z -> z  
 
 
+open Format
+let pp ppf c = 
+  let open Bohr in
+  fprintf ppf "@[@[%8.4f@] @[%8.4f@] @[%8.4f@]@]" c.x c.y c.z
+
 let pp_bohr ppf c = 
   let open Bohr in
-  Format.fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Bohr)@]" c.x c.y c.z
+  fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Bohr)@]" c.x c.y c.z
 
 let pp_angstrom ppf c = 
   let c = bohr_to_angstrom c in
   let open Angstrom in
-  Format.fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z
+  fprintf ppf "@[(@[%10f@], @[%10f@], @[%10f@] Angs)@]" c.x c.y c.z

Utils/Coordinate.mli

@@ -84,6 +84,8 @@ val norm : Bohr.t -> float
 
 (** {2 Printers} *)
 
+val pp: Format.formatter -> Bohr.t -> unit
+
 val pp_bohr: Format.formatter -> Bohr.t -> unit
 
 val pp_angstrom : Format.formatter -> Bohr.t -> unit

style.css

@@ -0,0 +1,86 @@
+img.ltxhtml { vertical-align : middle }
+.keyword { font-weight : bold ; color : Red }
+.keywordsign { color : #C04600 }
+.comment { color : Green }
+.constructor { color : Blue }
+.type { color : #5C6585 }
+.string { color : Maroon }
+.warning { color : Red ; font-weight : bold }
+.info { margin-left : 3em; margin-right: 3em }
+.param_info { margin-top: 4px; margin-left : 3em; margin-right : 3em }
+.code { color : #465F91 ; }
+.typetable { border-style : hidden }
+.paramstable { border-style : hidden ; padding: 5pt 5pt}
+tr { }
+td.typefieldcomment { font-size: smaller ;}
+div.sig_block {margin-left: 2em}
+*:target { background: yellow; }
+body {
+  font: 10pt sans-serif;
+  color: black;
+  text-align: left;
+  padding: 5px;
+  margin: 1.375em 5%;
+  min-width: 40ex;
+  max-width: 100ex;
+  background-color: White;
+}
+h1 {
+  font-size : 1.5em;
+  text-align: left;
+  margin-top: 0.5em;
+  padding-top: 0.8em;
+  margin-bottom: 1.0em;
+  padding-bottom: 0.0em;
+  border-top-style:solid;
+  border-width:1px;
+  border-color:#AAA;
+}
+h2 {
+  font-size : 1.3em;
+  text-align: left;
+  margin-top: 0.5em;
+  padding-top: 0.8em;
+  margin-bottom: 1.0em;
+  padding-bottom: 0.0em;
+  border-top-style:solid;
+  border-width:1px;
+  border-color:#AAA;
+}
+h3 {
+  font-size : 1.2em;
+  text-align: left;
+  margin-top: 0.5em;
+  padding-top: 0.8em;
+  margin-bottom: 1.0em;
+  padding-bottom: 0.0em;
+  font-style: italic;
+  font-weight: normal
+}
+a {color: #416DFF; text-decoration: none}
+a:hover {background-color: #ddd; text-decoration: underline}
+pre 
+{
+  font-family: monospace;
+}
+pre.verbatim, pre.codepre {
+  padding: 1.0em;
+  padding-right: 1.0em;
+  background-color:#F8F8F8;
+}
+.indextable {
+  border: 1px #ddd solid;
+  border-collapse: collapse;
+  font-size: 1.0em;
+}
+.indextable td, .indextable th {border: 1px #ddd solid; min-width: 80px}
+.indextable td.module {background-color: #eee ;  padding-left: 2px; padding-right: 2px}
+.indextable td.module a {color: #4E6272; text-decoration: none; display: block; width: 100%}
+.indextable td.module a:hover {text-decoration: underline; background-color: transparent}
+.deprecated {color: #888; font-style: italic}
+.indextable tr td div.info { margin-left: 2px; margin-right: 2px }
+ul.indexlist { margin-left: 0; padding-left: 0;}
+ul.indexlist li { list-style-type: none ; margin-left: 0; padding-left: 0; }
+ul.info-attributes {list-style: none; margin: 0; padding: 0; }
+div.info > p:first-child { margin-top:0; }
+div.info-desc > p:first-child { margin-top:0; margin-bottom:0; }