Pretty printing

Basis/Basis.ml

@@ -1,5 +1,6 @@
 type t
 
+(** Returns an array of the basis set per atom *)
 let of_nuclei_and_general_basis n b =
   Array.map (fun (e, center) ->
     List.assoc e b
@@ -14,7 +15,25 @@ let of_nuclei_and_general_basis n b =
 
 
 let to_string b =
-  Array.map (fun i -> Contracted_shell.to_string i) b
+  let line ="
-  |> Array.to_list
+-----------------------------------------------------------------------
-  |> String.concat "\n"
+" in 
+  "
+                          Atomic Basis set
+                          ----------------
+
+-----------------------------------------------------------------------
+Angular     Coordinates (Bohr)           Exponents       Coefficients
+Momentum  X         Y          Z
+-----------------------------------------------------------------------
+"
+  ^( Array.mapi (fun atom_id basis ->
+      Array.map (fun i -> 
+          Contracted_shell.to_string i) basis
+      |> Array.to_list
+      |> String.concat line
+    ) b
+    |> Array.to_list
+    |> String.concat line)
+    ^ line
 

Basis/Contracted_shell.ml

@@ -18,12 +18,14 @@ let norm_coef a i = a.norm_coef.(i)
 
 
 let to_string s =
+  let coord =
+    Coordinate.to_Bohr s.center
+  in
   let open Printf in
-  [ sprintf "center: %s" (Coordinate.to_string s.center) ; 
+  ( sprintf "%2s %10.6f %10.6f %10.6f " (Angular_momentum.to_string s.totAngMom)
-    sprintf "angular momentum: %s" (Angular_momentum.to_string s.totAngMom) ]
+      (Coordinate.x coord) (Coordinate.y coord) (Coordinate.z coord) ) ^
-  @ (Array.map2 (fun e c -> sprintf "expo: %e  coeff: %e" e c) s.expo s.coef
+  (Array.map2 (fun e c -> sprintf "%16.8e  %16.8e" e c) s.expo s.coef
-    |> Array.to_list) @ ["\n"]
+   |> Array.to_list |> String.concat (sprintf "\n%36s" " ") ) 
-  |> String.concat "\n"
 
 (** Normalization coefficient of contracted function i, which depends on the
     exponent and the angular momentum. Two conventions can be chosen : a single

Nuclei/Nuclei.ml

@@ -23,3 +23,29 @@ let of_zmt_file ~filename =
   |> Zmatrix.to_xyz
   |> Array.map (fun (e,x,y,z) -> (e, Coordinate.of_3_floats x y z ))
     
+let to_string atoms =
+    "
+                Nuclear Coordinates (Angstrom)
+                ------------------------------
+
+-----------------------------------------------------------------------
+   Center   Atomic   Element          Coordinates (Angstroms)
+            Number                 X             Y             Z
+-----------------------------------------------------------------------
+" ^
+    (Array.mapi (fun i (e, coord) ->
+         let coord =
+           Coordinate.to_Angstrom coord
+         in
+         Printf.sprintf " %5d    %5d    %5s   %12.6f  %12.6f  %12.6f"
+            (i+1)  (Element.to_int e)  (Element.to_string e) 
+           (Coordinate.x coord) (Coordinate.y coord) (Coordinate.z coord)
+       ) atoms
+     |> Array.to_list
+     |> String.concat "\n" ) ^
+"
+-----------------------------------------------------------------------
+
+"
+
+

Nuclei/Nuclei_lexer.mll

@@ -7,7 +7,7 @@ let white = [' ' '\t']+
 let word = [^' ' '\t' '\n']+
 let letter = ['A'-'Z' 'a'-'z']
 let integer = ['0'-'9']+ 
-let real = '-'? integer '.' integer (['e' 'E'] ('+'|'-')? integer)? 
+let real = '-'? (integer '.' integer | integer '.' | '.' integer) (['e' 'E'] ('+'|'-')? integer)? 
 
 
 rule read_all = parse
@@ -20,11 +20,12 @@ rule read_all = parse
 
 
 {
- let debug () =
+(* DEBUG
-   let ic = open_in "caffeine.xyz" in
+ let () =
+   let ic = open_in "h2o.xyz" in
    let lexbuf = Lexing.from_channel ic in
    while true do
-     let s = 
+     let s =
       match read_all lexbuf with
       | EOL -> "EOL"
       | SPACE w -> "SPACE("^w^")"
@@ -34,5 +35,6 @@ rule read_all = parse
       | EOF -> "EOF"
      in
      print_endline s
-   done; 
+   done;
+*)
 }

Nuclei/Xyz_parser.mly

@@ -34,14 +34,14 @@ title:
   | title_list EOL { $1 }
 
 text:
-  | WORD    {$1 }
+  | WORD    { $1 }
-  | SPACE   {$1 }
+  | SPACE   { $1 }
-  | FLOAT   {(string_of_float $1)}
+  | FLOAT   { (string_of_float $1)}
-  | INTEGER {(string_of_int $1)}
+  | INTEGER { (string_of_int $1)}
 
 title_list:
   | { "" }
-  | title_list text { $1 ^ $2 }
+  | title_list text { ($1 ^ $2) }
 
 atoms_xyz:
   | atoms_list EOL { List.rev $1 }

Utils/Coordinate.mli

@@ -12,5 +12,7 @@ val (|-) : t -> t -> t
 val (|+) : t -> t -> t
 val (|.) : float -> t -> t
 val dot  : t -> t -> float
+val to_Angstrom : t -> t
+val to_Bohr : t -> t
 val norm : t -> float
 

run_integrals.ml

@@ -24,11 +24,13 @@ let run ~coord ~basis =
   and general_basis =
     Gamess_reader.read ~filename:basis_file
   in
+  print_endline @@ Nuclei.to_string nuclei;
+
   let basis =
     Basis.of_nuclei_and_general_basis nuclei general_basis
   in
-  Array.map Basis.to_string basis
+  Basis.to_string basis
-  |> Array.iter print_endline 
+  |> print_endline 
 
 
 let () =