Zmatrix example

particles/lib/mass.ml

@@ -1,3 +1,3 @@
-(* [[file:../mass.org::*Atomic mass][Atomic mass:2]] *)
+(* [[file:~/QCaml/particles/mass.org::*Atomic%20mass][Atomic mass:2]] *)
 include Common.Non_negative_float
 (* Atomic mass:2 ends here *)

particles/lib/mass.mli

@@ -7,6 +7,6 @@
  * 
  *    #+NAME: types *)
 
-(* [[file:../mass.org::types][types]] *)
+(* [[file:~/QCaml/particles/mass.org::types][types]] *)
 include module type of Common.Non_negative_float
 (* types ends here *)

particles/lib/zmatrix.ml

@@ -1,4 +1,4 @@
-(* [[file:../zmatrix.org::*Type][Type:2]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::*Type][Type:2]] *)
 module StringMap = Map.Make(String)
 
 type atom_id  = int
@@ -18,12 +18,55 @@ type t = (line array * float StringMap.t)
 
 
 
-(* | ~of_string~     | Reads a z-matrix from a string                    |
+(*    | ~of_string~     | Reads a z-matrix from a string                    |
- * | ~to_xyz~        | Converts to xyz format, as in the ~Nuclei~ module |
+ *    | ~to_xyz~        | Converts to xyz format, as in the ~Nuclei~ module |
- * | ~to_xyz_string~ | Converts to xyz format, as a string               | *)
+ *    | ~to_xyz_string~ | Converts to xyz format, as a string               |
+ * 
+ *    #+begin_example
+ * let zmt = Zmatrix.of_string "
+ *  n
+ *  n    1 nn
+ *  h    1 hn         2 hnn
+ *  h    2 hn         1 hnn          3 dih4
+ *  h    1 hn         2 hnn          4 dih5
+ *  h    2 hn         1 hnn          3 dih5
+ * 
+ * nn          1.446
+ * hn          1.016
+ * hnn         106.0
+ * dih4        -54.38
+ * dih5         54.38
+ * " ;;
+ * - : Zmatrix.t = N  
+ * N       1 1.446000
+ * H       1 1.016000     2 106.000000
+ * H       2 1.016000     1 106.000000     3 -54.380000
+ * H       1 1.016000     2 106.000000     4 54.380000
+ * H       2 1.016000     1 106.000000     3 54.380000
+ * 
+ * 
+ * Zmatrix.to_xyz zmt ;;
+ * - : (Element.t * float * float * float) array =
+ * [|(N, 0., 0., 0.); (N, 0., 0., 1.446);
+ *   (H, -0.976641883073332107, 0., -0.280047553510071046);
+ *   (H, -0.568802835186988709, 0.793909757123734683, 1.726047553510071);
+ *   (H, 0.314092649983635563, 0.924756819385119, -0.280047553510071101);
+ *   (H, -0.568802835186988709, -0.793909757123734683, 1.726047553510071)|]
+ * 
+ * 
+ * Zmatrix.to_xyz_string zmt ;;
+ * - : string =
+ * "N 0.000000 0.000000 0.000000
+ * N 0.000000 0.000000 1.446000
+ * H -0.976642 0.000000 -0.280048
+ * H -0.568803 0.793910 1.726048
+ * H 0.314093 0.924757 -0.280048
+ * H -0.568803 -0.793910 1.726048"
+ *    #+end_example *)
 
+   
 
-(* [[file:../zmatrix.org::*Conversion][Conversion:2]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::*Conversion][Conversion:2]] *)
 let pi = Common.Constants.pi
 let to_radian = pi /. 180.
 
@@ -301,12 +344,12 @@ let to_xyz_string (l,map) =
   String.concat "\n" 
     ( to_xyz (l,map) 
       |> Array.map (fun (e,x,y,z) -> 
-          Printf.sprintf "%s %f %f %f\n" (Element.to_string e) x y z)
+          Printf.sprintf "%s %f %f %f" (Element.to_string e) x y z)
       |> Array.to_list
     )
 (* Conversion:2 ends here *)
 
-(* [[file:../zmatrix.org::*Printers][Printers:2]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::*Printers][Printers:2]] *)
 let pp ppf (a, map) =
   let f = string_of_line map in
   Format.fprintf ppf "@[";

particles/lib/zmatrix.mli

@@ -2,14 +2,14 @@
  * 
  *    #+NAME: types *)
 
-(* [[file:../zmatrix.org::types][types]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::types][types]] *)
 type t
 (* types ends here *)
 
 (* Conversion *)
 
 
-(* [[file:../zmatrix.org::*Conversion][Conversion:1]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::*Conversion][Conversion:1]] *)
 val of_string      : string -> t
 val to_xyz         : t -> (Element.t * float * float * float) array
 val to_xyz_string  : t -> string
@@ -18,6 +18,6 @@ val to_xyz_string  : t -> string
 (* Printers *)
 
 
-(* [[file:../zmatrix.org::*Printers][Printers:1]] *)
+(* [[file:~/QCaml/particles/zmatrix.org::*Printers][Printers:1]] *)
 val pp : Format.formatter -> t -> unit
 (* Printers:1 ends here *)

particles/zmatrix.org

@@ -53,6 +53,49 @@ val to_xyz_string  : t -> string
    | ~to_xyz~        | Converts to xyz format, as in the ~Nuclei~ module |
    | ~to_xyz_string~ | Converts to xyz format, as a string               |
 
+   #+begin_example
+let zmt = Zmatrix.of_string "
+ n
+ n    1 nn
+ h    1 hn         2 hnn
+ h    2 hn         1 hnn          3 dih4
+ h    1 hn         2 hnn          4 dih5
+ h    2 hn         1 hnn          3 dih5
+
+nn          1.446
+hn          1.016
+hnn         106.0
+dih4        -54.38
+dih5         54.38
+" ;;
+- : Zmatrix.t = N  
+N       1 1.446000
+H       1 1.016000     2 106.000000
+H       2 1.016000     1 106.000000     3 -54.380000
+H       1 1.016000     2 106.000000     4 54.380000
+H       2 1.016000     1 106.000000     3 54.380000
+
+
+Zmatrix.to_xyz zmt ;;
+- : (Element.t * float * float * float) array =
+[|(N, 0., 0., 0.); (N, 0., 0., 1.446);
+  (H, -0.976641883073332107, 0., -0.280047553510071046);
+  (H, -0.568802835186988709, 0.793909757123734683, 1.726047553510071);
+  (H, 0.314092649983635563, 0.924756819385119, -0.280047553510071101);
+  (H, -0.568802835186988709, -0.793909757123734683, 1.726047553510071)|]
+
+
+Zmatrix.to_xyz_string zmt ;;
+- : string =
+"N 0.000000 0.000000 0.000000
+N 0.000000 0.000000 1.446000
+H -0.976642 0.000000 -0.280048
+H -0.568803 0.793910 1.726048
+H 0.314093 0.924757 -0.280048
+H -0.568803 -0.793910 1.726048"
+   #+end_example
+
+   
    #+begin_src ocaml :tangle (eval ml) :exports none
 let pi = Common.Constants.pi
 let to_radian = pi /. 180.
@@ -331,7 +374,7 @@ let to_xyz_string (l,map) =
   String.concat "\n" 
     ( to_xyz (l,map) 
       |> Array.map (fun (e,x,y,z) -> 
-          Printf.sprintf "%s %f %f %f\n" (Element.to_string e) x y z)
+          Printf.sprintf "%s %f %f %f" (Element.to_string e) x y z)
       |> Array.to_list
     )
    #+end_src