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Zmatrix example

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This commit is contained in:
Anthony Scemama 2020-12-29 02:38:12 +01:00
parent 81fdc05a5c
commit a4582ffb67
5 changed files with 99 additions and 13 deletions
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2
particles/lib/mass.ml
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@ -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 *)

2
particles/lib/mass.mli
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@ -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 *)

57
particles/lib/zmatrix.ml
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@ -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 |
* | ~to_xyz~ | Converts to xyz format, as in the ~Nuclei~ module |
* | ~to_xyz_string~ | Converts to xyz format, as a string | *)
(* | ~of_string~ | Reads a z-matrix from a 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 *)
(* [[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 "@[";

6
particles/lib/zmatrix.mli
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@ -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 *)

45
particles/zmatrix.org
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@ -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