Added Molecule.of_xyz_file

ocaml/Makefile

@@ -1,3 +1,5 @@
+#TODO : Opam auto-installer in makefile
+
 # Check if QPACKAGE_ROOT is defined
 
 ifndef QPACKAGE_ROOT

ocaml/atom.ml

@@ -33,13 +33,13 @@ let of_string s =
   | [ name; charge; x; y; z ] ->
     { element = Element.of_string name ;
       charge  = Charge.of_string  charge ;
-      coord   = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
+      coord   = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
     }
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
     { element = e ;
       charge  = Charge.of_int (Element.charge e);
-      coord   = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
+      coord   = Point3d.of_string (String.concat [x; y; z] ~sep:" ")
     }
   | _ -> raise (AtomError s)
 ;;

ocaml/gto.ml

@@ -91,7 +91,7 @@ let find in_channel element =
 ;;
 
 let read_basis_of_element in_channel element =
-  find in_channel element ;
+  ignore (find in_channel element) ;
   read_basis in_channel ;
 ;;
 
@@ -100,5 +100,5 @@ let to_string { sym = sym ; lc = lc } =
   let f (p,c) = Printf.sprintf "( %s, %f )" (Primitive.to_string p) c
   in
   Printf.sprintf "[ %s : %s ]" (Symmetry.to_string sym)
-    (String.concat (List.map ~f:f lc) ?sep:(Some ", "))
+    (String.concat (List.map ~f:f lc) ~sep:", ")
 ;;

ocaml/molecule.ml

@@ -9,7 +9,7 @@ type t = {
   elec_beta  : Positive_int.t ;
 }
 
-let charge { nuclei  ; elec_alpha ; elec_beta } =
+let get_charge { nuclei  ; elec_alpha ; elec_beta } =
   let result = Positive_int.(to_int elec_alpha + to_int elec_beta) in
   let rec nucl_charge = function
   | a::rest -> Atom.(Charge.to_float a.charge) +. nucl_charge rest
@@ -18,12 +18,12 @@ let charge { nuclei  ; elec_alpha ; elec_beta } =
   nucl_charge nuclei  -. (Float.of_int result)
 ;;
 
-let multiplicity m = 
+let get_multiplicity m = 
   Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
 ;;
 
 let name m = 
-  let cm = Float.to_int (charge m) in
+  let cm = Float.to_int (get_charge m) in
   let c = 
      match cm with
      | 0 -> ""
@@ -32,7 +32,7 @@ let name m =
      | i when i>1 -> Printf.sprintf " (%d+)" i
      | i -> Printf.sprintf " (%d-)" (-i)
   in
-  let mult = Multiplicity.to_string (multiplicity m) in
+  let mult = Multiplicity.to_string (get_multiplicity m) in
   let { nuclei  ; elec_alpha ; elec_beta } = m in
   let rec build_list accu = function
   | a::rest ->
@@ -67,35 +67,47 @@ let to_string m =
   let n = List.length nuclei in
   let title = name m in
   [ Int.to_string n ; title ] @ (List.map ~f:Atom.to_string nuclei)
-  |> String.concat ?sep:(Some "\n")
+  |> String.concat ~sep:"\n"
 ;;
 
-let of_xyz_string s charge' multiplicity' =
+let of_xyz_string
+    ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
+    s =
   let l = String.split s ~on:'\n'
        |> List.filter ~f:(fun x -> x <> "")
        |> List.map ~f:Atom.of_string 
   in
-  let ne = ( charge { 
+  let ne = ( get_charge { 
         nuclei=l ;
         elec_alpha=(Positive_int.of_int 0) ;
         elec_beta=(Positive_int.of_int 0) } 
       |> Float.to_int 
-      )- charge' 
+      )- charge 
       |> Positive_int.of_int 
   in
-  let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity' in
+  let (na,nb) = Multiplicity.to_alpha_beta ne multiplicity in
   let result = 
   { nuclei = l ;
     elec_alpha = (Positive_int.of_int na) ;
     elec_beta  = (Positive_int.of_int nb) }
   in
-  if ((multiplicity result) <> multiplicity') then
+  if ((get_multiplicity result) <> multiplicity) then
      let msg = Printf.sprintf
       "With %d electrons multiplicity %d is impossible"
       (Positive_int.to_int ne)
-      (Multiplicity.to_int multiplicity')
+      (Multiplicity.to_int multiplicity)
      in
      raise (MultiplicityError msg);
   else () ;
   result
 ;;
+
+
+let of_xyz_file
+    ?(charge=0) ?(multiplicity=(Multiplicity.of_int 1))
+    filename =
+  let (_,buffer) = In_channel.read_all filename 
+  |> String.lsplit2_exn ~on:'\n' in
+  let (_,buffer) = String.lsplit2_exn buffer ~on:'\n' in
+  of_xyz_string ~charge:charge ~multiplicity:multiplicity buffer
+;;

ocaml/test_molecule.ml

@@ -10,14 +10,18 @@ H           1.0       0.54386314      0.00000000     -0.92559535
 "
   in
   
-  try ignore (Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 1))
-    with
-    | Molecule.MultiplicityError _ -> print_string "OK\n"
-  ;
   print_string "---\n";
-  let m = Molecule.of_xyz_string xyz 0 (Strictly_positive_int.of_int 1)
+  begin
+  try (
+    ignore (Molecule.of_xyz_string xyz ~multiplicity:(Multiplicity.of_int 2)) ;
+    print_string "Failed in MultiplicityError\n" )
+    with
+    | Molecule.MultiplicityError _ -> print_string "MultiplicityError OK\n"
+  end ;
+  print_string "---\n";
+  let m = Molecule.of_xyz_string xyz 
   in print_endline (Molecule.name m) ;
-  let m = Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 2)
+  let m = Molecule.of_xyz_string xyz ~charge:1 ~multiplicity:(Multiplicity.of_int 2)
   in print_endline (Molecule.name m) ;
 
   let xyz =
@@ -27,9 +31,14 @@ O        1.65102147      0.00000000     -2.35602344
 H        0.54386314      0.00000000     -0.92559535
 "
   in
-  let m = Molecule.of_xyz_string xyz (-2) (Strictly_positive_int.of_int 1)
+  let m = Molecule.of_xyz_string xyz ~charge:(-2) 
   in print_endline (Molecule.name m) ;
+  print_endline (Molecule.to_string m);
+  print_string "---------\n";
+
+  let m = Molecule.of_xyz_file "c2h6.xyz"  in
   print_string (Molecule.to_string m);
+
 ;;
 
 test_molecule ();;