Added molecule in ocaml

ocaml/.gitignore

@@ -0,0 +1,5 @@
+ezfio.ml
+*.byte
+*.native
+_build
+

ocaml/Makefile

@@ -1,19 +1,37 @@
+# Check if QPACKAGE_ROOT is defined
+
+ifndef QPACKAGE_ROOT
+$(info  -------------------- Error --------------------)
+$(info  QPACKAGE_ROOT undefined. Source the quantum_package.rc script)
+$(info  -----------------------------------------------)
+$(error )
+endif
+
 LIBS=
 PKGS=
 OCAMLCFLAGS=-g
 OCAMLBUILD=ocamlbuild -cflags $(OCAMLCFLAGS) -lflags -g
+MLFILES=$(wildcard *.ml) ezfio.ml
+MLIFILES=$(wildcard *.mli) 
+ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))
 
 
-test_elements.byte: 
+default: $(ALL_TESTS)
 
-%.inferred.mli: $(wildcard *.ml) 
+%.inferred.mli: $(MLFILES)
 	$(OCAMLBUILD) $*.inferred.mli -cflags -i -use-ocamlfind  $(PKGS)
 
-%.byte: $(wildcard *.ml) $(wildcard *.mli) 
+%.byte: $(MLFILES) $(MLIFILES)
 	$(OCAMLBUILD) $*.byte  -use-ocamlfind  $(PKGS)
 
-%.native: $(wildcard *.ml) $(wildcard *.mli)  
+%.native: $(MLFILES) $(MLIFILES)
 	$(OCAMLBUILD) $*.native -use-ocamlfind $(PKGS)
 
+ezfio.ml: ${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml
+	cp ${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml .
+
+${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml:
+	$(MAKE) -C ${QPACKAGE_ROOT}/src ezfio
+
 clean: 
 	rm -rf _build

ocaml/README.rst

@@ -0,0 +1,6 @@
+===============
+Ocaml scripts
+===============
+
+This directory contains all the scripts that control the input/output
+with the user.

ocaml/atom.ml

@@ -35,6 +35,12 @@ let of_string s =
       charge  = Charge.of_string  charge ;
       coord   = Point3d.of_string (String.concat [x; y; z] ?sep:(Some " "))
     }
+  | [ 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 " "))
+    }
   | _ -> raise (AtomError s)
 ;;
   
@@ -42,6 +48,6 @@ let to_string a =
   [ Element.to_string a.element ;
     Charge.to_string  a.charge ;
     Point3d.to_string a.coord ]
-  |> String.concat ?sep:(Some "  ")
+  |> String.concat ?sep:(Some "   ")
 ;;
 

ocaml/molecule.ml

@@ -0,0 +1,101 @@
+open Core.Std ;;
+open Qptypes ;;
+
+exception MultiplicityError of string;;
+
+type t = {
+  nuclei     : Atom.t list ;
+  elec_alpha : Positive_int.t ;
+  elec_beta  : Positive_int.t ;
+}
+
+let 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
+  | [] -> 0.
+  in
+  nucl_charge nuclei  -. (Float.of_int result)
+;;
+
+let multiplicity m = 
+  Multiplicity.of_alpha_beta m.elec_alpha m.elec_beta
+;;
+
+let name m = 
+  let cm = Float.to_int (charge m) in
+  let c = 
+     match cm with
+     | 0 -> ""
+     | 1 -> " (+)"
+     | (-1) -> " (-)"
+     | i when i>1 -> Printf.sprintf " (%d+)" i
+     | i -> Printf.sprintf " (%d-)" (-i)
+  in
+  let mult = Multiplicity.to_string (multiplicity m) in
+  let { nuclei  ; elec_alpha ; elec_beta } = m in
+  let rec build_list accu = function
+  | a::rest ->
+      begin
+        let e = a.Atom.element in
+        match (List.Assoc.find accu e) with
+        | None   -> build_list (List.Assoc.add accu e 1) rest
+        | Some i -> build_list (List.Assoc.add accu e (i+1)) rest
+      end
+  | [] -> accu
+  in
+  let rec build_name accu = function
+  | (a, n)::rest ->
+    let a = Element.to_string a in
+    begin
+      match n with 
+      | 1 -> build_name (a::accu) rest
+      | i when i>1 -> 
+        let tmp = Printf.sprintf "%s%d" a i
+        in build_name (tmp::accu) rest
+      | _ -> assert false
+    end
+  | [] -> accu
+  in
+  let result = build_list [] nuclei |> build_name [c ; ", " ; mult]
+  in
+  String.concat (result)
+;;
+
+let to_string m =
+  let { nuclei  ; elec_alpha ; elec_beta } = m in
+  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")
+;;
+
+let of_xyz_string s charge' multiplicity' =
+  let l = String.split s ~on:'\n'
+       |> List.filter ~f:(fun x -> x <> "")
+       |> List.map ~f:Atom.of_string 
+  in
+  let ne = ( charge { 
+        nuclei=l ;
+        elec_alpha=(Positive_int.of_int 0) ;
+        elec_beta=(Positive_int.of_int 0) } 
+      |> Float.to_int 
+      )- charge' 
+      |> Positive_int.of_int 
+  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
+     let msg = Printf.sprintf
+      "With %d electrons multiplicity %d is impossible"
+      (Positive_int.to_int ne)
+      (Multiplicity.to_int multiplicity')
+     in
+     raise (MultiplicityError msg);
+  else () ;
+  result
+;;

ocaml/multiplicity.ml

@@ -0,0 +1,35 @@
+open Qptypes ;;
+
+type t = Strictly_positive_int.t;;
+let of_int = Strictly_positive_int.of_int ;;
+let to_int = Strictly_positive_int.to_int ;;
+
+let to_string m = 
+  match (to_int m) with
+  | 1 -> "Singlet"
+  | 2 -> "Doublet"
+  | 3 -> "Triplet"
+  | 4 -> "Quartet"
+  | 5 -> "Quintet"
+  | 6 -> "Sextet"
+  | 7 -> "Septet"
+  | 8 -> "Octet"
+  | 9 -> "Nonet"
+  | i -> Printf.sprintf "%d-et" i
+;;
+   
+let of_alpha_beta a b =
+  let a = Positive_int.to_int a 
+  and b = Positive_int.to_int b
+  in
+  assert (a >= b);
+  of_int (1 + a - b)
+;;
+
+let to_alpha_beta ne m = 
+  let ne = Positive_int.to_int ne in
+  let nb = (ne-(to_int m)+1)/2 in
+  let na = ne - nb in
+  assert (na >= nb) ;
+  (na,nb)
+;;

ocaml/point3d.ml

@@ -30,6 +30,6 @@ let distance p1 p2 = sqrt (distance2 p1 p2)
 
 let to_string p =
   let { x=x ; y=y ; z=z } = p in
-  Printf.sprintf "%f %f %f" x y z
+  Printf.sprintf "%f  %f  %f" x y z
 ;;
   

ocaml/qptypes.ml

@@ -5,7 +5,7 @@ module Positive_float : sig
 end = struct
   type t = float
   let to_float x = x
-  let of_float x = ( assert (x > 0.) ; x )
+  let of_float x = ( assert (x >= 0.) ; x )
 end
 
 
@@ -16,7 +16,7 @@ module Strictly_positive_float : sig
 end = struct
   type t =float 
   let to_float x = x
-  let of_float x = ( assert (x >= 0.) ; x )
+  let of_float x = ( assert (x > 0.) ; x )
 end
 
 
@@ -27,7 +27,7 @@ module Positive_int : sig
 end = struct
   type t = int
   let to_int x = x
-  let of_int x = ( assert (x > 0) ; x )
+  let of_int x = ( assert (x >= 0) ; x )
 end
 
 
@@ -38,7 +38,7 @@ module Strictly_positive_int : sig
 end = struct
   type t = int
   let to_int x = x
-  let of_int x = ( assert (x >= 0) ; x )
+  let of_int x = ( assert (x > 0) ; x )
 end
 
 

ocaml/test_elements.ml

@@ -1,6 +1,6 @@
 let test_module () = 
-  let atom = Elements.of_string "Cobalt" in
-  Printf.printf "%s %d\n" (Elements.to_string atom) (Elements.charge atom)
+  let atom = Element.of_string "Cobalt" in
+  Printf.printf "%s %d\n" (Element.to_string atom) (Element.charge atom)
 ;;
 
 test_module ();;

ocaml/test_molecule.ml

@@ -0,0 +1,35 @@
+open Core.Std ;;
+open Qptypes ;;
+
+let test_molecule () =
+  let xyz =
+"
+H           1.0       0.54386314      0.00000000     -3.78645152
+O           8.0       1.65102147      0.00000000     -2.35602344
+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)
+  in print_endline (Molecule.name m) ;
+  let m = Molecule.of_xyz_string xyz 1 (Strictly_positive_int.of_int 2)
+  in print_endline (Molecule.name m) ;
+
+  let xyz =
+"
+H        0.54386314      0.00000000     -3.78645152
+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)
+  in print_endline (Molecule.name m) ;
+  print_string (Molecule.to_string m);
+;;
+
+test_molecule ();;

src/Makefile.common

@@ -96,6 +96,7 @@ $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_
 	@cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
 	@cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
 
+ezfio: $(EZFIO)
 
 # Create symbolic links of other modules
 

src/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs BiInts Bitmask CISD CISD_SC2_selected CISD_selected DensityMatrix Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Perturbation SC2 Selectors_full SingleRefMethod Utils
-