Merge branch 'master' of github.com:LCPQ/quantum_package

Makefile

@@ -28,13 +28,14 @@ EZFIO: bin/irpf90
 bin/irpf90:
 	$(info $(BLUE)===== Fetching IRPF90 from the web ===== $(BLACK))
 	@sleep 1
-	@$(FETCH_FROM_WEB) "$(WWW_SERVER)/$(IRPF90_TGZ)" $(IRPF90_TGZ) || \
+	#@$(FETCH_FROM_WEB) "$(WWW_SERVER)/$(IRPF90_TGZ)" $(IRPF90_TGZ) || \
-	  (echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1)
+	#  (echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1)
-	tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ)
+	#tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ)
-	$(MAKE) -C irpf90 | tee install_irpf90.log
+	#$(MAKE) -C irpf90 | tee install_irpf90.log
-	rm -rf -- $$PWD/bin/irpf90 $$PWD/bin/irpman
+	#rm -rf -- $$PWD/bin/irpf90 $$PWD/bin/irpman
-	ln -s $$PWD/irpf90/bin/irpf90 $$PWD/bin/irpf90
+	echo $$PWD/irpf90/bin/irpf90 $$\@ > $$PWD/bin/irpf90
-	ln -s $$PWD/irpf90/bin/irpman $$PWD/bin/irpman
+	echo $$PWD/irpf90/bin/irpman $$\@ > $$PWD/bin/irpman
+	chmod +x $$PWD/bin/irpf90 $$PWD/bin/irpman
 
 doc:
 	$(MAKE) -C doc

ocaml/Generic_input_of_rst.ml

@@ -0,0 +1,60 @@
+open Core.Std;;
+open Qptypes;;
+
+
+let fail_msg str (ex,range) = 
+    let msg = match ex with
+    | Failure msg -> msg
+    | _ -> raise ex
+    in
+    let range = match range with
+      | Sexp.Annotated.Atom (range,_)  -> range
+      | Sexp.Annotated.List (range,_,_)  -> range
+    in
+    let open Sexp.Annotated in
+    let start_pos = range.start_pos.offset
+    and end_pos = range.end_pos.offset
+    in
+    let pre  = String.sub ~pos:0 ~len:start_pos str
+    and mid  = String.sub ~pos:start_pos ~len:(end_pos-start_pos) str
+    and post = String.sub ~pos:(end_pos)
+      ~len:((String.length str)-(end_pos)) str
+    in
+    let str = Printf.sprintf "%s ## %s ## %s" pre mid post
+    in
+    let str = String.tr str ~target:'(' ~replacement:' '
+      |> String.split ~on:')'
+      |> List.map ~f:String.strip 
+      |> List.filter ~f:(fun x -> 
+          match String.substr_index x ~pos:0 ~pattern:"##" with
+          | None -> false
+          | Some _ -> true
+         )
+      |> String.concat ~sep:"\n"
+    in
+    Printf.eprintf "Error:  (%s)\n\n  %s\n\n" msg str;
+;;
+
+
+let evaluate_sexp t_of_sexp s =
+  let sexp = ("("^s^")") in
+  match ( Sexp.of_string_conv sexp t_of_sexp ) with
+  | `Result r -> Some r
+  | `Error ex -> ( fail_msg sexp ex; None)
+;;
+
+let of_rst t_of_sexp s =
+  Rst_string.to_string s
+  |> String.split ~on:'\n'
+  |> List.filter ~f:(fun line ->
+      String.contains line '=')
+  |> List.map ~f:(fun line ->
+      "("^(
+      String.tr line ~target:'=' ~replacement:' '
+      )^")" )
+  |> String.concat
+  |> evaluate_sexp t_of_sexp
+;;
+
+
+

ocaml/Makefile

@@ -11,7 +11,7 @@ endif
 LIBS=
 PKGS=
 OCAMLCFLAGS="-g -warn-error A"
-OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
+OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -ocamlopt ocamlc.opt
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 
 ALL_TESTS=$(patsubst %.ml,%.byte,$(wildcard test_*.ml))

ocaml/qptypes_generator.ml

@@ -228,9 +228,9 @@ let parse_input_ezfio input=
         and (min, max) = String.lsplit2_exn ~on:':' c
         and msg = d
         in 
-        let name :: typ :: ezfio_func :: min :: max :: msg :: [] = 
+        let (name, typ, ezfio_func, min, max, msg) = 
-        match (name :: typ :: ezfio_func :: min :: max :: msg :: []) with
+        match (List.map [ name ; typ ; ezfio_func ; min ; max ; msg ] ~f:String.strip) with
-        | l -> List.map ~f:String.strip  l
+        | [ name ; typ ; ezfio_func ; min ; max ; msg ] -> (name, typ, ezfio_func, min, max, msg)
         | _ -> assert false
         in
         Printf.sprintf ezfio_template 

ocaml/test_basis.ml

@@ -9,12 +9,12 @@ let test_module () =
       In_channel.create (Qpackage.root^"/data/basis/"^(String.lowercase b))
     in
 
+(*
     let molecule =
       let xyz_file = "F2.xyz" in
       Molecule.of_xyz_file xyz_file 
     in
-
+*)
-    let nuclei = molecule.Molecule.nuclei in
 
     let basis = 
       (Basis.read_element basis_channel (Nucl_number.of_int 1) Element.F) @ 

ocaml/test_input.ml

@@ -16,7 +16,10 @@ let test_bielec_intergals () =
   in
   print_endline output;
   let rst = Input.Bielec_integrals.to_rst b in
-  let b2 = Input.Bielec_integrals.of_rst rst in
+  let b2 = match Input.Bielec_integrals.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   if (b = b2) then
     print_endline "OK"
   else
@@ -43,8 +46,11 @@ let test_dets () =
   in
   print_endline (Input.Determinants.to_rst b |> Rst_string.to_string ) ;
   print_endline (Input.Determinants.sexp_of_t b |> Sexplib.Sexp.to_string ) ;
-  let r = Input.Determinants.to_rst b in
+  let rst = Input.Determinants.to_rst b in
-  let b2 = Input.Determinants.of_rst r in
+  let b2 = match Input.Determinants.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   if (b2 = b) then
     print_endline "OK"
   else
@@ -57,7 +63,10 @@ let test_cisd_sc2 () =
   in
   print_endline (Input.Cisd_sc2.to_string b);
   let rst = Input.Cisd_sc2.to_rst b in
-  let b2 = Input.Cisd_sc2.of_rst rst in
+  let b2 = match Input.Cisd_sc2.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   if (b = b2) then
     print_endline "OK"
   else
@@ -71,8 +80,11 @@ let test_electrons () =
   in
   print_endline (Input.Electrons.to_string b);
   let rst = Input.Electrons.to_rst b in
-  let new_b = Input.Electrons.of_rst rst in
+  let b2 = match Input.Electrons.of_rst rst with
-  if (b = new_b) then
+  | Some x -> x
+  | None -> assert false
+  in
+  if (b = b2) then
     print_endline "OK"
   else
     print_endline "Failed in rst"
@@ -84,9 +96,12 @@ let test_fci () =
   in
   print_endline (Input.Full_ci.to_string b);
   let rst = Input.Full_ci.to_rst b in
-  let new_b = Input.Full_ci.of_rst rst in
+  let b2 = match Input.Full_ci.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   print_endline (Input.Full_ci.to_string b);
-  if (b = new_b) then
+  if (b = b2) then
     print_endline "OK"
   else
     print_endline "Failed in rst"
@@ -98,9 +113,12 @@ let test_hf () =
   in
   print_endline (Input.Hartree_fock.to_string b);
   let rst = Input.Hartree_fock.to_rst b in
-  let new_b = Input.Hartree_fock.of_rst rst in
+  let b2 = match Input.Hartree_fock.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   print_endline (Input.Hartree_fock.to_string b);
-  if (b = new_b) then
+  if (b = b2) then
     print_endline "OK"
   else
     print_endline "Failed in rst"
@@ -117,9 +135,12 @@ let test_nucl () =
   Ezfio.set_file "F2.ezfio" ;
   let b = Input.Nuclei.read () in
   let rst = Input.Nuclei.to_rst b in
-  let new_b = Input.Nuclei.of_rst rst in
+  let b2 = match Input.Nuclei.of_rst rst with
+  | Some x -> x
+  | None -> assert false
+  in
   print_endline (Input.Nuclei.to_string b);
-  if (b = new_b) then
+  if (b = b2) then
     print_endline "OK"
   else
     print_endline "Failed in rst"

src/Perturbation/selection.irp.f

@@ -148,7 +148,6 @@ subroutine make_s2_eigenfunction
   integer, parameter             :: bufsze = 1000
   logical, external              :: is_in_wavefunction
 
-  print *,  irp_here
 !  !TODO DEBUG
 !  do i=1,N_det
 !   do j=i+1,N_det