Updated OCaml

install/scripts/install_ocaml.sh

@@ -5,7 +5,7 @@ QP_ROOT=$PWD
 cd -
 
 # Normal installation
-PACKAGES="core.v0.10.0 cryptokit ocamlfind sexplib.v0.10.0 zmq ppx_sexp_conv ppx_deriving"
+PACKAGES="core cryptokit ocamlfind sexplib zmq ppx_sexp_conv ppx_deriving"
 
 # Needed for ZeroMQ
 export C_INCLUDE_PATH="${QP_ROOT}"/include:"${C_INCLUDE_PATH}"
@@ -65,7 +65,7 @@ fi
 cd Downloads || exit 1
 chmod +x  ocaml.sh || exit 1
 
-echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.06.0 || exit 1
+echo N | ./ocaml.sh ${QP_ROOT}/bin/ 4.07.1 || exit 1
 
 ${QP_ROOT}/bin/opam config setup -a -q || exit 1
 

ocaml/Gamess.ml

@@ -79,14 +79,14 @@ let read_until_found f tries =
         begin 
           try
             Some (read_mos x f)
-          with Not_found ->
+          with Caml.Not_found ->
             None
         end
         ) None tries 
   in
   match result with
   | Some mos -> mos
-  | None -> raise Not_found
+  | None -> raise Caml.Not_found
 
 let read_natural_mos f =
   let tries = [
@@ -430,7 +430,7 @@ let create_cas_input ?(vecfile="") ~guess ~nstate s n_e n_a =
           in
           try
             string_of_guess (Natural (norb, vecfile))
-          with Not_found ->
+          with Caml.Not_found ->
             string_of_guess (Canonical (norb, vecfile))
     end
   ;

ocaml/Input_ao_basis.ml

@@ -1,38 +1,101 @@
-(* =~=~ *)
-(* Init *)
-(* =~=~ *)
-
 open Qptypes;;
 open Qputils;;
 open Core;;
 
 module Ao_basis : sig
-(* Generate type *)
   type t = 
-     {
+    { ao_basis        : AO_basis_name.t;
-       disk_access_ao_one_integrals   : Disk_access.t;
+      ao_num          : AO_number.t ;
+      ao_prim_num     : AO_prim_number.t array;
+      ao_prim_num_max : AO_prim_number.t;
+      ao_nucl         : Nucl_number.t array;
+      ao_power        : Symmetry.Xyz.t array;
+      ao_coef         : AO_coef.t array;
+      ao_expo         : AO_expo.t array;
+      ao_cartesian    : bool;
     } [@@deriving sexp]
   ;;
   val read : unit -> t option
-  val write : t-> unit
   val to_string : t -> string
+  val to_basis  : t -> Basis.t
+  val write  : t -> unit
+  val to_md5 : t -> MD5.t
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t option
 end = struct
-(* Generate type *)
   type t = 
-     {
+    { ao_basis        : AO_basis_name.t;
-       disk_access_ao_one_integrals   : Disk_access.t;
+      ao_num          : AO_number.t ;
+      ao_prim_num     : AO_prim_number.t array;
+      ao_prim_num_max : AO_prim_number.t;
+      ao_nucl         : Nucl_number.t array;
+      ao_power        : Symmetry.Xyz.t array;
+      ao_coef         : AO_coef.t array;
+      ao_expo         : AO_expo.t array;
+      ao_cartesian    : bool;
     } [@@deriving sexp]
   ;;
 
   let get_default = Qpackage.get_ezfio_default "ao_basis";;
 
-(* =~=~=~=~=~=~==~=~=~=~=~=~ *)
+  let read_ao_basis () = 
-(* Generate Special Function *)
+    Ezfio.get_ao_basis_ao_basis ()
-(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)
+    |> AO_basis_name.of_string
+  ;;
+
+  let read_ao_num () =
+    Ezfio.get_ao_basis_ao_num ()
+    |> AO_number.of_int
+  ;;
+
+  let read_ao_prim_num () =
+    Ezfio.get_ao_basis_ao_prim_num () 
+    |> Ezfio.flattened_ezfio
+    |> Array.map ~f:AO_prim_number.of_int
+  ;;
+
+  let read_ao_prim_num_max () =
+    Ezfio.get_ao_basis_ao_prim_num ()
+    |> Ezfio.flattened_ezfio
+    |> Array.fold ~f:(fun x y -> if x>y then x else y) ~init:0
+    |> AO_prim_number.of_int
+  ;;
+
+  let read_ao_nucl () =
+    let nmax = Nucl_number.get_max () in
+    Ezfio.get_ao_basis_ao_nucl () 
+    |> Ezfio.flattened_ezfio
+    |> Array.map ~f:(fun x-> Nucl_number.of_int ~max:nmax x)
+  ;;
+
+  let read_ao_power () =
+    let x = Ezfio.get_ao_basis_ao_power () in
+    let dim = x.Ezfio.dim.(0) in
+    let data = Ezfio.flattened_ezfio x in
+    let result = Array.init dim ~f:(fun x -> "") in
+    for i=1 to dim
+    do
+      if (data.(i-1) > 0) then
+        result.(i-1) <- result.(i-1)^"x"^(Int.to_string data.(i-1));
+      if (data.(dim+i-1) > 0) then
+        result.(i-1) <- result.(i-1)^"y"^(Int.to_string data.(dim+i-1));
+      if (data.(2*dim+i-1) > 0) then
+        result.(i-1) <- result.(i-1)^"z"^(Int.to_string data.(2*dim+i-1));
+    done;
+    Array.map ~f:Symmetry.Xyz.of_string result
+  ;;
+
+  let read_ao_coef () =
+    Ezfio.get_ao_basis_ao_coef () 
+    |> Ezfio.flattened_ezfio
+    |> Array.map ~f:AO_coef.of_float
+  ;;
+
+  let read_ao_expo () =
+    Ezfio.get_ao_basis_ao_expo ()
+    |> Ezfio.flattened_ezfio
+    |> Array.map ~f:AO_expo.of_float
+  ;;
 
-(* Read snippet for ao_cartesian *)
   let read_ao_cartesian () =
     if not (Ezfio.has_ao_basis_ao_cartesian ()) then
        get_default "ao_cartesian"
@@ -41,133 +104,191 @@ end = struct
     ;
     Ezfio.get_ao_basis_ao_cartesian ()
   ;;
-(* Write snippet for ao_cartesian *)
-  let write_ao_cartesian =
-     Ezfio.set_ao_basis_ao_cartesian
-  ;;
 
-(* Read snippet for ao_prim_num_max *)
+  let to_long_basis b =
-  let read_ao_prim_num_max () =
+    let ao_num = AO_number.to_int b.ao_num in
-    if not (Ezfio.has_ao_basis_ao_prim_num_max ()) then
+    let gto_array = Array.init (AO_number.to_int b.ao_num)
-       get_default "ao_prim_num_max"
+      ~f:(fun i ->
-       |> Int.of_string
+        let s = Symmetry.Xyz.to_symmetry b.ao_power.(i) in
-       |> Ezfio.set_ao_basis_ao_prim_num_max
+        let ao_prim_num = AO_prim_number.to_int b.ao_prim_num.(i) in
-    ;
+        let prims = List.init ao_prim_num ~f:(fun j ->
-    Ezfio.get_ao_basis_ao_prim_num_max ()
+          let prim = { GaussianPrimitive.sym  = s ;
-  ;;
+                       GaussianPrimitive.expo = b.ao_expo.(ao_num*j+i)
-(* Write snippet for ao_prim_num_max *)
-  let write_ao_prim_num_max =
-     Ezfio.set_ao_basis_ao_prim_num_max
-  ;;
-
-(* Read snippet for disk_access_ao_one_integrals *)
-  let read_disk_access_ao_one_integrals () =
-    if not (Ezfio.has_ao_basis_disk_access_ao_one_integrals ()) then
-       get_default "disk_access_ao_one_integrals"
-       |> String.of_string
-       |> Ezfio.set_ao_basis_disk_access_ao_one_integrals
-    ;
-    Ezfio.get_ao_basis_disk_access_ao_one_integrals ()
-      |> Disk_access.of_string
-  ;;
-(* Write snippet for disk_access_ao_one_integrals *)
-  let write_disk_access_ao_one_integrals var = 
-    Disk_access.to_string var
-    |> Ezfio.set_ao_basis_disk_access_ao_one_integrals
-  ;;
-
-(* Read snippet for integral_kinetic *)
-  let read_integral_kinetic () =
-    if not (Ezfio.has_ao_basis_integral_kinetic ()) then
-       get_default "integral_kinetic"
-       |> Float.of_string
-       |> Ezfio.set_ao_basis_integral_kinetic
-    ;
-    Ezfio.get_ao_basis_integral_kinetic ()
-  ;;
-(* Write snippet for integral_kinetic *)
-  let write_integral_kinetic =
-     Ezfio.set_ao_basis_integral_kinetic
-  ;;
-
-(* Read snippet for integral_nuclear *)
-  let read_integral_nuclear () =
-    if not (Ezfio.has_ao_basis_integral_nuclear ()) then
-       get_default "integral_nuclear"
-       |> Float.of_string
-       |> Ezfio.set_ao_basis_integral_nuclear
-    ;
-    Ezfio.get_ao_basis_integral_nuclear ()
-  ;;
-(* Write snippet for integral_nuclear *)
-  let write_integral_nuclear =
-     Ezfio.set_ao_basis_integral_nuclear
-  ;;
-
-(* Read snippet for integral_overlap *)
-  let read_integral_overlap () =
-    if not (Ezfio.has_ao_basis_integral_overlap ()) then
-       get_default "integral_overlap"
-       |> Float.of_string
-       |> Ezfio.set_ao_basis_integral_overlap
-    ;
-    Ezfio.get_ao_basis_integral_overlap ()
-  ;;
-(* Write snippet for integral_overlap *)
-  let write_integral_overlap =
-     Ezfio.set_ao_basis_integral_overlap
-  ;;
-
-(* Read snippet for integral_pseudo *)
-  let read_integral_pseudo () =
-    if not (Ezfio.has_ao_basis_integral_pseudo ()) then
-       get_default "integral_pseudo"
-       |> Float.of_string
-       |> Ezfio.set_ao_basis_integral_pseudo
-    ;
-    Ezfio.get_ao_basis_integral_pseudo ()
-  ;;
-(* Write snippet for integral_pseudo *)
-  let write_integral_pseudo =
-     Ezfio.set_ao_basis_integral_pseudo
-  ;;
-
-(* =~=~=~=~=~=~=~=~=~=~=~=~ *)
-(* Generate Global Function *)
-(* =~=~=~=~=~=~=~=~=~=~=~=~ *)
-
-(* Read all *)
-   let read() = 
-     Some
-     {
-       disk_access_ao_one_integrals   = read_disk_access_ao_one_integrals ();
                      }
+          in
+          let coef = b.ao_coef.(ao_num*j+i) in
+          (prim,coef)
+        ) in
+        Gto.of_prim_coef_list prims
+      )
+    in
+    let rec do_work accu sym gto nucl =
+      match (sym, gto, nucl) with
+        | (s::srest, g::grest, n::nrest) -> 
+          do_work ((s,g,n)::accu) srest grest nrest
+        | ([],[],[]) -> List.rev accu
+        | _ -> assert false
+    in
+    do_work [] 
+      (Array.to_list b.ao_power)
+      (Array.to_list gto_array)
+      (Array.to_list b.ao_nucl)
   ;;
-(* Write all *)
+  let to_basis b =
-   let write{ 
+    to_long_basis b
-              disk_access_ao_one_integrals;
+    |> Long_basis.to_basis
-            } =
-     write_disk_access_ao_one_integrals   disk_access_ao_one_integrals;
   ;;
-(* to_string*)
+      
-   let to_string b =
+  let to_md5 b =
-     Printf.sprintf "
+    let short_basis = to_basis b in
-   disk_access_ao_one_integrals = %s
+    Basis.to_md5 short_basis
-   "
-       (Disk_access.to_string b.disk_access_ao_one_integrals)
   ;;
-(* to_rst*)
+    
+
+ 
+  let write_md5 b =
+    to_md5 b
+    |> MD5.to_string 
+    |> Ezfio.set_ao_basis_ao_md5 
+  ;;
+
+  let write_ao_basis name =
+    AO_basis_name.to_string name
+    |> Ezfio.set_ao_basis_ao_basis
+  ;;
+
+  let write b =
+   let { ao_basis        ;
+         ao_num          ;
+         ao_prim_num     ;
+         ao_prim_num_max ;
+         ao_nucl         ;
+         ao_power        ;
+         ao_coef         ;
+         ao_expo         ;
+         ao_cartesian    ;
+       } = b
+     in
+     write_md5 b ;
+     write_ao_basis ao_basis;
+  ;;
+
+
+  let read () =
+    if (Ezfio.has_ao_basis_ao_basis ()) then
+      begin
+        let result = 
+          { ao_basis        = read_ao_basis ();
+            ao_num          = read_ao_num () ;
+            ao_prim_num     = read_ao_prim_num ();
+            ao_prim_num_max = read_ao_prim_num_max ();
+            ao_nucl         = read_ao_nucl ();
+            ao_power        = read_ao_power ();
+            ao_coef         = read_ao_coef () ;
+            ao_expo         = read_ao_expo () ;
+            ao_cartesian    = read_ao_cartesian () ;
+          }
+        in
+        to_md5 result
+        |> MD5.to_string
+        |> Ezfio.set_ao_basis_ao_md5 ;
+        Some result
+      end
+    else
+      None
+  ;;
+    
+
   let to_rst b =
+    let print_sym = 
+      let l = List.init (Array.length b.ao_power) ~f:(
+         fun i -> ( (i+1),b.ao_nucl.(i),b.ao_power.(i) ) ) in
+      let rec do_work = function
+      | [] -> []
+      | (i,n,x)::tail  -> 
+          (Printf.sprintf " %5d  %6d     %-8s\n" i (Nucl_number.to_int n) (Symmetry.Xyz.to_string x))::
+          (do_work tail)
+      in do_work l
+      |> String.concat
+    in
+
+    let short_basis = to_basis b in
     Printf.sprintf "
-   Read/Write AO one-electron integrals from/to disk [ Write | Read | None ] ::
+Name of the AO basis ::
 
-     disk_access_ao_one_integrals = %s
+  ao_basis = %s
+
+Cartesian coordinates (6d,10f,...) ::
+
+  ao_cartesian = %s
+
+Basis set (read-only) ::
+  
+%s
+
+
+======= ========= ===========
+ Basis   Nucleus   Symmetries
+======= ========= ===========
+%s
+======= ========= ===========
+
+"   (AO_basis_name.to_string b.ao_basis)
+    (Bool.to_string b.ao_cartesian)
+    (Basis.to_string short_basis 
+       |> String.split ~on:'\n'
+       |> List.map ~f:(fun x-> "  "^x)
+       |> String.concat ~sep:"\n"
+    ) print_sym
   
-   "
-       (Disk_access.to_string b.disk_access_ao_one_integrals)
   |> Rst_string.of_string
   ;;
-  include Generic_input_of_rst;;
-  let of_rst = of_rst t_of_sexp;;
 
+  let read_rst s = 
+    let s = Rst_string.to_string s
+    |> String.split ~on:'\n'
+    in
+    let rec extract_basis = function
+    | [] -> failwith "Error in basis set"
+    | line :: tail ->
+      let line = String.strip line in
+      if line = "Basis set (read-only) ::" then
+        String.concat tail ~sep:"\n"
+      else
+        extract_basis tail
+    in
+    extract_basis s
+  ;;
+
+  let to_string b =
+    Printf.sprintf "
+ao_basis        = %s
+ao_num          = %s
+ao_prim_num     = %s
+ao_prim_num_max = %s
+ao_nucl         = %s
+ao_power        = %s
+ao_coef         = %s
+ao_expo         = %s
+ao_cartesian    = %s
+md5             = %s
+"
+    (AO_basis_name.to_string b.ao_basis)
+    (AO_number.to_string b.ao_num)
+    (b.ao_prim_num |> Array.to_list |> List.map
+      ~f:(AO_prim_number.to_string) |> String.concat ~sep:", " )
+    (AO_prim_number.to_string b.ao_prim_num_max)
+    (b.ao_nucl |> Array.to_list |> List.map ~f:Nucl_number.to_string |>
+      String.concat ~sep:", ")
+    (b.ao_power |> Array.to_list |> List.map ~f:(fun x->
+      "("^(Symmetry.Xyz.to_string x)^")" )|> String.concat ~sep:", ")
+    (b.ao_coef  |> Array.to_list |> List.map ~f:AO_coef.to_string
+      |> String.concat ~sep:", ")
+    (b.ao_expo  |> Array.to_list |> List.map ~f:AO_expo.to_string
+      |> String.concat ~sep:", ")
+    (b.ao_cartesian |> Bool.to_string) 
+    (to_md5 b |> MD5.to_string )
+
+  ;;
 end
+

ocaml/Input_mo_basis.ml

@@ -1,131 +1,229 @@
-(* =~=~ *)
+open Qptypes
-(* Init *)
+open Qputils
-(* =~=~ *)
+open Core
 
-open Qptypes;;
-open Qputils;;
-open Core;;
 
 module Mo_basis : sig
-(* Generate type *)
   type t = 
-     {
+      { mo_tot_num      : MO_number.t ;
-       disk_access_mo_one_integrals   : Disk_access.t;
+        mo_label        : MO_label.t;
+        mo_class        : MO_class.t array;
+        mo_occ          : MO_occ.t array;
+        mo_coef         : (MO_coef.t array) array;
+        ao_md5          : MD5.t;
       } [@@deriving sexp]
-   ;;
   val read : unit -> t option
-  val write : t-> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t option
 end = struct
-(* Generate type *)
   type t = 
-     {
+      { mo_tot_num      : MO_number.t ;
-       disk_access_mo_one_integrals   : Disk_access.t;
+        mo_label        : MO_label.t;
+        mo_class        : MO_class.t array;
+        mo_occ          : MO_occ.t array;
+        mo_coef         : (MO_coef.t array) array;
+        ao_md5          : MD5.t;
       } [@@deriving sexp]
-   ;;
+  let get_default = Qpackage.get_ezfio_default "mo_basis"
 
-  let get_default = Qpackage.get_ezfio_default "mo_basis";;
+  let read_mo_label () = 
-
+    if not (Ezfio.has_mo_basis_mo_label ()) then
-(* =~=~=~=~=~=~==~=~=~=~=~=~ *)
+      Ezfio.set_mo_basis_mo_label "None"
-(* Generate Special Function *)
-(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)
-
-(* Read snippet for disk_access_mo_one_integrals *)
-  let read_disk_access_mo_one_integrals () =
-    if not (Ezfio.has_mo_basis_disk_access_mo_one_integrals ()) then
-       get_default "disk_access_mo_one_integrals"
-       |> String.of_string
-       |> Ezfio.set_mo_basis_disk_access_mo_one_integrals
     ;
-    Ezfio.get_mo_basis_disk_access_mo_one_integrals ()
+    Ezfio.get_mo_basis_mo_label ()
-      |> Disk_access.of_string
+    |> MO_label.of_string
-  ;;
-(* Write snippet for disk_access_mo_one_integrals *)
-  let write_disk_access_mo_one_integrals var = 
-    Disk_access.to_string var
-    |> Ezfio.set_mo_basis_disk_access_mo_one_integrals
-  ;;
 
-(* Read snippet for integral_kinetic *)
-  let read_integral_kinetic () =
-    if not (Ezfio.has_mo_basis_integral_kinetic ()) then
-       get_default "integral_kinetic"
-       |> Float.of_string
-       |> Ezfio.set_mo_basis_integral_kinetic
-    ;
-    Ezfio.get_mo_basis_integral_kinetic ()
-  ;;
-(* Write snippet for integral_kinetic *)
-  let write_integral_kinetic =
-     Ezfio.set_mo_basis_integral_kinetic
-  ;;
 
-(* Read snippet for integral_nuclear *)
+  let read_ao_md5 () = 
-  let read_integral_nuclear () =
+    let ao_md5 = 
-    if not (Ezfio.has_mo_basis_integral_nuclear ()) then
+      match (Input_ao_basis.Ao_basis.read ()) with
-       get_default "integral_nuclear"
+      | None -> failwith "Unable to read AO basis"
-       |> Float.of_string
+      | Some result -> Input_ao_basis.Ao_basis.to_md5 result
-       |> Ezfio.set_mo_basis_integral_nuclear
+    in
-    ;
+    let result = 
-    Ezfio.get_mo_basis_integral_nuclear ()
+      if not (Ezfio.has_mo_basis_ao_md5 ()) then
-  ;;
+        begin
-(* Write snippet for integral_nuclear *)
+          MD5.to_string ao_md5
-  let write_integral_nuclear =
+          |> Ezfio.set_mo_basis_ao_md5 
-     Ezfio.set_mo_basis_integral_nuclear
+        end;
-  ;;
+      Ezfio.get_mo_basis_ao_md5 ()
+      |> MD5.of_string
+    in
+    if (ao_md5 <> result) then
+      failwith "The current MOs don't correspond to the current AOs.";
+    result
 
-(* Read snippet for integral_pseudo *)
-  let read_integral_pseudo () =
-    if not (Ezfio.has_mo_basis_integral_pseudo ()) then
-       get_default "integral_pseudo"
-       |> Float.of_string
-       |> Ezfio.set_mo_basis_integral_pseudo
-    ;
-    Ezfio.get_mo_basis_integral_pseudo ()
-  ;;
-(* Write snippet for integral_pseudo *)
-  let write_integral_pseudo =
-     Ezfio.set_mo_basis_integral_pseudo
-  ;;
 
-(* =~=~=~=~=~=~=~=~=~=~=~=~ *)
+  let read_mo_tot_num () =
-(* Generate Global Function *)
+    Ezfio.get_mo_basis_mo_tot_num ()
-(* =~=~=~=~=~=~=~=~=~=~=~=~ *)
+    |> MO_number.of_int
 
-(* Read all *)
+
-   let read() = 
+  let read_mo_class () =
+    if not (Ezfio.has_mo_basis_mo_class ()) then
+      begin
+        let mo_tot_num = MO_number.to_int (read_mo_tot_num ()) in
+        let data = 
+          Array.init mo_tot_num ~f:(fun _ -> MO_class.(to_string (Active [])))
+          |> Array.to_list
+        in
+        Ezfio.ezfio_array_of_list ~rank:1 
+          ~dim:[| mo_tot_num |] ~data:data
+        |> Ezfio.set_mo_basis_mo_class
+      end;
+    Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_class () )
+    |> Array.map ~f:MO_class.of_string
+
+
+  let read_mo_occ () =
+    if not (Ezfio.has_mo_basis_mo_label ()) then
+      begin
+        let elec_alpha_num = Ezfio.get_electrons_elec_alpha_num () 
+        and elec_beta_num = Ezfio.get_electrons_elec_beta_num ()
+        and mo_tot_num = MO_number.to_int (read_mo_tot_num ()) in
+        let data = Array.init mo_tot_num ~f:(fun i ->
+            if (i<elec_beta_num) then 2.
+            else if (i < elec_alpha_num) then 1.
+            else 0.) |> Array.to_list in
+        Ezfio.ezfio_array_of_list ~rank:1 
+          ~dim:[| mo_tot_num |] ~data:data
+        |> Ezfio.set_mo_basis_mo_occ
+      end;
+    Ezfio.flattened_ezfio (Ezfio.get_mo_basis_mo_occ () )
+    |> Array.map ~f:MO_occ.of_float
+
+
+  let read_mo_coef () =
+    let a = Ezfio.get_mo_basis_mo_coef () 
+            |> Ezfio.flattened_ezfio
+            |> Array.map ~f:MO_coef.of_float
+    in
+    let mo_tot_num = read_mo_tot_num () |> MO_number.to_int in
+    let ao_num = (Array.length a)/mo_tot_num in
+    Array.init mo_tot_num ~f:(fun j ->
+        Array.sub ~pos:(j*ao_num) ~len:(ao_num) a
+      )
+
+
+  let read () =
+    if (Ezfio.has_mo_basis_mo_tot_num ()) then
       Some
-     {
+        { mo_tot_num      = read_mo_tot_num ();
-       disk_access_mo_one_integrals   = read_disk_access_mo_one_integrals ();
+          mo_label        = read_mo_label () ;
+          mo_class        = read_mo_class ();
+          mo_occ          = read_mo_occ ();
+          mo_coef         = read_mo_coef ();
+          ao_md5          = read_ao_md5 ();
         }
-   ;;
+    else
-(* Write all *)
+      None
-   let write{ 
+
-              disk_access_mo_one_integrals;
+
-            } =
+  let mo_coef_to_string mo_coef =
-     write_disk_access_mo_one_integrals   disk_access_mo_one_integrals;
+    let ao_num = Array.length mo_coef.(0) 
-   ;;
+    and mo_tot_num = Array.length mo_coef in
-(* to_string*)
+    let rec print_five imin imax =
-   let to_string b =
+      match (imax-imin+1) with 
-     Printf.sprintf "
+      | 1 ->
-   disk_access_mo_one_integrals = %s
+        let header = [ Printf.sprintf "  #%15d" (imin+1) ; ] in
-   "
+        let new_lines = 
-       (Disk_access.to_string b.disk_access_mo_one_integrals)
+          List.init ao_num ~f:(fun i ->
-   ;;
+              Printf.sprintf "  %3d %15.10f " (i+1)
-(* to_rst*)
+                (MO_coef.to_float mo_coef.(imin  ).(i)) )
+        in header @ new_lines
+      | 2 ->
+        let header = [ Printf.sprintf "  #%15d %15d" (imin+1) (imin+2) ; ] in
+        let new_lines = 
+          List.init ao_num ~f:(fun i ->
+              Printf.sprintf "  %3d %15.10f %15.10f" (i+1)
+                (MO_coef.to_float mo_coef.(imin  ).(i))
+                (MO_coef.to_float mo_coef.(imin+1).(i)) )
+        in header @ new_lines
+      | 3 ->
+        let header = [ Printf.sprintf "  #%15d %15d %15d"
+                         (imin+1) (imin+2) (imin+3); ] in
+        let new_lines = 
+          List.init ao_num ~f:(fun i ->
+              Printf.sprintf "  %3d %15.10f %15.10f %15.10f" (i+1)
+                (MO_coef.to_float mo_coef.(imin  ).(i))
+                (MO_coef.to_float mo_coef.(imin+1).(i))
+                (MO_coef.to_float mo_coef.(imin+2).(i)) )
+        in header @ new_lines
+      | 4 ->
+        let header = [ Printf.sprintf "  #%15d %15d %15d %15d"
+                         (imin+1) (imin+2) (imin+3) (imin+4) ; ] in
+        let new_lines = 
+          List.init ao_num ~f:(fun i ->
+              Printf.sprintf "  %3d %15.10f %15.10f %15.10f %15.10f" (i+1)
+                (MO_coef.to_float mo_coef.(imin  ).(i))
+                (MO_coef.to_float mo_coef.(imin+1).(i))
+                (MO_coef.to_float mo_coef.(imin+2).(i))
+                (MO_coef.to_float mo_coef.(imin+3).(i)) )
+        in header @ new_lines
+      | 5 ->
+        let header = [ Printf.sprintf "  #%15d %15d %15d %15d %15d"
+                         (imin+1) (imin+2) (imin+3) (imin+4) (imin+5) ; ] in
+        let new_lines = 
+          List.init ao_num ~f:(fun i ->
+              Printf.sprintf "  %3d %15.10f %15.10f %15.10f %15.10f %15.10f" (i+1)
+                (MO_coef.to_float mo_coef.(imin  ).(i))
+                (MO_coef.to_float mo_coef.(imin+1).(i))
+                (MO_coef.to_float mo_coef.(imin+2).(i))
+                (MO_coef.to_float mo_coef.(imin+3).(i))
+                (MO_coef.to_float mo_coef.(imin+4).(i)) )
+        in header @ new_lines 
+      | _ -> assert false
+    in
+    let rec create_list accu i = 
+      if (i+4 < mo_tot_num) then
+        create_list ( (print_five i (i+3) |> String.concat ~sep:"\n")::accu ) (i+4)
+      else
+        (print_five i (mo_tot_num-1) |> String.concat ~sep:"\n")::accu |> List.rev
+    in
+    create_list [] 0 |> String.concat ~sep:"\n\n"
+
+
   let to_rst b =
     Printf.sprintf "
-   Read/Write MO one-electron integrals from/to disk [ Write | Read | None ] ::
+Label of the molecular orbitals ::
 
-     disk_access_mo_one_integrals = %s
+  mo_label = %s
 
-   "
+Total number of MOs ::
-       (Disk_access.to_string b.disk_access_mo_one_integrals)
+
+  mo_tot_num = %s
+
+MO coefficients ::
+
+%s
+"
+      (MO_label.to_string b.mo_label)
+      (MO_number.to_string b.mo_tot_num)
+      (mo_coef_to_string b.mo_coef)
     |> Rst_string.of_string
-   ;;
+
-  include Generic_input_of_rst;;
+
-  let of_rst = of_rst t_of_sexp;;
+
+  let to_string b =
+    Printf.sprintf "
+mo_label        = %s
+mo_tot_num      = \"%s\"
+mo_clas         = %s
+mo_occ          = %s
+mo_coef         = %s
+"
+      (MO_label.to_string b.mo_label)
+      (MO_number.to_string b.mo_tot_num)
+      (b.mo_class |> Array.to_list |> List.map
+         ~f:(MO_class.to_string) |> String.concat ~sep:", " )
+      (b.mo_occ |> Array.to_list |> List.map
+         ~f:(MO_occ.to_string) |> String.concat ~sep:", " )
+      (b.mo_coef |> Array.map
+         ~f:(fun x-> Array.map ~f:MO_coef.to_string x |> String.concat_array
+                       ~sep:"," ) |>
+       String.concat_array ~sep:"\n" )
+
 
 end
+
+

ocaml/Input_nuclei_by_hand.ml

@@ -196,7 +196,7 @@ Nuclear coordinates in xyz format (Angstroms) ::
     in
     (* Find lines containing the xyz data *)
     let rec extract_begin = function
-    | [] -> raise Not_found
+    | [] -> raise Caml.Not_found
     | line::tail ->
       let line = String.strip line in
       if (String.length line > 3) &&

ocaml/Molecule.ml

@@ -62,7 +62,7 @@ let name m =
         try
           let i = List.assoc e accu in
           build_list ( (e,i+1)::(List.remove_assoc e accu) ) rest
-        with Not_found -> build_list ( (e,1)::accu ) rest
+        with Caml.Not_found -> build_list ( (e,1)::accu ) rest
       end
   | [] -> accu
   in

ocaml/Qpackage.ml

@@ -63,7 +63,7 @@ let executables = lazy (
      )
   in
   In_channel.with_file filename ~f:func
-  |> List.sort ~cmp:(fun (x,_) (y,_) -> 
+  |> List.sort ~compare:(fun (x,_) (y,_) -> 
       if x < y then -1
       else if x > y then 1
       else 0) 
@@ -80,14 +80,14 @@ let get_ezfio_default_in_file ~directory ~data ~filename =
           rest
         else
           find_dir rest
-    | [] -> raise Not_found
+    | [] -> raise Caml.Not_found
   in 
   let rec find_data = function
     | line :: rest ->
         if (line = "") then
-          raise Not_found
+          raise Caml.Not_found
         else if (line.[0] <> ' ') then
-          raise Not_found
+          raise Caml.Not_found
         else 
           begin
             match (String.lsplit2 ~on:' ' (String.strip line)) with
@@ -96,9 +96,9 @@ let get_ezfio_default_in_file ~directory ~data ~filename =
                   String.strip r
                 else
                   find_data rest
-              | None -> raise Not_found
+              | None -> raise Caml.Not_found
           end
-    | [] -> raise Not_found
+    | [] -> raise Caml.Not_found
   in
   find_dir lines
     |> find_data ;
@@ -111,7 +111,7 @@ let get_ezfio_default directory data =
   | []           -> 
       begin
         Printf.printf "%s/%s not found\n%!" directory data;
-        raise Not_found
+        raise Caml.Not_found
       end
   | filename :: tail ->
     let filename = 
@@ -120,7 +120,7 @@ let get_ezfio_default directory data =
     try
       get_ezfio_default_in_file ~directory ~data ~filename
     with
-    | Not_found -> aux tail
+    | Caml.Not_found -> aux tail
   in
   Sys.readdir dirname
   |> Array.to_list

ocaml/Queuing_system.ml

@@ -83,7 +83,7 @@ let pop_task ~client_id q =
       }
     and found =
       try Some (TasksMap.find task_id q.tasks)
-      with Not_found -> None
+      with Caml.Not_found -> None
     in new_q, Some task_id, found 
   | [] -> q, None, None
     
@@ -104,7 +104,7 @@ let end_task ~task_id ~client_id q =
   let () =
     let client_id_check = 
       try RunningMap.find task_id running with
-      Not_found -> failwith "Task already finished"
+      Caml.Not_found -> failwith "Task already finished"
     in
     assert (client_id_check = client_id)
   in

ocaml/qp_create_ezfio_from_xyz.ml

@@ -89,7 +89,7 @@ let list_basis () =
        | _ :: a :: _ -> String.strip a
       )
   in 
-  List.sort basis_list ~cmp:String.ascending
+  List.sort basis_list ~compare:String.ascending
   |> String.concat ~sep:"\n" 
 
 
@@ -131,7 +131,7 @@ let run ?o b au c d m p cart xyz_file =
     match Hashtbl.find basis_table key with
     | Some in_channel -> 
         in_channel
-    | None -> raise Not_found
+    | None -> raise Caml.Not_found
   in
   
   let temp_filename =
@@ -563,13 +563,13 @@ let run ?o b au c d m p cart xyz_file =
             in
             try
               Basis.read_element (basis_channel key) i e
-            with Not_found ->
+            with Caml.Not_found ->
               let key =
                 Element x.Atom.element
               in
               try
                 Basis.read_element (basis_channel key) i e
-              with Not_found ->
+              with Caml.Not_found ->
                 failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
                  (Element.to_string x.Atom.element) )
           with

ocaml/qp_find_pi_space.ml

@@ -99,8 +99,12 @@ let run ?(sym="None") ?(apply="no") fc ezfio_filename =
                 let ic =
                   Unix.open_process_in ("qp_set_frozen_core.py -q "^ezfio_filename)
                 in
-                let result = int_of_string @@ input_line ic in
+                let result = int_of_string @@
-                close_in ic; result
+                match In_channel.input_line ic with 
+                | Some line -> line
+                | None -> failwith "Failed in qp_set_frozen_core"
+                in
+                In_channel.close ic; result
               else 0
             in
             let command = 

ocaml/qp_overlap_of_wf.ml

@@ -54,7 +54,7 @@ let () =
       Hashtbl.fold (fun k c (accu,norm,norm') ->
         let (c',c) =
           try  (Hashtbl.find wf' k, c)
-          with Not_found -> (0.,0.)
+          with Caml.Not_found -> (0.,0.)
         in
         (accu +. c *. c' , 
         norm +. c *. c  , 

plugins/Full_CI_ZMQ/pt2_stoch_routines.irp.f

@@ -17,7 +17,7 @@ END_PROVIDER
   e = elec_num - n_core_orb * 2
   pt2_n_tasks_max = 1+min((e*(e-1))/2, int(dsqrt(dble(N_det_selectors)))/10)
   do i=1,N_det_generators
-    pt2_F(i) = 1 + dble(pt2_n_tasks_max)*maxval(dsqrt(dabs(psi_coef_sorted_gen(i,1:N_states))))
+    pt2_F(i) = 1 + int(dble(pt2_n_tasks_max)*maxval(dsqrt(dabs(psi_coef_sorted_gen(i,1:N_states)))))
   enddo
   
   if(N_det_generators < 1024) then

plugins/Full_CI_ZMQ/selection.irp.f

@@ -86,10 +86,10 @@ double precision function get_phase_bi(phasemask, s1, s2, h1, p1, h2, p2, Nint)
 
 
   ! Put the phasemask bits at position 0, and add them all
-  h1_bit = ishft(phasemask(h1_int,s1),-h1_bit)
+  h1_bit = int(ishft(phasemask(h1_int,s1),-h1_bit))
-  p1_bit = ishft(phasemask(p1_int,s1),-p1_bit)
+  p1_bit = int(ishft(phasemask(p1_int,s1),-p1_bit))
-  h2_bit = ishft(phasemask(h2_int,s2),-h2_bit)
+  h2_bit = int(ishft(phasemask(h2_int,s2),-h2_bit))
-  p2_bit = ishft(phasemask(p2_int,s2),-p2_bit)
+  p2_bit = int(ishft(phasemask(p2_int,s2),-p2_bit))
 
   np = h1_bit + p1_bit + h2_bit + p2_bit
 

src/AO_one_e_integrals/EZFIO.cfg

@@ -3,28 +3,24 @@ type: double precision
 doc: Nucleus-electron integrals in AO basis set
 size: (ao_basis.ao_num,ao_basis.ao_num)
 interface: ezfio
-default: false
 
 [integral_kinetic]
 type: double precision
 doc: Kinetic energy integrals in AO basis set
 size: (ao_basis.ao_num,ao_basis.ao_num)
 interface: ezfio
-default: false
 
 [integral_pseudo]
 type: double precision
 doc: Pseudopotential integrals in AO basis set
 size: (ao_basis.ao_num,ao_basis.ao_num)
 interface: ezfio
-default: false
 
 [integral_overlap]
 type: double precision
 doc: Overlap integrals in AO basis set
 size: (ao_basis.ao_num,ao_basis.ao_num)
 interface: ezfio
-default: false
 
 [disk_access_ao_one_integrals]
 type: Disk_access

src/MO_one_e_integrals/EZFIO.cfg

@@ -3,21 +3,18 @@ type: double precision
 doc: Nucleus-electron integrals in MO basis set
 size: (mo_basis.mo_tot_num,mo_basis.mo_tot_num)
 interface: ezfio
-default: false
 
 [integral_kinetic]
 type: double precision
 doc: Kinetic energy integrals in MO basis set
 size: (mo_basis.mo_tot_num,mo_basis.mo_tot_num)
 interface: ezfio
-default: false
 
 [integral_pseudo]
 type: double precision
 doc: Pseudopotential integrals in MO basis set
 size: (mo_basis.mo_tot_num,mo_basis.mo_tot_num)
 interface: ezfio
-default: false
 
 
 [disk_access_mo_one_integrals]