Improved qp_edit

data/ezfio_defaults

@@ -18,7 +18,7 @@ cis_dressed
 determinants
   n_states                   1
   n_states_diag              determinants_n_states
-  n_det_max_jacobi           5000
+  n_det_max_jacobi           1000
   threshold_generators       0.99
   threshold_selectors        0.999
   read_wf                    False

ocaml/Input_ao_basis.ml

@@ -14,7 +14,7 @@ module Ao_basis : sig
       ao_expo         : AO_expo.t array;
     } with sexp
   ;;
-  val read : unit -> t
+  val read : unit -> t option
   val to_string : t -> string
   val to_md5 : t -> MD5.t
   val to_rst : t -> Rst_string.t
@@ -93,15 +93,19 @@ end = struct
   ;;
 
   let read () =
-    { ao_basis        = read_ao_basis ();
+    if (Ezfio.has_ao_basis_ao_basis ()) then
-      ao_num          = read_ao_num () ;
+      Some
-      ao_prim_num     = read_ao_prim_num ();
+      { ao_basis        = read_ao_basis ();
-      ao_prim_num_max = read_ao_prim_num_max ();
+        ao_num          = read_ao_num () ;
-      ao_nucl         = read_ao_nucl ();
+        ao_prim_num     = read_ao_prim_num ();
-      ao_power        = read_ao_power ();
+        ao_prim_num_max = read_ao_prim_num_max ();
-      ao_coef         = read_ao_coef () ;
+        ao_nucl         = read_ao_nucl ();
-      ao_expo         = read_ao_expo () ;
+        ao_power        = read_ao_power ();
-    }
+        ao_coef         = read_ao_coef () ;
+        ao_expo         = read_ao_expo () ;
+      }
+    else
+      None
   ;;
     
   let to_long_basis b =

ocaml/Input_bi_integrals.ml

@@ -13,7 +13,7 @@ module Bielec_integrals : sig
       direct             : bool;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -150,7 +150,7 @@ end = struct
     if (result.read_mo_integrals &&
         result.write_mo_integrals) then
           failwith "Read and Write MO integrals are both true.";
-    result
+    Some result
   ;;
 
   let write b =

ocaml/Input_bitmasks.ml

@@ -10,7 +10,7 @@ module Bitmasks : sig
       generators         : int64 array;
     } with sexp
   ;;
-  val read : unit -> t
+  val read : unit -> t option 
   val to_string : t -> string
 end = struct
   type t = 
@@ -77,11 +77,15 @@ end = struct
   ;;
 
   let read () = 
-    { n_int              = read_n_int ();
+    if (Ezfio.has_mo_basis_mo_tot_num ()) then
-      bit_kind           = read_bit_kind ();
+      Some
-      n_mask_gen         = read_n_mask_gen ();
+      { n_int              = read_n_int ();
-      generators         = read_generators ();
+        bit_kind           = read_bit_kind ();
-    }
+        n_mask_gen         = read_n_mask_gen ();
+        generators         = read_generators ();
+      }
+    else
+      None
   ;;
 
   let to_string b =

ocaml/Input_cis.ml

@@ -12,7 +12,7 @@ module Cis_dressed : sig
       en_2_2             : bool;
     } with sexp
   ;;
-  val read : unit -> t
+  val read : unit -> t option
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
   val of_rst : Rst_string.t -> t option
@@ -86,6 +86,7 @@ end = struct
   ;;
 
   let read () = 
+    Some
     { n_state_cis        = read_n_state_cis ();
       n_core_cis         = read_n_core_cis ();
       n_act_cis          = read_n_act_cis ();

ocaml/Input_cisd_sc2.ml

@@ -9,7 +9,7 @@ module Cisd_sc2 : sig
       do_pt2_end         : bool;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -71,6 +71,7 @@ end = struct
 
 
   let read () = 
+    Some
     { n_det_max_cisd_sc2  = read_n_det_max_cisd_sc2 ();
       pt2_max             = read_pt2_max ();
       do_pt2_end          = read_do_pt2_end ();

ocaml/Input_determinants.ml

@@ -19,7 +19,7 @@ module Determinants : sig
       psi_coef               : Det_coef.t array;
       psi_det                : Determinant.t array;
     } with sexp
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -311,21 +311,25 @@ end = struct
 
 
   let read () =
-    { n_int                  = read_n_int ()                ;
+    if (Ezfio.has_mo_basis_mo_tot_num ()) then
-      bit_kind               = read_bit_kind ()             ;
+      Some
-      mo_label               = read_mo_label ()             ;
+      { n_int                  = read_n_int ()                ;
-      n_det                  = read_n_det ()                ;
+        bit_kind               = read_bit_kind ()             ;
-      n_states               = read_n_states ()             ;
+        mo_label               = read_mo_label ()             ;
-      n_states_diag          = read_n_states_diag ()        ;
+        n_det                  = read_n_det ()                ;
-      n_det_max_jacobi       = read_n_det_max_jacobi ()     ;
+        n_states               = read_n_states ()             ;
-      threshold_generators   = read_threshold_generators () ;
+        n_states_diag          = read_n_states_diag ()        ;
-      threshold_selectors    = read_threshold_selectors ()  ;
+        n_det_max_jacobi       = read_n_det_max_jacobi ()     ;
-      read_wf                = read_read_wf ()              ;
+        threshold_generators   = read_threshold_generators () ;
-      expected_s2            = read_expected_s2 ()          ;
+        threshold_selectors    = read_threshold_selectors ()  ;
-      s2_eig                 = read_s2_eig ()               ;
+        read_wf                = read_read_wf ()              ;
-      psi_coef               = read_psi_coef ()             ;
+        expected_s2            = read_expected_s2 ()          ;
-      psi_det                = read_psi_det ()              ;
+        s2_eig                 = read_s2_eig ()               ;
-    }
+        psi_coef               = read_psi_coef ()             ;
+        psi_det                = read_psi_det ()              ;
+      }
+    else
+      None
   ;;
 
   let write { n_int                ;

ocaml/Input_electrons.ml

@@ -8,7 +8,7 @@ module Electrons : sig
       elec_beta_num      : Elec_beta_number.t;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit
   val read_elec_num : unit -> Elec_number.t
   val to_string : t -> string
@@ -53,9 +53,13 @@ end = struct
 
 
   let read () = 
-    { elec_alpha_num      = read_elec_alpha_num ();
+    if (Ezfio.has_electrons_elec_alpha_num ()) then
-      elec_beta_num       = read_elec_beta_num ();
+      Some
-    }
+      { elec_alpha_num      = read_elec_alpha_num ();
+        elec_beta_num       = read_elec_beta_num ();
+      }
+    else
+      None
   ;;
 
   let write { elec_alpha_num ; elec_beta_num } =

ocaml/Input_full_ci.ml

@@ -9,7 +9,7 @@ module Full_ci : sig
       do_pt2_end         : bool;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t-> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -69,9 +69,10 @@ end = struct
 
 
   let read () = 
-    { n_det_max_fci    = read_n_det_max_fci ();
+    Some
-    pt2_max            = read_pt2_max ();
+    { n_det_max_fci = read_n_det_max_fci ();
-    do_pt2_end         = read_do_pt2_end ();
+      pt2_max       = read_pt2_max ();
+      do_pt2_end    = read_do_pt2_end ();
     }
   ;;
 

ocaml/Input_hartree_fock.ml

@@ -8,7 +8,7 @@ module Hartree_fock : sig
       thresh_scf         : Threshold.t;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -54,6 +54,7 @@ end = struct
 
 
   let read () = 
+    Some
     { n_it_scf_max       = read_n_it_scf_max ();
       thresh_scf         = read_thresh_scf ();
     }

ocaml/Input_mo_basis.ml

@@ -10,7 +10,7 @@ module Mo_basis : sig
       mo_coef         : (MO_coef.t array) array;
     } with sexp
   ;;
-  val read : unit -> t
+  val read : unit -> t option
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
 end = struct
@@ -68,11 +68,15 @@ end = struct
   ;;
 
   let read () =
-    { mo_tot_num      = read_mo_tot_num ();
+    if (Ezfio.has_mo_basis_mo_tot_num ()) then
-      mo_label        = read_mo_label () ;
+      Some
-      mo_occ          = read_mo_occ ();
+      { mo_tot_num      = read_mo_tot_num ();
-      mo_coef         = read_mo_coef ();
+        mo_label        = read_mo_label () ;
-    }
+        mo_occ          = read_mo_occ ();
+        mo_coef         = read_mo_coef ();
+      }
+    else
+      None
   ;;
 
   let mo_coef_to_string mo_coef =

ocaml/Input_nuclei.ml

@@ -10,7 +10,7 @@ module Nuclei : sig
       nucl_coord      : Point3d.t array;
     } with sexp
   ;;
-  val read  : unit -> t
+  val read  : unit -> t option
   val write : t -> unit 
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
@@ -111,11 +111,15 @@ end = struct
 
 
   let read () =
-    { nucl_num        = read_nucl_num ();
+    if (Ezfio.has_nuclei_nucl_num ()) then
-      nucl_label      = read_nucl_label () ;
+      Some
-      nucl_charge     = read_nucl_charge ();
+      { nucl_num        = read_nucl_num ();
-      nucl_coord      = read_nucl_coord ();
+        nucl_label      = read_nucl_label () ;
-    }
+        nucl_charge     = read_nucl_charge ();
+        nucl_coord      = read_nucl_coord ();
+      }
+    else
+      None
   ;;
 
   let write { nucl_num    ;

ocaml/qp_edit.ml

@@ -43,73 +43,93 @@ let make_header kw =
 ;;
 
 let get s = 
-  let header = (make_header s) 
+  let header = (make_header s) in
-  and rst = let open Input in
+  let f (read,to_rst) = 
-  match s with
+    match read () with
-  | Full_ci ->
+    | Some text -> header ^ (Rst_string.to_string (to_rst text))
-    Full_ci.(to_rst (read ()))
+    | None      -> ""
-  | Hartree_fock ->
+  in
-    Hartree_fock.(to_rst (read ()))
+  let rst = 
-  | Mo_basis ->
+    try
-    Mo_basis.(to_rst (read ()))
+      begin
-  | Electrons ->
+         let open Input in
-    Electrons.(to_rst (read ()))
+         match s with
-  | Determinants ->
+         | Full_ci ->
-    Determinants.(to_rst (read ()))
+           f Full_ci.(read, to_rst)
-  | Cisd_sc2 ->
+         | Hartree_fock ->
-    Cisd_sc2.(to_rst (read ()))
+           f Hartree_fock.(read, to_rst)
-  | Nuclei ->
+         | Mo_basis ->
-    Nuclei.(to_rst (read ()))
+           f Mo_basis.(read, to_rst)
-  | Ao_basis ->
+         | Electrons ->
-    Ao_basis.(to_rst (read ()))
+           f Electrons.(read, to_rst)
-  | Bielec_integrals -> 
+         | Cisd_sc2 ->
-    Bielec_integrals.(to_rst (read ()))
+           f Cisd_sc2.(read, to_rst)
- 
+         | Nuclei ->
-  in header^(Rst_string.to_string rst)
+           f Nuclei.(read, to_rst)
+         | Ao_basis ->
+           f Ao_basis.(read, to_rst)
+         | Bielec_integrals -> 
+           f Bielec_integrals.(read, to_rst)
+         | Determinants ->
+           f Determinants.(read, to_rst)
+      end
+    with
+    | Sys_error msg -> (Printf.eprintf "Info: %s\n%!" msg ; "")
+  in 
+  rst
 ;;
 
 let set str s = 
   let header = (make_header s) in
-  let index_begin = String.substr_index_exn ~pos:0 ~pattern:header str in
+  match String.substr_index ~pos:0 ~pattern:header str with
-  let index_begin = index_begin + (String.length header) in
+  | None -> ()
-  let index_end   = 
+  | Some idx -> 
-    match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
+    begin
-      ~pattern:"==" str) with
+      let index_begin = idx + (String.length header) in
-      | Some i -> i
+      let index_end   = 
-      | None -> String.length str
+        match ( String.substr_index ~pos:(index_begin+(String.length header)+1)
-  in
+          ~pattern:"==" str) with
-  let l = index_end - index_begin in
+          | Some i -> i
-  let str = String.sub ~pos:index_begin ~len:l str
+          | None -> String.length str
-  |> Rst_string.of_string
+      in
-  in
+      let l = index_end - index_begin in
-  let write (of_rst,w) =
+      let str = String.sub ~pos:index_begin ~len:l str
-    match of_rst str with
+      |> Rst_string.of_string
-    | Some data -> w data
+      in
-    | None -> ()
+      let write (of_rst,w) s =
-  in
+        try
-  let open Input in
+        match of_rst str with
-    match s with
+        | Some data -> w data
-    | Hartree_fock     -> write Hartree_fock.(of_rst, write)
+        | None -> ()
-    | Full_ci          -> write Full_ci.(of_rst, write)
+        with
-    | Electrons        -> write Electrons.(of_rst, write)
+        | _ -> (Printf.eprintf "Info: Read error in %s\n%!"
-    | Cisd_sc2         -> write Cisd_sc2.(of_rst, write)
+               (keyword_to_string s))
-    | Bielec_integrals -> write Bielec_integrals.(of_rst, write)
+      in
-    | Determinants     -> write Determinants.(of_rst, write)
+      let open Input in
-    | Nuclei           -> write Nuclei.(of_rst, write)
+        match s with
-    | Ao_basis         -> () (* TODO *)
+        | Hartree_fock     -> write Hartree_fock.(of_rst, write) s
-    | Mo_basis         -> () (* TODO *)
+        | Full_ci          -> write Full_ci.(of_rst, write) s
- 
+        | Electrons        -> write Electrons.(of_rst, write) s
+        | Cisd_sc2         -> write Cisd_sc2.(of_rst, write) s
+        | Bielec_integrals -> write Bielec_integrals.(of_rst, write) s
+        | Determinants     -> write Determinants.(of_rst, write) s
+        | Nuclei           -> write Nuclei.(of_rst, write) s
+        | Ao_basis         -> () (* TODO *)
+        | Mo_basis         -> () (* TODO *)
+    end 
 ;;
 
 
 let create_temp_file ezfio_filename fields =
   let temp_filename  = Filename.temp_file "qp_edit_" ".rst" in
-  Out_channel.with_file temp_filename ~f:(fun out_channel ->
+  begin
-    (file_header ezfio_filename) :: (List.map ~f:get fields) 
+      Out_channel.with_file temp_filename ~f:(fun out_channel ->
-    |> String.concat ~sep:"\n" 
+        (file_header ezfio_filename) :: (List.map ~f:get fields) 
-    |> Out_channel.output_string out_channel 
+        |> String.concat ~sep:"\n" 
-  );
+        |> Out_channel.output_string out_channel 
-  temp_filename
+      )
+  end
+  ; temp_filename
 ;;
 
 let run ezfio_filename =

ocaml/qp_print.ml

@@ -51,7 +51,10 @@ let run_i ~action ezfio_filename =
 
 
   let compute_charge () =
-    let input = Input.Electrons.read () in
+    let input = match Input.Electrons.read () with
+    | Some x -> x
+    | None   -> assert false
+    in
     let nucl_charge = Ezfio.get_nuclei_nucl_charge ()
       |> Ezfio.flattened_ezfio |> Array.map ~f:(Float.to_int) 
     and n_alpha = input.Input.Electrons.elec_alpha_num
@@ -63,7 +66,10 @@ let run_i ~action ezfio_filename =
   in
 
   let compute_multiplicity () =
-    let input = Input.Electrons.read () in
+    let input = match Input.Electrons.read () with
+    | Some x -> x
+    | None   -> assert false
+    in
     let n_alpha = input.Input.Electrons.elec_alpha_num
     and n_beta  = input.Input.Electrons.elec_beta_num 
     in Multiplicity.of_alpha_beta n_alpha n_beta

ocaml/test_input.ml

@@ -2,7 +2,9 @@ open Qptypes;;
 
 let test_ao () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Ao_basis.read ()
+  let b = match Input.Ao_basis.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Ao_basis.to_string b);
   print_endline (Input.Ao_basis.to_rst b |> Rst_string.to_string);
@@ -10,7 +12,9 @@ let test_ao () =
 
 let test_bielec_intergals () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Bielec_integrals.read ()
+  let b = match Input.Bielec_integrals.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   let output = Input.Bielec_integrals.to_string b
   in
@@ -28,21 +32,27 @@ let test_bielec_intergals () =
 
 let test_bitmasks () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Bitmasks.read ()
+  let b = match Input.Bitmasks.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Bitmasks.to_string b);
 ;;
 
 let test_cis () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Cis_dressed.read ()
+  let b = match Input.Cis_dressed.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Cis_dressed.to_string b);
 ;;
 
 let test_dets () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Determinants.read ()
+  let b = match Input.Determinants.read () with
+  | Some x -> x
+  | None -> assert false
   in
   print_endline (Input.Determinants.to_rst b |> Rst_string.to_string ) ;
   print_endline (Input.Determinants.sexp_of_t b |> Sexplib.Sexp.to_string ) ;
@@ -59,7 +69,9 @@ let test_dets () =
 
 let test_cisd_sc2 () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Cisd_sc2.read ()
+  let b = match Input.Cisd_sc2.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Cisd_sc2.to_string b);
   let rst = Input.Cisd_sc2.to_rst b in
@@ -76,7 +88,9 @@ let test_cisd_sc2 () =
 
 let test_electrons () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Electrons.read ()
+  let b = match Input.Electrons.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Electrons.to_string b);
   let rst = Input.Electrons.to_rst b in
@@ -92,7 +106,9 @@ let test_electrons () =
 
 let test_fci () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Full_ci.read ()
+  let b = match Input.Full_ci.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Full_ci.to_string b);
   let rst = Input.Full_ci.to_rst b in
@@ -109,7 +125,9 @@ let test_fci () =
 
 let test_hf () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Hartree_fock.read ()
+  let b = match Input.Hartree_fock.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Hartree_fock.to_string b);
   let rst = Input.Hartree_fock.to_rst b in
@@ -126,14 +144,19 @@ let test_hf () =
 
 let test_mo () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Mo_basis.read ()
+  let b = match Input.Mo_basis.read () with
+  | Some x -> x
+  | None   -> assert false
   in
   print_endline (Input.Mo_basis.to_string b);
 ;;
 
 let test_nucl () =
   Ezfio.set_file "F2.ezfio" ;
-  let b = Input.Nuclei.read () in
+  let b = match Input.Nuclei.read () with
+  | Some x -> x
+  | None   -> assert false
+  in
   let rst = Input.Nuclei.to_rst b in
   let b2 = match Input.Nuclei.of_rst rst with
   | Some x -> x