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

README.md

@@ -0,0 +1,8 @@
+Quantum package
+===============
+
+[![Gitter](https://badges.gitter.im/Join Chat.svg)](https://gitter.im/LCPQ/quantum_package?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+Set of quantum chemistry programs and libraries.
+
+For more information, you can visit the [wiki of the project](http://github.com/LCPQ/quantum_package/wiki>)

README.rst

@@ -1,9 +0,0 @@
-===============
-Quantum package
-===============
-
-Set of quantum chemistry programs and libraries.
-
-For more information, you can visit the
-`wiki of the project <http://github.com/LCPQ/quantum_package/wiki>`_
-

ocaml/Input_bi_integrals.ml

@@ -17,7 +17,7 @@ module Bielec_integrals : sig
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t 
+  val of_rst : Rst_string.t -> t option 
 end = struct
   type t = 
     { read_ao_integrals  : bool;
@@ -220,20 +220,8 @@ Direct calculation of integrals ::
   |> Rst_string.of_string
   ;;
 
-  let of_rst s =
+  include Generic_input_of_rst;;
-    let s = Rst_string.to_string s
+  let of_rst = of_rst t_of_sexp;;
-    |> String.split ~on:'\n'
-    |> List.filter ~f:(fun line ->
-        String.contains line '=')
-    |> List.map ~f:(fun line ->
-        "("^(
-        String.tr line ~target:'=' ~replacement:' '
-        )^")" )
-    |> String.concat
-    in
-    Sexp.of_string ("("^s^")")
-    |> t_of_sexp
-  ;;
 
 end
 

ocaml/Input_cis.ml

@@ -15,6 +15,7 @@ module Cis_dressed : sig
   val read : unit -> t
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { n_state_cis        : States_number.t;
@@ -145,6 +146,10 @@ Epstein-Nesbet 2x2 diagonalization ::
 
    |> Rst_string.of_string
   ;;
+
+  include Generic_input_of_rst;;
+  let of_rst = of_rst t_of_sexp;;
+
 end
 
 

ocaml/Input_cisd_sc2.ml

@@ -13,7 +13,7 @@ module Cisd_sc2 : sig
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { n_det_max_cisd_sc2 : Det_number_max.t;
@@ -118,22 +118,8 @@ Compute E(PT2) at the end ::
    |> Rst_string.of_string
   ;;
 
-  let of_rst s =
+  include Generic_input_of_rst;;
-    let s = Rst_string.to_string s
+  let of_rst = of_rst t_of_sexp;;
-    |> String.split ~on:'\n'
-    |> List.filter ~f:(fun line ->
-        String.contains line '=')
-    |> List.map ~f:(fun line ->
-        "("^(
-        String.tr line ~target:'=' ~replacement:' '
-        )^")" )
-    |> String.concat
-    in
-    Sexp.of_string ("("^s^")")
-    |> t_of_sexp
-  ;;
-
-
 
 end
 

ocaml/Input_determinants.ml

@@ -23,7 +23,7 @@ module Determinants : sig
   val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t 
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { n_int                  : N_int_number.t;
@@ -538,8 +538,8 @@ psi_det                = %s
     and n_int = Printf.sprintf "(n_int %d)" (N_int_number.get_max ()) in
     let s = String.concat [ header ; bitkind ; n_int ; psi_coef ; psi_det]
     in
-    Sexp.of_string ("("^s^")")
+
-    |> t_of_sexp
+    Generic_input_of_rst.evaluate_sexp t_of_sexp s
   ;;
 
 end

ocaml/Input_electrons.ml

@@ -13,7 +13,7 @@ module Electrons : sig
   val read_elec_num : unit -> Elec_number.t
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { elec_alpha_num     : Elec_alpha_number.t;
@@ -91,20 +91,8 @@ elec_num           = %s
         (Elec_number.to_string (read_elec_num ()))
   ;;
 
-  let of_rst s =
+  include Generic_input_of_rst;;
-    let s = Rst_string.to_string s
+  let of_rst = of_rst t_of_sexp;;
-    |> String.split ~on:'\n'
-    |> List.filter ~f:(fun line ->
-        String.contains line '=')
-    |> List.map ~f:(fun line ->
-        "("^(
-        String.tr line ~target:'=' ~replacement:' '
-        )^")" )
-    |> String.concat
-    in
-    Sexp.of_string ("("^s^")")
-    |> t_of_sexp
-  ;;
 
 end
 

ocaml/Input_full_ci.ml

@@ -10,9 +10,10 @@ module Full_ci : sig
     } with sexp
   ;;
   val read  : unit -> t
+  val write : t-> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { n_det_max_fci      : Det_number_max.t;
@@ -33,6 +34,11 @@ end = struct
     |> Det_number_max.of_int
   ;;
 
+  let write_n_det_max_fci ndet = 
+    Det_number_max.to_int ndet
+    |> Ezfio.set_full_ci_n_det_max_fci
+  ;;
+
   let read_pt2_max () = 
     if not (Ezfio.has_full_ci_pt2_max ()) then
        get_default "pt2_max"
@@ -43,6 +49,11 @@ end = struct
     |> PT2_energy.of_float
   ;;
 
+  let write_pt2_max pt2_max = 
+    PT2_energy.to_float pt2_max
+    |> Ezfio.set_full_ci_pt2_max
+  ;;
+
   let read_do_pt2_end () = 
     if not (Ezfio.has_full_ci_do_pt2_end ()) then
        get_default "do_pt2_end"
@@ -52,6 +63,10 @@ end = struct
     Ezfio.get_full_ci_do_pt2_end ()
   ;;
 
+  let write_do_pt2_end =
+    Ezfio.set_full_ci_do_pt2_end
+  ;;
+
 
   let read () = 
     { n_det_max_fci    = read_n_det_max_fci ();
@@ -60,6 +75,16 @@ end = struct
     }
   ;;
 
+
+  let write { n_det_max_fci ;
+              pt2_max       ;
+              do_pt2_end    ;
+            } = 
+     write_n_det_max_fci n_det_max_fci;
+     write_pt2_max       pt2_max;
+     write_do_pt2_end    do_pt2_end;
+  ;;
+
   let to_string b =
     Printf.sprintf "
 n_det_max_fci = %s
@@ -92,20 +117,8 @@ Compute E(PT2) at the end ::
     |> Rst_string.of_string
     ;;
 
-  let of_rst s =
+  include Generic_input_of_rst;;
-    let s = Rst_string.to_string s
+  let of_rst = of_rst t_of_sexp;;
-    |> String.split ~on:'\n'
-    |> List.filter ~f:(fun line ->
-        String.contains line '=')
-    |> List.map ~f:(fun line ->
-        "("^(
-        String.tr line ~target:'=' ~replacement:' '
-        )^")" )
-    |> String.concat
-    in
-    Sexp.of_string ("("^s^")")
-    |> t_of_sexp
-  ;;
 
 
 end

ocaml/Input_hartree_fock.ml

@@ -9,9 +9,10 @@ module Hartree_fock : sig
     } with sexp
   ;;
   val read  : unit -> t
+  val write : t -> unit
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t 
+  val of_rst : Rst_string.t -> t  option
 end = struct
   type t = 
     { n_it_scf_max       : Strictly_positive_int.t;
@@ -31,14 +32,25 @@ end = struct
     |> Strictly_positive_int.of_int
   ;;
 
-  let read_thresh_scf() = 
+  let write_n_it_scf_max n_it_scf_max = 
+    Strictly_positive_int.to_int n_it_scf_max
+    |> Ezfio.set_hartree_fock_n_it_scf_max
+  ;;
+
+  let read_thresh_scf () = 
     if not (Ezfio.has_hartree_fock_thresh_scf()) then
        get_default "thresh_scf"
        |> Float.of_string
        |> Ezfio.set_hartree_fock_thresh_scf
     ;
     Ezfio.get_hartree_fock_thresh_scf ()
-    |> Threshold.of_float ;;
+    |> Threshold.of_float
+  ;;
+
+  let write_thresh_scf thresh_scf =
+    Threshold.to_float thresh_scf
+    |> Ezfio.set_hartree_fock_thresh_scf
+  ;;
 
 
   let read () = 
@@ -47,6 +59,15 @@ end = struct
     }
   ;;
 
+
+  let write { n_it_scf_max ;
+              thresh_scf ;
+            } =
+    write_n_it_scf_max n_it_scf_max;
+    write_thresh_scf   thresh_scf
+  ;;
+
+
   let to_string b =
     Printf.sprintf "
 n_it_scf_max = %s
@@ -72,21 +93,8 @@ SCF convergence criterion (on energy) ::
     |> Rst_string.of_string
   ;;
 
-  let of_rst s =
+  include Generic_input_of_rst;;
-    let s = Rst_string.to_string s
+  let of_rst = of_rst t_of_sexp;;
-    |> String.split ~on:'\n'
-    |> List.filter ~f:(fun line ->
-        String.contains line '=')
-    |> List.map ~f:(fun line ->
-        "("^(
-        String.tr line ~target:'=' ~replacement:' '
-        )^")" )
-    |> String.concat
-    in
-    Sexp.of_string ("("^s^")")
-    |> t_of_sexp
-  ;;
-
 
 end
 

ocaml/Input_nuclei.ml

@@ -14,7 +14,7 @@ module Nuclei : sig
   val write : t -> unit 
   val to_string : t -> string
   val to_rst : t -> Rst_string.t
-  val of_rst : Rst_string.t -> t
+  val of_rst : Rst_string.t -> t option
 end = struct
   type t = 
     { nucl_num        : Nucl_number.t ;
@@ -203,6 +203,7 @@ Nuclear coordinates in xyz format (Angstroms) ::
       | _ -> failwith "Error in xyz format"
     in
     (* Create the Nuclei.t data structure *)
+    let result = 
       { nucl_num = List.length atom_list
           |> Nucl_number.of_int ~max:nmax;
         nucl_label = List.map atom_list ~f:(fun x ->
@@ -212,6 +213,7 @@ Nuclear coordinates in xyz format (Angstroms) ::
         nucl_coord = List.map atom_list ~f:(fun x ->
           x.Atom.coord ) |> Array.of_list ;
       }
+    in Some result
   ;;
 
 end

ocaml/Makefile

@@ -10,7 +10,7 @@ endif
 
 LIBS=
 PKGS=
-OCAMLCFLAGS="-g"
+OCAMLCFLAGS="-g -warn-error A"
 OCAMLBUILD=ocamlbuild -j 0 -syntax camlp4o -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS)
 MLFILES=$(wildcard *.ml) ezfio.ml Qptypes.ml
 MLIFILES=$(wildcard *.mli) 

ocaml/README.rst

@@ -4,3 +4,10 @@ Ocaml scripts
 
 This directory contains all the scripts that control the input/output
 with the user.
+
+All executables start with `qp_` and all tests start with `test_`. Modules
+file names start with a capital letter.
+
+Info on how to extend the `qp_edit` tool is given in
+`README_qp_edit.rst <https://github.com/LCPQ/quantum_package/blob/master/ocaml/README_qp_edit.rst>`_.
+

ocaml/README_qp_edit.rst

@@ -0,0 +1,209 @@
+Adding a new block
+==================
+
+In this section, we assume we will add the `New_keyword` keyword.
+
+Create the `Input_new_keyword.ml` file
+--------------------------------------
+
+Copy for example the `Input_full_ci.ml` file as a starting point.
+
+The template is the following, where `r_x`, `r_y`, ..., `last_r` are the records
+of the block.
+
+.. code-block:: ocaml
+
+  module New_keyword : sig
+    type t =
+      {  r_x    : Type_of_x.t
+         r_y    : Y_type.t
+        ...
+         last_r : bool
+      } with sexp
+    ;;
+    val read  : unit -> t
+    val write : t -> unit
+    val to_rst : t -> Rst_string.t
+    val of_rst : Rst_string.t -> t option
+  end = struct
+    type t =
+      {  r_x    : Type_of_x.t
+         r_y    : Y_type.t
+        ...
+         last_r : bool
+      } with sexp
+    ;;
+
+    let get_default = Qpackage.get_ezfio_default "new_keyword";;
+
+
+    ...
+
+  end
+
+The following functions need to be defined
+
+.. code-block:: ocaml
+
+    val read   : unit -> t
+    val write  : t -> unit
+    val to_rst : t -> Rst_string.t
+    val of_rst : Rst_string.t -> t option
+
+
+The type `t` has to be defined in a same way in the `sig` and the `struct`.
+
+For each record of the type `t`, use types defined in the `Qptypes.ml` file as
+much as possible.
+
+The `get_default` function will fetch the default values in the `ezfio_defaults` file
+in the `new_keyword` block.
+
+For each record `r_x` of the type `t`, create a `read_r_x ()` function
+and a `write_r_x r_x` function that performs the I/O in the EZFIO.
+To set a default value in the `read_r_x` function, use the following template
+(assuming that the `Type_of_x` is built from a `double precision` value in
+the EZFIO file).
+
+.. code-block:: ocaml
+
+  let read_r_x () =
+    if not (Ezfio.has_new_keyword_r_x ()) then
+       get_default "r_x"
+       |> Float.of_string
+       |> Ezfio.set_new_keyword_r_x
+    ;
+    Ezfio.get_new_keyword_r_x ()
+    |> Type_of_x.of_float
+  ;;
+
+  let write_r_x r_x =
+    Type_of_x.to_float r_x
+    |> Ezfio.set_new_keyword_r_x
+  ;;
+
+
+Then, create a `read` and a `write` function as
+
+.. code-block:: ocaml
+
+  let read () =
+    { r_x      = read_r_x () ;
+      r_y      = read_r_y () ;
+      ...
+      last_r   = read_last_r () ;
+    }
+  ;;
+
+  let write { r_x ;
+              r_y
+              ...
+              last_r ;
+            } = 
+    write_r_x r_x;
+    write_r_y r_y;
+    ...
+    write_last_r last_r;
+  ;;
+
+Finally, create the functions to write an RST string as
+
+.. code-block:: ocaml
+
+  let to_rst b =
+    Printf.sprintf "
+  You can put here some documentation as long as there is no equal sign.
+  The record entries should be indented on the right with  a blank line
+  before and a blank line after, as they would be in a rst file.
+
+  Here is the text for r_x
+
+    r_x = %s
+
+  And here is the text for r_y
+
+    r_y = %s
+
+  ...
+  Finally, the text for last_r
+
+    last_r = %s
+  "
+      (Type_of_x.to_string  b.r_x)
+      (Y_type.to_string     b.r_y)
+      ...
+      (Bool.to_string       b.last_r)
+  ;;
+
+
+and you can use the generic `of_rst` function to read it back:
+
+.. code-block:: ocaml
+
+  include Generic_input_of_rst;;
+  let of_rst = of_rst t_of_sexp;;
+
+  
+
+Add module to `Input.ml` file
+-----------------------------
+
+Append module to the `Input.ml` file. Use the name of the `Input_new_keyword.ml` without the
+`.ml` suffix.
+
+.. code-block:: ocaml
+
+  include Input_new_keyword;;
+
+
+In the `qp_edit.ml` file
+------------------------
+
+vim search strings are given in brackets.
+
+1. (`/type keyword`) : Add a new entry to the keyword type corresponding to the block to add:
+
+.. code-block:: ocaml
+
+  type keyword =
+  ...
+  | New_keyword
+  ;;
+
+
+
+2. (`/keyword_to_string`) : Add a new entry to the `keyword_to_string` function for the title of the block
+
+.. code-block:: ocaml
+
+  let keyword_to_string = function
+  ...
+  | New_keyword -> "My new keyword"
+  ;;
+
+
+3. (`/let get s`) : Add a new call to the to_rst function of the `Input.New_keyword` module
+
+.. code-block:: ocaml
+
+  let get s =
+    let header = (make_header s)
+      and rst = let open Input in
+      match s with
+      ...
+      | New_keyword ->
+        New_keyword.(to_rst (read ()))
+      ...
+      
+
+4. (`/let set s`) : Add a new call to the of_rst function of the `Input.New_keyword` module
+
+.. code-block:: ocaml
+
+    let open Input in
+      match s with
+      ...
+      | New_keyword -> write New_keyword.(of_rst, write)
+      ...
+    ;;  
+

ocaml/qp_edit.ml

@@ -44,25 +44,26 @@ let make_header kw =
 
 let get s = 
   let header = (make_header s) 
-  and rst = match s with
+  and rst = let open Input in
+  match s with
   | Full_ci ->
-    Input.Full_ci.(to_rst (read ()))
+    Full_ci.(to_rst (read ()))
   | Hartree_fock ->
-    Input.Hartree_fock.(to_rst (read ()))
+    Hartree_fock.(to_rst (read ()))
   | Mo_basis ->
-    Input.Mo_basis.(to_rst (read ()))
+    Mo_basis.(to_rst (read ()))
   | Electrons ->
-    Input.Electrons.(to_rst (read ()))
+    Electrons.(to_rst (read ()))
   | Determinants ->
-    Input.Determinants.(to_rst (read ()))
+    Determinants.(to_rst (read ()))
   | Cisd_sc2 ->
-    Input.Cisd_sc2.(to_rst (read ()))
+    Cisd_sc2.(to_rst (read ()))
   | Nuclei ->
-    Input.Nuclei.(to_rst (read ()))
+    Nuclei.(to_rst (read ()))
   | Ao_basis ->
-    Input.Ao_basis.(to_rst (read ()))
+    Ao_basis.(to_rst (read ()))
   | Bielec_integrals -> 
-    Input.Bielec_integrals.(to_rst (read ()))
+    Bielec_integrals.(to_rst (read ()))
  
   in header^(Rst_string.to_string rst)
 ;;
@@ -81,30 +82,22 @@ let set str s =
   let str = String.sub ~pos:index_begin ~len:l str
   |> Rst_string.of_string
   in
+  let write (of_rst,w) =
+    match of_rst str with
+    | Some data -> w data
+    | None -> ()
+  in
+  let open Input in
     match s with
-  (*
+    | Hartree_fock     -> write Hartree_fock.(of_rst, write)
-  | Full_ci ->
+    | Full_ci          -> write Full_ci.(of_rst, write)
-  | Hartree_fock ->
+    | Electrons        -> write Electrons.(of_rst, write)
-  | Mo_basis ->
+    | Cisd_sc2         -> write Cisd_sc2.(of_rst, write)
-    *)
+    | Bielec_integrals -> write Bielec_integrals.(of_rst, write)
-  | Electrons ->
+    | Determinants     -> write Determinants.(of_rst, write)
-      Input.Electrons.of_rst str 
+    | Nuclei           -> write Nuclei.(of_rst, write)
-      |> Input.Electrons.write
+    | Ao_basis         -> () (* TODO *)
-  | Determinants ->
+    | Mo_basis         -> () (* TODO *)
-      Input.Determinants.of_rst str 
-      |> Input.Determinants.write
-  | Cisd_sc2 ->
-      Input.Cisd_sc2.of_rst str 
-      |> Input.Cisd_sc2.write
-  | Nuclei ->
-      Input.Nuclei.of_rst str 
-      |> Input.Nuclei.write
-  | Bielec_integrals -> 
-      Input.Bielec_integrals.of_rst str 
-      |> Input.Bielec_integrals.write
-    (*
-  | Ao_basis ->
-    *)
  
 ;;
 
@@ -132,8 +125,6 @@ let run ezfio_filename =
     List.map ~f:get [
       Ao_basis ; 
       Mo_basis ; 
-      Full_ci ;
-      Hartree_fock ;
     ])
    in
   String.concat output
@@ -144,7 +135,9 @@ let run ezfio_filename =
       Nuclei ;
       Electrons ;
       Bielec_integrals ;
+      Hartree_fock ;
       Cisd_sc2 ;
+      Full_ci ;
       Determinants ;
   ]
   in