From 586c5e343520d3d177a275805c8b09f2044354a8 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Tue, 25 Jul 2017 16:09:19 +0200
Subject: [PATCH] Working on aux basis

---
 ocaml/qp_add_aux_basis.ml | 206 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 206 insertions(+)
 create mode 100644 ocaml/qp_add_aux_basis.ml

diff --git a/ocaml/qp_add_aux_basis.ml b/ocaml/qp_add_aux_basis.ml
new file mode 100644
index 00000000..529dca9c
--- /dev/null
+++ b/ocaml/qp_add_aux_basis.ml
@@ -0,0 +1,206 @@
+open Qputils
+open Qptypes
+open Core.Std
+
+let spec =
+  let open Command.Spec in
+  empty 
+  +> flag "o" (optional string)
+     ~doc:"file Name of the new EZFIO file. Default is suffixed by .RI"
+  +> flag "b" (required string)
+     ~doc:"string Name of basis set."
+  +> anon (" EZFIO file)" %: file )
+
+type element =
+| Element of Element.t
+| Int_elem of (Nucl_number.t * Element.t)
+
+    
+(** Returns the list of available basis sets *)
+let list_basis () =
+  let basis_list = 
+    Qpackage.root ^ "/install/emsl/EMSL_api.py list_basis | grep \"-RI\" " 
+    |> Unix.open_process_in 
+    |> In_channel.input_lines
+    |> List.map ~f:(fun x -> 
+       match String.split x ~on:'\'' with
+       | [] -> ""
+       | a :: [] 
+       | _ :: a :: _ -> String.strip a
+      )
+  in 
+  List.sort basis_list ~cmp:String.ascending
+  |> String.concat ~sep:"\n" 
+
+
+(** Run the program *)
+let run ?o b ezfio_file =
+
+  let new_filename = 
+    match o with
+    | Some filename -> filename
+    | None -> ezfio_file ^ ".RI"
+  in
+  let () =
+    match Sys.is_directory new_filename with
+    | `Yes ->  failwith "Output directory exists"
+    | _ -> ()
+  in
+  let status =
+    Printf.sprintf "cp -r %s %s" ezfio_file new_filename
+    |> Unix.system 
+  in
+  ignore status;
+
+  Ezfio.set_file new_filename;
+
+ (**********
+  Basis set
+  **********)
+
+  let basis_table =
+     Hashtbl.Poly.create ()
+  in
+
+  (* Open basis set channels *)
+  let basis_channel element =
+    let key =
+      match element with
+      | Element e -> Element.to_string e
+      | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i)  (Element.to_string e)
+    in
+    match Hashtbl.find basis_table key with
+    | Some in_channel -> 
+        in_channel
+    | None -> raise Not_found
+  in
+  
+  let temp_filename =
+    Filename.temp_file "qp_create_" ".basis"
+  in
+  let () = 
+    Sys.remove temp_filename
+  in
+
+  let fetch_channel basis =
+    let command =
+      Qpackage.root ^ "/scripts/get_basis.sh \"" ^ temp_filename 
+          ^ "." ^ basis ^ "\" \"" ^ basis ^"\""
+    in
+    let long_basis = 
+      Qpackage.root ^ "/data/basis/" ^ basis
+    in
+    match 
+      Sys.is_file basis,
+      Sys.is_file long_basis
+    with
+    | `Yes, _    -> In_channel.create basis
+    | `No , `Yes -> In_channel.create long_basis
+    | _ -> 
+      begin
+        let filename = 
+          Unix.open_process_in command
+          |> In_channel.input_all
+          |> String.strip
+        in
+        let new_channel =
+          In_channel.create filename
+        in
+        Unix.unlink filename;
+        new_channel
+      end
+  in
+
+  let rec build_basis = function
+  | [] -> ()
+  | elem_and_basis_name :: rest -> 
+    begin
+      match (String.lsplit2 ~on:':' elem_and_basis_name) with
+      | None -> (* Principal basis *)
+        begin
+          let basis = 
+            elem_and_basis_name 
+          in
+          let new_channel =
+            fetch_channel basis
+          in
+          List.iter nuclei ~f:(fun elem->
+            let key = 
+              Element.to_string elem.Atom.element
+            in
+            match Hashtbl.add basis_table ~key:key ~data:new_channel with
+            | `Ok -> ()
+            | `Duplicate -> ()
+          )
+        end
+      | Some (key, basis) -> (*Aux basis *)
+        begin
+          let elem  = 
+            try
+              Element (Element.of_string key)
+            with Element.ElementError _ ->
+              let result = 
+                match (String.split ~on:',' key) with
+                | i :: k :: [] -> (Nucl_number.of_int @@ int_of_string i, Element.of_string k)
+                | _ -> failwith "Expected format is int,Element:basis"
+              in Int_elem result
+          and basis =
+            String.lowercase basis
+          in
+          let key = 
+             match elem with
+             | Element e -> Element.to_string e
+             | Int_elem (i,e) -> Printf.sprintf "%d,%s" (Nucl_number.to_int i) (Element.to_string e)
+          in
+          let new_channel =
+            fetch_channel basis
+          in
+          begin
+            match Hashtbl.add basis_table ~key:key ~data:new_channel with
+            | `Ok -> ()
+            | `Duplicate ->
+              let e = 
+                match elem with
+                | Element e -> e
+                | Int_elem (_,e) -> e
+              in
+              failwith ("Duplicate definition of basis for "^(Element.to_long_string e))
+          end
+       end
+    end;
+    build_basis rest
+  in
+  String.split ~on:'|' b
+  |> List.rev_map ~f:String.strip 
+  |> build_basis
+  in
+
+  let basis =
+    Input.AO_basis.read ()
+  in
+  ()
+
+
+let command = 
+    Command.basic 
+    ~summary: "Quantum Package command"
+    ~readme:(fun () -> "
+
+=== Available basis sets ===
+
+" ^ (list_basis ()) ^ "
+
+============================
+
+Extents the basis set to add an auxiliary basis set.
+" )
+    spec
+    (fun o b ezfio_file () -> run ?o b ezfio_file )
+
+
+let () =
+    Command.run command
+
+
+
+