From 61c380f31e19049c88ae7df313106111c1a0aac7 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 25 Feb 2019 14:36:59 +0100
Subject: [PATCH] Added Command_line module

---
 _tags               |  2 +-
 run_hartree_fock.ml | 77 ++++++++++++++++++++++++---------------------
 2 files changed, 43 insertions(+), 36 deletions(-)

diff --git a/_tags b/_tags
index c7598f6..0f8a66a 100644
--- a/_tags
+++ b/_tags
@@ -1,4 +1,4 @@
-true: package(str,unix,bigarray,lacaml,alcotest,zarith)
+true: package(str,unix,bigarray,lacaml,alcotest,zarith,getopt)
 <*.byte>  : linkdep(Utils/math_functions.o), custom
 <*.native>: linkdep(Utils/math_functions.o)
 <odoc-ltxhtml>: not_hygienic
diff --git a/run_hartree_fock.ml b/run_hartree_fock.ml
index d378bc7..7f8fe77 100644
--- a/run_hartree_fock.ml
+++ b/run_hartree_fock.ml
@@ -1,38 +1,50 @@
-let out_file    : string option ref = ref None
-let basis_file  : string option ref = ref None
-let nuclei_file : string option ref = ref None
-let charge      : int ref = ref 0
-let multiplicity: int ref = ref 1
+let () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QCaml command");
+    set_description_doc "Runs a Hartree-Fock calculation";
+    set_specs
+      [ { short='b' ; long="basis" ; opt=Mandatory;
+          arg=With_arg "<string>";
+          doc="Name of the file containing the basis set"; } ;
 
+        { short='x' ; long="xyz" ; opt=Mandatory;
+          arg=With_arg "<string>";
+          doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
 
-let speclist = [
-  ( "-b" , Arg.String (fun x -> basis_file := Some x),
-    "File containing the atomic basis set") ;
-  ( "-c" , Arg.String (fun x -> nuclei_file := Some x),
-    "File containing the nuclear coordinates") ;
-  ( "-o" , Arg.String (fun x -> out_file := Some x) ,
-    "Output file") ;
-  ( "-charge" , Arg.Int (fun x -> charge := x),
-    "Charge of the system") ;
-  ( "-mult" , Arg.Int (fun x -> multiplicity := x),
-    "Spin multiplicity of the system") ;
-]
+        { short='m' ; long="multiplicity" ; opt=Optional;
+          arg=With_arg "<int>";
+          doc="Spin multiplicity (2S+1). Default is singlet"; } ;
 
-let run ~out =
-  (*
-  let gc = Gc.get () in
-  Gc.set { gc with minor_heap_size=(262144 / 16) };
-  *)
-  let basis_file = 
-    match !basis_file with
-    | None -> raise (Invalid_argument "Basis set file should be specified with -b")
+        { short='c' ; long="charge" ; opt=Optional;
+          arg=With_arg "<int>";
+          doc="Total charge of the molecule. Default is 0"; } ;
+      ]
+  end;
+
+  (* Handle options *)
+  let basis_file  = 
+    match Command_line.get "basis" with
     | Some x -> x
-  and nuclei_file = 
-    match !nuclei_file with
-    | None -> raise (Invalid_argument "Coordinate file should be specified with -c")
+    | None -> assert false
+  in
+
+  let nuclei_file = 
+    match Command_line.get "xyz" with
     | Some x -> x
-  and charge = !charge
-  and multiplicity = !multiplicity
+    | None -> assert false
+  in
+
+  let charge = 
+    match Command_line.get "charge" with
+    | Some x -> int_of_string x
+    | None   -> 0
+  in
+
+  let multiplicity =
+    match Command_line.get "multiplicity" with
+    | Some x -> int_of_string x
+    | None -> 1
   in
 
   let s =
@@ -44,8 +56,3 @@ let run ~out =
   |> print_endline
 
 
-let () =
-  let usage_msg = "Available options:" in
-  Arg.parse speclist (fun _ -> ()) usage_msg;
-  run ~out:!out_file
-