Better CLI

qcaml-tools/dune

@@ -4,7 +4,6 @@
     quack_integrals
  )
  (libraries
-        qcaml.common
      qcaml
  )
 )

qcaml-tools/quack_input.ml

@@ -5,23 +5,82 @@ let quack_dir =
 let quack_basis_filename = quack_dir ^ "/input/basis"
 let quack_molecule_filename = quack_dir ^ "/input/molecule"
 
+module Command_line = Qcaml.Common.Command_line
+module Util = Qcaml.Common.Util
 
-let basis_file       : string option ref = ref None
+let () =
-let nuclei_file      : string option ref = ref None
+  let open Command_line in
-let charge           : int    option ref = ref None
+  begin
-let multiplicity     : int    option ref = ref None
+    set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
+    set_description_doc "Prepares the input data for QuAcK.
+Writes $QUACK_DIR/input/basis and $QUACK_DIR/input/molecule.
+If $QUACK_DIR is not set, $QUACK_DIR is replaces by the current
+directory.";
+    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 = [
+        { short='m' ; long="multiplicity" ; opt=Optional;
-  ( "-b" , Arg.String (fun x -> basis_file := Some x),
+          arg=With_arg "<int>";
-    "File containing the atomic basis set") ;
+          doc="Spin multiplicity (2S+1). Default is singlet"; } ;
-  ( "-c" , Arg.Int    (fun x -> charge := Some x),
+
-    "Total charge of the system") ;
+        { short='c' ; long="charge" ; opt=Optional;
-  ( "-m" , Arg.Int    (fun x -> multiplicity := Some x),
+          arg=With_arg "<int>";
-    "Multiplicity of the system") ;
+          doc="Total charge of the molecule. Specify negative charges with 'm' instead of the minus sign, for example m1 instead of -1. Default is 0"; } ;
-  ( "-x" , Arg.String (fun x -> nuclei_file := Some x),
+
-    "File containing the nuclear coordinates") ;
+        { short='f' ; long="frozen-core" ; opt=Optional;
+          arg=Without_arg ;
+          doc="Freeze core MOs. Default is false"; } ;
+
+        { short='r' ; long="rydberg" ; opt=Optional;
+          arg=With_arg "<int>" ;
+          doc="Number of Rydberg electrons. Default is 0"; } ;
       ]
+  end;
+
+  (* Handle options *)
+  let basis_file  = Util.of_some @@ Command_line.get "basis" in
+  let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
+  let frozen_core = Command_line.get_bool "frozen-core" in
+
+  let charge =
+    match Command_line.get "charge" with
+    | Some x -> ( if x.[0] = 'm' then
+                    ~- (int_of_string (String.sub x 1 (String.length x - 1)))
+                  else
+                    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 rydberg =
+    match Command_line.get "rydberg" with
+    | Some x -> int_of_string x
+    | None -> 0
+  in
+
+
+  let nuclei = 
+    Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
+  in
+
+  let electrons =
+    Qcaml.Particles.Electrons.of_atoms ~multiplicity ~charge nuclei
+  in
+
+  let basis = 
+    Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
+  in
 
 
   let print_basis nuclei basis =
@@ -40,7 +99,8 @@ let print_basis nuclei basis =
           Format.fprintf ocf "%a" Qcaml.Gaussian.General_basis.pp_gcs x) b
       ) dict;
     close_out oc
-    
+  in
+  print_basis nuclei basis;
 
 
   let print_molecule nuclei electrons =
@@ -48,8 +108,12 @@ let print_molecule nuclei electrons =
     let nat  = Array.length nuclei in
     let nela = Qcaml.Particles.Electrons.n_alfa electrons in
     let nelb = Qcaml.Particles.Electrons.n_beta electrons in
-  let ncore = Qcaml.Particles.Nuclei.small_core nuclei in
+    let ncore = 
-  let nryd  = 0 in
+      if frozen_core then
+        Qcaml.Particles.Nuclei.small_core nuclei 
+      else 0
+    in
+    let nryd = rydberg in
     Printf.fprintf oc "# nAt nEla nElb nCore nRyd\n";
     Printf.fprintf oc " %4d %4d %4d %5d %4d\n" nat nela nelb ncore nryd;
     Printf.fprintf oc "# Znuc   x            y           z\n";
@@ -60,49 +124,10 @@ let print_molecule nuclei electrons =
           coord.x coord.y coord.z
         ) nuclei;
     close_out oc
-    
-
-
-
-let run () =
-  let basis_file =
-    match !basis_file with
-    | None -> raise (Invalid_argument "Basis set file should be specified with -b")
-    | Some x -> x
-  and nuclei_file =
-    match !nuclei_file with
-    | None -> raise (Invalid_argument "Coordinate file should be specified with -x")
-    | Some x -> x
-  and charge = 
-    match !charge with
-    | None -> 0
-    | Some c -> c
-  and multiplicity = 
-    match !multiplicity with
-    | None -> 1
-    | Some m -> m
   in    
-
-  let nuclei = 
-    Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
-  in
-
-  let electrons =
-    Qcaml.Particles.Electrons.of_atoms ~multiplicity ~charge nuclei
-  in
-
-  let basis = 
-    Qcaml.Gaussian.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
-  in
-
-  (* Print basis *)
   print_molecule nuclei electrons;
-  print_basis nuclei basis;
+
   ()
 
-let () =
-  let usage_msg = "Available options:" in
-  Arg.parse speclist (fun _ -> ()) usage_msg;
-  run ()
 
 

qcaml-tools/quack_integrals.ml

@@ -1,30 +1,32 @@
-let out_file         : string option ref = ref None
+module Command_line = Qcaml.Common.Command_line
-let basis_file       : string option ref = ref None
+module Util = Qcaml.Common.Util
-let nuclei_file      : string option ref = ref None
-let charge           : int    option ref = ref None
-let multiplicity     : int    option ref = ref None
-let range_separation : float  option ref = ref None
 
+let () =
+  let open Command_line in
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - QuAcK command");
+    set_description_doc "Computes the one- and two-electron integrals on the Gaussian atomic basis set.";
+    set_specs
+      [ { short='b' ; long="basis" ; opt=Mandatory;
+          arg=With_arg "<string>";
+          doc="Name of the file containing the basis set"; } ;
 
-let speclist = [
+        { short='x' ; long="xyz" ; opt=Mandatory;
-  ( "-b" , Arg.String (fun x -> basis_file := Some x),
+          arg=With_arg "<string>";
-    "File containing the atomic basis set") ;
+          doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
-  ( "-x" , Arg.String (fun x -> nuclei_file := Some x),
+
-    "File containing the nuclear coordinates") ;
+        { short='u' ; long="range-separation" ; opt=Optional;
-  ( "-u" , Arg.Float  (fun x -> range_separation := Some x),
+          arg=With_arg "<float>";
-    "Value of mu, the range separation factor") ;
+          doc="Range-separation parameter."; } ;
       ]
+  end;
 
-let run () =
+  let basis_file  = Util.of_some @@ Command_line.get "basis" in
-  let basis_file =
+  let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
-    match !basis_file with
+  let range_separation = 
-    | None -> raise (Invalid_argument "Basis set file should be specified with -b")
+    match Command_line.get "range-separation" with
-    | Some x -> x
+    | None -> None
-  and nuclei_file =
+    | Some mu -> Some (float_of_string mu) 
-    match !nuclei_file with
-    | None -> raise (Invalid_argument "Coordinate file should be specified with -x")
-    | Some x -> x
-  and range_separation = !range_separation
   in
 
   let nuclei =
@@ -56,8 +58,4 @@ let run () =
   | None -> ()
 
 
-let () =
-  let usage_msg = "Available options:" in
-  Arg.parse speclist (fun _ -> ()) usage_msg;
-  run ()