From 14158742bf9e9ed706d8b7258fdb6a9f152a175e Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Jun 2017 09:42:52 +0200
Subject: [PATCH] Review

---
 ocaml/qp_run.ml                               | 12 ++++----
 plugins/Hartree_Fock/SCF.irp.f                |  3 +-
 .../qp_convert_output_to_ezfio.py             | 28 ++++++++++++-------
 3 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/ocaml/qp_run.ml b/ocaml/qp_run.ml
index e8c8d05a..17d31cea 100644
--- a/ocaml/qp_run.ml
+++ b/ocaml/qp_run.ml
@@ -120,10 +120,11 @@ let run slave exe ezfio_file =
     | Some (_,x) -> x^" "
     | None -> assert false
   in
-  match (Sys.command (prefix^exe^ezfio_file)) with
-  | 0 -> ()
-  | i -> Printf.printf "Program exited with code %d.\n%!" i;
-  ;
+  let exit_code = 
+    match (Sys.command (prefix^exe^ezfio_file)) with
+    | 0 -> 0
+    | i -> (Printf.printf "Program exited with code %d.\n%!" i; i)
+  in
 
   TaskServer.stop ~port:port_number;
   Thread.join task_thread;
@@ -132,7 +133,8 @@ let run slave exe ezfio_file =
 
   let duration = Time.diff (Time.now()) time_start 
   |> Core.Span.to_string in
-  Printf.printf "Wall time : %s\n\n" duration
+  Printf.printf "Wall time : %s\n\n" duration;
+  exit exit_code
 
 let spec = 
   let open Command.Spec in
diff --git a/plugins/Hartree_Fock/SCF.irp.f b/plugins/Hartree_Fock/SCF.irp.f
index 853e34c9..64263e83 100644
--- a/plugins/Hartree_Fock/SCF.irp.f
+++ b/plugins/Hartree_Fock/SCF.irp.f
@@ -5,7 +5,6 @@ program scf
 ! output: hartree_fock.energy
 ! optional: mo_basis.mo_coef
   END_DOC
-!  call debug
   call create_guess
   call orthonormalize_mos
   call run
@@ -56,7 +55,7 @@ subroutine run
 
 ! Choose SCF algorithm
 
-!    call damping_SCF
+!    call damping_SCF   ! Deprecated routine
   call Roothaan_Hall_SCF
   
 end
diff --git a/scripts/ezfio_interface/qp_convert_output_to_ezfio.py b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py
index 122ce1fe..2a9bc087 100755
--- a/scripts/ezfio_interface/qp_convert_output_to_ezfio.py
+++ b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py
@@ -309,16 +309,16 @@ def write_ezfio(res, filename):
             array_l_max_block.append(l_max_block)
             array_z_remove.append(z_remove)
 
-            x = [[coef_n_zeta.split() for coef_n_zeta in l.split('\n')] \
+            x = [[ filter(None,coef_n_zeta.split()) for coef_n_zeta in l.split('\n')] \
                for l in array_party[1:] ]
-            x = []
-            for l in array_party[1:]:
-              y = []
-              for coef_n_zeta in l.split('\n'):
-                z = coef_n_zeta.split()
-                if z : y.append(z)
-              x.append(y)
-            matrix.append(x)
+#            x = []
+#            for l in array_party[1:]:
+#              y = []
+#              for coef_n_zeta in l.split('\n'):
+#                z = coef_n_zeta.split()
+#                if z : y.append(z)
+#              x.append(y)
+#            matrix.append(x)
         return (matrix, array_l_max_block, array_z_remove)
 
     def get_local_stuff(matrix):
@@ -444,4 +444,12 @@ if __name__ == '__main__':
         print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
 
     write_ezfio(res_file, ezfio_file)
-    os.system("qp_run save_ortho_mos "+ezfio_file)
+    if os.system("qp_run save_ortho_mos "+ezfio_file) != 0:
+      print """Warning: You need to run 
+
+         qp_run save_ortho_mos """+ezfio_file+"""
+
+to be sure your MOs will be orthogonal, which is not the case when
+the MOs are read from output files (not enough precision in output)."""
+
+