Merge branch 'dev-stable' of https://github.com/QuantumPackage/qp2 into dev-stable

ocaml/Atom.ml

@@ -22,10 +22,15 @@ let of_string ~units s =
     }
   | [ name; x; y; z ] ->
     let e = Element.of_string name in
-    { element = e ;
-      charge  = Element.to_charge e;
-      coord   = Point3d.of_string ~units (String.concat " " [x; y; z])
-    }
+    begin
+      try
+      { element = e ;
+        charge  = Element.to_charge e;
+        coord   = Point3d.of_string ~units (String.concat " " [x; y; z])
+      }
+      with
+      | err -> (Printf.eprintf "name = \"%s\"\nxyz = (%s,%s,%s)\n%!" name x y z ; raise err)
+    end
   | _ -> raise (AtomError s)
 
 

ocaml/Molecule.ml

@@ -142,13 +142,21 @@ let of_xyz_string
   result
 
 
+let regexp_r = Str.regexp {|
|}
+let regexp_t = Str.regexp {|	|}
+
 
 let of_xyz_file
     ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1))
     ?(units=Units.Angstrom)
     filename =
   let lines =
-    match Io_ext.input_lines filename with
+    Io_ext.input_lines filename
+    |> List.map (fun s -> Str.global_replace regexp_r "" s)
+    |> List.map (fun s -> Str.global_replace regexp_t " " s)
+  in
+  let lines =
+    match lines with
     | natoms :: title :: rest ->
           let natoms = 
             try
@@ -173,6 +181,8 @@ let of_zmt_file
     ?(units=Units.Angstrom)
     filename =
   Io_ext.read_all filename
+  |> Str.global_replace regexp_r ""
+  |> Str.global_replace regexp_t " "
   |> Zmatrix.of_string
   |> Zmatrix.to_xyz_string
   |> of_xyz_string ~charge ~multiplicity ~units

ocaml/Point3d.ml

@@ -24,7 +24,9 @@ let of_string ~units s =
   let l = s
           |> String_ext.split ~on:' '
           |> List.filter (fun x -> x <> "")
-          |> list_map float_of_string
+          |> list_map (fun x ->
+                 try float_of_string x with
+                 | Failure msg -> (Printf.eprintf "Bad string: \"%s\"\n%!" x ; failwith msg) )
           |> Array.of_list
   in
   { x = l.(0) *. f ;

plugins/local/tc_keywords/EZFIO.cfg

@@ -106,7 +106,7 @@ doc: If |true|, the MO basis is assumed to be bi-orthonormal
 interface: ezfio,provider,ocaml
 default: True
 
-[symetric_fock_tc]
+[symmetric_fock_tc]
 type: logical
 doc: If |true|, using F+F^t as Fock TC
 interface: ezfio,provider,ocaml

plugins/local/tc_scf/fock_hermit.irp.f

@@ -4,7 +4,7 @@
 BEGIN_PROVIDER [ double precision, good_hermit_tc_fock_mat, (mo_num, mo_num)]
 
   BEGIN_DOC
-! good_hermit_tc_fock_mat = Hermitian Upper triangular Fock matrix 
+! good_hermit_tc_fock_mat = Hermitian Upper triangular Fock matrix
 !
 ! The converged eigenvectors of such matrix yield to orthonormal vectors satisfying the left Brillouin theorem
   END_DOC
@@ -14,11 +14,11 @@ BEGIN_PROVIDER [ double precision, good_hermit_tc_fock_mat, (mo_num, mo_num)]
   good_hermit_tc_fock_mat = Fock_matrix_tc_mo_tot
   do j = 1, mo_num
     do i = 1, j-1
-      good_hermit_tc_fock_mat(i,j) = Fock_matrix_tc_mo_tot(j,i) 
+      good_hermit_tc_fock_mat(i,j) = Fock_matrix_tc_mo_tot(j,i)
     enddo
   enddo
 
-END_PROVIDER 
+END_PROVIDER
 
 BEGIN_PROVIDER [ double precision, hermit_average_tc_fock_mat, (mo_num, mo_num)]
 
@@ -35,7 +35,7 @@ BEGIN_PROVIDER [ double precision, hermit_average_tc_fock_mat, (mo_num, mo_num)]
     enddo
   enddo
 
-END_PROVIDER 
+END_PROVIDER
 
 
 ! ---
@@ -44,13 +44,13 @@ BEGIN_PROVIDER [ double precision, grad_hermit]
  BEGIN_DOC
  ! square of gradient of the energy
  END_DOC
- if(symetric_fock_tc)then
+ if(symmetric_fock_tc)then
   grad_hermit = grad_hermit_average_tc_fock_mat
  else
   grad_hermit = grad_good_hermit_tc_fock_mat
  endif
 
-END_PROVIDER 
+END_PROVIDER
 
 BEGIN_PROVIDER [ double precision, grad_good_hermit_tc_fock_mat]
   implicit none
@@ -64,7 +64,7 @@ BEGIN_PROVIDER [ double precision, grad_good_hermit_tc_fock_mat]
       grad_good_hermit_tc_fock_mat += dabs(good_hermit_tc_fock_mat(i,j))
     enddo
   enddo
-END_PROVIDER 
+END_PROVIDER
 
 ! ---
 
@@ -80,7 +80,7 @@ BEGIN_PROVIDER [ double precision, grad_hermit_average_tc_fock_mat]
       grad_hermit_average_tc_fock_mat += dabs(hermit_average_tc_fock_mat(i,j))
     enddo
   enddo
-END_PROVIDER 
+END_PROVIDER
 
 
 ! ---
@@ -95,8 +95,8 @@ subroutine save_good_hermit_tc_eigvectors()
   sign = 1
   label = "Canonical"
   output = .False.
-  
-  if(symetric_fock_tc)then
+
+  if(symmetric_fock_tc)then
    call mo_as_eigvectors_of_mo_matrix(hermit_average_tc_fock_mat, mo_num, mo_num, label, sign, output)
   else
    call mo_as_eigvectors_of_mo_matrix(good_hermit_tc_fock_mat, mo_num, mo_num, label, sign, output)

src/utils/util.irp.f

@@ -327,12 +327,12 @@ subroutine wall_time(t)
 end
 
 BEGIN_PROVIDER [ integer, nproc ]
+  use omp_lib
   implicit none
   BEGIN_DOC
   ! Number of current OpenMP threads
   END_DOC
 
-  integer, external              :: omp_get_num_threads
   nproc = 1
   !$OMP PARALLEL
   !$OMP MASTER