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

bin/qp_convert_output_to_ezfio

@@ -224,14 +224,18 @@ def write_ezfio(res, filename):
           exponent += [p.expo for p in b.prim]
           ang_mom.append(str.count(s, "z"))
           shell_prim_num.append(len(b.prim))
-          shell_index += [nshell_tot+1] * len(b.prim)
+          shell_index += [nshell_tot] * len(b.prim)
+
+    shell_num = len(ang_mom)
+    assert(shell_index[0] = 1)
+    assert(shell_index[-1] = shell_num)
 
     # ~#~#~#~#~ #
     # W r i t e #
     # ~#~#~#~#~ #
 
     ezfio.set_basis_basis("Read from ResultsFile")
-    ezfio.set_basis_shell_num(len(ang_mom))
+    ezfio.set_basis_shell_num(shell_num)
     ezfio.set_basis_basis_nucleus_index(nucl_index)
     ezfio.set_basis_prim_num(len(coefficient))
 

ocaml/Angmom.ml

@@ -26,8 +26,7 @@ let of_string = function
   | "J" | "j" -> J
   | "K" | "k" -> K
   | "L" | "l" -> L
-  | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L,
+  | x -> raise (Failure ("Angmom should be S|P|D|F|G|H|I|J|K|L, not "^x^"."))
-not "^x^"."))
 
 let of_char = function
   | 'S' | 's' -> S

ocaml/Basis.ml

@@ -17,7 +17,7 @@ let read in_channel at_number =
 (** Find an element in the basis set file *)
 let find in_channel element =
   seek_in in_channel 0;
-  let element_read = ref Element.X in
+  let element_read = ref Element.Og in
   while !element_read <> element
   do
     let buffer = input_line in_channel in

ocaml/Element.ml

@@ -20,7 +20,7 @@ type t = X
 
 let of_string x =
   match (String.capitalize_ascii (String.lowercase_ascii x)) with
-|  "X"   |   "Dummy"        ->  X
+|  "X"   |   "Ghost"        ->  X
 |  "H"   |   "Hydrogen"     ->  H
 |  "He"  |   "Helium"       ->  He
 |  "Li"  |   "Lithium"      ->  Li
@@ -265,7 +265,7 @@ let to_string = function
 
 
 let to_long_string = function
-| X   -> "Dummy"
+| X   -> "Ghost"
 | H   -> "Hydrogen"
 | He  -> "Helium"
 | Li  -> "Lithium"

ocaml/qp_create_ezfio.ml

@@ -6,8 +6,8 @@ type element =
 | Element of Element.t
 | Int_elem of (Nucl_number.t * Element.t)
 
-(** Handle dummy atoms placed on bonds *)
+(** Handle ghost atoms placed on bonds *)
-let dummy_centers ~threshold ~molecule ~nuclei =
+let ghost_centers ~threshold ~molecule ~nuclei =
   let d =
     Molecule.distance_matrix molecule
   in
@@ -68,11 +68,11 @@ let run ?o b au c d m p cart xyz_file =
       (Molecule.of_file xyz_file ~charge:(Charge.of_int c)
         ~multiplicity:(Multiplicity.of_int m) )
   in
-  let dummy =
+  let ghost =
-    dummy_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
+    ghost_centers ~threshold:d ~molecule ~nuclei:molecule.Molecule.nuclei
   in
   let nuclei =
-    molecule.Molecule.nuclei @ dummy
+    molecule.Molecule.nuclei @ ghost
   in
 
 
@@ -145,8 +145,6 @@ let run ?o b au c d m p cart xyz_file =
                 | 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_ascii basis
           in
           let key =
              match elem with
@@ -313,7 +311,7 @@ let run ?o b au c d m p cart xyz_file =
         }
       in
       let nuclei =
-        molecule.Molecule.nuclei @ dummy
+        molecule.Molecule.nuclei @ ghost
       in
 
 
@@ -491,11 +489,7 @@ let run ?o b au c d m p cart xyz_file =
         |> List.rev
         |> list_map (fun (x,i) ->
           try
-            let e =
+            let e = x.Atom.element in
-              match x.Atom.element with
-              | Element.X -> Element.H
-              | e -> e
-            in
             let key =
               Int_elem (i,x.Atom.element)
             in
@@ -507,6 +501,12 @@ let run ?o b au c d m p cart xyz_file =
               in
               try
                 Basis.read_element (basis_channel key) i e
+              with _ ->
+                try
+                  if e = Element.X then
+                    Basis.read_element (basis_channel key) i (Element.H)
+                  else
+                    raise Not_found
                 with Not_found ->
                   failwith (Printf.sprintf "Basis not found for atom %d (%s)" (Nucl_number.to_int i)
                   (Element.to_string x.Atom.element) )
@@ -710,9 +710,9 @@ If a file with the same name as the basis set exists, this file will be read.  O
         arg=With_arg "<int>";
         doc="Total charge of the molecule. Default is 0. For negative values, use m instead of -, for ex m1"} ;
 
-      { opt=Optional ; short='d'; long="dummy";
+      { opt=Optional ; short='g'; long="ghost";
         arg=With_arg "<float>";
-        doc="Add dummy atoms. x * (covalent radii of the atoms)."} ;
+        doc="Add ghost atoms. x * (covalent radii of the atoms)."} ;
 
       { opt=Optional ; short='m'; long="multiplicity";
         arg=With_arg "<int>";
@@ -756,8 +756,8 @@ If a file with the same name as the basis set exists, this file will be read.  O
                     int_of_string x )
   in
 
-  let dummy =
+  let ghost =
-    match Command_line.get "dummy" with
+    match Command_line.get "ghost" with
     | None -> 0.
     | Some x -> float_of_string x
   in
@@ -782,7 +782,7 @@ If a file with the same name as the basis set exists, this file will be read.  O
     | x::_ -> x
   in
 
-  run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
+  run ?o:output basis au charge ghost multiplicity pseudo cart xyz_filename
   )
   with
 (*  | Failure txt  -> Printf.eprintf "Fatal error: %s\n%!" txt *)

plugins/local/cipsi_tc_bi_ortho/run_pt2_slave.irp.f

@@ -31,11 +31,12 @@ subroutine run_pt2_slave(thread,iproc,energy)
 
   double precision, intent(in)    :: energy(N_states_diag)
   integer,  intent(in)            :: thread, iproc
-  if (N_det > 100000 ) then
   call run_pt2_slave_large(thread,iproc,energy)
-  else
+!  if (N_det > 100000 ) then
-    call run_pt2_slave_small(thread,iproc,energy)
+!   call run_pt2_slave_large(thread,iproc,energy)
-  endif
+! else
+!   call run_pt2_slave_small(thread,iproc,energy)
+! endif
 end
 
 subroutine run_pt2_slave_small(thread,iproc,energy)
@@ -178,15 +179,12 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
   type(pt2_type) :: pt2_data
   integer :: n_tasks, k, N
   integer :: i_generator, subset
+  integer :: ifirst
 
   integer :: bsize ! Size of selection buffers
   logical :: sending
-  double precision :: time_shift
-
   PROVIDE global_selection_buffer global_selection_buffer_lock
 
-  call random_number(time_shift)
-  time_shift = time_shift*15.d0
 
   zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()
 
@@ -198,15 +196,13 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
 
   zmq_socket_push      = new_zmq_push_socket(thread)
 
+  ifirst = 0
   b%N = 0
   buffer_ready = .False.
   n_tasks = 1
 
   sending = .False.
   done = .False.
-  double precision :: time0, time1
-  call wall_time(time0)
-  time0 = time0+time_shift
   do while (.not.done)
 
     integer, external :: get_tasks_from_taskserver
@@ -233,28 +229,29 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
       ASSERT (b%N == bsize)
     endif
 
+    double precision :: time0, time1
+    call wall_time(time0)
     call pt2_alloc(pt2_data,N_states)
     b%cur = 0
     call select_connected(i_generator,energy,pt2_data,b,subset,pt2_F(i_generator))
+    call wall_time(time1)
 
     integer, external :: tasks_done_to_taskserver
     if (tasks_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id,n_tasks) == -1) then
       done = .true.
     endif
     call sort_selection_buffer(b)
-
+    call push_pt2_results_async_recv(zmq_socket_push,b%mini,sending)
-    call wall_time(time1)
-!    if (time1-time0 > 15.d0) then
     call omp_set_lock(global_selection_buffer_lock)
     global_selection_buffer%mini = b%mini
     call merge_selection_buffers(b,global_selection_buffer)
+    if (ifirst /= 0 ) then
       b%cur=0
+    else
+      ifirst = 1
+    endif
     call omp_unset_lock(global_selection_buffer_lock)
-      call wall_time(time0)
+    if ( iproc == 1 ) then
-!    endif
-
-    call push_pt2_results_async_recv(zmq_socket_push,b%mini,sending)
-    if ( iproc == 1 .or. i_generator < 100 .or. done) then
       call omp_set_lock(global_selection_buffer_lock)
       call push_pt2_results_async_send(zmq_socket_push, (/i_generator/), (/pt2_data/), global_selection_buffer, (/task_id/), 1,sending)
       global_selection_buffer%cur = 0

plugins/local/cipsi_tc_bi_ortho/run_selection_slave.irp.f

@@ -7,17 +7,20 @@ subroutine run_selection_slave(thread, iproc, energy)
 
   double precision, intent(in)    :: energy(N_states)
   integer,  intent(in)            :: thread, iproc
-
   integer                        :: rc, i
+
   integer                        :: worker_id, task_id(1), ctask, ltask
   character*(512)                :: task
-  integer(ZMQ_PTR)             :: zmq_to_qp_run_socket
+
-  integer(ZMQ_PTR)             :: zmq_socket_push
   integer(ZMQ_PTR),external      :: new_zmq_to_qp_run_socket
+  integer(ZMQ_PTR)               :: zmq_to_qp_run_socket
+
   integer(ZMQ_PTR), external     :: new_zmq_push_socket
+  integer(ZMQ_PTR)               :: zmq_socket_push
+
   type(selection_buffer) :: buf, buf2
-  type(pt2_type)               :: pt2_data
   logical :: done, buffer_ready
+  type(pt2_type) :: pt2_data
 
   PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
   PROVIDE psi_bilinear_matrix_rows psi_det_sorted_tc_order psi_bilinear_matrix_order

plugins/local/cipsi_tc_bi_ortho/zmq_selection.irp.f

@@ -11,7 +11,7 @@ subroutine ZMQ_selection(N_in, pt2_data)
   integer, external              :: omp_get_thread_num
   type(pt2_type), intent(inout)  :: pt2_data
 
-  PROVIDE psi_det psi_coef N_det qp_max_mem N_states pt2_F s2_eig N_det_generators
+!  PROVIDE psi_det psi_coef N_det qp_max_mem N_states pt2_F s2_eig N_det_generators
 
   N = max(N_in,1)
   N = min(N, (elec_alpha_num * (mo_num-elec_alpha_num))**2)
@@ -61,7 +61,6 @@ subroutine ZMQ_selection(N_in, pt2_data)
   ipos=1
   task = ' '
 
- 
  do i= 1, N_det_generators
     do j=1,pt2_F(i)
       write(task(ipos:ipos+30),'(I9,1X,I9,1X,I9,''|'')') j, i, N

src/cipsi/run_pt2_slave.irp.f

@@ -186,6 +186,7 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
   type(pt2_type) :: pt2_data
   integer :: n_tasks, k, N
   integer :: i_generator, subset
+  integer :: ifirst
 
   integer :: bsize ! Size of selection buffers
   logical :: sending
@@ -202,6 +203,7 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
 
   zmq_socket_push      = new_zmq_push_socket(thread)
 
+  ifirst = 0
   b%N = 0
   buffer_ready = .False.
   n_tasks = 1
@@ -250,7 +252,11 @@ subroutine run_pt2_slave_large(thread,iproc,energy)
     call omp_set_lock(global_selection_buffer_lock)
     global_selection_buffer%mini = b%mini
     call merge_selection_buffers(b,global_selection_buffer)
+    if (ifirst /= 0 ) then
       b%cur=0
+    else
+      ifirst = 1
+    endif
     call omp_unset_lock(global_selection_buffer_lock)
     if ( iproc == 1 ) then
       call omp_set_lock(global_selection_buffer_lock)

src/tools/diagonalize_h.irp.f

@@ -20,4 +20,5 @@ subroutine routine
  call diagonalize_CI
  print*,'N_det = ',N_det
  call save_wavefunction_general(N_det,N_states,psi_det_sorted,size(psi_coef_sorted,1),psi_coef_sorted)
+ call print_mol_properties
 end

src/tools/print_energy.irp.f

@@ -14,5 +14,6 @@ end
 
 subroutine run
  implicit none
+ call print_mol_properties
  print *,  psi_energy + nuclear_repulsion
 end