Merge branch 'dev' into csf_verified

README.md

@@ -1,6 +1,7 @@
 # Quantum Package 2.2
 
-<img src="https://raw.githubusercontent.com/QuantumPackage/qp2/master/data/qp2.png" width="250">
+<!--- img src="https://raw.githubusercontent.com/QuantumPackage/qp2/master/data/qp2.png" width="250" --->
+<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2021-12/Risorsa%2014_0.png"  width="250">
 
 
 [![DOI](https://zenodo.org/badge/167513335.svg)](https://zenodo.org/badge/latestdoi/167513335)
@@ -34,6 +35,12 @@ https://arxiv.org/abs/1902.08154
 * [Download the latest release](http://github.com/QuantumPackage/qp2/releases)
 * [Read the documentation](https://quantum-package.readthedocs.io) 
 
+# Discussion list
+
+For any questions or announcements regarding QuantumPackage, you can join our discussion list by registering [here](https://groupes.renater.fr/sympa/subscribe/quantum_package) or by sending an email to `quantum_package-request@groupes.renater.fr` .
+You can also look over its [archives](https://groupes.renater.fr/sympa/arc/quantum_package).
+
+
 # Build status
 
 * Master [![master build status](https://travis-ci.com/QuantumPackage/qp2.svg?branch=master)](https://travis-ci.org/QuantumPackage/qp2)
@@ -44,9 +51,19 @@ https://arxiv.org/abs/1902.08154
 
 # Credits
 
+* [TREX Center of Excellence](https://trex-coe.eu)
+* [ERC PTEROSOR](https://lcpq.github.io/PTEROSOR)
 * [CNRS](http://www.cnrs.fr)
 * [Laboratoire de Chimie et Physique Quantiques](http://lcpq.ups-tlse.fr)
 * [Laboratoire de Chimie Théorique](http://www.lct.jussieu.fr)
 * [Argonne  Leadership Computing  Facility](http://alcf.anl.gov)
 * [CALMIP](https://www.calmip.univ-toulouse.fr)
 
+
+------------------------------
+
+<img src="https://lcpq.github.io/PTEROSOR/img/ERC.png" width="200" />
+
+[TREX: Targeting Real Chemical Accuracy at the Exascale](https://trex-coe.eu) project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.
+
+[PTEROSOR](https://lcpq.github.io/PTEROSOR) project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 863481).

bin/qp_convert_output_to_ezfio

@@ -146,6 +146,17 @@ def write_ezfio(res, filename):
     ezfio.set_ao_basis_ao_nucl(at)
     ezfio.set_ao_basis_ao_prim_num(num_prim)
     ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
+    try:
+      normf = res.normf
+      if normf == 0:
+        ezfio.set_ao_basis_ao_normalized(True)
+      elif normf == 1:
+        ezfio.set_ao_basis_ao_normalized(False)
+      else:
+        print("BUG in NORMF")
+        sys.exit(0)
+    except AttributeError:
+      ezfio.set_ao_basis_ao_normalized(True)
 
     # ~#~#~#~#~#~#~ #
     # P a r s i n g #

configure

@@ -180,7 +180,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
 fi
 
 if [[ ${PACKAGES} = all ]] ; then
-        PACKAGES="zlib ninja zeromq f77zmq gmp ocaml docopt resultsFile bats"
+        PACKAGES="zlib ninja zeromq f77zmq gmp ocaml docopt resultsFile bats bse"
 fi
 
 
@@ -354,12 +354,6 @@ echo "                 ||----w |     "
 echo "                 ||     ||     "
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo ""
-echo "If you have PIP, you can install the Basis Set Exchange command-line tool:"
-echo ""
-echo "  ./configure -i bse"
-echo ""
-echo "This will enable the usage of qp_basis to install extra basis sets."
-echo ""
 echo ""
 printf "\e[m\n"
 

data/basis/cc-pv5z_ecp_bfd

@@ -555,7 +555,7 @@ g 1 1.00
 g 1 1.00
 1 0.457496     1.000000
 
-MAGNESIUM 
+MAGNESIUM
 s 9 1.00
 1 0.030975     0.165290
 2 0.062959     0.506272

etc/qp.rc

@@ -80,8 +80,6 @@ function qp()
       if [[ -d $NAME ]] ; then
         [[ -d $EZFIO_FILE ]] && ezfio unset_file
         ezfio set_file $NAME
-      else
-        qp_create_ezfio -h | more
       fi
       unset _ARGS
       ;;

ocaml/Command_line.ml

@@ -1,3 +1,5 @@
+exception Error of string
+
 type short_opt     = char
 type long_opt      = string 
 type optional      = Mandatory | Optional 
@@ -181,15 +183,16 @@ let set_specs specs_in =
     Getopt.parse_cmdline cmd_specs (fun x -> anon_args := !anon_args @ [x]);
 
     if show_help () then
-        (help () ; exit 0);
+        help ()
+    else
+        (* Check that all mandatory arguments are set *)
+        List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
+        |> List.iter (fun x -> 
+            match get x.long with
+            | Some _ -> ()
+            | None -> raise (Error ("--"^x.long^" option is missing."))
+            )
 
-    (* Check that all mandatory arguments are set *)
-    List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
-    |> List.iter (fun x -> 
-        match get x.long with
-        | Some _ -> ()
-        | None -> failwith ("Error: --"^x.long^" option is missing.")
-        )
 ;;
 
 

ocaml/Command_line.mli

@@ -59,6 +59,8 @@ let () =
 *)
 
 
+exception Error of string
+
 type short_opt = char
 
 type long_opt = string

ocaml/Molecule.ml

@@ -101,7 +101,7 @@ let to_string_general ~f m =
   |> String.concat "\n"
 
 let to_string =
-  to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x)
+  to_string_general ~f:(fun x -> Atom.to_string ~units:Units.Angstrom x)
 
 let to_xyz =
   to_string_general ~f:Atom.to_xyz
@@ -113,7 +113,7 @@ let of_xyz_string
     s =
   let l = String_ext.split s ~on:'\n'
        |> List.filter (fun x -> x <> "")
-       |> list_map (fun x -> Atom.of_string units x)
+       |> list_map (fun x -> Atom.of_string ~units x)
   in
   let ne = ( get_charge {
         nuclei=l ;

ocaml/qp_create_ezfio.ml

@@ -677,6 +677,7 @@ let run ?o b au c d m p cart xyz_file =
 
 let () =
 
+  try (
 
   let open Command_line in
   begin
@@ -734,7 +735,7 @@ If a file with the same name as the basis set exists, this file will be read.  O
 
   let basis =
     match Command_line.get "basis" with
-    | None -> assert false
+    | None -> ""
     | Some x -> x
   in
 
@@ -773,10 +774,14 @@ If a file with the same name as the basis set exists, this file will be read.  O
 
   let xyz_filename =
     match Command_line.anon_args () with
-    | [x] -> x
+    | []  -> failwith "input file is missing"
-    | _ -> (Command_line.help () ; failwith "input file is missing")
+    | x::_ -> x
   in
 
   run ?o:output basis au charge dummy multiplicity pseudo cart xyz_filename
+  )
+  with
+  | Failure txt  -> Printf.eprintf "Fatal error: %s\n%!" txt
+  | Command_line.Error txt  -> Printf.eprintf "Command line error: %s\n%!" txt
 
 

ocaml/qp_run.ml

@@ -110,7 +110,7 @@ let run slave ?prefix exe ezfio_file =
   let task_thread =
      let thread =
       Thread.create ( fun () ->
-         TaskServer.run port_number )
+         TaskServer.run ~port:port_number )
      in
      thread ();
   in

src/cisd/30.cisd.bats

@@ -4,7 +4,7 @@ source $QP_ROOT/tests/bats/common.bats.sh
 source $QP_ROOT/quantum_package.rc
 
 function run() {
-  thresh=1.e-5
+  thresh=2.e-5
   test_exe cisd || skip
   qp edit --check
   qp set determinants n_states  2

src/davidson/diagonalization_hcsf_dressed.irp.f

@@ -1,4 +1,5 @@
-subroutine davidson_diag_h_csf(dets_in,u_in,dim_in,energies,sze,sze_csf,N_st,N_st_diag,Nint,dressing_state,converged)
+subroutine davidson_diag_h_csf(dets_in, u_in, dim_in, energies, sze, sze_csf, &
+                               N_st, N_st_diag, Nint, dressing_state,converged)
   use bitmasks
   implicit none
   BEGIN_DOC

src/davidson/diagonalize_ci.irp.f

@@ -69,13 +69,21 @@ END_PROVIDER
 
    do_csf = s2_eig .and. only_expected_s2 .and. csf_based
 
-   if (diag_algorithm == "Davidson") then
+   if (diag_algorithm == 'Davidson') then
 
      if (do_csf) then
        if (sigma_vector_algorithm == 'det') then
-         call davidson_diag_H_csf(psi_det,CI_eigenvectors, &
+         call davidson_diag_H_csf (psi_det,                  &
-           size(CI_eigenvectors,1),CI_electronic_energy,               &
+                                   CI_eigenvectors,          &
-           N_det,N_csf,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
+                                   size(CI_eigenvectors,1),  &
+                                   CI_electronic_energy,     &
+                                   N_det,                    &
+                                   N_csf,                    &
+                                   min(N_csf,N_states),      &
+                                   min(N_csf,N_states_diag), &
+                                   N_int,                    &
+                                   0,                        &
+                                   converged)
        else if (sigma_vector_algorithm == 'cfg') then
           call davidson_diag_H_cfg(psi_det,CI_eigenvectors, &
           size(CI_eigenvectors,1),CI_electronic_energy,               &
@@ -85,9 +93,17 @@ END_PROVIDER
           stop 'bug'
        endif
      else
-       call davidson_diag_HS2(psi_det,CI_eigenvectors, CI_s2, &
+       call davidson_diag_HS2(psi_det,                  &
-         size(CI_eigenvectors,1),CI_electronic_energy,               &
+                              CI_eigenvectors,          &
-         N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
+                              CI_s2,                    &
+                              size(CI_eigenvectors,1),  &
+                              CI_electronic_energy,     &
+                              N_det,                    &
+                              min(N_det,N_states),      &
+                              min(N_det,N_states_diag), &
+                              N_int,                    &
+                              0,                        &
+                              converged)
      endif
 
      integer :: N_states_diag_save
@@ -108,9 +124,17 @@ END_PROVIDER
           CI_electronic_energy_tmp(1:N_states_diag_save) = CI_electronic_energy(1:N_states_diag_save)
           CI_eigenvectors_tmp(1:N_det,1:N_states_diag_save) = CI_eigenvectors(1:N_det,1:N_states_diag_save)
 
-          call davidson_diag_H_csf(psi_det,CI_eigenvectors_tmp, &
+          call davidson_diag_H_csf (psi_det,                      &
-            size(CI_eigenvectors_tmp,1),CI_electronic_energy_tmp,               &
+                                    CI_eigenvectors_tmp,          &
-            N_det,N_csf,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
+                                    size(CI_eigenvectors_tmp,1),  &
+                                    CI_electronic_energy_tmp,     &
+                                    N_det,                        &
+                                    N_csf,                        &
+                                    min(N_csf,N_states),          &
+                                    min(N_csf,N_states_diag),     &
+                                    N_int,                        &
+                                    0,                            &
+                                    converged)
 
           CI_electronic_energy(1:N_states_diag_save) = CI_electronic_energy_tmp(1:N_states_diag_save)
           CI_eigenvectors(1:N_det,1:N_states_diag_save) = CI_eigenvectors_tmp(1:N_det,1:N_states_diag_save)
@@ -128,9 +152,17 @@ END_PROVIDER
           CI_eigenvectors_tmp(1:N_det,1:N_states_diag_save) = CI_eigenvectors(1:N_det,1:N_states_diag_save)
           CI_s2_tmp(1:N_states_diag_save) = CI_s2(1:N_states_diag_save)
 
-          call davidson_diag_HS2(psi_det,CI_eigenvectors_tmp, CI_s2_tmp, &
+          call davidson_diag_HS2(psi_det,                     &
-            size(CI_eigenvectors_tmp,1),CI_electronic_energy_tmp,               &
+                                 CI_eigenvectors_tmp,             &
-            N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
+                                 CI_s2_tmp,                       &
+                                 size(CI_eigenvectors_tmp,1),     &
+                                 CI_electronic_energy_tmp,        &
+                                 N_det,                       &
+                                 min(N_det,N_states),         &
+                                 min(N_det,N_states_diag),    &
+                                 N_int,                       &
+                                 0,                           &
+                                 converged)
 
           CI_electronic_energy(1:N_states_diag_save) = CI_electronic_energy_tmp(1:N_states_diag_save)
           CI_eigenvectors(1:N_det,1:N_states_diag_save) = CI_eigenvectors_tmp(1:N_det,1:N_states_diag_save)

src/fci/40.fci.bats

@@ -40,7 +40,14 @@ function run_stoch() {
   run_stoch -49.14097596  0.0001  10000
 }
 
-@test "NH3" { # 0:00:11
+@test "F2" { # 4.07m
+  [[ -n $TRAVIS ]] && skip
+  qp set_file f2.ezfio
+  qp set_frozen_core
+  run_stoch -199.307512211742 0.002  100000
+}
+
+@test "NH3" { # 10.6657s
   qp set_file nh3.ezfio
   qp set_mo_class --core="[1-4]" --act="[5-72]"
   run -56.24474908 1.e-5  10000
@@ -179,10 +186,3 @@ function run_stoch() {
   run_stoch -93.0980746734051 5.e-4  50000
 }
 
-@test "F2" { # 0:03:34
-  [[ -n $TRAVIS ]] && skip
-  qp set_file f2.ezfio
-  qp set_frozen_core
-  run_stoch -199.307512211742 0.002  100000
-}
-

src/tools/truncate_wf.irp.f

@@ -54,11 +54,23 @@ subroutine routine_s2
  double precision, allocatable :: psi_coef_tmp(:,:)
  integer :: i,j,k
  double precision :: accu(N_states)
+ integer :: weights(0:16), ix
+ double precision :: x
 
- print *,  'Weights of the CFG'
+ weights(:) = 0
  do i=1,N_det
-   print *,  i, real(weight_configuration(det_to_configuration(i),:)), real(sum(weight_configuration(det_to_configuration(i),:)))
+   x = -dlog(1.d-32+sum(weight_configuration(det_to_configuration(i),:)))/dlog(10.d0)
+   ix = min(int(x), 16)
+   weights(ix) += 1
  enddo
+
+ print *,  'Histogram of the weights of the CFG'
+ do i=0,15
+   print *, '  10^{-', i, '}   ', weights(i) 
+ end do
+ print *, '< 10^{-', 15, '}   ', weights(16) 
+
+
  print*, 'Min weight of the configuration?'
  read(5,*) wmin