PTEROSOR/QuantumPackage
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Merge branch 'dev' into csf_verified

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Anthony Scemama 2022-09-15 11:06:02 +02:00 committed by GitHub
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19
README.md
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@ -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).

11
bin/qp_convert_output_to_ezfio
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@ -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 #

8
configure vendored
View File

@ -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"

2
data/basis/cc-pv5z_ecp_bfd
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@ -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

2
etc/qp.rc
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@ -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
;;

19
ocaml/Command_line.ml
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@ -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.")
)
;;

2
ocaml/Command_line.mli
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@ -59,6 +59,8 @@ let () =
*)
exception Error of string
type short_opt = char
type long_opt = string

4
ocaml/Molecule.ml
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@ -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 ;

11
ocaml/qp_create_ezfio.ml
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@ -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
| _ -> (Command_line.help () ; failwith "input file is missing")
| [] -> 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

2
ocaml/qp_run.ml
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@ -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

2
src/cisd/30.cisd.bats
View File

@ -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

3
src/davidson/diagonalization_hcsf_dressed.irp.f
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@ -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

58
src/davidson/diagonalize_ci.irp.f
View File

@ -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, &
size(CI_eigenvectors,1),CI_electronic_energy, &
N_det,N_csf,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
call davidson_diag_H_csf (psi_det, &
CI_eigenvectors, &
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, &
size(CI_eigenvectors,1),CI_electronic_energy, &
N_det,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
call davidson_diag_HS2(psi_det, &
CI_eigenvectors, &
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, &
size(CI_eigenvectors_tmp,1),CI_electronic_energy_tmp, &
N_det,N_csf,min(N_det,N_states),min(N_det,N_states_diag),N_int,0,converged)
call davidson_diag_H_csf (psi_det, &
CI_eigenvectors_tmp, &
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, &
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)
call davidson_diag_HS2(psi_det, &
CI_eigenvectors_tmp, &
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)

16
src/fci/40.fci.bats
View File

@ -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
}

16
src/tools/truncate_wf.irp.f
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@ -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