Merge pull request #56 from scemama/master

merge
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Emmanuel Giner 2019-01-15 17:54:33 +01:00 committed by GitHub
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149
LICENSE
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@ -1,23 +1,21 @@
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The GNU Affero General Public License is a free, copyleft license for
software and other kinds of works, specifically designed to ensure
cooperation with the community in the case of network server software.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
our General Public Licenses are intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
software for all its users.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
@ -26,44 +24,34 @@ them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
Developers that use our General Public Licenses protect your rights
with two steps: (1) assert copyright on the software, and (2) offer
you this License which gives you legal permission to copy, distribute
and/or modify the software.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
A secondary benefit of defending all users' freedom is that
improvements made in alternate versions of the program, if they
receive widespread use, become available for other developers to
incorporate. Many developers of free software are heartened and
encouraged by the resulting cooperation. However, in the case of
software used on network servers, this result may fail to come about.
The GNU General Public License permits making a modified version and
letting the public access it on a server without ever releasing its
source code to the public.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
The GNU Affero General Public License is designed specifically to
ensure that, in such cases, the modified source code becomes available
to the community. It requires the operator of a network server to
provide the source code of the modified version running there to the
users of that server. Therefore, public use of a modified version, on
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code of the modified version.
For the developers' and authors' protection, the GPL clearly explains
that there is no warranty for this free software. For both users' and
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changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run
modified versions of the software inside them, although the manufacturer
can do so. This is fundamentally incompatible with the aim of
protecting users' freedom to change the software. The systematic
pattern of such abuse occurs in the area of products for individuals to
use, which is precisely where it is most unacceptable. Therefore, we
have designed this version of the GPL to prohibit the practice for those
products. If such problems arise substantially in other domains, we
stand ready to extend this provision to those domains in future versions
of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents.
States should not allow patents to restrict development and use of
software on general-purpose computers, but in those that do, we wish to
avoid the special danger that patents applied to a free program could
make it effectively proprietary. To prevent this, the GPL assures that
patents cannot be used to render the program non-free.
An older license, called the Affero General Public License and
published by Affero, was designed to accomplish similar goals. This is
a different license, not a version of the Affero GPL, but Affero has
released a new version of the Affero GPL which permits relicensing under
this license.
The precise terms and conditions for copying, distribution and
modification follow.
@ -72,7 +60,7 @@ modification follow.
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"This License" refers to version 3 of the GNU Affero General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
@ -549,35 +537,45 @@ to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
interacting with it remotely through a computer network (if your version
supports such interaction) an opportunity to receive the Corresponding
Source of your version by providing access to the Corresponding Source
from a network server at no charge, through some standard or customary
means of facilitating copying of software. This Corresponding Source
shall include the Corresponding Source for any work covered by version 3
of the GNU General Public License that is incorporated pursuant to the
following paragraph.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
under version 3 of the GNU General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
but the work with which it is combined will remain governed by version
3 of the GNU General Public License.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
the GNU Affero General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU General
Program specifies that a certain numbered version of the GNU Affero General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published
GNU Affero General Public License, you may choose any version ever published
by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU General Public License can be used, that proxy's
versions of the GNU Affero General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
@ -632,43 +630,32 @@ state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Quantum Package
Copyright (C) 2018 Anthony Scemama, Emmanuel Giner
Copyright (C) 2019 Anthony Scemama, Emmanuel Giner
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
GNU Affero General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Quantum Package Copyright (C) 2018 Anthony Scemam, Emmanuel Giner
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
If your software can interact with users remotely through a computer
network, you should also make sure that it provides a way for users to
get its source. For example, if your program is a web application, its
interface could display a "Source" link that leads users to an archive
of the code. There are many ways you could offer source, and different
solutions will be better for different programs; see section 13 for the
specific requirements.
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
For more information on this, and how to apply and follow the GNU AGPL, see
<https://www.gnu.org/licenses/>.

11
TODO
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@ -55,17 +55,10 @@ Refaire les benchmarks
# Documentation de qpsh
# Documentation de /etc
# Extrapolation qui prend aussi en compe la variance
# Extrapolation qui prend aussi en compe la variance? a tester
# Parler dans le papier de rPT2
# Toto
Si un provider est un programme, generer une page a lui tout seul avec le man
Options obligatoires dans Command_line.ml
Documentation des commandes a updater
# Completion foireuse:
qp create_ezfio_from_xyz -b 6-31g ./<Tab>
qp create_ezfio_from_xyz -b <Tab>
# Verifier la doc des commandes avec les options - et --
# qp_stop : pour forcer a terminer proprement le programme (kill clean)

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@ -88,11 +88,20 @@ IRPF90
The code can be automatically indented with :command:`irp_indent`.
Mathematical formulas in the `BEGIN_DOC...END_DOC` sections sould be written
in LaTeX format, between `$` symbols.
Lines sould not be longer than 80 characters.
Mathematical formulas in the `BEGIN_DOC...END_DOC` sections sould be written in
LaTeX format, between `$` symbols.
All the providers, subroutines and functions should have a
`BEGIN_DOC...END_DOC` block.
Providers should never be present in the same file as a main program.
String must not use double quotes (`"`) but single quotes (`'`).
After a `read` statement there should be no comma.
Only standard Fortran is allowed : Intel or GNU extensions are forbidden.

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@ -0,0 +1,17 @@
.. _qp_update:
=========
qp_update
=========
.. program:: qp_update
This command makes an update of the |QP| to the latest stable version.
Usage
-----
.. code:: bash
qp_update [-h]

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@ -2,7 +2,7 @@
source ${QP_ROOT}/etc/autocomplete.rc
_Complete()
_configure_Complete()
{
local cur
@ -31,5 +31,5 @@ _Complete()
esac
}
complete -F _Complete configure
complete -F _configure_Complete configure

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@ -20,13 +20,13 @@ Usage:
qp set DIRECTORY ITEM : Array values read from stdin
qp run PROGRAM
qp man PROGRAM
qp man PROGRAM
qp srun PROGRAM
qp mpirun PROGRAM
qp set_frozen_core
qp create_ezfio_from_xyz
qp create_ezfio_from_xyz
qp convert_output_to_ezfio
qp update
qp set_mo_class
@ -50,19 +50,21 @@ function qp()
"create_ezfio_from_xyz")
shift
# Replace ':' by spaces
for arg in $@ ; do
if [[ $arg =~ -* ]] ; then
_ARGS+=("\"${arg//:/ }\"")
else
_ARGS+=("${arg}")
fi
for arg in "$@" ; do
case $arg in
*:*)
_ARGS+=("\"${arg//:/ }\"") ;;
*)
_ARGS+=("${arg}") ;;
esac
done
NAME=$(eval "qp_create_ezfio_from_xyz ${_ARGS}")
echo qp_create_ezfio_from_xyz "${_ARGS[@]}"
NAME=$(qp_create_ezfio_from_xyz "${_ARGS[@]}")
if [[ -d $NAME ]] ; then
[[ -d $EZFIO_FILE ]] && ezfio unset_file
ezfio set_file $NAME
else
echo $NAME | more
qp_create_ezfio_from_xyz -h | more
fi
unset _ARGS
;;
@ -74,12 +76,12 @@ function qp()
"set_mo_class")
shift
qp_set_mo_class "$@" -- ${EZFIO_FILE}
qp_set_mo_class "$@" -- ${EZFIO_FILE}
;;
"edit")
shift
qp_edit "$@" -- ${EZFIO_FILE}
qp_edit "$@" -- ${EZFIO_FILE}
;;
"run")
@ -113,7 +115,7 @@ function qp()
}
PS1="\$(_check_ezfio)\n$PS1"
;;
"plugins")
shift
qp_plugins $@
@ -128,7 +130,7 @@ function qp()
_qp_usage
;;
esac
}
@ -144,7 +146,7 @@ function _get_basis_sets () {
_Complete()
_qp_Complete()
{
local cur
@ -211,7 +213,7 @@ _Complete()
uninstall)
COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
return 0;;
create)
create)
COMPREPLY=( $(compgen -W "-n " -- $cur ) )
return 0;;
*)
@ -258,7 +260,7 @@ _Complete()
return 0
;;
set|has|get)
COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) )
COMPREPLY=( $(compgen -d "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) )
return 0
;;
edit)
@ -278,7 +280,7 @@ _Complete()
case "${prev}" in
set_file)
COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) )
COMPREPLY=( $(compgen -W "$(for i in ./* ; do [[ -f ${i}/ezfio/.version ]] && echo $i ; done)" -- ${cur} ) )
return 0
;;
*)
@ -290,4 +292,4 @@ _Complete()
fi
}
complete -F _Complete qp
complete -F _qp_Complete qp

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@ -98,10 +98,11 @@ def main(arguments):
l_result = [f for f in os.listdir(QP_PLUGINS) if f not in [".gitignore", "local"]]
else:
# Search in src all directories with a NEED file
# Search in QP_PLUGINS all directories with a NEED file
l_tmp = [dirname for (dirname, _, filenames) in \
os.walk(QP_PLUGINS, followlinks=False) \
for f in filenames if f == 'NEED']
for f in filenames if f == 'NEED' and \
"IRPF90_temp" not in dirname]
# Find directories which contain modules
l_tmp = [os.path.split(f) for f in l_tmp]

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@ -84,7 +84,7 @@ if [[ $NPROC -gt 1 ]] ; then
done
echo "Starting slaves"
srun -n $((${SLURM_NTASKS}-1)) \
qp_run -slave $PROG $INPUT > $INPUT.slaves.out
qp_run --slave $PROG $INPUT > $INPUT.slaves.out
fi
wait

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@ -116,6 +116,11 @@ subroutine ZMQ_pt2(E, pt2,relative_error, error, variance, norm, N_in)
integer(ZMQ_PTR), external :: new_zmq_to_qp_run_socket
type(selection_buffer) :: b
PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
PROVIDE psi_bilinear_matrix_transp_order psi_selectors_coef_transp psi_det_sorted
if (N_det < max(10,N_states)) then
pt2=0.d0

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@ -26,6 +26,8 @@ subroutine run_selection_slave(thread,iproc,energy)
PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
PROVIDE psi_bilinear_matrix_transp_order N_int pt2_F
PROVIDE psi_selectors_coef_transp psi_det_sorted
zmq_to_qp_run_socket = new_zmq_to_qp_run_socket()

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@ -3,23 +3,9 @@ use bitmasks
BEGIN_PROVIDER [ double precision, selection_weight, (N_states) ]
implicit none
BEGIN_DOC
! Weights in the state-average calculation of the density matrix
! Weights used in the selection criterion
END_DOC
logical :: exists
selection_weight(:) = 1.d0
if (used_weight == 0) then
selection_weight(:) = c0_weight(:)
else if (used_weight == 1) then
selection_weight(:) = 1./N_states
else
call ezfio_has_determinants_state_average_weight(exists)
if (exists) then
call ezfio_get_determinants_state_average_weight(selection_weight)
endif
endif
selection_weight(:) = selection_weight(:)+1.d-31
selection_weight(:) = selection_weight(:)/(sum(selection_weight(:)))
selection_weight(1:N_states) = c0_weight(1:N_states)
END_PROVIDER
@ -171,9 +157,25 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
double precision :: rss
double precision, external :: memory_of_double, memory_of_int
rss = memory_of_int( (8*N_int+5)*N_det + N_det_alpha_unique + 4*N_int*N_det_selectors)
rss += memory_of_double(mo_num*mo_num*(N_states+1))
PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
PROVIDE psi_bilinear_matrix_transp_order psi_selectors_coef_transp
rss = memory_of_double( &
N_int*2*N_det & ! preinteresting_det
+ N_int*2*N_det & ! fullminilist
+ N_int*2*N_det_selectors & ! minilist
+ N_states*mo_num*mo_num & ! mat
) + memory_of_int( &
+ (N_det+1)*2 & ! preinteresting, prefullinteresting,
+ (N_det+1)*2 & ! interesting, fullinteresting
+ mo_num*mo_num/2 & ! banned
+ mo_num/2 & ! bannedOrb
)
call check_mem(rss,irp_here)
allocate (preinteresting_det(N_int,2,N_det))
monoAdo = .true.
@ -200,11 +202,6 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
allocate (indices(N_det), &
exc_degree(max(N_det_alpha_unique,N_det_beta_unique)))
PROVIDE psi_bilinear_matrix_columns_loc psi_det_alpha_unique psi_det_beta_unique
PROVIDE psi_bilinear_matrix_rows psi_det_sorted_order psi_bilinear_matrix_order
PROVIDE psi_bilinear_matrix_transp_rows_loc psi_bilinear_matrix_transp_columns
PROVIDE psi_bilinear_matrix_transp_order
k=1
do i=1,N_det_alpha_unique
call get_excitation_degree_spin(psi_det_alpha_unique(1,i), &
@ -561,11 +558,11 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d
variance(istate) = variance(istate) + alpha_h_psi * alpha_h_psi
norm(istate) = norm(istate) + coef * coef
if (h0_type == "Variance") then
sum_e_pert = sum_e_pert - alpha_h_psi * alpha_h_psi * selection_weight(istate)
else
! if (h0_type == "Variance") then
! sum_e_pert = sum_e_pert - alpha_h_psi * alpha_h_psi * selection_weight(istate)
! else
sum_e_pert = sum_e_pert + e_pert * selection_weight(istate)
endif
! endif
end do
if(sum_e_pert <= buf%mini) then
@ -590,7 +587,7 @@ subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, intere
integer(bit_kind) :: perMask(N_int, 2), mobMask(N_int, 2), negMask(N_int, 2)
integer(bit_kind) :: phasemask(N_int,2)
PROVIDE psi_selectors_coef_transp
PROVIDE psi_selectors_coef_transp psi_det_sorted
mat = 0d0
do i=1,N_int

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@ -36,9 +36,9 @@ default: True
[used_weight]
type: integer
doc: 0: 1./(c_0^2), 1: 1/N_states, 2: input state-average weight, 3: 1/(Norm_L3(Psi))
doc: Weight used in the calculation of the one-electron density matrix. 0: 1./(c_0^2), 1: 1/N_states, 2: input state-average weight, 3: 1/(Norm_L3(Psi))
interface: ezfio,provider,ocaml
default: 0
default: 1
[threshold_generators]
type: Threshold

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@ -5,7 +5,7 @@ source $QP_ROOT/quantum_package.rc
function run() {
thresh=1.e-8
thresh=1.e-9
test_exe scf || skip
qp set_file $1
qp edit --check
@ -21,7 +21,7 @@ function run() {
}
@test "SO" { # 0.539000
run so.ezfio -25.7175263371942
run so.ezfio -25.7175126082701
}
@test "HCO" { # 0.636700

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@ -15,7 +15,7 @@ default: 0.0001
type: Normalized_float
doc: Stop stochastic |PT2| when the relative error is smaller than `PT2_relative_error`
interface: ezfio,provider,ocaml
default: 0.005
default: 0.002
[correlation_energy_ratio_max]
type: Normalized_float
@ -24,9 +24,4 @@ doc: The selection process stops at a fixed correlation ratio (useful for gettin
interface: ezfio,provider,ocaml
default: 1.00
[h0_type]
type: Perturbation
doc: Type of zeroth-order Hamiltonian [ EN | Barycentric | Variance | SOP ]
interface: ezfio,provider,ocaml
default: EN

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@ -0,0 +1,12 @@
BEGIN_PROVIDER [ character*32,h0_type ]
implicit none
BEGIN_DOC
! Type of zeroth-order Hamiltonian
END_DOC
if (s2_eig) then
h0_type = 'SOP'
else
h0_type = 'EN'
endif
END_PROVIDER