LCPQ
/
qp2
mirror of https://github.com/QuantumPackage/qp2.git
9
1
Fork 0
Code Releases Activity

Merge branch 'dev' into dev-lcpq

This commit is contained in:
Anthony Scemama 2019-07-24 13:18:23 +02:00
parent ecf8e0bb96 2db0173057
commit 133a05c683
18 changed files with 137 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

21
GITHUB.md
View File

@ -2,20 +2,23 @@ GitHub Branches
===============
master:
The current up-to-date working branch, that users download It should
only contain the latest release and bug fixes.
The current up-to-date working branch, that users download. It should
only contain the latest stable release and bug fixes.
develop-lcpq:
Toulouse development branch
develop-lct:
Paris development branch
develop:
dev:
It is a fork of the *master* branch with new developments that will be
merged in the *master* branch for the next release. Other development
branches should be merged on this one.
bugfix:
A fork of the *master* on which the bug fixes are made.
dev-lcpq:
Toulouse development branch
dev-lct:
Paris development branch
gh-pages:
This is an independent branch, containing only the web site of QP2.

13
INSTALL.rst
View File

@ -143,7 +143,7 @@ IRPF90
to Parameters (IRP) method.
* Download the latest version of IRPF90
here : `<https://github.com/scemama/irpf90/releases/latest>`_ and move
here : `<https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz>`_ and move
the downloaded archive in the :file:`${QP_ROOT}/external` directory
* Extract the archive and go into the :file:`irpf90-*` directory to run
@ -328,7 +328,7 @@ OCaml
echo ${QP_ROOT}/bin
${QP_ROOT}/external/opam_installer.sh --no-backup --fresh
You the :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and
use it as an answer to where :command:`opam` should be installed.
@ -337,7 +337,14 @@ OCaml
.. code:: bash
opam init --disable-sandboxing --comp=4.07.0
opam init --comp=4.07.1
eval `${QP_ROOT}/bin/opam env`
If the installation fails because of bwrap, you can initialize opam using:
.. code:: bash
opam init --disable-sandboxing --comp=4.07.1
eval `${QP_ROOT}/bin/opam env`
* Install the required external OCaml libraries

2
README.md
View File

@ -5,7 +5,7 @@
[*Quantum package 2.0: an open-source determinant-driven suite of programs*](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176)\
Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\
J. Chem. Theory Comput., 15:6, 3591--3609, (2019)\
[J. Chem. Theory Comput. 2019, 15, 6, 3591-3609](https://doi.org/10.1021/acs.jctc.9b00176)\
https://arxiv.org/abs/1902.08154
```

1
REPLACE
View File

@ -834,3 +834,4 @@ qp_name potential_sr_c_alpha_ao_pbe --rename=potential_c_alpha_ao_sr_pbe
qp_name potential_sr_c_beta_ao_pbe --rename=potential_c_beta_ao_sr_pbe
qp_name potential_sr_xc_alpha_ao_pbe --rename=potential_xc_alpha_ao_sr_pbe
qp_name potential_sr_xc_beta_ao_pbe --rename=potential_xc_beta_ao_sr_pbe
qp_name disk_access_nuclear_repulsion --rename=io_nuclear_repulsion

22
configure vendored
View File

@ -297,27 +297,37 @@ EOF
${QP_ROOT}/bin
EOF
rm ${QP_ROOT}/external/opam_installer.sh
source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
${QP_ROOT}/bin/opam init --verbose --yes
opam switch create ocaml-base-compiler.4.07.1
opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
eval $(${QP_ROOT}/bin/opam env)
eval $(opam env)
opam install -y ${OCAML_PACKAGES} || exit 1
else
# Conventional commands
execute << EOF
chmod +x "\${QP_ROOT}"/external/opam_installer.sh
"\${QP_ROOT}"/external/opam_installer.sh --no-backup
EOF
execute << EOF
rm --force \${QP_ROOT}/bin/opam
export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam}
echo \${QP_ROOT}/bin \
| sh \${QP_ROOT}/external/opam_installer.sh
rm \${QP_ROOT}/external/opam_installer.sh
source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
\${QP_ROOT}/bin/opam init --verbose --yes
eval \$(\${QP_ROOT}/bin/opam env)
EOF
rm \${QP_ROOT}/external/opam_installer.sh
source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
opam switch create ocaml-base-compiler.4.07.1 || exit 1
opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
eval $(opam env)
EOF
execute << EOF
opam install -y \${OCAML_PACKAGES} || exit 1
EOF
fi

10
docs/source/research.bib
View File

@ -1,4 +1,14 @@
%%% ARXIV TO BE UPDATED %%%
@article{Giner2019Jul,
author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\ifmmode\mbox{\c{c}}\else\c{c}\fi}ois},
title = {{Chemically Accurate Excitation Energies With Small Basis Sets}},
journal = {arXiv},
year = {2019},
month = {Jul},
eprint = {1907.01245},
url = {https://arxiv.org/abs/1907.01245}
}
@article{Dash2019May,
author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia},
title = {{Excited states with selected CI-QMC: chemically accurate excitation energies and geometries}},

7
src/ao_one_e_ints/README.rst
View File

@ -6,9 +6,8 @@ All the one-electron integrals in the |AO| basis are here.
The most important providers for usual quantum-chemistry calculation are:
* `ao_kinetic_integral` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_ao_ints.irp.f`)
* `ao_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_ao_ints.irp.f`)
* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis (see :file:`ao_mono_ints.irp.f`)
* `ao_kinetic_integrals` which are the kinetic operator integrals on the |AO| basis
* `ao_integrals_n_e` which are the nuclear-elctron operator integrals on the |AO| basis
* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis
Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_ao.irp.f`.

2
src/cipsi/run_pt2_slave.irp.f
View File

@ -148,7 +148,7 @@ subroutine run_pt2_slave_small(thread,iproc,energy)
integer, external :: disconnect_from_taskserver
do i=1,300
if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) /= -2) exit
call sleep(1)
call usleep(500)
print *, 'Retry disconnect...'
end do

72
src/cipsi/run_selection_slave.irp.f
View File

@ -74,7 +74,7 @@ subroutine run_selection_slave(thread,iproc,energy)
if(done .or. ctask == size(task_id)) then
do i=1, ctask
if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
call sleep(1)
call usleep(100)
if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
ctask = 0
done = .true.
@ -85,6 +85,7 @@ subroutine run_selection_slave(thread,iproc,energy)
if(ctask > 0) then
call sort_selection_buffer(buf)
! call merge_selection_buffers(buf,buf2)
print *, task_id(1), pt2(1), buf%cur, ctask
call push_selection_results(zmq_socket_push, pt2, variance, norm, buf, task_id(1), ctask)
! buf%mini = buf2%mini
pt2(:) = 0d0
@ -132,23 +133,24 @@ subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_
print *, 'f77_zmq_send( zmq_socket_push, b%cur, 4, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)'
endif
if (b%cur > 0) then
rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, variance, 8*N_states, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)
if(rc /= 8*N_states) then
print *, 'f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)'
endif
rc = f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)
if(rc /= 8*b%cur) then
print *, 'f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)'
@ -203,22 +205,26 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
print *, 'f77_zmq_recv( zmq_socket_pull, N, 4, 0)'
endif
pt2(:) = 0.d0
variance(:) = 0.d0
norm(:) = 0.d0
rc = f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)'
endif
rc = f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)'
endif
rc = f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
endif
if (N>0) then
rc = f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)'
endif
rc = f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, variance, N_states*8, 0)'
endif
rc = f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)
if(rc /= 8*N_states) then
print *, 'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
endif
rc = f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)
if(rc /= 8*N) then
print *, 'f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)'
@ -228,10 +234,6 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
if(rc /= bit_kind*N_int*2*N) then
print *, 'f77_zmq_recv( zmq_socket_pull, det(1,1,1), bit_kind*N_int*2*N, 0)'
endif
else
pt2(:) = 0.d0
variance(:) = 0.d0
norm(:) = 0.d0
endif
rc = f77_zmq_recv( zmq_socket_pull, ntask, 4, 0)

2
src/cipsi/slave_cipsi.irp.f
View File

@ -63,7 +63,7 @@ subroutine run_slave_main
if (mpi_master) then
call wait_for_states(states,zmq_state,size(states))
if (zmq_state(1:64) == old_state(1:64)) then
call sleep(1)
call usleep(200)
cycle
else
old_state(1:64) = zmq_state(1:64)

2
src/ezfio_files/ezfio.irp.f
View File

@ -39,6 +39,8 @@ BEGIN_PROVIDER [ character*(128), ezfio_filename ]
write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
call system(command)
PROVIDE file_lock
END_PROVIDER
BEGIN_PROVIDER [ character*(128), ezfio_work_dir ]

9
src/fci/pt2.irp.f
View File

@ -43,8 +43,13 @@ subroutine run
E_CI_before(:) = psi_energy(:) + nuclear_repulsion
relative_error=PT2_relative_error
call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
norm,0) ! Stochastic PT2
if (do_pt2) then
call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
norm,0) ! Stochastic PT2
else
call ZMQ_selection(0, pt2, variance, norm)
endif
do k=1,N_states
rpt2(k) = pt2(k)/(1.d0 + norm(k))
enddo

2
src/nuclei/EZFIO.cfg
View File

@ -21,7 +21,7 @@ type: double precision
size: (nuclei.nucl_num,3)
interface: ezfio
[disk_access_nuclear_repulsion]
[io_nuclear_repulsion]
doc: Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
type: Disk_access
interface: ezfio,provider,ocaml

4
src/nuclei/nuclei.irp.f
View File

@ -143,7 +143,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
END_DOC
PROVIDE mpi_master nucl_coord nucl_charge nucl_num
if (disk_access_nuclear_repulsion.EQ.'Read') then
if (io_nuclear_repulsion == 'Read') then
logical :: has
if (mpi_master) then
@ -194,7 +194,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
call write_time(6)
call write_double(6,nuclear_repulsion,'Nuclear repulsion energy')
if (disk_access_nuclear_repulsion.EQ.'Write') then
if (io_nuclear_repulsion == 'Write') then
if (mpi_master) then
call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion)
endif

6
src/utils/c_funcs.c Normal file
View File

@ -0,0 +1,6 @@
#include <unistd.h>
void usleep_c(int s)
{
usleep((useconds_t) s);
}

21
src/utils/c_functions.f90 Normal file
View File

@ -0,0 +1,21 @@
module c_functions
use iso_c_binding
interface
subroutine usleep_c(us) bind (C,name="usleep_c")
use iso_c_binding
integer(c_int), value :: us
end subroutine usleep_c
end interface
end module
subroutine usleep(us)
use c_functions
use iso_c_binding
implicit none
integer, intent(in) :: us
integer(c_int) :: u
u = us
call usleep_c(u)
end

3
src/utils/memory.irp.f
View File

@ -15,6 +15,7 @@ BEGIN_PROVIDER [ integer, qp_max_mem ]
END_PROVIDER
subroutine resident_memory(value)
use c_functions
implicit none
BEGIN_DOC
! Returns the current used memory in gigabytes used by the current process.
@ -25,6 +26,8 @@ subroutine resident_memory(value)
double precision, intent(out) :: value
call omp_set_lock(file_lock)
call usleep(10)
value = 0.d0
iunit = getUnitAndOpen('/proc/self/status','r')
do

5
src/zmq/utils.irp.f
View File

@ -275,7 +275,6 @@ IRP_ENDIF
rc = f77_zmq_bind(new_zmq_pull_socket, zmq_socket_pull_tcp_address)
if (rc /= 0) then
icount = icount-1
! call sleep(3)
zmq_socket_pull_tcp_address = 'tcp://*:'//zmq_port(2+icount*100)//' '
zmq_socket_push_tcp_address = trim(qp_run_address)//':'//zmq_port(2+icount*100)//' '
else
@ -752,7 +751,8 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
add_task_to_taskserver = 0
allocate(character(len=len(task)+10+len(zmq_state)) :: message)
sze = len(trim(task)) + len(trim(zmq_state))+11
allocate(character(len=sze) :: message)
message='add_task '//trim(zmq_state)//' '//trim(task)
sze = len(message)
rc = f77_zmq_send(zmq_to_qp_run_socket, message, sze, 0)
@ -768,6 +768,7 @@ integer function add_task_to_taskserver(zmq_to_qp_run_socket,task)
add_task_to_taskserver = -1
return
endif
deallocate(message)
end