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Merge branch 'dev' into dev-lct

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Anthony Scemama 2019-07-24 13:18:47 +02:00
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21
GITHUB.md
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@ -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.

11
INSTALL.rst
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@ -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
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@ -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
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@ -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

20
configure vendored
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@ -303,23 +303,31 @@ 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 --comp=4.07.1 --disable-sandboxing
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 --comp=4.07.1 --disable-sandboxing
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
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@ -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
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@ -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
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@ -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
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@ -73,7 +73,7 @@ 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.
@ -84,6 +84,7 @@ 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
@ -131,23 +132,24 @@ 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)'
@ -202,22 +204,26 @@ 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)'
@ -227,10 +233,6 @@ 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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -0,0 +1,6 @@
#include <unistd.h>
void usleep_c(int s)
{
usleep((useconds_t) s);
}

21
src/utils/c_functions.f90 Normal file
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@ -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
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@ -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
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@ -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