mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-08-24 21:21:47 +02:00
Merge branch 'dev' into dev-lcpq
This commit is contained in:
commit
133a05c683
21
GITHUB.md
21
GITHUB.md
@ -2,20 +2,23 @@ GitHub Branches
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===============
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master:
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The current up-to-date working branch, that users download It should
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only contain the latest release and bug fixes.
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The current up-to-date working branch, that users download. It should
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only contain the latest stable release and bug fixes.
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develop-lcpq:
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Toulouse development branch
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develop-lct:
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Paris development branch
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develop:
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dev:
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It is a fork of the *master* branch with new developments that will be
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merged in the *master* branch for the next release. Other development
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branches should be merged on this one.
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bugfix:
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A fork of the *master* on which the bug fixes are made.
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dev-lcpq:
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Toulouse development branch
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dev-lct:
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Paris development branch
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gh-pages:
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This is an independent branch, containing only the web site of QP2.
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|
13
INSTALL.rst
13
INSTALL.rst
@ -143,7 +143,7 @@ IRPF90
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to Parameters (IRP) method.
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* Download the latest version of IRPF90
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here : `<https://github.com/scemama/irpf90/releases/latest>`_ and move
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here : `<https://gitlab.com/scemama/irpf90/-/archive/v1.7.2/irpf90-v1.7.2.tar.gz>`_ and move
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the downloaded archive in the :file:`${QP_ROOT}/external` directory
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* Extract the archive and go into the :file:`irpf90-*` directory to run
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@ -328,7 +328,7 @@ OCaml
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echo ${QP_ROOT}/bin
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${QP_ROOT}/external/opam_installer.sh --no-backup --fresh
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You the :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
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The :command:`opam` command can be installed in the :file:`${QP_ROOT}/bin`
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directory. To do this, take the output of ``echo ${QP_ROOT}/bin`` and
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use it as an answer to where :command:`opam` should be installed.
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@ -337,7 +337,14 @@ OCaml
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.. code:: bash
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opam init --disable-sandboxing --comp=4.07.0
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opam init --comp=4.07.1
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eval `${QP_ROOT}/bin/opam env`
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If the installation fails because of bwrap, you can initialize opam using:
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.. code:: bash
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opam init --disable-sandboxing --comp=4.07.1
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eval `${QP_ROOT}/bin/opam env`
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* Install the required external OCaml libraries
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@ -5,7 +5,7 @@
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[*Quantum package 2.0: an open-source determinant-driven suite of programs*](https://pubs.acs.org/doi/10.1021/acs.jctc.9b00176)\
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Y. Garniron, K. Gasperich, T. Applencourt, A. Benali, A. Ferté, J. Paquier, B. Pradines, R. Assaraf, P. Reinhardt, J. Toulouse, P. Barbaresco, N. Renon, G. David, J. P. Malrieu, M. Véril, M. Caffarel, P. F. Loos, E. Giner and A. Scemama\
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J. Chem. Theory Comput., 15:6, 3591--3609, (2019)\
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[J. Chem. Theory Comput. 2019, 15, 6, 3591-3609](https://doi.org/10.1021/acs.jctc.9b00176)\
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https://arxiv.org/abs/1902.08154
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```
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1
REPLACE
1
REPLACE
@ -834,3 +834,4 @@ qp_name potential_sr_c_alpha_ao_pbe --rename=potential_c_alpha_ao_sr_pbe
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qp_name potential_sr_c_beta_ao_pbe --rename=potential_c_beta_ao_sr_pbe
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qp_name potential_sr_xc_alpha_ao_pbe --rename=potential_xc_alpha_ao_sr_pbe
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qp_name potential_sr_xc_beta_ao_pbe --rename=potential_xc_beta_ao_sr_pbe
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qp_name disk_access_nuclear_repulsion --rename=io_nuclear_repulsion
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18
configure
vendored
18
configure
vendored
@ -297,27 +297,37 @@ EOF
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${QP_ROOT}/bin
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EOF
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rm ${QP_ROOT}/external/opam_installer.sh
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source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
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${QP_ROOT}/bin/opam init --verbose --yes
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opam switch create ocaml-base-compiler.4.07.1
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opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
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eval $(${QP_ROOT}/bin/opam env)
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eval $(opam env)
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opam install -y ${OCAML_PACKAGES} || exit 1
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else
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# Conventional commands
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execute << EOF
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chmod +x "\${QP_ROOT}"/external/opam_installer.sh
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"\${QP_ROOT}"/external/opam_installer.sh --no-backup
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EOF
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execute << EOF
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rm --force \${QP_ROOT}/bin/opam
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export OPAMROOT=\${OPAMROOT:-\${QP_ROOT}/external/opam}
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echo \${QP_ROOT}/bin \
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| sh \${QP_ROOT}/external/opam_installer.sh
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EOF
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rm \${QP_ROOT}/external/opam_installer.sh
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source \${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
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\${QP_ROOT}/bin/opam init --verbose --yes
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eval \$(\${QP_ROOT}/bin/opam env)
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opam switch create ocaml-base-compiler.4.07.1 || exit 1
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opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing
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eval $(opam env)
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EOF
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execute << EOF
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opam install -y \${OCAML_PACKAGES} || exit 1
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EOF
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fi
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@ -1,4 +1,14 @@
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%%% ARXIV TO BE UPDATED %%%
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@article{Giner2019Jul,
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author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\ifmmode\mbox{\c{c}}\else\c{c}\fi}ois},
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title = {{Chemically Accurate Excitation Energies With Small Basis Sets}},
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journal = {arXiv},
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year = {2019},
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month = {Jul},
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eprint = {1907.01245},
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url = {https://arxiv.org/abs/1907.01245}
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}
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@article{Dash2019May,
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author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia},
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title = {{Excited states with selected CI-QMC: chemically accurate excitation energies and geometries}},
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@ -6,9 +6,8 @@ All the one-electron integrals in the |AO| basis are here.
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The most important providers for usual quantum-chemistry calculation are:
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* `ao_kinetic_integral` which are the kinetic operator integrals on the |AO| basis (see :file:`kin_ao_ints.irp.f`)
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* `ao_nucl_elec_integral` which are the nuclear-elctron operator integrals on the |AO| basis (see :file:`pot_ao_ints.irp.f`)
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* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis (see :file:`ao_mono_ints.irp.f`)
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* `ao_kinetic_integrals` which are the kinetic operator integrals on the |AO| basis
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* `ao_integrals_n_e` which are the nuclear-elctron operator integrals on the |AO| basis
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* `ao_one_e_integrals` which are the the h_core operator integrals on the |AO| basis
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Note that you can find other interesting integrals related to the position operator in :file:`spread_dipole_ao.irp.f`.
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@ -148,7 +148,7 @@ subroutine run_pt2_slave_small(thread,iproc,energy)
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integer, external :: disconnect_from_taskserver
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do i=1,300
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if (disconnect_from_taskserver(zmq_to_qp_run_socket,worker_id) /= -2) exit
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call sleep(1)
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call usleep(500)
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print *, 'Retry disconnect...'
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end do
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@ -74,7 +74,7 @@ subroutine run_selection_slave(thread,iproc,energy)
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if(done .or. ctask == size(task_id)) then
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do i=1, ctask
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if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
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call sleep(1)
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call usleep(100)
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if (task_done_to_taskserver(zmq_to_qp_run_socket,worker_id,task_id(i)) == -1) then
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ctask = 0
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done = .true.
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@ -85,6 +85,7 @@ subroutine run_selection_slave(thread,iproc,energy)
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if(ctask > 0) then
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call sort_selection_buffer(buf)
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! call merge_selection_buffers(buf,buf2)
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print *, task_id(1), pt2(1), buf%cur, ctask
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call push_selection_results(zmq_socket_push, pt2, variance, norm, buf, task_id(1), ctask)
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! buf%mini = buf2%mini
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pt2(:) = 0d0
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@ -132,7 +133,6 @@ subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_
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print *, 'f77_zmq_send( zmq_socket_push, b%cur, 4, ZMQ_SNDMORE)'
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endif
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if (b%cur > 0) then
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rc = f77_zmq_send( zmq_socket_push, pt2, 8*N_states, ZMQ_SNDMORE)
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if(rc /= 8*N_states) then
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@ -149,6 +149,8 @@ subroutine push_selection_results(zmq_socket_push, pt2, variance, norm, b, task_
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print *, 'f77_zmq_send( zmq_socket_push, norm, 8*N_states, ZMQ_SNDMORE)'
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endif
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if (b%cur > 0) then
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rc = f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)
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if(rc /= 8*b%cur) then
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print *, 'f77_zmq_send( zmq_socket_push, b%val(1), 8*b%cur, ZMQ_SNDMORE)'
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@ -203,7 +205,10 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
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print *, 'f77_zmq_recv( zmq_socket_pull, N, 4, 0)'
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endif
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if (N>0) then
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pt2(:) = 0.d0
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variance(:) = 0.d0
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norm(:) = 0.d0
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rc = f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)
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if(rc /= 8*N_states) then
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print *, 'f77_zmq_recv( zmq_socket_pull, pt2, N_states*8, 0)'
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@ -219,6 +224,7 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
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print *, 'f77_zmq_recv( zmq_socket_pull, norm, N_states*8, 0)'
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endif
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if (N>0) then
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rc = f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)
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if(rc /= 8*N) then
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print *, 'f77_zmq_recv( zmq_socket_pull, val(1), 8*N, 0)'
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@ -228,10 +234,6 @@ subroutine pull_selection_results(zmq_socket_pull, pt2, variance, norm, val, det
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if(rc /= bit_kind*N_int*2*N) then
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print *, 'f77_zmq_recv( zmq_socket_pull, det(1,1,1), bit_kind*N_int*2*N, 0)'
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endif
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else
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pt2(:) = 0.d0
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variance(:) = 0.d0
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norm(:) = 0.d0
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endif
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rc = f77_zmq_recv( zmq_socket_pull, ntask, 4, 0)
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|
@ -63,7 +63,7 @@ subroutine run_slave_main
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if (mpi_master) then
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call wait_for_states(states,zmq_state,size(states))
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if (zmq_state(1:64) == old_state(1:64)) then
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call sleep(1)
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call usleep(200)
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cycle
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else
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old_state(1:64) = zmq_state(1:64)
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|
@ -39,6 +39,8 @@ BEGIN_PROVIDER [ character*(128), ezfio_filename ]
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write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
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call system(command)
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PROVIDE file_lock
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END_PROVIDER
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BEGIN_PROVIDER [ character*(128), ezfio_work_dir ]
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|
@ -43,8 +43,13 @@ subroutine run
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E_CI_before(:) = psi_energy(:) + nuclear_repulsion
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relative_error=PT2_relative_error
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if (do_pt2) then
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call ZMQ_pt2(psi_energy_with_nucl_rep,pt2,relative_error,error, variance, &
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norm,0) ! Stochastic PT2
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else
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call ZMQ_selection(0, pt2, variance, norm)
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endif
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do k=1,N_states
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rpt2(k) = pt2(k)/(1.d0 + norm(k))
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enddo
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|
@ -21,7 +21,7 @@ type: double precision
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size: (nuclei.nucl_num,3)
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interface: ezfio
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[disk_access_nuclear_repulsion]
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[io_nuclear_repulsion]
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doc: Read/Write Nuclear Repulsion from/to disk [ Write | Read | None ]
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type: Disk_access
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interface: ezfio,provider,ocaml
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|
@ -143,7 +143,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
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END_DOC
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PROVIDE mpi_master nucl_coord nucl_charge nucl_num
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if (disk_access_nuclear_repulsion.EQ.'Read') then
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if (io_nuclear_repulsion == 'Read') then
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logical :: has
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if (mpi_master) then
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@ -194,7 +194,7 @@ BEGIN_PROVIDER [ double precision, nuclear_repulsion ]
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call write_time(6)
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call write_double(6,nuclear_repulsion,'Nuclear repulsion energy')
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if (disk_access_nuclear_repulsion.EQ.'Write') then
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if (io_nuclear_repulsion == 'Write') then
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if (mpi_master) then
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call ezfio_set_nuclei_nuclear_repulsion(nuclear_repulsion)
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endif
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|
6
src/utils/c_funcs.c
Normal file
6
src/utils/c_funcs.c
Normal file
@ -0,0 +1,6 @@
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#include <unistd.h>
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||||
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||||
void usleep_c(int s)
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||||
{
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||||
usleep((useconds_t) s);
|
||||
}
|
21
src/utils/c_functions.f90
Normal file
21
src/utils/c_functions.f90
Normal file
@ -0,0 +1,21 @@
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||||
module c_functions
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use iso_c_binding
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||||
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||||
interface
|
||||
subroutine usleep_c(us) bind (C,name="usleep_c")
|
||||
use iso_c_binding
|
||||
integer(c_int), value :: us
|
||||
end subroutine usleep_c
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||||
end interface
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||||
|
||||
end module
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||||
|
||||
subroutine usleep(us)
|
||||
use c_functions
|
||||
use iso_c_binding
|
||||
implicit none
|
||||
integer, intent(in) :: us
|
||||
integer(c_int) :: u
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||||
u = us
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||||
call usleep_c(u)
|
||||
end
|
@ -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
|
||||
|
@ -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
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user