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Merge branch 'develop' into develop-manus
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commit
2783eabec3
29
INSTALL.rst
29
INSTALL.rst
@ -43,6 +43,7 @@ Requirements
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- `Zlib`_
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- `GNU Patch`_
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- |ZeroMQ| : networking library
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- `GMP <https://gmplib.org/>`_ : Gnu Multiple Precision Arithmetic Library
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- |OCaml| compiler with |OPAM| package manager
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- |Ninja| : a parallel build system
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@ -84,6 +85,7 @@ The following packages are supported by the :command:`configure` installer:
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* irpf90
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* zeromq
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* f77zmq
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* gmp
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* ocaml ( :math:`\approx` 10 minutes)
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* ezfio
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* docopt
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@ -110,11 +112,11 @@ If the :command:`configure` executable fails to install a specific dependency
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-----------------------------------------------------------------------------
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If the :command:`configure` executable does not succeed to install a specific dependency,
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there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|
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there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|.
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Before doing anything below, try to install the packages with your package manager
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(:command:`apt`, :command:`yum`, etc)
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(:command:`apt`, :command:`yum`, etc).
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Ninja
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@ -216,6 +218,29 @@ With Debian or Ubuntu, you can use
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sudo apt install zlib1g-dev
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GMP
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---
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GMP is the GNU Multiple Precision Arithmetic Library.
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* Download the latest version of gmp here:
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`<ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2>`_
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and move it in the :file:`${QP_ROOT}/external` directory
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* Extract the archive, go into the :file:`gmp-*` directory and run
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the following commands
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.. code:: bash
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./configure --prefix=${QP_ROOT}
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make
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make install
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With Debian or Ubuntu, you can use
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.. code:: bash
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sudo apt install libgmp-dev
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OCaml
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9
TODO
9
TODO
@ -57,6 +57,13 @@ Doc: plugins et qp_plugins
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Ajouter les symetries dans devel
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Compiler ezfio avec openmp
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# Parallelize i_H_psi
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IMPORTANT:
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Davidson Diagonalization
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------------------------
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Not enough memory: aborting in davidson_diag_hjj_sjj
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67
config/cray.cfg
Normal file
67
config/cray.cfg
Normal file
@ -0,0 +1,67 @@
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# Common flags
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##############
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#
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# -mkl=[parallel|sequential] : Use the MKL library
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# --ninja : Allow the utilisation of ninja. It is mandatory !
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# --align=32 : Align all provided arrays on a 32-byte boundary
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#
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[COMMON]
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FC : ftn -dynamic -fpic
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LAPACK_LIB :
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IRPF90 : irpf90
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IRPF90_FLAGS : --ninja --align=32 -DMPI
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# For KNL, use:
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#IRPF90_FLAGS : --ninja --align=64 -DMPI
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# Global options
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################
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#
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# 1 : Activate
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# 0 : Deactivate
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#
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[OPTION]
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MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
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CACHE : 0 ; Enable cache_compile.py
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OPENMP : 1 ; Append OpenMP flags
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# Optimization flags
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####################
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#
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# -xHost : Compile a binary optimized for the current architecture
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# -O2 : O3 not better than O2.
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# -ip : Inter-procedural optimizations
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# -ftz : Flushes denormal results to zero
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#
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[OPT]
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FCFLAGS : -xCORE-AVX2 -O2 -ip -ftz -g -traceback -qopt-prefetch=5 -qopt-prefetch-issue-excl-hint -unroll-aggressive
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#
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#For KNL, use:
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#FCFLAGS : -xMIC-AVX512 -O2 -ip -ftz -g -traceback -qopt-prefetch=5 -qopt-prefetch-issue-excl-hint -unroll-aggressive
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#
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# Profiling flags
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#################
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#
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[PROFILE]
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FC : -p -g
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FCFLAGS : -xSSE4.2 -O2 -ip -ftz -qopt-prefetch
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# Debugging flags
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#################
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#
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# -traceback : Activate backtrace on runtime
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# -fpe0 : All floating point exaceptions
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# -C : Checks uninitialized variables, array subscripts, etc...
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# -g : Extra debugging information
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# -xSSE2 : Valgrind needs a very simple x86 executable
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#
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[DEBUG]
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FC : -g -traceback
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FCFLAGS : -xCORE-AVX2 -C -fpe0 -traceback
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# OpenMP flags
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#################
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#
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[OPENMP]
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FC : -qopenmp
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IRPF90_FLAGS : --openmp
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23
configure
vendored
23
configure
vendored
@ -183,7 +183,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
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fi
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if [[ ${PACKAGES} = all ]] ; then
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PACKAGES="zlib ninja irpf90 zeromq f77zmq ocaml ezfio docopt resultsFile bats"
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PACKAGES="zlib ninja irpf90 zeromq f77zmq gmp ocaml ezfio docopt resultsFile bats"
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fi
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@ -200,6 +200,21 @@ for PACKAGE in ${PACKAGES} ; do
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EOF
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elif [[ ${PACKAGE} = gmp ]] ; then
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download \
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"ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2" \
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"${QP_ROOT}"/external/gmp.tar.bz2
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execute << EOF
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cd "\${QP_ROOT}"/external
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tar --bzip2 --extract --file gmp.tar.bz2
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rm gmp.tar.bz2
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cd gmp*
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./configure --prefix=$QP_ROOT && make -j 8
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make install
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EOF
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elif [[ ${PACKAGE} = irpf90 ]] ; then
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# When changing version of irpf90, don't forget to update etc/irpf90.rc
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@ -388,6 +403,12 @@ if [[ ${F77ZMQ} = $(not_found) ]] ; then
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fail
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fi
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GMP=$(find_lib -lgmp)
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if [[ ${ZLIB} = $(not_found) ]] ; then
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error "GMP (gmp) is not installed."
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fail
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fi
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OPAM=$(find_exe opam)
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if [[ ${OPAM} = $(not_found) ]] ; then
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error "OPAM (ocaml) package manager is not installed."
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@ -35,6 +35,17 @@
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%%%% PUBLISHED PAPERS
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@phdthesis{yann_garniron_2019_2558127,
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author = {Yann Garniron},
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title = {{Development and parallel implementation of
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selected configuration interaction methods}},
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school = {Université de Toulouse},
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year = 2019,
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month = feb,
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doi = {10.5281/zenodo.2558127},
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url = {https://doi.org/10.5281/zenodo.2558127}
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}
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@article{Giner_2018,
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doi = {10.1063/1.5052714},
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url = {https://doi.org/10.1063%2F1.5052714},
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@ -10,10 +10,10 @@
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# export QP_NTHREADS_PT2=32
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# Number of threads for MKL
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# exort MKL_NUM_THREADS=16
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# export MKL_NUM_THREADS=16
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# Number of threads for OpenMP
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# exort OMP_NUM_THREADS=16
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# export OMP_NUM_THREADS=16
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# Name of the network interface to be chosen
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# export QP_NIC=ib0
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@ -163,7 +163,7 @@ _qp_Complete()
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create_ezfio)
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case "${prev}" in
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create_ezfio)
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COMPREPLY=( $(compgen -W "-b -a -c -d -h -m -o -p -x" -- $cur ) )
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COMPREPLY=( $(compgen -W "-b -a -c -d -h -m -o -p -x $(\ls)" -- $cur ) )
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return 0
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;;
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-m|-d|-c)
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1
ocaml/.gitignore
vendored
1
ocaml/.gitignore
vendored
@ -9,6 +9,7 @@ Input_ao_two_e_erf_ints.ml
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Input_ao_two_e_ints.ml
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Input_auto_generated.ml
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Input_becke_numerical_grid.ml
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Input_champ.ml
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Input_davidson.ml
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Input_density_for_dft.ml
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Input_determinants.ml
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@ -11,7 +11,7 @@ END_PROVIDER
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implicit none
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logical, external :: testTeethBuilding
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integer :: i,j
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pt2_n_tasks_max = elec_beta_num*elec_beta_num + elec_alpha_num*elec_beta_num - n_core_orb*2
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pt2_n_tasks_max = elec_alpha_num*elec_alpha_num + elec_alpha_num*elec_beta_num - n_core_orb*2
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pt2_n_tasks_max = min(pt2_n_tasks_max,1+N_det_generators/10000)
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call write_int(6,pt2_n_tasks_max,'pt2_n_tasks_max')
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@ -609,6 +609,12 @@ BEGIN_PROVIDER[ double precision, pt2_u, (N_det_generators)]
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BEGIN_PROVIDER[ integer, pt2_J, (N_det_generators)]
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&BEGIN_PROVIDER[ integer, pt2_R, (N_det_generators)]
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implicit none
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BEGIN_DOC
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! pt2_J contains the list of generators after ordering them according to the
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! Monte Carlo sampling.
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!
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! pt2_R(i) is the number of combs drawn when determinant i is computed.
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END_DOC
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integer :: N_c, N_j
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integer :: U, t, i
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double precision :: v
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@ -286,7 +286,11 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
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end if
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end do
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deallocate(indices)
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! !$OMP CRITICAL
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! print *, 'Step1: ', i_generator, preinteresting(0)
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! !$OMP END CRITICAL
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allocate(banned(mo_num, mo_num,2), bannedOrb(mo_num, 2))
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allocate (mat(N_states, mo_num, mo_num))
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maskInd = -1
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@ -485,6 +489,9 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d
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call spot_isinwf(mask, fullminilist, i_generator, fullinteresting(0), banned, fullMatch, fullinteresting)
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if(fullMatch) cycle
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! !$OMP CRITICAL
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! print *, 'Step3: ', i_generator, h1, interesting(0)
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! !$OMP END CRITICAL
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call splash_pq(mask, sp, minilist, i_generator, interesting(0), bannedOrb, banned, mat, interesting)
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@ -623,6 +630,11 @@ end
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subroutine splash_pq(mask, sp, det, i_gen, N_sel, bannedOrb, banned, mat, interesting)
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use bitmasks
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implicit none
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BEGIN_DOC
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! Computes the contributions A(r,s) by
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! comparing the external determinant to all the internal determinants det(i).
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! an applying two particles (r,s) to the mask.
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END_DOC
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integer, intent(in) :: sp, i_gen, N_sel
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integer, intent(in) :: interesting(0:N_sel)
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@ -1198,6 +1210,10 @@ end
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subroutine spot_isinwf(mask, det, i_gen, N, banned, fullMatch, interesting)
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use bitmasks
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implicit none
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BEGIN_DOC
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! Identify the determinants in det which are in the internal space. These are
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! the determinants that can be produced by creating two particles on the mask.
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END_DOC
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integer, intent(in) :: i_gen, N
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integer, intent(in) :: interesting(0:N)
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@ -1217,16 +1233,19 @@ subroutine spot_isinwf(mask, det, i_gen, N, banned, fullMatch, interesting)
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end do
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genl : do i=1, N
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! If det(i) can't be generated by the mask, cycle
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do j=1, N_int
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if(iand(det(j,1,i), mask(j,1)) /= mask(j, 1)) cycle genl
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if(iand(det(j,2,i), mask(j,2)) /= mask(j, 2)) cycle genl
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end do
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! If det(i) < det(i_gen), it hs already been considered
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if(interesting(i) < i_gen) then
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fullMatch = .true.
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return
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end if
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! Identify the particles
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do j=1, N_int
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myMask(j, 1) = iand(det(j, 1, i), negMask(j, 1))
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myMask(j, 2) = iand(det(j, 2, i), negMask(j, 2))
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|
@ -29,7 +29,7 @@ subroutine run_stochastic_cipsi
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pt2 = -huge(1.e0)
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rpt2 = -huge(1.e0)
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norm = 0.d0
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variance = 0.d0
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variance = huge(1.e0)
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if (s2_eig) then
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call make_s2_eigenfunction
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@ -64,6 +64,7 @@ subroutine run_stochastic_cipsi
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do while ( &
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(N_det < N_det_max) .and. &
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(maxval(abs(pt2(1:N_states))) > pt2_max) .and. &
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(maxval(abs(variance(1:N_states))) > variance_max) .and. &
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(correlation_energy_ratio <= correlation_energy_ratio_max) &
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)
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write(*,'(A)') '--------------------------------------------------------------------------------'
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|
@ -90,7 +90,7 @@ subroutine ZMQ_selection(N_in, pt2, variance, norm)
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mem = 8.d0 * N_det * (N_int * 2.d0 * 3.d0 + 3.d0 + 5.d0) / (1024.d0**3)
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call write_double(6,mem,'Estimated memory/thread (Gb)')
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if (qp_max_mem > 0) then
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nproc_target = max(1,int(dble(qp_max_mem)/mem))
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nproc_target = max(1,int(dble(qp_max_mem)/(0.1d0 + mem)))
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nproc_target = min(nproc_target,nproc)
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endif
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|
@ -4,7 +4,7 @@
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use map_module
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implicit none
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BEGIN_DOC
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! Alpha Fock matrix in AO basis set
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! Alpha and Beta Fock matrices in AO basis set
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END_DOC
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integer :: i,j,k,l,k1,r,s
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|
@ -20,9 +20,15 @@ subroutine save_iterations(e_, pt2_,n_)
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END_DOC
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integer, intent(in) :: n_
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double precision, intent(in) :: e_(N_states), pt2_(N_states)
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integer :: i
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if (N_iter > 100) then
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return
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if (N_iter == 101) then
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do i=2,N_iter-1
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energy_iterations(1:N_states,N_iter-1) = energy_iterations(1:N_states,N_iter)
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pt2_iterations(1:N_states,N_iter-1) = pt2_iterations(1:N_states,N_iter)
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enddo
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N_iter = N_iter-1
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TOUCH N_iter
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endif
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energy_iterations(1:N_states,N_iter) = e_(1:N_states)
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|
@ -10,6 +10,12 @@ doc: The selection process stops when the largest |PT2| (for all the state) is l
|
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interface: ezfio,provider,ocaml
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default: 0.0001
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[variance_max]
|
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type: Positive_float
|
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doc: The selection process stops when the largest variance (for all the state) is lower than `variance_max` in absolute value
|
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interface: ezfio,provider,ocaml
|
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default: 0.0
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[pt2_relative_error]
|
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type: Normalized_float
|
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doc: Stop stochastic |PT2| when the relative error is smaller than `pT2_relative_error`
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|
@ -1,7 +1,7 @@
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BEGIN_PROVIDER [ double precision, eigenvectors_Fock_matrix_mo, (ao_num,mo_num) ]
|
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implicit none
|
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BEGIN_DOC
|
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! Eigenvector of the Fock matrix in the MO basis obtained with level shift.
|
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! Eigenvectors of the Fock matrix in the MO basis obtained with level shift.
|
||||
END_DOC
|
||||
|
||||
integer :: i,j
|
||||
|
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