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Merge branch 'bugfix' of github.com:QuantumPackage/qp2 into bugfix

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This commit is contained in:
Anthony Scemama 2019-10-21 14:13:32 +02:00
commit 9ef3e904de
50 changed files with 1561 additions and 469 deletions
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2
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

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

71
bin/qp_tunnel
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@ -1,71 +0,0 @@
#!/usr/bin/env python2
"""
Creates an ssh tunnel for using slaves on another network.
Launch a server on the front-end node of the cluster on which the master
process runs. Then start a client ont the front-end node of the distant
cluster.
Usage:
qp_tunnel server EZFIO_DIR
qp_tunnel client <address> EZFIO_DIR
Options:
-h --help
"""
import os
import sys
import zmq
try:
import qp_path
except ImportError:
print "source .quantum_package.rc"
raise
from docopt import docopt
from ezfio import ezfio
def get_address(filename):
with open(os.path.join(filename,'work','qp_run_address'),'r') as f:
a = f.readlines()[0].strip()
return a
def set_address(filename,address):
with open(os.path.join(filename,'work','qp_run_address'),'r') as f:
backup = f.readlines()
with open(os.path.join(filename,'work','qp_run_address'),'w') as f:
f.write('\n'.join([address]+backup))
def main_server(arguments,filename):
destination = get_address(filename)
print destination
def main_client(arguments,filename):
destination = arguments["<address>"]
print destination
def main(arguments):
"""Main function"""
print arguments
filename = arguments["EZFIO_DIR"]
if arguments["server"]:
return main_server(arguments, filename)
if arguments["client"]:
return main_client(arguments, filename)
if __name__ == '__main__':
ARGUMENTS = docopt(__doc__)
main(ARGUMENTS)

29
configure vendored
View File

@ -290,6 +290,9 @@ EOF
# Special commands for Travis CI
chmod +x "${QP_ROOT}"/external/opam_installer.sh
rm --force ${QP_ROOT}/bin/opam
if [[ -n ${NO_CACHE} ]] ; then
rm -rf ${HOME}/.opam
fi
export OPAMROOT=${HOME}/.opam
cat << EOF | bash ${QP_ROOT}/external/opam_installer.sh --no-backup
${QP_ROOT}/bin
@ -310,21 +313,21 @@ EOF
else
# Conventional commands
execute << EOF
chmod +x "\${QP_ROOT}"/external/opam_installer.sh
"\${QP_ROOT}"/external/opam_installer.sh --no-backup
chmod +x "${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 --force ${QP_ROOT}/bin/opam
export OPAMROOT=${OPAMROOT:-${QP_ROOT}/external/opam}
echo ${QP_ROOT}/bin \
| sh ${QP_ROOT}/external/opam_installer.sh
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
@ -423,18 +426,18 @@ if [[ ${ZLIB} = $(not_found) ]] ; then
fail
fi
BWRAP=$(find_exe bwrap)
if [[ ${BWRAP} = $(not_found) ]] ; then
error "Bubblewrap (bwrap) is not installed."
fail
fi
LIBCAP=$(find_lib -lcap)
if [[ ${LIBCAP} = $(not_found) ]] ; then
error "Libcap (libcap) is not installed."
fail
fi
BWRAP=$(find_exe bwrap)
if [[ ${BWRAP} = $(not_found) ]] ; then
error "Bubblewrap (bwrap) is not installed."
fail
fi
OPAM=$(find_exe opam)
if [[ ${OPAM} = $(not_found) ]] ; then
error "OPAM (ocaml) package manager is not installed."

10
data/basis/6-31++g
View File

@ -8,6 +8,16 @@ S 1
S 1
1 0.0360000 1.0000000
HELIUM
S 3
1 0.3842163400E+02 0.4013973935E-01
2 0.5778030000E+01 0.2612460970E+00
3 0.1241774000E+01 0.7931846246E+00
S 1
1 0.2979640000E+00 1.0000000
S 1
1 0.8600000000E-01 0.1000000000E+01
LITHIUM
S 6
1 642.4189200 0.0021426

25
data/basis/6-31++g_star_star
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@ -1,14 +1,27 @@
HYDROGEN
S 3
1 18.7311370 0.03349460
2 2.8253937 0.23472695
3 0.6401217 0.81375733
1 0.1873113696E+02 0.3349460434E-01
2 0.2825394365E+01 0.2347269535E+00
3 0.6401216923E+00 0.8137573261E+00
S 1
1 0.1612778 1.0000000
1 0.1612777588E+00 1.0000000
S 1
1 0.0360000 1.0000000
1 0.3600000000E-01 0.1000000000E+01
P 1
1 1.1000000 1.0000000
1 0.1100000000E+01 1.0000000
HELIUM
S 3
1 0.3842163400E+02 0.4013973935E-01
2 0.5778030000E+01 0.2612460970E+00
3 0.1241774000E+01 0.7931846246E+00
S 1
1 0.2979640000E+00 1.0000000
S 1
1 0.8600000000E-01 0.1000000000E+01
P 1
1 0.1100000000E+01 1.0000000
LITHIUM
S 6

16
data/basis/6-31+g_star
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@ -1,3 +1,19 @@
HYDROGEN
S 3
1 0.1873113696E+02 0.3349460434E-01
2 0.2825394365E+01 0.2347269535E+00
3 0.6401216923E+00 0.8137573261E+00
S 1
1 0.1612777588E+00 1.0000000
HELIUM
S 3
1 0.3842163400E+02 0.4013973935E-01
2 0.5778030000E+01 0.2612460970E+00
3 0.1241774000E+01 0.7931846246E+00
S 1
1 0.2979640000E+00 1.0000000
LITHIUM
S 6
1 642.4189200 0.0021426

12
data/basis/6-311++g_2d_2p
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@ -14,6 +14,18 @@ P 1
P 1
1 0.3750000 1.0000000
HELIUM
S 3
1 98.12430 0.0287452
2 14.76890 0.208061
3 3.318830 0.837635
S 1
1 0.874047 1.000000
S 1
1 0.244564 1.000000
P 1
1 0.750 1.000000
LITHIUM
S 6
1 900.4600000 0.00228704

20
data/basis/6-311+g_star
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@ -1,3 +1,23 @@
HYDROGEN
S 3
1 33.86500 0.0254938
2 5.094790 0.190373
3 1.158790 0.852161
S 1
1 0.325840 1.000000
S 1
1 0.102741 1.000000
HELIUM
S 3
1 98.12430 0.0287452
2 14.76890 0.208061
3 3.318830 0.837635
S 1
1 0.874047 1.000000
S 1
1 0.244564 1.000000
LITHIUM
S 6
1 900.4600000 0.00228704

20
data/basis/6-311G_star
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@ -1,3 +1,23 @@
HYDROGEN
S 3
1 33.86500 0.0254938
2 5.094790 0.190373
3 1.158790 0.852161
S 1
1 0.325840 1.000000
S 1
1 0.102741 1.000000
HELIUM
S 3
1 98.12430 0.0287452
2 14.76890 0.208061
3 3.318830 0.837635
S 1
1 0.874047 1.000000
S 1
1 0.244564 1.000000
LITHIUM
S 6
1 900.4600000 0.00228704

16
data/basis/6-31g_star
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@ -1,3 +1,19 @@
HYDROGEN
S 3
1 18.7311370 0.03349460
2 2.8253937 0.23472695
3 0.6401217 0.81375733
S 1
1 0.1612778 1.0000000
HELIUM
S 3
1 38.4216340 0.0237660
2 5.7780300 0.1546790
3 1.2417740 0.4696300
S 1
1 0.2979640 1.0000000
LITHIUM
S 6
1 642.4189200 0.0021426

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87
docs/source/research.bib
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@ -1,6 +1,16 @@
%%% ARXIV TO BE UPDATED %%%
@article{Hollett2019Aug,
author = {Hollett, Joshua W. and Loos, Pierre-Fran{\c{c}}ois},
title = {{Capturing static and dynamic correlation with $\Delta \text{NO}$-MP2 and $\Delta \text{NO}$-CCSD}},
journal = {arXiv},
year = {2019},
month = {Aug},
eprint = {1908.09914},
url = {https://arxiv.org/abs/1908.09914}
}
@article{Giner2019Jul,
author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\ifmmode\mbox{\c{c}}\else\c{c}\fi}ois},
author = {Giner, Emmanuel and Scemama, Anthony and Toulouse, Julien and Loos, Pierre-Fran{\c{c}}ois},
title = {{Chemically Accurate Excitation Energies With Small Basis Sets}},
journal = {arXiv},
year = {2019},
@ -9,29 +19,66 @@
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}},
journal = {arXiv},
year = {2019},
month = {May},
eprint = {1905.06737},
url = {https://arxiv.org/abs/1905.06737}
}
@article{Burton2019May,
author = {Burton, Hugh G. A. and Thom, Alex J. W.},
title = {{A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction}},
journal = {arXiv},
year = {2019},
month = {May},
eprint = {1905.02626},
url = {https://arxiv.org/abs/1905.02626}
}
%%%% PUBLISHED PAPERS
@article{Burton2019Sep,
author = {Burton, Hugh G. A. and Thom, Alex J. W.},
title = {{General Approach for Multireference Ground and Excited States Using Nonorthogonal Configuration Interaction}},
journal = {J. Chem. Theory Comput.},
volume = {15},
number = {9},
pages = {4851--4861},
year = {2019},
month = {Sep},
issn = {1549-9618},
publisher = {American Chemical Society},
doi = {10.1021/acs.jctc.9b00441}
}
@article{Dash_2019,
author = {Dash, Monika and Feldt, Jonas and Moroni, Saverio and Scemama, Anthony and Filippi, Claudia},
title = {{Excited States with Selected Configuration Interaction-Quantum Monte Carlo: Chemically Accurate Excitation Energies and Geometries}},
journal = {J. Chem. Theory Comput.},
volume = {15},
number = {9},
pages = {4896--4906},
year = {2019},
month = {Sep},
issn = {1549-9618},
publisher = {American Chemical Society},
doi = {10.1021/acs.jctc.9b00476}
}
@article{Ferte_2019,
doi = {10.1063/1.5082638},
url = {https://doi.org/10.1063%2F1.5082638},
year = 2019,
month = {feb},
publisher = {{AIP} Publishing},
volume = {150},
number = {8},
pages = {084103},
author = {Anthony Fert{\'{e}} and Emmanuel Giner and Julien Toulouse},
title = {Range-separated multideterminant density-functional theory with a short-range correlation functional of the on-top pair density},
journal = {The Journal of Chemical Physics}
}
@article{Caffarel_2019,
doi = {10.1063/1.5114703},
url = {https://doi.org/10.1063%2F1.5114703},
year = 2019,
month = {aug},
publisher = {{AIP} Publishing},
volume = {151},
number = {6},
pages = {064101},
author = {Michel Caffarel},
title = {Evaluating two-electron-repulsion integrals over arbitrary orbitals using zero variance Monte Carlo: Application to full configuration interaction calculations with Slater-type orbitals},
journal = {The Journal of Chemical Physics}
}
@article{Loos_2019,
doi = {10.1021/acs.jpclett.9b01176},
url = {https://doi.org/10.1021%2Facs.jpclett.9b01176},

89
docs/source/users_guide/qp_tunnel.rst Normal file
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@ -0,0 +1,89 @@
.. _qp_tunnel:
=========
qp_tunnel
=========
.. TODO
.. program:: qp_tunnel
Establishes a tunnel to allow communications between machines within
different networks, for example multiple MPI slave jobs running on
different clusters.
Usage
-----
.. code:: bash
qp_tunnel [-g] (ADDRESS|EZFIO_DIR)
``EZFIO_DIR`` is the name of the |EZFIO| directory containing the data,
and ``ADDRESS`` is the address of another tunnel.
.. option:: -h, --help
Displays the help message
.. option:: -g, --get-input
Download the EZFIO directory from the remote instance of qp_tunnel.
Example
-------
.. code:: text
+-------------------+ +------------------+
| | | |
| N1_1 N1_2 N1_3 | | N2_1 N2_2 N2_3 |
| | | | | | | | | |
| +----+----+ | | +----+----+ |
| | | | | |
| C1 F1 | | F2 C2 |
| +---------=----=--------+ |
| | | |
+-------------------+ +------------------+
Imagine you have two clusters, C1 and C2. Each cluster is accessible via SSH
on a front-end named respectively F1 and F2. Groups of nodes N1 and N2 have
been reserved by the batch scheduling system on both clusters.
Each node in N1 is on the same network as the other nodes of N1, but they
can't access the network on which the nodes of N2 are.
1) Start a parallel simulation on the cluster C1, running on nodes N1.
We assume that there is a shared file system, such that F1 can access
the EZFIO directory. We also assume that F1 can communicate with the
nodes of N1.
2) Run a tunnel on the front-end F1 and keep it running:
.. code:: bash
me@f1 $ qp_tunnel my_directory.ezfio
Connect to:
tcp://31.122.230.47:42379
Ready
3) On the front-end F2, run another instance connecting to the other one,
which will fetch the |EZFIO| directory:
.. code:: bash
me@f2 $ qp_tunnel --get-input tcp://31.122.230.47:42379
Connect to:
tcp://31.122.209.139:42379
Communication [ OK ]
Getting input... my_directory.ezfio ...done
Ready
4) Keep the tunnel running, and you can now run a slave simulation within the
nodes N2.

2
docs/source/users_guide/quickstart.rst
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@ -115,7 +115,7 @@ create an |EZFIO| database with the 6-31G basis set:
.. code:: bash
qp create_ezfio -b "6-31G" hcn.xyz -o hcn
qp create_ezfio -b "6-31g" hcn.xyz -o hcn
The EZFIO database now contains data relative to the nuclear coordinates
and the atomic basis set:

139
man/qp_tunnel.1 Normal file
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@ -0,0 +1,139 @@
.\" Man page generated from reStructuredText.
.
.TH "QP_TUNNEL" "1" "Jun 15, 2019" "2.0" "Quantum Package"
.SH NAME
qp_tunnel \- | Quantum Package >
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.sp
Establishes a tunnel to allow communications between machines within
different networks, for example multiple MPI slave jobs running on
different clusters.
.SH USAGE
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
qp_tunnel [\-g] (ADDRESS|EZFIO_DIR)
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
\fBEZFIO_DIR\fP is the name of the \fI\%EZFIO\fP directory containing the data,
and \fBADDRESS\fP is the address of another tunnel.
.INDENT 0.0
.TP
.B \-h, \-\-help
Displays the help message
.UNINDENT
.INDENT 0.0
.TP
.B \-g, \-\-get\-input
Download the EZFIO directory from the remote instance of qp_tunnel.
.UNINDENT
.SH EXAMPLE
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
+\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+ +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+
| | | |
| N1_1 N1_2 N1_3 | | N2_1 N2_2 N2_3 |
| | | | | | | | | |
| +\-\-\-\-+\-\-\-\-+ | | +\-\-\-\-+\-\-\-\-+ |
| | | | | |
| C1 F1 | | F2 C2 |
| +\-\-\-\-\-\-\-\-\-=\-\-\-\-=\-\-\-\-\-\-\-\-+ |
| | | |
+\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+ +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
Imagine you have two clusters, C1 and C2. Each cluster is accessible via SSH
on a front\-end named respectively F1 and F2. Groups of nodes N1 and N2 have
been reserved by the batch scheduling system on both clusters.
Each node in N1 is on the same network as the other nodes of N1, but they
can’t access the network on which the nodes of N2 are.
.INDENT 0.0
.IP 1. 3
Start a parallel simulation on the cluster C1, running on nodes N1.
We assume that there is a shared file system, such that F1 can access
the EZFIO directory. We also assume that F1 can communicate with the
nodes of N1.
.IP 2. 3
Run a tunnel on the front\-end F1 and keep it running:
.UNINDENT
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
me@f1 $ qp_tunnel my_directory.ezfio
Connect to:
tcp://31.122.230.47:42379
Ready
.ft P
.fi
.UNINDENT
.UNINDENT
.INDENT 0.0
.IP 3. 3
On the front\-end F2, run another instance connecting to the other one,
which will fetch the \fI\%EZFIO\fP directory:
.UNINDENT
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
me@f2 $ qp_tunnel \-\-get\-input tcp://31.122.230.47:42379
Connect to:
tcp://31.122.209.139:42379
Communication [ OK ]
Getting input... my_directory.ezfio ...done
Ready
.ft P
.fi
.UNINDENT
.UNINDENT
.INDENT 0.0
.IP 4. 3
Keep the tunnel running, and you can now run a slave simulation within the
nodes N2.
.UNINDENT
.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2019, A. Scemama, E. Giner
.\" Generated by docutils manpage writer.
.

2
man/rotate_mos.1
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@ -34,7 +34,7 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
.INDENT 3.5
Rotates molecular orbitals i and j by combining them as
$1/sqrt{2} ( phi_i + phi_j )$ and
$1/sqrt{2} ( phi_i \- phi_j )$.
$1/sqrt{2} ( phi_i - phi_j )$.
.sp
Needs:
.INDENT 0.0

55
man/test.1 Normal file
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@ -0,0 +1,55 @@
.\" Man page generated from reStructuredText.
.
.TH "TEST" "1" "Jun 15, 2019" "2.0" "Quantum Package"
.SH NAME
test \- | Quantum Package >
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.INDENT 0.0
.INDENT 3.5
Calls:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBtwo_e_integrals_index()\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBtwo_e_integrals_index_reverse()\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2019, A. Scemama, E. Giner
.\" Generated by docutils manpage writer.
.

2
ocaml/.merlin
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@ -1,4 +1,4 @@
PKG core ZMQ cryptokit
PKG core zmq cryptokit
B _build/

214
ocaml/Bitlist.ml
View File

@ -7,82 +7,61 @@ Type for bits strings
list of Bits
*)
type t = Bit.t list
type t = int64 array
let n_int = Array.length
(* Create a zero bit list *)
let zero n_int =
Array.make (N_int_number.to_int n_int) 0L
(* String representation *)
let to_string b =
let rec do_work accu = function
| [] -> accu
| head :: tail ->
let new_accu = (Bit.to_string head) ^ accu
in do_work new_accu tail
let int64_to_string x =
String.init 64 (fun i ->
if Int64.logand x @@ Int64.shift_left 1L i <> 0L then
'+'
else
'-')
in
do_work "" b
Array.map int64_to_string b
|> Array.to_list
|> String.concat ""
let of_string ?(zero='0') ?(one='1') s =
List.init (String.length s) (String.get s)
|> List.rev_map ( fun c ->
if (c = zero) then Bit.Zero
else if (c = one) then Bit.One
else (failwith ("Error in bitstring ") ) )
let n_int = ( (String.length s - 1) lsr 6 ) + 1 in
let result = Array.make n_int 0L in
String.iteri (fun i c ->
if c = one then
begin
let iint = i lsr 6 in (* i / 64 *)
let k = i - (iint lsl 6) in
result.(iint) <- Int64.logor result.(iint) @@ Int64.shift_left 1L k;
end) s;
result
let of_string_mp s =
List.init (String.length s) (String.get s)
|> List.rev_map (function
| '-' -> Bit.Zero
| '+' -> Bit.One
| _ -> failwith ("Error in bitstring ") )
let of_string_mp = of_string ~zero:'-' ~one:'+'
(* Create a bit list from an int64 *)
let of_int64 i =
let rec do_work accu = function
| 0L -> Bit.Zero :: accu |> List.rev
| 1L -> Bit.One :: accu |> List.rev
| i ->
let b =
match (Int64.logand i 1L ) with
| 0L -> Bit.Zero
| 1L -> Bit.One
| _ -> raise (Failure "i land 1 not in (0,1)")
in
do_work (b :: accu) (Int64.shift_right_logical i 1)
in
let adjust_length result =
let rec do_work accu = function
| 64 -> List.rev accu
| i when i>64 -> raise (Failure "Error in of_int64 > 64")
| i when i<0 -> raise (Failure "Error in of_int64 < 0")
| i -> do_work (Bit.Zero :: accu) (i+1)
in
do_work (List.rev result) (List.length result)
in
adjust_length (do_work [] i)
let of_int64 i = [| i |]
(* Create an int64 from a bit list *)
let to_int64 l =
assert ( (List.length l) <= 64) ;
let rec do_work accu = function
| [] -> accu
| Bit.Zero::tail -> do_work Int64.(shift_left accu 1) tail
| Bit.One::tail -> do_work Int64.(logor one (shift_left accu 1)) tail
in do_work Int64.zero (List.rev l)
let to_int64 = function
| [| i |] -> i
| _ -> failwith "N_int > 1"
(* Create a bit list from a list of int64 *)
let of_int64_list l =
List.map of_int64 l
|> List.concat
(* Create a bit list from an array of int64 *)
let of_int64_array l =
Array.map of_int64 l
|> Array.to_list
|> List.concat
external of_int64_array : int64 array -> t = "%identity"
external to_int64_array : t -> int64 array = "%identity"
(* Create a bit list from a list of int64 *)
let of_int64_list l =
Array.of_list l |> of_int64_array
(* Compute n_int *)
@ -91,101 +70,64 @@ let n_int_of_mo_num mo_num =
N_int_number.of_int ( (mo_num-1)/bit_kind_size + 1 )
(* Create a zero bit list *)
let zero n_int =
let n_int = N_int_number.to_int n_int in
let a = Array.init n_int (fun i-> 0L) in
of_int64_list ( Array.to_list a )
(* Create an int64 list from a bit list *)
let to_int64_list l =
let rec do_work accu buf counter = function
| [] ->
begin
match buf with
| [] -> accu
| _ -> (List.rev buf)::accu
end
| i::tail ->
if (counter < 64) then
do_work accu (i::buf) (counter+1) tail
else
do_work ( (List.rev (i::buf))::accu) [] 1 tail
in
let l = do_work [] [] 1 l
in
List.rev_map to_int64 l
to_int64_array l |> Array.to_list
(* Create an array of int64 from a bit list *)
let to_int64_array l =
to_int64_list l
|> Array.of_list
(* Create a bit list from a list of MO indices *)
let of_mo_number_list n_int l =
let n_int = N_int_number.to_int n_int in
let length = n_int*64 in
let a = Array.make length (Bit.Zero) in
List.iter (fun i-> a.((MO_number.to_int i)-1) <- Bit.One) l;
Array.to_list a
let result = zero n_int in
List.iter (fun j ->
let i = (MO_number.to_int j) - 1 in
let iint = i lsr 6 in (* i / 64 *)
let k = i - (iint lsl 6) in
result.(iint) <- Int64.logor result.(iint) @@ Int64.shift_left 1L k;
) l;
result
let to_mo_number_list l =
let a = Array.of_list l in
let mo_num = MO_number.get_max () in
let rec do_work accu = function
| 0 -> accu
| i ->
begin
let new_accu =
match a.(i-1) with
| Bit.One -> (MO_number.of_int ~max:mo_num i)::accu
| Bit.Zero -> accu
in
do_work new_accu (i-1)
end
let rec aux_one x shift accu = function
| -1 -> accu
| i -> if Int64.logand x (Int64.shift_left 1L i) <> 0L then
aux_one x shift ( (i+shift) ::accu) (i-1)
else
aux_one x shift accu (i-1)
in
do_work [] (List.length l)
Array.mapi (fun i x ->
let shift = (i lsr 6) lsl 6 + 1 in
aux_one x shift [] 63
) l
|> Array.to_list
|> List.concat
|> List.map MO_number.of_int
(* logical operations on bit_list *)
let logical_operator2 op a b =
let rec do_work_binary result a b =
match a, b with
| [], [] -> result
| [], _ | _ , [] -> raise (Failure "Lists should have same length")
| (ha::ta), (hb::tb) ->
let newbit = op ha hb
in do_work_binary (newbit::result) ta tb
let and_operator a b = Array.map2 Int64.logand a b
let xor_operator a b = Array.map2 Int64.logxor a b
let or_operator a b = Array.map2 Int64.logor a b
let not_operator b = Array.map Int64.lognot b
let pop_sign =
let mask =
(Int64.pred (Int64.shift_left 1L 63))
in
List.rev (do_work_binary [] a b)
let logical_operator1 op b =
let rec do_work_unary result b =
match b with
| [] -> result
| (hb::tb) ->
let newbit = op hb
in do_work_unary (newbit::result) tb
in
List.rev (do_work_unary [] b)
let and_operator a b = logical_operator2 Bit.and_operator a b
let xor_operator a b = logical_operator2 Bit.xor_operator a b
let or_operator a b = logical_operator2 Bit.or_operator a b
let not_operator b = logical_operator1 Bit.not_operator b
fun x -> Int64.logand mask x
let popcnt b =
List.fold_left (fun accu -> function
| Bit.One -> accu+1
| Bit.Zero -> accu
) 0 b
Array.fold_left (fun accu x ->
if x >= 0L then
accu + (Z.popcount @@ Z.of_int64 x)
else
accu + 1 + (Z.popcount @@ Z.of_int64 (pop_sign x))
) 0 b

2
ocaml/Bitlist.mli
View File

@ -1,4 +1,4 @@
type t = Bit.t list
type t
(** The zero bit list *)
val zero : Qptypes.N_int_number.t -> t

35
ocaml/Determinant.ml
View File

@ -3,7 +3,8 @@ open Sexplib.Std
type t = int64 array [@@deriving sexp]
let to_int64_array (x:t) = (x:int64 array)
external to_int64_array : t -> int64 array = "%identity"
external of_int64_array_no_check : int64 array -> t = "%identity"
let to_alpha_beta x =
@ -24,19 +25,6 @@ let to_bitlist_couple x =
in (xa,xb)
let bitlist_to_string ~mo_num x =
let len =
MO_number.to_int mo_num
in
let s =
List.map (function
| Bit.Zero -> "-"
| Bit.One -> "+"
) x
|> String.concat ""
in
String.sub s 0 len
let of_int64_array ~n_int ~alpha ~beta x =
@ -47,38 +35,29 @@ let of_int64_array ~n_int ~alpha ~beta x =
in
if ( (Bitlist.popcnt a) <> alpha) then
begin
let mo_num = MO_number.get_max () in
let mo_num = MO_number.of_int mo_num ~max:mo_num in
failwith (Printf.sprintf "Expected %d electrons in alpha determinant
%s" alpha (bitlist_to_string ~mo_num:mo_num a) )
%s" alpha (Bitlist.to_string a) )
end;
if ( (Bitlist.popcnt b) <> beta ) then
begin
let mo_num = MO_number.get_max () in
let mo_num = MO_number.of_int mo_num ~max:mo_num in
failwith (Printf.sprintf "Expected %d electrons in beta determinant
%s" beta (bitlist_to_string ~mo_num:mo_num b) )
%s" beta (Bitlist.to_string b) )
end;
x
let of_int64_array_no_check x = x
let of_bitlist_couple ?n_int ~alpha ~beta (xa,xb) =
let of_bitlist_couple ~n_int ~alpha ~beta (xa,xb) =
let ba, bb =
Bitlist.to_int64_array xa ,
Bitlist.to_int64_array xb
and n_int =
match n_int with
| Some x -> x
| None -> Bitlist.n_int_of_mo_num (List.length xa)
in
of_int64_array ~n_int ~alpha ~beta (Array.concat [ba;bb])
let to_string ~mo_num x =
let (xa,xb) = to_bitlist_couple x in
[ " " ; bitlist_to_string ~mo_num xa ; "\n" ;
" " ; bitlist_to_string ~mo_num xb ]
[ " " ; Bitlist.to_string xa ; "\n" ;
" " ; Bitlist.to_string xb ]
|> String.concat ""

2
ocaml/Determinant.mli
View File

@ -24,7 +24,7 @@ val to_alpha_beta : t -> (int64 array)*(int64 array)
val to_bitlist_couple : t -> Bitlist.t * Bitlist.t
(** Create from a bit list *)
val of_bitlist_couple : ?n_int:Qptypes.N_int_number.t ->
val of_bitlist_couple : n_int:Qptypes.N_int_number.t ->
alpha:Qptypes.Elec_alpha_number.t ->
beta:Qptypes.Elec_beta_number.t ->
Bitlist.t * Bitlist.t -> t

151
ocaml/Input_determinants_by_hand.ml
View File

@ -7,14 +7,14 @@ module Determinants_by_hand : sig
{ n_int : N_int_number.t;
bit_kind : Bit_kind.t;
n_det : Det_number.t;
n_det_qp_edit : Det_number.t;
n_states : States_number.t;
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
psi_det : Determinant.t array;
state_average_weight : Positive_float.t array;
} [@@deriving sexp]
val read : unit -> t
val read_maybe : unit -> t option
val read : ?full:bool -> unit -> t option
val write : t -> unit
val to_string : t -> string
val to_rst : t -> Rst_string.t
@ -28,6 +28,7 @@ end = struct
{ n_int : N_int_number.t;
bit_kind : Bit_kind.t;
n_det : Det_number.t;
n_det_qp_edit : Det_number.t;
n_states : States_number.t;
expected_s2 : Positive_float.t;
psi_coef : Det_coef.t array;
@ -38,8 +39,6 @@ end = struct
let get_default = Qpackage.get_ezfio_default "determinants";;
let n_det_read_max = 10_000 ;;
let read_n_int () =
if not (Ezfio.has_determinants_n_int()) then
Ezfio.get_mo_basis_mo_num ()
@ -80,11 +79,27 @@ end = struct
|> Det_number.of_int
;;
let read_n_det_qp_edit () =
if not (Ezfio.has_determinants_n_det_qp_edit ()) then
begin
let n_det = read_n_det () |> Det_number.to_int in
Ezfio.set_determinants_n_det_qp_edit n_det
end;
Ezfio.get_determinants_n_det_qp_edit ()
|> Det_number.of_int
;;
let write_n_det n =
Det_number.to_int n
|> Ezfio.set_determinants_n_det
;;
let write_n_det_qp_edit n =
let n_det = read_n_det () |> Det_number.to_int in
min n_det (Det_number.to_int n)
|> Ezfio.set_determinants_n_det_qp_edit
;;
let read_n_states () =
if not (Ezfio.has_determinants_n_states ()) then
Ezfio.set_determinants_n_states 1
@ -178,7 +193,7 @@ end = struct
|> Ezfio.set_determinants_expected_s2
;;
let read_psi_coef () =
let read_psi_coef ~read_only () =
if not (Ezfio.has_determinants_psi_coef ()) then
begin
let n_states =
@ -189,24 +204,33 @@ end = struct
~data:(List.init n_states (fun i -> if (i=0) then 1. else 0. ))
|> Ezfio.set_determinants_psi_coef
end;
Ezfio.get_determinants_psi_coef ()
begin
if read_only then
Ezfio.get_determinants_psi_coef_qp_edit ()
else
Ezfio.get_determinants_psi_coef ()
end
|> Ezfio.flattened_ezfio
|> Array.map Det_coef.of_float
;;
let write_psi_coef ~n_det ~n_states c =
let n_det = Det_number.to_int n_det
and c = Array.to_list c
|> List.map Det_coef.to_float
and c =
Array.map Det_coef.to_float c
|> Array.to_list
and n_states =
States_number.to_int n_states
in
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
|> Ezfio.set_determinants_psi_coef
let r =
Ezfio.ezfio_array_of_list ~rank:2 ~dim:[| n_det ; n_states |] ~data:c
in
Ezfio.set_determinants_psi_coef r;
Ezfio.set_determinants_psi_coef_qp_edit r
;;
let read_psi_det () =
let read_psi_det ~read_only () =
let n_int = read_n_int ()
and n_alpha = Ezfio.get_electrons_elec_alpha_num ()
|> Elec_alpha_number.of_int
@ -232,19 +256,26 @@ end = struct
|> Ezfio.set_determinants_psi_det ;
end ;
let n_int = N_int_number.to_int n_int in
let psi_det_array = Ezfio.get_determinants_psi_det () in
let psi_det_array =
if read_only then
Ezfio.get_determinants_psi_det_qp_edit ()
else
Ezfio.get_determinants_psi_det ()
in
let dim = psi_det_array.Ezfio.dim
and data = Ezfio.flattened_ezfio psi_det_array
in
assert (n_int = dim.(0));
assert (dim.(1) = 2);
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
List.init dim.(2) (fun i ->
if read_only then
assert (dim.(2) = (Det_number.to_int (read_n_det_qp_edit ())))
else
assert (dim.(2) = (Det_number.to_int (read_n_det ())));
Array.init dim.(2) (fun i ->
Array.sub data (2*n_int*i) (2*n_int) )
|> List.map (Determinant.of_int64_array
|> Array.map (Determinant.of_int64_array
~n_int:(N_int_number.of_int n_int)
~alpha:n_alpha ~beta:n_beta )
|> Array.of_list
;;
let write_psi_det ~n_int ~n_det d =
@ -252,40 +283,45 @@ end = struct
|> Array.concat
|> Array.to_list
in
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[| N_int_number.to_int n_int ; 2 ; Det_number.to_int n_det |] ~data:data
|> Ezfio.set_determinants_psi_det
let r =
Ezfio.ezfio_array_of_list ~rank:3 ~dim:[| N_int_number.to_int n_int ; 2 ; Det_number.to_int n_det |] ~data:data
in
Ezfio.set_determinants_psi_det r;
Ezfio.set_determinants_psi_det_qp_edit r
;;
let read () =
let read ?(full=true) () =
let n_det_qp_edit = read_n_det_qp_edit () in
let n_det = read_n_det () in
let read_only =
if full then false else n_det_qp_edit <> n_det
in
if (Ezfio.has_mo_basis_mo_num ()) then
try
Some
{ n_int = read_n_int () ;
bit_kind = read_bit_kind () ;
n_det = read_n_det () ;
n_det_qp_edit = read_n_det_qp_edit () ;
expected_s2 = read_expected_s2 () ;
psi_coef = read_psi_coef () ;
psi_det = read_psi_det () ;
psi_coef = read_psi_coef ~read_only () ;
psi_det = read_psi_det ~read_only () ;
n_states = read_n_states () ;
state_average_weight = read_state_average_weight () ;
}
with _ -> None
else
failwith "No molecular orbitals, so no determinants"
;;
let read_maybe () =
let n_det =
read_n_det ()
in
if ( (Det_number.to_int n_det) < n_det_read_max ) then
try Some (read ()) with
| Failure _ -> None
else
(* No molecular orbitals, so no determinants *)
None
;;
let write { n_int ;
bit_kind ;
n_det ;
n_det_qp_edit ;
expected_s2 ;
psi_coef ;
psi_det ;
@ -297,9 +333,13 @@ end = struct
write_n_det n_det;
write_n_states n_states;
write_expected_s2 expected_s2;
write_psi_coef ~n_det:n_det ~n_states:n_states psi_coef ;
write_psi_det ~n_int:n_int ~n_det:n_det psi_det;
write_state_average_weight state_average_weight;
if n_det <= n_det_qp_edit then
begin
write_n_det_qp_edit n_det;
write_psi_coef ~n_det:n_det ~n_states:n_states psi_coef ;
write_psi_det ~n_int:n_int ~n_det:n_det psi_det
end;
write_state_average_weight state_average_weight
;;
@ -316,11 +356,13 @@ end = struct
|> States_number.to_int
and ndet =
Det_number.to_int b.n_det
and ndet_qp_edit =
Det_number.to_int b.n_det_qp_edit
in
let coefs_string i =
Array.init nstates (fun j ->
let ishift =
j*ndet
j*ndet_qp_edit
in
if (ishift < Array.length b.psi_coef) then
b.psi_coef.(i+ishift)
@ -331,7 +373,7 @@ end = struct
)
|> Array.to_list |> String.concat "\t"
in
Array.init ndet (fun i ->
Array.init ndet_qp_edit (fun i ->
Printf.sprintf " %s\n%s\n"
(coefs_string i)
(Determinant.to_string ~mo_num:mo_num b.psi_det.(i)
@ -363,7 +405,7 @@ Determinants ::
"
(b.expected_s2 |> Positive_float.to_string)
(b.n_det |> Det_number.to_string)
(b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat "\t")
(b.state_average_weight |> Array.map Positive_float.to_string |> Array.to_list |> String.concat "\t")
det_text
|> Rst_string.of_string
;;
@ -387,10 +429,10 @@ psi_det = %s
(b.n_states |> States_number.to_string)
(b.expected_s2 |> Positive_float.to_string)
(b.state_average_weight |> Array.to_list |> List.map Positive_float.to_string |> String.concat ",")
(b.psi_coef |> Array.to_list |> List.map Det_coef.to_string
(b.psi_coef |> Array.map Det_coef.to_string |> Array.to_list
|> String.concat ", ")
(b.psi_det |> Array.to_list |> List.map (Determinant.to_string
~mo_num) |> String.concat "\n\n")
(b.psi_det |> Array.map (Determinant.to_string ~mo_num) |> Array.to_list
|> String.concat "\n\n")
;;
let of_rst r =
@ -472,6 +514,7 @@ psi_det = %s
(* Handle determinants *)
let psi_det =
let n_int = N_int_number.of_int @@ (MO_number.get_max () - 1) / 64 + 1 in
let n_alpha = Ezfio.get_electrons_elec_alpha_num ()
|> Elec_alpha_number.of_int
and n_beta = Ezfio.get_electrons_elec_beta_num ()
@ -483,8 +526,8 @@ psi_det = %s
begin
let newdet =
(Bitlist.of_string ~zero:'-' ~one:'+' alpha ,
Bitlist.of_string ~zero:'-' ~one:'+' beta)
|> Determinant.of_bitlist_couple ~alpha:n_alpha ~beta:n_beta
Bitlist.of_string ~zero:'-' ~one:'+' beta)
|> Determinant.of_bitlist_couple ~n_int ~alpha:n_alpha ~beta:n_beta
|> Determinant.sexp_of_t
|> Sexplib.Sexp.to_string
in
@ -492,9 +535,6 @@ psi_det = %s
end
| _::tail -> read_dets accu tail
in
let dets =
List.map String_ext.rev dets
in
let a =
read_dets [] dets
|> String.concat ""
@ -510,9 +550,11 @@ psi_det = %s
Printf.sprintf "(n_int %d)" (N_int_number.get_max ())
and n_states =
Printf.sprintf "(n_states %d)" (States_number.to_int @@ read_n_states ())
and n_det_qp_edit =
Printf.sprintf "(n_det_qp_edit %d)" (Det_number.to_int @@ read_n_det_qp_edit ())
in
let s =
String.concat "" [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det]
String.concat "" [ header ; bitkind ; n_int ; n_states ; psi_coef ; psi_det ; n_det_qp_edit ]
in
@ -527,7 +569,9 @@ psi_det = %s
Det_number.to_int n_det_new
in
let det =
read ()
match read () with
| Some x -> x
| None -> failwith "No determinants in file"
in
let n_det_old, n_states =
Det_number.to_int det.n_det,