From fdcd8c3a8f5a3b3eb0f9ed99acccd257d6f305dd Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 19 Aug 2019 17:42:54 +0200 Subject: [PATCH 1/8] Fixing opam installation --- configure | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/configure b/configure index 2599fbbc..368151f6 100755 --- a/configure +++ b/configure @@ -301,9 +301,9 @@ ${QP_ROOT}/bin 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 +# source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true +# +# opam switch create ocaml-base-compiler.4.07.1 opam init --verbose --yes --compiler=4.07.1 --disable-sandboxing eval $(opam env) @@ -322,8 +322,8 @@ EOF | 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 +# 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 From 9f6cedde853c9b170b303bb902bbefcaa513993f Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 26 Sep 2019 11:00:31 +0200 Subject: [PATCH 2/8] Fixed 6-31 basis sets --- data/basis/6-31++g | 10 ++++++++++ data/basis/6-31++g_star_star | 25 +++++++++++++++++++------ data/basis/6-31+g_star | 16 ++++++++++++++++ data/basis/6-311++g_2d_2p | 12 ++++++++++++ data/basis/6-311+g_star | 20 ++++++++++++++++++++ data/basis/6-311G_star | 20 ++++++++++++++++++++ data/basis/6-31g_star | 16 ++++++++++++++++ 7 files changed, 113 insertions(+), 6 deletions(-) diff --git a/data/basis/6-31++g b/data/basis/6-31++g index 7e36d0f9..e1994202 100644 --- a/data/basis/6-31++g +++ b/data/basis/6-31++g @@ -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 diff --git a/data/basis/6-31++g_star_star b/data/basis/6-31++g_star_star index ae124833..4f4ead25 100644 --- a/data/basis/6-31++g_star_star +++ b/data/basis/6-31++g_star_star @@ -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 diff --git a/data/basis/6-31+g_star b/data/basis/6-31+g_star index 663f7af8..bc112c64 100644 --- a/data/basis/6-31+g_star +++ b/data/basis/6-31+g_star @@ -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 diff --git a/data/basis/6-311++g_2d_2p b/data/basis/6-311++g_2d_2p index 5cf54355..de8f54b4 100644 --- a/data/basis/6-311++g_2d_2p +++ b/data/basis/6-311++g_2d_2p @@ -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 diff --git a/data/basis/6-311+g_star b/data/basis/6-311+g_star index 9a6bd86f..14ec3a44 100644 --- a/data/basis/6-311+g_star +++ b/data/basis/6-311+g_star @@ -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 diff --git a/data/basis/6-311G_star b/data/basis/6-311G_star index 21621a45..c9cb224c 100644 --- a/data/basis/6-311G_star +++ b/data/basis/6-311G_star @@ -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 diff --git a/data/basis/6-31g_star b/data/basis/6-31g_star index 2e79dff2..12291b80 100644 --- a/data/basis/6-31g_star +++ b/data/basis/6-31g_star @@ -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 From d91de1bc2b841cb69f19ed6f0c456948116de04a Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Thu, 26 Sep 2019 12:48:43 +0200 Subject: [PATCH 3/8] Bug in quickstart --- docs/source/users_guide/quickstart.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/users_guide/quickstart.rst b/docs/source/users_guide/quickstart.rst index 2883ed96..f0620c5a 100644 --- a/docs/source/users_guide/quickstart.rst +++ b/docs/source/users_guide/quickstart.rst @@ -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: From 924d505d170c0bb11116daa9efe7834288cd806e Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 21 Oct 2019 14:11:47 +0200 Subject: [PATCH 4/8] Use irpf90 v1.7.6 --- configure | 66 +++++++++++++++++++++++-------------------------------- 1 file changed, 27 insertions(+), 39 deletions(-) diff --git a/configure b/configure index 368151f6..f8160aef 100755 --- a/configure +++ b/configure @@ -9,6 +9,20 @@ eval set -- "$TEMP" export QP_ROOT="$( cd "$(dirname "$0")" ; pwd -P )" echo "QP_ROOT="$QP_ROOT +BATS_URL="https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" +BUBBLE_URL="https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz" +DOCOPT_URL="https://github.com/docopt/docopt/archive/0.6.2.tar.gz" +EZFIO_URL="https://gitlab.com/scemama/EZFIO/-/archive/v1.4.0/EZFIO-v1.4.0.tar.gz" +F77ZMQ_URL="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" +GMP_URL="ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2" +IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v1.7.6/irpf90-v1.7.6.tar.gz" +LIBCAP_URL="https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" +NINJA_URL="https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip" +OCAML_URL="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" +RESULTS_URL="https://gitlab.com/scemama/resultsFile/-/archive/master/resultsFile-master.tar.gz" +ZEROMQ_URL="https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" +ZLIB_URL="https://www.zlib.net/zlib-1.2.11.tar.gz" + function help() { @@ -183,9 +197,7 @@ for PACKAGE in ${PACKAGES} ; do if [[ ${PACKAGE} = ninja ]] ; then - download \ - "https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip" \ - "${QP_ROOT}"/external/ninja.zip + download ${NINJA_URL} "${QP_ROOT}"/external/ninja.zip execute << EOF rm -f "\${QP_ROOT}"/bin/ninja unzip "\${QP_ROOT}"/external/ninja.zip -d "\${QP_ROOT}"/bin @@ -194,9 +206,7 @@ EOF elif [[ ${PACKAGE} = gmp ]] ; then - download \ - "ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2" \ - "${QP_ROOT}"/external/gmp.tar.bz2 + download ${GMP_URL} "${QP_ROOT}"/external/gmp.tar.bz2 execute << EOF cd "\${QP_ROOT}"/external tar --bzip2 --extract --file gmp.tar.bz2 @@ -208,9 +218,7 @@ EOF elif [[ ${PACKAGE} = libcap ]] ; then - download \ - "https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" \ - "${QP_ROOT}"/external/libcap.tar.gz + download ${LIBCAP_URL} "${QP_ROOT}"/external/libcap.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file libcap.tar.gz @@ -221,9 +229,7 @@ EOF elif [[ ${PACKAGE} = bwrap ]] ; then - download \ - "https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz" \ - "${QP_ROOT}"/external/bwrap.tar.xz + download ${BUBBLE_URL} "${QP_ROOT}"/external/bwrap.tar.xz execute << EOF cd "\${QP_ROOT}"/external tar --xz --extract --file bwrap.tar.xz @@ -236,9 +242,7 @@ EOF elif [[ ${PACKAGE} = irpf90 ]] ; then # When changing version of irpf90, don't forget to update etc/irpf90.rc - download \ - "https://gitlab.com/scemama/irpf90/-/archive/v1.7.5/irpf90-v1.7.5.tar.gz" \ - "${QP_ROOT}"/external/irpf90.tar.gz + download ${IRPF90_URL} "${QP_ROOT}"/external/irpf90.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file irpf90.tar.gz @@ -250,9 +254,7 @@ EOF elif [[ ${PACKAGE} = zeromq ]] ; then - download \ - "https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz" \ - "${QP_ROOT}"/external/zeromq.tar.gz + download ${ZEROMQ_URL} "${QP_ROOT}"/external/zeromq.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file zeromq.tar.gz @@ -266,9 +268,7 @@ EOF elif [[ ${PACKAGE} = f77zmq ]] ; then - download \ - "https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" \ - "${QP_ROOT}"/external/f77_zmq.tar.gz + download ${F77ZMQ_URL} "${QP_ROOT}"/external/f77_zmq.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file f77_zmq.tar.gz @@ -284,9 +284,7 @@ EOF elif [[ ${PACKAGE} = ocaml ]] ; then - download \ - "https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" \ - "${QP_ROOT}"/external/opam_installer.sh + download ${OCAML_URL} "${QP_ROOT}"/external/opam_installer.sh if [[ -n ${TRAVIS} ]] ; then # Special commands for Travis CI @@ -335,9 +333,7 @@ EOF elif [[ ${PACKAGE} = ezfio ]] ; then - download \ - "https://gitlab.com/scemama/EZFIO/-/archive/v1.4.0/EZFIO-v1.4.0.tar.gz" \ - "${QP_ROOT}"/external/ezfio.tar.gz + download ${EZFIO_URL} "${QP_ROOT}"/external/ezfio.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file ezfio.tar.gz @@ -348,9 +344,7 @@ EOF elif [[ ${PACKAGE} = zlib ]] ; then - download \ - "https://www.zlib.net/zlib-1.2.11.tar.gz" \ - "${QP_ROOT}"/external/zlib.tar.gz + download ${ZLIB_URL} "${QP_ROOT}"/external/zlib.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file zlib.tar.gz @@ -363,9 +357,7 @@ EOF elif [[ ${PACKAGE} = docopt ]] ; then - download \ - "https://github.com/docopt/docopt/archive/0.6.2.tar.gz" \ - "${QP_ROOT}"/external/docopt.tar.gz + download ${DOCOPT_URL} "${QP_ROOT}"/external/docopt.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file docopt.tar.gz @@ -376,9 +368,7 @@ EOF elif [[ ${PACKAGE} = resultsFile ]] ; then - download \ - "https://gitlab.com/scemama/resultsFile/-/archive/master/resultsFile-master.tar.gz" \ - "${QP_ROOT}"/external/resultsFile.tar.gz + download ${RESULTS_URL} "${QP_ROOT}"/external/resultsFile.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar --gunzip --extract --file resultsFile.tar.gz @@ -388,9 +378,7 @@ EOF elif [[ ${PACKAGE} = bats ]] ; then - download \ - "https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" \ - "${QP_ROOT}"/external/bats.tar.gz + download ${BATS_URL} "${QP_ROOT}"/external/bats.tar.gz execute << EOF cd "\${QP_ROOT}"/external tar -zxf bats.tar.gz From 8732c2176580b25f664cc3506abc8e2eb6551f60 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 21 Oct 2019 14:32:17 +0200 Subject: [PATCH 5/8] Fix IRPF90 Path --- etc/irpf90.rc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/irpf90.rc b/etc/irpf90.rc index 474af1a2..42ec4502 100644 --- a/etc/irpf90.rc +++ b/etc/irpf90.rc @@ -1,7 +1,7 @@ # Configuration of IRPF90 package # Set the path of IRPF90 here: -export IRPF90_PATH=${QP_ROOT}/external/irpf90-v1.7.5 +export IRPF90_PATH=${QP_ROOT}/external/irpf90-v1.7.6 export PATH=${PATH}:${IRPF90_PATH}/bin export IRPF90=${IRPF90_PATH}/bin/irpf90 From e61cf32ea3df4839288b8850e3b706acb1398868 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 21 Oct 2019 17:40:54 +0200 Subject: [PATCH 6/8] Force GCC for dependencies --- configure | 3 +++ 1 file changed, 3 insertions(+) diff --git a/configure b/configure index 21df1b71..3b17f8ac 100755 --- a/configure +++ b/configure @@ -3,6 +3,9 @@ # Quantum Package configuration script # +# Force GCC instead of ICC for dependencies +export CC=gcc + TEMP=$(getopt -o c:i:h -l config:,install:,help -n $0 -- "$@") || exit 1 eval set -- "$TEMP" From 328672f6be2343dc8b2f8b9d6bc7a1bb291eef7d Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 30 Oct 2019 15:28:46 +0100 Subject: [PATCH 7/8] Comments --- src/cipsi/pt2_stoch_routines.irp.f | 13 +++++++------ src/cipsi/selection.irp.f | 3 ++- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/src/cipsi/pt2_stoch_routines.irp.f b/src/cipsi/pt2_stoch_routines.irp.f index 70e86fca..281b0c5d 100644 --- a/src/cipsi/pt2_stoch_routines.irp.f +++ b/src/cipsi/pt2_stoch_routines.irp.f @@ -77,6 +77,7 @@ logical function testTeethBuilding(minF, N) tilde_cW(i) = tilde_cW(i-1) + tilde_w(i) enddo tilde_cW(:) = tilde_cW(:) + 1.d0 + deallocate(tilde_w) n0 = 0 testTeethBuilding = .false. @@ -89,19 +90,19 @@ logical function testTeethBuilding(minF, N) r = tilde_cW(n0 + minF) Wt = (1d0 - u0) * f if (dabs(Wt) <= 1.d-3) then - return + exit endif if(Wt >= r - u0) then testTeethBuilding = .true. - return + exit end if n0 += 1 -! if(N_det_generators - n0 < minF * N) then if(n0 > minFN) then - return + exit end if end do - stop "exited testTeethBuilding" + deallocate(tilde_cW) + end function @@ -768,7 +769,7 @@ END_PROVIDER tilde_cW(i) = tilde_cW(i-1) + tilde_w(i) enddo tilde_cW(:) = tilde_cW(:) + 1.d0 - + pt2_n_0(1) = 0 do pt2_u_0 = tilde_cW(pt2_n_0(1)) diff --git a/src/cipsi/selection.irp.f b/src/cipsi/selection.irp.f index e9ab6c2e..3585940e 100644 --- a/src/cipsi/selection.irp.f +++ b/src/cipsi/selection.irp.f @@ -346,6 +346,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d call isort(indices,iorder,nmax) deallocate(iorder) + ! Start with 32 elements. Size will double along with the filtering. allocate(preinteresting(0:32), prefullinteresting(0:32), & interesting(0:32), fullinteresting(0:32)) preinteresting(:) = 0 @@ -477,7 +478,7 @@ subroutine select_singles_and_doubles(i_generator,hole_mask,particle_mask,fock_d if (nt > 4) exit endif end do - case default + case default mobMask(1:N_int,1) = iand(negMask(1:N_int,1), psi_det_sorted(1:N_int,1,preinteresting(ii))) mobMask(1:N_int,2) = iand(negMask(1:N_int,2), psi_det_sorted(1:N_int,2,preinteresting(ii))) nt = 0 From 55736addf2baede3dbbfa9f6de9976253a2db00a Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 19 Nov 2019 18:07:51 +0100 Subject: [PATCH 8/8] Update tests --- src/fci/40.fci.bats | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fci/40.fci.bats b/src/fci/40.fci.bats index 46b511c0..7e30878a 100644 --- a/src/fci/40.fci.bats +++ b/src/fci/40.fci.bats @@ -71,7 +71,7 @@ function run_stoch() { @test "HBO" { # 13.3144s [[ -n $TRAVIS ]] && skip qp set_file hbo.ezfio - run -100.213733051634 1.e-4 100000 + run -100.212721540746 1.e-3 100000 } @test "H2O" { # 11.3727s @@ -89,7 +89,7 @@ function run_stoch() { @test "SO" { # 13.4952s [[ -n $TRAVIS ]] && skip qp set_file so.ezfio - run -26.011918121362 3.e-4 100000 + run -26.0060656855457 1.e-3 100000 } @test "H2S" { # 13.6745s