From fdcd8c3a8f5a3b3eb0f9ed99acccd257d6f305dd Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Mon, 19 Aug 2019 17:42:54 +0200
Subject: [PATCH 1/6] 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 <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Sep 2019 11:00:31 +0200
Subject: [PATCH 2/6] 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 <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Sep 2019 12:48:43 +0200
Subject: [PATCH 3/6] 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 <scemama@irsamc.ups-tlse.fr>
Date: Mon, 21 Oct 2019 14:11:47 +0200
Subject: [PATCH 4/6] 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 <scemama@irsamc.ups-tlse.fr>
Date: Mon, 21 Oct 2019 14:32:17 +0200
Subject: [PATCH 5/6] 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 <scemama@irsamc.ups-tlse.fr>
Date: Mon, 21 Oct 2019 17:40:54 +0200
Subject: [PATCH 6/6] 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"