Develop (#10)

* fixed laplacian of aos * corrected the laplacians of aos * added dft_one_e * added new feature for new dft functionals * changed the configure to add new functionals * changed the configure * added dft_one_e/README.rst * added README.rst in new_functionals * added source/programmers_guide/new_ks.rst * Thesis Yann * Added gmp installation in configure * improved qp_e_conv_fci * Doc * Typos * Added variance_max * Fixed completion in qp_create * modif TODO * fixed DFT potential for n_states gt 1 * improved pot pbe * trying to improve sr PBE * fixed potential pbe * fixed the vxc smashed for pbe sr and normal * Comments in selection * bug fixed by peter * Fixed bug with zero beta electrons * Update README.rst * Update e_xc_new_func.irp.f * Update links.rst * Update quickstart.rst * Update quickstart.rst * updated cipsi * Fixed energies of non-expected s2 (#9) * Moved diag_algorithm in Davdison
QuantumPackage · Feb 22, 2019 · 49e9488 · 49e9488
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diff --git a/INSTALL.rst b/INSTALL.rst
@@ -8,7 +8,7 @@ repository <https://github.com/LCPQ/quantum_package>`_.
 
 .. code:: bash
 
-  git clone https://github.com/LCPQ/quantum_package
+  git clone https://github.com/QuantumPackage/qp2
 
 
 Before anything, go into your :file:`quantum_package` directory and run
@@ -43,6 +43,7 @@ Requirements
 - `Zlib`_
 - `GNU Patch`_
 - |ZeroMQ| : networking library
+- `GMP <https://gmplib.org/>`_ : Gnu Multiple Precision Arithmetic Library
 - |OCaml| compiler with |OPAM| package manager 
 - |Ninja| : a parallel build system
 
@@ -84,6 +85,7 @@ The following packages are supported by the :command:`configure` installer:
 * irpf90 
 * zeromq 
 * f77zmq
+* gmp
 * ocaml  ( :math:`\approx` 10 minutes)
 * ezfio 
 * docopt 
@@ -110,11 +112,11 @@ If the :command:`configure` executable fails to install a specific dependency
 -----------------------------------------------------------------------------
 
 If the :command:`configure` executable does not succeed to install a specific dependency, 
-there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|
+there are some proposition of how to download and install the minimal dependencies to compile and use the |QP|.
 
 
 Before doing anything below, try to install the packages with your package manager
-(:command:`apt`, :command:`yum`, etc)
+(:command:`apt`, :command:`yum`, etc).
 
 
 Ninja
@@ -216,6 +218,29 @@ With Debian or Ubuntu, you can use
 
    sudo apt install zlib1g-dev
 
+GMP
+---
+
+GMP is the GNU Multiple Precision Arithmetic Library.
+
+* Download the latest version of gmp here:
+  `<ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2>`_
+  and move it in the :file:`${QP_ROOT}/external` directory
+
+* Extract the archive, go into the :file:`gmp-*` directory and run
+  the following commands
+
+.. code:: bash
+
+   ./configure --prefix=${QP_ROOT}
+   make
+   make install
+
+With Debian or Ubuntu, you can use
+
+.. code:: bash
+
+   sudo apt install libgmp-dev
 
 
 OCaml

diff --git a/TODO b/TODO
@@ -57,4 +57,13 @@ Doc: plugins et qp_plugins
 
 Ajouter les symetries dans devel
 
-Compiler ezfio avec openmp
+
+# Parallelize i_H_psi
+
+
+IMPORTANT:
+
+Davidson Diagonalization
+------------------------
+
+ Not enough memory: aborting in davidson_diag_hjj_sjj
diff --git a/bin/qp_e_conv_fci b/bin/qp_e_conv_fci
@@ -1,19 +1,96 @@
 #!/bin/bash
-file=$1
 
+# Check the QP_ROOT directory
 if [[ -z ${QP_ROOT} ]] ; then
   >&2 echo "please source quantum_package.rc"
   exit 1
 fi
+
 source ${QP_ROOT}/quantum_package.rc
 
-qp_run print_e_conv $1
-nstates=`cat ${1}/determinants/n_states`
+TEMP=$(getopt -o h -l ,help -n $0 -- "$@") || exit 1 # get the input / options 
+eval set -- "$TEMP"
+
+function help(){
+     cat <<EOF
+
+ Check the convergence of a CIPSI calculation
+ 
+ Usage:
+   $(basename $0)  EZFIO
+ 
+ Output: 
+ 
+      For each ELECTRONIC STATE \$i, produces plain text files 
+        *  for the convergence of the TOTAL variational and E+PT2 energies
+           files  EZFIO.\$i.conv 
+        *  gnuplot file to generate pdf image of the converge
+           files  EZFIO.\$i.conv.plt 
+        *  if gnuplot is available, creates the pdf image
+           files  EZFIO.\$i.conv.pdf 
+
+      For each EXCITED STATE \$i, produces plain text files
+        *  for the convergence of the ENERGY DIFFERENCE with the ground state
+           files  EZFIO.\$i.delta_e.conv 
+        *  gnuplot file to generate pdf image of the converge
+           files  EZFIO.\$i.delta_e.conv.plt 
+        *  if gnuplot is available, creates the pdf image
+           files  EZFIO.\$i.delta_e.conv.pdf 
+
+
+ Note: 
+    If you're in qpsh mode and that a EZFIO is set, this will be taken as the EZFIO file
+
+ Options:
+   -h, --help                            Print the HELP message
+ 
+ Example: ground state calculation on the EZFIO h2o.ezfio 
+
+          $(basename $0) h2o.ezfio 
+
+          produces h2o.ezfio.1.conv, h2o.ezfio.1.conv.plt and h2o.ezfio.1.conv.pdf if gnuplot is available 
+ 
+ 
+EOF
+     exit
+}
+
+ while true ; do
+     case "$1" in
+         -h|-help|--help)
+             help
+             exit 0;;
+         --) shift  ; break ;;
+     "") help ; break ;;
+     esac
+ done
+
+ezfio=${1%/} # take off the / at the end
+
+if [[ ! -z ${EZFIO_FILE}   ]] ; then
+ file=${EZFIO_FILE}
+else 
+ file=$ezfio
+fi
+
+
+if [[ -z ${file} ]] ; then
+ >&2 echo "You did not specify any EZFIO directory. "
+ exit 1
+
+fi
+
+
+gnuplot_ok=`hash gnuplot`
+
+
+qp_run print_e_conv $file 
+nstates=`cat ${file}/determinants/n_states`
 echo $nstates
 
 
 for i in $(seq 1 $nstates) ; do
-  out=${1}.${i}.conv
+  out=${file}.${i}.conv
 cat << EOF > ${out}.plt
 set term pdf
 set output "$out.pdf"
@@ -25,13 +102,14 @@ plot "$out" w lp title "E_{var} state $i", "$out" u 1:3 w lp title "E_{var} + PT
 
 EOF
 
-gnuplot ${out}.plt
-#rm ${out}.plt
+if [[  -z ${gnuplot_ok} ]] ; then
+ gnuplot ${out}.plt
+fi
 
 done
 
 for i in $(seq 2 $nstates) ; do
-  out=${1}.${i}.delta_e.conv
+  out=${file}.${i}.delta_e.conv
 cat << EOF > ${out}.plt
 set term pdf
 set output "$out.pdf"
@@ -42,6 +120,7 @@ set ylabel "Energy difference (a.u.)"
 plot "$out" w lp title "Delta E_{var} state $i", "$out" u 1:3 w lp title "Delta E_{var} + PT2 state $i"
 
 EOF
+if [[  -z ${gnuplot_ok} ]] ; then
   gnuplot ${out}.plt
-# rm ${out}.plt
+fi
 done
diff --git a/config/cray.cfg b/config/cray.cfg
@@ -0,0 +1,67 @@
+# Common flags
+##############
+#
+# -mkl=[parallel|sequential] : Use the MKL library
+# --ninja                 : Allow the utilisation of ninja. It is mandatory !
+# --align=32                 : Align all provided arrays on a 32-byte boundary
+#
+[COMMON]
+FC           : ftn -dynamic -fpic
+LAPACK_LIB   : 
+IRPF90       : irpf90
+IRPF90_FLAGS : --ninja --align=32 -DMPI  
+# For KNL, use:
+#IRPF90_FLAGS : --ninja --align=64 -DMPI  
+
+# Global options
+################
+#
+# 1 : Activate
+# 0 : Deactivate
+# 
+[OPTION]
+MODE    : OPT        ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
+CACHE   : 0          ; Enable cache_compile.py
+OPENMP  : 1          ; Append OpenMP flags
+
+# Optimization flags
+####################
+#
+# -xHost                     : Compile a binary optimized for the current architecture
+# -O2                        : O3 not better than O2.
+# -ip                        : Inter-procedural optimizations
+# -ftz                       : Flushes denormal results to zero
+#
+[OPT]
+FCFLAGS  : -xCORE-AVX2 -O2 -ip -ftz -g -traceback -qopt-prefetch=5 -qopt-prefetch-issue-excl-hint -unroll-aggressive 
+#
+#For KNL, use:
+#FCFLAGS : -xMIC-AVX512 -O2 -ip -ftz -g -traceback -qopt-prefetch=5 -qopt-prefetch-issue-excl-hint -unroll-aggressive 
+#
+# Profiling flags
+#################
+#
+[PROFILE]
+FC       : -p -g
+FCFLAGS  : -xSSE4.2 -O2 -ip -ftz -qopt-prefetch
+
+# Debugging flags
+#################
+#
+# -traceback   : Activate backtrace on runtime
+# -fpe0        : All floating point exaceptions
+# -C           : Checks uninitialized variables,  array subscripts, etc...
+# -g           : Extra debugging information
+# -xSSE2       : Valgrind needs a very simple x86 executable
+#
+[DEBUG]
+FC      : -g -traceback
+FCFLAGS : -xCORE-AVX2 -C -fpe0 -traceback
+
+# OpenMP flags
+#################
+#
+[OPENMP]
+FC           : -qopenmp
+IRPF90_FLAGS : --openmp
+
diff --git a/configure b/configure
@@ -9,6 +9,12 @@ eval set -- "$TEMP"
 export QP_ROOT="$( cd "$(dirname "$0")" ; pwd -P )"
 echo "QP_ROOT="$QP_ROOT
 
+# Check if the module to create new DFT functionals exists or not
+if [[ ! -d ${QP_ROOT}/src/new_functionals  ]] ; then
+   cp -r ${QP_ROOT}/scripts/functionals/do_not_touch_func ${QP_ROOT}/src/new_functionals
+fi
+
+
 
 function help()
 {
@@ -175,7 +181,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
 fi
 
 if [[ ${PACKAGES} = all ]] ; then
-        PACKAGES="zlib ninja irpf90 zeromq f77zmq ocaml ezfio docopt resultsFile bats"
+        PACKAGES="zlib ninja irpf90 zeromq f77zmq gmp ocaml ezfio docopt resultsFile bats"
 fi
 
 
@@ -192,6 +198,21 @@ for PACKAGE in ${PACKAGES} ; do
 EOF
 
 
+    elif [[ ${PACKAGE} = gmp ]] ; then
+
+            download \
+              "ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2" \
+              "${QP_ROOT}"/external/gmp.tar.bz2
+            execute << EOF
+              cd "\${QP_ROOT}"/external
+              tar --bzip2 --extract --file gmp.tar.bz2
+              rm gmp.tar.bz2
+              cd gmp*
+              ./configure --prefix=$QP_ROOT && make -j 8
+              make install
+EOF
+
+
     elif [[ ${PACKAGE} = irpf90 ]] ; then
 
             # When changing version of irpf90, don't forget to update etc/irpf90.rc
@@ -380,6 +401,12 @@ if [[ ${F77ZMQ} = $(not_found) ]] ; then
         fail
 fi
 
+GMP=$(find_lib -lgmp)
+if [[ ${ZLIB} = $(not_found) ]] ; then
+        error "GMP (gmp) is not installed."
+        fail
+fi
+
 OPAM=$(find_exe opam)
 if [[ ${OPAM} = $(not_found) ]] ; then
         error "OPAM (ocaml) package manager is not installed."
@@ -443,7 +470,7 @@ else
       echo "See  ./configure --help  for more details." 
       echo ""
 fi
-   
+
 exit 0
 
 

diff --git a/docs/ref b/docs/ref
@@ -4,7 +4,7 @@
 * option provider :option:`name_of_module provider`
 * subroutine      :c:func:`my_subroutine` 
 * module          :ref:`module`
-* provider        :c:data:`my_subroutine` 
+* provider        :c:data:`my_provider` 
 * qp_command      :ref:`qp_command`
 * linux command   :command:`qp_command`
 * linux command with option :command:`qp_command -o`