Lots of cleaning in scripts and Makefiles

.gitignore

@@ -5,4 +5,5 @@ EMSL_Basis
 bin/
 *.log
 quantum_package_static.tar.gz
-
+resultsFile
+opam_installer.sh

scripts/archive_ezfio.sh

@@ -1,78 +0,0 @@
-#!/bin/bash
-#
-# Computes the MD5 digest of an EZFIO file, and creates a tar.
-# Thu Apr  3 16:55:50 CEST 2014
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  print "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-fi
-
-function archive()
-{
-  FILE="$1"
-  MD5="$2"
-  ARCHIVE="${QPACKAGE_ROOT}/data/cache/$MD5"
-  if [[ -f "$ARCHIVE" ]]
-  then
-    if ! diff "$FILE" "${QPACKAGE_ROOT}/data/cache/$MD5" &> /dev/null
-    then
-      echo "Something went wrong. The file"
-      echo "${QPACKAGE_ROOT}/data/cache/$MD5"
-      echo "is different from $FILE"
-      echo "Aborting"
-      return 1
-    fi
-  else
-    cp "$FILE" "${QPACKAGE_ROOT}/data/cache/$MD5"
-  fi
-}
-
-
-
-
-EZFIO_FILE=$(basename ${1})
-
-if [[ -z ${EZFIO_FILE} ]]
-then
-  echo "Usage: $(basename $0) <EZFIO_FILE>"
-  exit 1
-fi
-
-
-cd "${QPACKAGE_ROOT}/EZFIO/src"
-FILES=($(python << EOF | sort
-from read_config import * 
-for group in groups:
-  if group == "ezfio":
-    continue
-  for d in groups[group]:
-    if d[2] == ():
-      suffix = ""
-    else:
-      suffix = ".gz"
-    print group+'/'+d[0]+suffix
-print "ezfio/creation"
-print "ezfio/library"
-EOF
-))
-cd $OLDPWD
-
-MD5_FILE=$(basename "${EZFIO_FILE}" .ezfio).md5
-rm -f -- "${MD5_FILE}"
-for FILE in ${FILES[@]}
-do
-  FILE="${EZFIO_FILE}/${FILE}"
-  MD5=$(md5sum "${FILE}" 2>/dev/null | cut -d ' ' -f 1)
-  if [[ ! -z $MD5 ]]
-  then
-    if ! archive "$FILE" "$MD5"
-    then
-      rm -- "${MD5_FILE}"
-      exit 1
-    fi
-    echo "$MD5" "$FILE" >> "${MD5_FILE}"
-  fi
-done
-

scripts/build_modules.sh

@@ -0,0 +1,34 @@
+#!/bin/bash 
+#
+# This script should run from the directory $QPACKAGE_ROOT/src
+
+source ${QPACKAGE_ROOT}/scripts/run_Makefile_global.sh
+
+NPROC=$(cat /proc/cpuinfo | grep MHz | wc -l)
+
+export IN_MAKE=1
+
+for MODULE in $@
+do
+  if [[ ! -d ${MODULE} ]]
+  then
+    error "Module ${MODULE} doesn't exist"
+  fi
+  cd ${MODULE}
+  echo ${MODULE}  
+  ${QPACKAGE_ROOT}/scripts/run_Makefile_common.sh
+  if [[ $# -eq 1 ]] 
+  then
+    env make -j ${NPROC} all 
+  else
+    env make -j ${NPROC} all &> make.log 
+    if [[ $? -ne 0 ]]
+    then
+      cat make.log
+      error "
+Build failed for module $MODULE
+"
+    fi
+  fi
+  cd ${OLDPWD}
+done

scripts/check_dependencies.sh

@@ -10,13 +10,13 @@
 # read in the Makefile.
 # Thu Apr  3 01:44:23 CEST 2014
 
-function unique_list()
+if [[ -z ${QPACKAGE_ROOT} ]]
-{
+then
-  for d in $@
+  print "The QPACKAGE_ROOT environment variable is not set."
-  do
+  print "Please reload the quantum_package.rc file."
-    echo $d
+  exit -1
-  done | sort | uniq
+fi
-}
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 
 if [[ -z $1 ]]
 then

scripts/clean_modules.sh

@@ -0,0 +1,36 @@
+#!/bin/bash 
+#
+# Cleans a module directory 
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+function do_clean()
+{
+  rm -rf -- \
+    IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
+    ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe)
+}
+
+if [[ -z $1 ]]
+then
+  check_current_dir_is_module
+  do_clean
+else
+  check_current_dir_is_src
+  for i in $@
+  do
+    if [[ -d $i ]]
+    then
+       cd $i
+       do_clean
+       cd $OLDPWD
+    fi
+  done
+fi
+

scripts/create_Makefile.sh

@@ -6,17 +6,17 @@
 # module directory.
 # Thu Apr  3 01:44:41 CEST 2014
 
-MODULE=$(basename "$PWD")
+if [[ -z ${QPACKAGE_ROOT} ]]
-
-if [[ "$MODULE" == "src" ]]
 then
-  echo "Error: This script should not be run in the src directory."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  exit 1
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
 
 cat << EOF > Makefile
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

scripts/create_Makefile_depend.sh

@@ -6,9 +6,19 @@
 # files included by including other modules.
 # Thu Apr  3 01:44:09 CEST 2014
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
 SRC=""
 OBJ=""
-DEPS="$(cat NEEDED_MODULES)"
+DEPS="$NEEDED_MODULES"
 
 for M in ${DEPS}
 do

scripts/create_Needed_modules.sh

@@ -4,13 +4,15 @@
 # This script is supposed to run in a module directory.
 # Thu Apr  3 13:38:38 CEST 2014
 
-MODULE=$(basename $PWD)
+if [[ -z ${QPACKAGE_ROOT} ]]
-
-if [[ $MODULE == "src" ]]
 then
-  echo "Error: This script should not be run in the src directory."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  exit 1
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
 
 OUTPUT=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh $@)
 echo ${OUTPUT} > NEEDED_MODULES

scripts/create_gitignore.sh

@@ -5,6 +5,16 @@
 # Tue Jan 13 14:18:05 CET 2015
 #
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
 cat << EOF > .gitignore
 #
 # Do not modify this file. Add your ignored files to the gitignore

scripts/create_module.sh

@@ -7,7 +7,17 @@
 # All remaining aruments are dependencies.
 # Thu Apr  3 01:44:58 CEST 2014
 
-DEBUG=1
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_src
+
+DEBUG=0
 
 # If DEBUG=1, the print debug info.
 function debug()
@@ -36,13 +46,6 @@ function fail()
 }
 
 
-if [[ -z $QPACKAGE_ROOT ]]
-then
-  echo "Error:"
-  echo "QPACKAGE_ROOT environment variable is not set."
-  echo "source quantum_package.rc"
-  exit 1
-fi
 
 MODULE=$1
 
@@ -68,7 +71,7 @@ debug "Module does not already exist: OK"
 
 
 # Set up dependencies
-ALL_MODULES="$(cat NEEDED_MODULES)"
+ALL_MODULES="${NEEDED_MODULES}"
 echo "Select which modules you are sure you will need:  (press q to quit)"  
 NEEDED_MODULES=""
 select M in ${ALL_MODULES}

scripts/create_rst_templates.sh

@@ -3,24 +3,15 @@
 # Creates the rst files when creating a new module.
 # Thu Apr  3 11:54:16 CEST 2014
 
-MODULE=$(basename $PWD)
+if [[ -z ${QPACKAGE_ROOT} ]]
-
-if [[ $MODULE == "src" ]]
 then
-  echo "Error: This script should not be run in the src directory."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  exit 1
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 
-function asksure() {
+check_current_dir_is_module
-  echo -n $@ "(Y/N) "
-  answer=w
-  while [[ $answer != [YyNn] ]]
-  do
-     read answer
-     [[ $answer = [Yy] ]] && retval=0 || retval=1
-  done
-  return $retval
-}
 
 README="True"
 if [[ -f README.rst ]]

scripts/ezfio_interface.py

@@ -184,15 +184,26 @@ def save_ezfio_provider(path_head, dict_code_provider):
 
     path = "{0}/ezfio_interface.irp.f".format(path_head)
 
-    print "Path = {}".format(path)
+#    print "Path = {}".format(path)
 
-    with open(path, "w") as f:
+    try:
-        f.write("!DO NOT MODIFY BY HAND \n")
+        f = open(path, "r")
-        f.write("!Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py \n")
+    except IOError:
-        f.write("!from file {0}/EZFIO.cfg\n".format(path_head))
+        old_output = ""
-        f.write("\n")
+    else:
-        for provider_name, code in dict_code_provider.iteritems():
+        old_output = f.read()
-            f.write(code + "\n")
+        f.close()
+
+    output =   "! DO NOT MODIFY BY HAND\n" + \
+               "! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py\n" + \
+               "! from file {0}/EZFIO.cfg\n".format(path_head) + \
+               "\n" 
+    for provider_name, code in dict_code_provider.iteritems():
+        output += code + "\n"
+
+    if output != old_output:
+        with open(path, "w") as f:
+            f.write(output)
 
 
 def create_ezfio_config(dict_ezfio_cfg, opt, folder):
@@ -220,10 +231,19 @@ def save_ezfio_config(folder, str_ezfio_config):
     path = "{0}/config/{1}.ezfio_interface_config".format(ezfio_dir,
                                                           folder)
 
-    print "Path = {}".format(path)
+#    print "Path = {}".format(path)
 
-    with open(path, "w") as f:
+    try:
-        f.write(str_ezfio_config)
+        f = open(path, "r")
+    except IOError:
+        old_output = ""
+    else:
+        old_output = f.read()
+        f.close()
+
+    if str_ezfio_config != old_output:
+        with open(path, "w") as f:
+            f.write(str_ezfio_config)
 
 def main():
     """Take in argument a EZFIO.cfg"""
@@ -238,28 +258,25 @@ def main():
     path = os.path.expanduser(path)
     path = os.path.expandvars(path)
     path = os.path.abspath(path)
-    print path
+#    print path
 
     path_dirname = os.path.dirname(path)
     folder = [i for i in path_dirname.split("/") if i][-1]
     folder = folder.lower()
 
-    print "Find a EZFIO.cfg in {}".format(path)
+#    print "Found a EZFIO.cfg in {}".format(path)
     dict_info_provider = get_dict_config_file(path,folder)
 
-    print "Generating the ezfio_interface.irp.f: \n"
+#    print "Generating the ezfio_interface.irp.f: \n"
     d_config = create_ezfio_provider(dict_info_provider)
-#    for provider, code in d_config.iteritems():
-#        print code
 
-    print "Saving the ezfio_interface.irp.f"
+#    print "Saving the ezfio_interface.irp.f"
     save_ezfio_provider(path_dirname, d_config)
 
-    print "Generating the ezfio_config"
+#    print "Generating the ezfio_config"
     config_ezfio = create_ezfio_config(dict_info_provider, "config", folder)
-#    print config_ezfio
 
-    print "Saving ezfio_config"
+#    print "Saving ezfio_config"
     save_ezfio_config(folder, config_ezfio)
 
 

scripts/get_basis.sh

@@ -8,6 +8,13 @@
 # Prints in stdout the name of a temporary file containing the basis set.
 #
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+
 export EMSL_API_ROOT="${QPACKAGE_ROOT}"/EMSL_Basis/
 export PYTHONPATH="${EMSL_API_ROOT}":${PYTHONPATH}
 
@@ -15,8 +22,11 @@ tmpfile="$1"
 shift
 
 # Case insensitive basis in input
-basis=$( ${EMSL_API_ROOT}/EMSL_api.py list_basis | cut -d "'" -f 2 | grep -i "^${1}\$")
+#basis=$( ${EMSL_API_ROOT}/EMSL_api.py list_basis | cut -d "'" -f 2 | grep -i "^${1}\$")
+
+basis="$1"
 shift
+
 atoms=""
 
 for atom in $@

scripts/install_curl.sh

@@ -6,12 +6,11 @@
 CURL="curl-7.30.0.ermine"
 CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
+  print "Please reload the quantum_package.rc file."
-  exit 1
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}

scripts/install_emsl.sh

@@ -6,18 +6,18 @@
 BASE="EMSL_Basis_Set_Exchange_Local"
 URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
+  print "Please reload the quantum_package.rc file."
-  exit 1
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}
 
 ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
+rm -rf EMSL_Basis
 mv ${BASE}-master EMSL_Basis
 
 

scripts/install_ezfio.sh

@@ -6,17 +6,15 @@
 BASE="ezfio"
 URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
+  print "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
+  print "Please reload the quantum_package.rc file."
-  exit 1
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}
 
-
 rm -rf -- EZFIO
 ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1

scripts/install_ocaml.sh

@@ -45,7 +45,8 @@ then
     done
   fi
 fi
-scripts/fetch_from_web.py "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
+${QPACKAGE_ROOT}/scripts/fetch_from_web.py \
+   "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
 chmod +x opam_installer.sh
 echo N | ./opam_installer.sh ${QPACKAGE_ROOT}/bin 
 
@@ -53,6 +54,7 @@ if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]; then
    echo "Installation of OPAM failed"
    exit 2
 fi
+rm opam_installer.sh
 ${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/quantum_package.rc 
 
 source ${QPACKAGE_ROOT}/quantum_package.rc

scripts/prepare_ezfio.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+# Prepares the EZFIO library before running make
+# Wed Mar 25 21:25:11 CET 2015
+
+echo "Building EZFIO library"
+echo "=-=-=-=-=-=-=-=-=-=-=-"
+
+# Interpret all the EZFIO.cfg files
+for dir in ${QPACKAGE_ROOT}/src/*/ 
+do 
+  cd $dir || exit -1
+  ${QPACKAGE_ROOT}/scripts/ezfio_interface.py
+done
+
+# For old-style directories. Will be removed some day...
+cp ${QPACKAGE_ROOT}/src{/*,}/*.ezfio_config ${QPACKAGE_ROOT}/EZFIO/config 
+
+

scripts/prepare_module.sh

@@ -1,15 +0,0 @@
-#!/bin/bash
-# This script is used by module Makefiles, and should not be used by users.
-# Checks if all the other module directories are properly linked in the
-# current directory. If not, the links are created.
-# Wed Apr  2 14:35:42 CEST 2014
-
-for dir in $@
-do
-  if [[ ! -h $dir ]] ;
-  then
-    ln -s ../$dir $dir
-  fi
-done
-
-

scripts/qp_include.sh

@@ -0,0 +1,80 @@
+#!/bin/bash
+#
+# Useful functions in all scripts
+
+# Make a list unique
+function unique_list()
+{
+  for d in $@
+  do
+    echo $d
+  done | sort | uniq
+}
+
+function check_current_dir_is_src()
+{
+  if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
+  then
+     return 0
+  else
+     echo "Current directory should be \$QPACKAGE_ROOT/src"
+     exit -1
+  fi
+}
+
+function check_current_dir_is_module()
+{
+  cd ..
+  if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
+  then
+     cd $OLDPWD
+     return 0
+  else
+     cd $OLDPWD
+     echo "Current directory should be \$QPACKAGE_ROOT/src"
+     exit -1
+  fi
+}
+if [[ -f NEEDED_MODULES ]]
+then
+  NEEDED_MODULES=$(cat NEEDED_MODULES)
+fi
+
+# List of executables in the current directory
+function ls_exe()
+{
+  find . -perm /u+x -type f
+}
+
+function asksure() {
+  echo -n $@ "(Y/N) "
+  answer=w
+  while [[ $answer != [YyNn] ]]
+  do
+     read answer
+     [[ $answer = [Yy] ]] && retval=0 || retval=1
+  done
+  return $retval
+}
+
+function error()
+{
+  echo "-------------------- Error --------------------"
+  printf "$@\n"
+  echo "-----------------------------------------------"
+  exit -1
+}
+
+if [[ -z ${DEBUG} ]]
+then
+  function info ()
+  {
+    :
+  }
+else
+  function info ()
+  {
+    echo "$@"
+  }
+fi
+

scripts/run_Makefile_common.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+#
+# Checks to run in every Module directory before building
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
+# Check if the NEEDED_MODULES file is consistent
+INCLUDE_DIRS="${NEEDED_MODULES} include"
+NEEDED_MODULES_OK=$( ${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${NEEDED_MODULES} )
+if [[ $? -ne 0 ]] 
+then
+  error "
+Your NEEDED_MODULES file is inconsistent. It should be
+${NEEDED_MODULES_OK}
+"
+else
+  info "NEEDED_MODULES files is consistent"
+fi
+
+# Check if README.rst exists
+if [[ ! -f README.rst ]] 
+then
+  ${QPACKAGE_ROOT}/scripts/create_rst_templates.sh
+  error "
+README.rst was not present, so I created a
+default one for you.
+You should document it before you compile, as
+well as the ASSUMPTIONS.rst file.
+"
+else
+  info "README.rst is present"
+fi
+
+
+# Check if ASSUMPTIONS.rst exists
+if [[ ! -f ASSUMPTIONS.rst ]] 
+then
+  error "This is a Bug. At that point, the ASSUMPTIONS.rst) file should exist."
+else
+  info "ASSUMPTIONS.rst is present."
+fi
+
+
+# Create symbolic links of other modules
+if [[ $PWD != ${QPACKAGE_ROOT}/src ]]
+then
+  for dir in ${INCLUDE_DIRS}
+  do
+    if [[ ! -h $dir ]] ;
+    then
+      ln -s ../$dir $dir
+    fi
+  done
+fi
+
+# Update Makefile.depend
+${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
+
+# Update EZFIO interface
+${QPACKAGE_ROOT}/scripts/ezfio_interface.py
+

scripts/run_Makefile_global.sh

@@ -0,0 +1,81 @@
+#!/bin/bash
+# Makes several checks before compiling.
+# Wed Mar 25 21:22:18 CET 2015
+
+# Required EZFIO version
+EZFIO_REQUIRED_VERSION=1.1
+
+# Required IRPF90 version
+IRPF90_REQUIRED_VERSION=1.5
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_src
+
+
+# Check if the user's config exists
+if [[ ! -f  ${QPACKAGE_ROOT}/src/Makefile.config ]] 
+then
+  error "
+Makefile.config is not present.
+You can create Makefile.config
+by modifying Makefile.config.example
+"
+else
+  info "Makefile.config is present"
+fi
+
+
+IRPF90_VERSION=$( ${IRPF90} -v )
+python << EOF
+import sys
+irp_version = float("${IRPF90_VERSION}".rsplit('.',1)[0])
+irp_required_version = float($IRPF90_REQUIRED_VERSION)
+if irp_version < irp_required_version:
+  sys.exit(-1)
+EOF
+
+if [[ $? -ne 0 ]]
+then
+  error "
+Current IRPF90 version :
+\$ ${IRPF90} -v
+${IRPF90_VERSION}.
+
+IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
+To upgrade IRPF90, run :                       
+  ${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh   
+"
+else
+  info "irpf90 version is OK"
+fi
+
+
+# Check EZFIO version
+EZFIO_VERSION=$(cat ${QPACKAGE_ROOT}/EZFIO/version | cut -d '=' -f 2)
+python << EOF
+import sys
+ezfio_version = float("${EZFIO_VERSION}".rsplit('.',1)[0])
+ezfio_required_version = float($EZFIO_REQUIRED_VERSION)
+if ezfio_version < ezfio_required_version:
+  sys.exit(-1)
+EOF
+
+if [[ $? -ne 0 ]]
+then
+  error "
+Current EZFIO version : ${EZFIO_VERSION}
+EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
+To upgrade EZFIO, run :                       
+  ${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh   
+"
+else
+  info "EZFIO version is OK"
+fi
+

scripts/save_current_mos.sh

@@ -4,6 +4,13 @@
 # directory, where xxx is the corresponding mo_label.
 # Wed Apr  2 14:35:15 CEST 2014
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+
 EZFIO=$1
 
 if [[ -z ${EZFIO} ]]

scripts/unarchive_ezfio.sh

@@ -1,54 +0,0 @@
-#!/bin/bash
-#
-# Reads a *.md5 file, then fetches the proper data in the
-# cache and re-creates the EZFIO database.
-# If the cache data is not present, download it from 
-# $QPACKAGE_CACHE_URL
-# Fri Apr  4 01:02:53 CEST 2014
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  print "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-fi
-
-EZFIO_FILE=$(basename $(basename ${1} .md5))
-
-if [[ -z $1 ]]
-then
-  echo "Usage: $(basename $0) <EZFIO_FILE.md5>"
-  exit 1
-fi
-
-if [[ ! -f ${EZFIO_FILE}.md5 ]]
-then
-  echo "Error: ${EZFIO_FILE}.md5 does not exist."
-  exit 1
-fi
-
-key=($(cut -d ' ' -f 1 ${EZFIO_FILE}.md5))
-filename=($(cut -d ' ' -f 2 ${EZFIO_FILE}.md5))
-
-if [[ -z ${QPACKAGE_CACHE_URL} ]]
-then
-  echo "Error: The QPACKAGE_CACHE_URL environment variable is not set."  
-  exit 1
-fi
-
-VERSION=$( cut -d '=' -f 2 < ${QPACKAGE_ROOT}/EZFIO/version)
-for i in ${!key[@]}
-do
-  MD5=${key[$i]}
-  file=${filename[$i]}
-  if [[ ! -d $file ]]
-  then
-    mkdir -p $(dirname $file)
-    echo ${VERSION} > $(dirname $file)/.version
-  fi
-  if [[ ! -f ${QPACKAGE_ROOT}/data/cache/${MD5} ]]
-  then
-    ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${QPACKAGE_CACHE_URL}/${MD5} ${QPACKAGE_ROOT}/data/cache/${MD5}
-  fi
-  cp ${QPACKAGE_ROOT}/data/cache/${MD5} ${file}
-done
-echo ${VERSION} > ${EZFIO_FILE}.ezfio/.version

scripts/upgrade_ezfio.sh

@@ -12,7 +12,7 @@ fi
 cd -- ${QPACKAGE_ROOT}
 mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
 
-make EZFIO
+${QPACKAGE_ROOT}/scripts/install_ezfio.sh
 
 if [[ $? -eq 0 ]]
 then

setup_environment.sh

@@ -75,6 +75,9 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
 " $BLACK
 
 
+mkdir -f install_logs
+mv *.log install_logs/
+
 if [[ $1 == "--robot" ]] ; 
 then
   exit 0

src/AOs/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/BiInts/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Bitmask/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=bitmasks_module.f90

src/CAS_SD_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CID/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CID_SC2_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CID_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CIS/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CISD/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CISD_SC2_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/CISD_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/DDCI_selected/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Dets/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=H_apply_template.f

src/Electrons/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Ezfio_files/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/FCIdump/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Full_CI/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Generators_CAS/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Generators_full/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Generators_restart/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Hartree_Fock/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/MOGuess/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/MOs/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/MP2/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Makefile

@@ -1,19 +1,24 @@
-default: all
+ifndef QPACKAGE_ROOT
+  $(error "QPACKAGE_ROOT is not defined. Please source quantum_package.rc")
+endif
 
-SRC=
+include Makefile.config
-OBJ=
 
 ALL_MODULES=$(shell cat NEEDED_MODULES)
+EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
+EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 
-.PHONY: executables all all_clean $(ALL_MODULES)
+.PHONY: $(ALL_MODULES)
 
-all: $(ALL_MODULES)
 
-all_clean:
+default: $(EZFIO)
-	@for i in $(ALL_MODULES) ; do cd $$i ; make veryclean ; make clean_links ; cd .. ; done
+	$(QPACKAGE_ROOT)/scripts/build_modules.sh $(ALL_MODULES)
 
-$(ALL_MODULES): FORCE
+veryclean:
-	cd $@ ; make -j $$(cat /proc/cpuinfo | grep MHz | wc -l)
+	$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
+
+$(ALL_MODULES): $(EZFIO)
+	$(QPACKAGE_ROOT)/scripts/build_modules.sh $@ 
 
 executables: $(ALL_MODULES)
 	rm -f executables ; \
@@ -21,7 +26,15 @@ executables: $(ALL_MODULES)
 	  do printf "%-30s %s\n" $$(basename $$EXE) $$EXE | sed "s|$(QPACKAGE_ROOT)|\$$QPACKAGE_ROOT|g" >> executables ;\
 	done
 
-# Dummy rule to enable to force recompilation
+# Define the EZFIO rules
-FORCE:
+$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
+	$(QPACKAGE_ROOT)/scripts/prepare_ezfio.sh
+	cd $(EZFIO_DIR);\
+	export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ;\
+	$(MAKE) ;\
+	$(MAKE) Python
+
+# Frequent typos
+clena: clean
+veryclena: veryclean
 
-veryclean: all_clean

src/Makefile.common

@@ -1,160 +1,34 @@
-.PHONY: default
+.PHONY: default silent
+
+ifneq ($(IN_MAKE),1) 
+
+default:
+	@$(MAKE) -C $(QPACKAGE_ROOT)/src $$(basename $(PWD))
+
+veryclean:
+	 clean_modules.sh
+
+else  # Called by scripts/build_module.sh
 
 default: all .gitignore
 
-# Required EZFIO version
-EZFIO_VERSION=1.1
-
-# Required IRPF90 version
-IRPF90_VERSION=1.4
-
-# Check if QPACKAGE_ROOT is defined
-
-ifndef QPACKAGE_ROOT
-$(info  -------------------- Error --------------------)
-$(info  QPACKAGE_ROOT undefined. Run the setup_environment.sh script)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  QPACKAGE_ROOT is defined.)
-endif
-
-
-# Check if the user's config exists
-
-MAKEFILE_OK=$(shell ls $(QPACKAGE_ROOT)/src/Makefile.config 2> /dev/null && echo True || echo False)
-ifeq ($(MAKEFILE_OK),False)
-$(info  -------------------- Error --------------------)
-$(info Makefile.config is not present.)
-$(info You can create Makefile.config)
-$(info by modifying Makefile.config.example)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  Makefile.config is present.)
-endif
-
-
 # Include the user's config
-
 include $(QPACKAGE_ROOT)/src/Makefile.config
 
-
-# Check the  version of IRPF90
-
-IRP_VERSION_OK=$(shell $(IRPF90) -v | python -c "import sys ; print float(sys.stdin.readline().rsplit('.',1)[0]) >= $(IRPF90_VERSION)")
-ifeq ($(IRP_VERSION_OK),False)
-$(info  -------------------- Error --------------------)
-$(info  IRPF90 version >= $(IRPF90_VERSION) is required)
-$(info  To upgrade IRPF90, run :                       )
-$(info    $(QPACKAGE_ROOT)/scripts/upgrade_irpf90.sh   )
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  irpf90 version is OK.)
-endif
-
-
 # Create the NEEDED_MODULES variable, needed for IRPF90
-
 NEEDED_MODULES=$(shell cat NEEDED_MODULES)
 
-
-# Check if the NEEDED_MODULES file is consistent
-
-NEEDED_MODULES_OK=$(shell X=`$(QPACKAGE_ROOT)/scripts/check_dependencies.sh $(NEEDED_MODULES)` && echo OK || echo $$X)
-ifneq ($(NEEDED_MODULES_OK),OK)
-$(info  -------------------- Error --------------------)
-$(info Your NEEDED_MODULES file is inconsistent. It should be)
-$(info $(NEEDED_MODULES_OK))
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  NEEDED_MODULES files is consistent.)
-endif
-
-
 # Check and update dependencies
-
 include Makefile.depend
 
 
-# Check if README.rst exists
-
-README_RST_OK=$(shell ls README.rst 2>/dev/null || echo False)
-ifeq ($(README_RST_OK), False)
-$(shell $(QPACKAGE_ROOT)/scripts/create_rst_templates.sh)
-$(info  -------------------- Error --------------------)
-$(info  README.rst was not present, so I created a)
-$(info  default one for you.)
-$(info  You should document it before you compile, as)
-$(info  well as the ASSUMPTIONS.rst file.)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  README.rst is present.)
-endif
-
-
-# Check if ASSUMPTIONS.rst exists
-
-ASSUMPTIONS_RST_OK=$(shell ls ASSUMPTIONS.rst || echo False)
-ifeq ($(ASSUMPTIONS_RST_OK), False)
-$(info  -------------------- Error --------------------)
-$(info This is a Bug. At that point, the ASSUMPTIONS.rst)
-$(info file should exist.)
-$(info  -----------------------------------------------)
-#else
-#$(info  ASSUMPTIONS.rst is present.)
-endif
-
-
 # Define the Makefile common variables
-
 EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
 EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 INCLUDE_DIRS=$(NEEDED_MODULES) include
 
-# Check EZFIO version
-
-EZFIO_VERSION_OK=$(shell cat $(EZFIO_DIR)/version | cut -d '=' -f 2 | python -c "import sys ; print float(sys.stdin.readline().rsplit('.',1)[0]) >= $(EZFIO_VERSION)")
-ifeq ($(EZFIO_VERSION_OK),False)
-$(info  -------------------- Error --------------------)
-$(info  EZFIO version >= $(EZFIO_VERSION) is required  )
-$(info  To upgrade EZFIO, run :                        )
-$(info    $(QPACKAGE_ROOT)/scripts/upgrade_ezfio.sh    )
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  EZFIO version is OK.)
-endif
-
-# Define the EZFIO rules
-
-$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
-	@echo Building EZFIO library
-	@echo =-=-=-=-=-=-=-=-=-=-=-
-	for dir in $(QPACKAGE_ROOT)/src/*/ ;\
-	do \
-	        cd $$dir && \
-		$(QPACKAGE_ROOT)/scripts/ezfio_interface.py && \
-		cd .. ;\
-	done
-	cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
-	cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
-
-ezfio: $(EZFIO)
-
-
-# Create symbolic links of other modules
-
-ifneq ($(PWD),$(QPACKAGE_ROOT)/src)
-$(shell $(QPACKAGE_ROOT)/scripts/prepare_module.sh $(INCLUDE_DIRS))
 clean_links:
 	rm -f $(INCLUDE_DIRS) $$(basename $$PWD)
-else
-clean_links:
-endif
 
 LIB+=$(EZFIO) $(MKL)
 IRPF90+=$(patsubst %, -I %, $(INCLUDE_DIRS)) $(IRPF90_FLAGS)
@@ -163,22 +37,14 @@ irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp
 	- $(IRPF90)
 	- update_README.py
 
-Makefile.depend: Makefile
-	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh
-
-ifneq ( $(PWD), $($(QPACKAGE_ROOT)/src))
 include irpf90.make
+
 endif
 
-# Dummy rule to enable to force recompilation
-FORCE:
-
-vercylean: veryclean
-
 .gitignore:
 	$(QPACKAGE_ROOT)/scripts/create_gitignore.sh 
 
-
 # Frequent typos
 clena: clean
 veryclena: veryclean
+vercylean: veryclean

src/Molden/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/MonoInts/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/NEEDED_MODULES

@@ -1 +1 @@
-AOs BiInts Bitmask Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD_selected DDCI_selected
+AOs BiInts Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD_selected DDCI_selected

src/Nuclei/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Output/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Perturbation/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=perturbation_template.f

src/Properties/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Selectors_full/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Selectors_no_sorted/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/SingleRefMethod/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=

src/Utils/Makefile

@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=map_module.f90