Bash calls ezfio.py

Bash/ezfio.sh

@@ -1,5 +1,13 @@
 #!/bin/bash
 
+EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/..  ; pwd -P )
+
+function _ezfio_py()
+{
+  python ${EZFIO_ROOT}/Python/ezfio.py $@
+}
+
+
 function _ezfio_usage()
 {
       echo "
@@ -78,8 +86,7 @@ function _ezfio_set_file()
 
   if [[ ! -d $1 ]]
   then
-    echo "No such directory: $1"
+    mkdir -p $1 || return 1
-    return 1
   fi
   export EZFIO_FILE=$1
   _ezfio_info "Set file ${EZFIO_FILE}"
@@ -109,18 +116,7 @@ function _ezfio_has()
       return 0
   fi
 
-  if [[ -f  ${EZFIO_FILE}/${1,,}/${2,,} ]]
+  _ezfio_py has $@ && return 0 || return 1
-  then
-      _ezfio_info "EZFIO has $1 / $2"
-      return 0
-  elif [[ -f  ${EZFIO_FILE}/${1,,}/${2,,}.gz ]]
-  then
-      _ezfio_info "EZFIO has $1 / $2"
-      return 0
-  else
-      _ezfio_info "EZFIO doesn't have $1 / $2"
-      return 1
-  fi
 }
 
 function _ezfio_get()
@@ -129,29 +125,15 @@ function _ezfio_get()
 
   if [[ -z $1 ]] 
   then
-    ls ${EZFIO_FILE}
+    ls ${EZFIO_FILE} && return 0 || return 1
-    return 0
   fi
 
-  _ezfio_has $@ || return 1
-
   if [[ -z $2 ]]
   then
-      ls ${EZFIO_FILE}/${1,,}
+      ls ${EZFIO_FILE}/${1,,} && return 0 || return 1
-      return 0
   fi
 
-  if [[ -f ${EZFIO_FILE}/${1,,}/${2,,} ]]
+  _ezfio_py get $@ && return 0 || return 1
-  then
-    cat ${EZFIO_FILE}/${1,,}/${2,,}
-  elif [[ -f ${EZFIO_FILE}/${1,,}/${2,,}.gz ]]
-  then
-    zcat ${EZFIO_FILE}/${1,,}/${2,,}.gz
-  else
-    _ezfio_info "EZFIO doesn't have $1 / $2"
-    return 1
-  fi
-  return 0
 }
 
 function _ezfio_set()
@@ -160,15 +142,11 @@ function _ezfio_set()
   _require_first_argument  $@ || return 1
   _require_second_argument $@ || return 2
 
-  if [[ ! -d ${EZFIO_FILE}/${1,,} ]]
+  if [[ -z $3 ]]
   then
-    mkdir -p ${EZFIO_FILE}/${1,,}
+    _ezfio_py set $@ || return 1
-  fi
-  if [[ ! -z "$3" ]]
-  then
-    echo "$3" > ${EZFIO_FILE}/${1,,}/${2,,}
   else
-    zcat > ${EZFIO_FILE}/${1,,}/${2,,}.gz
+    echo $3 | _ezfio_py set $1 $2 || return 1
   fi
   return 0
 }
@@ -234,6 +212,9 @@ _Complete()
   prev="${COMP_WORDS[COMP_CWORD-1]}"
   prev2="${COMP_WORDS[COMP_CWORD-2]}"
 
+  if [[ -n ${EZFIO_FILE} && -d ${EZFIO_FILE} ]]
+  then
+
     case "${prev2}" in
       set|has|get)
         COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE}/${prev} ; ls | sed 's/\.gz//' )" -- $cur ) )
@@ -246,27 +227,36 @@ _Complete()
         COMPREPLY=()
         return 0
         ;;
-    set_file)
-      COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) )
-      return 0
-      ;;
       set|has|get)
         COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) )
         return 0
         ;;
       *)
-      if [[ -z ${EZFIO_FILE} ]]
-      then
-        COMPREPLY=( $(compgen -W 'set_file \
-                                  set_verbose unset_verbose -h' -- $cur ) )
-      else
         COMPREPLY=( $(compgen -W 'has get set unset_file \
                                   set_verbose unset_verbose -h' -- $cur ) )
-      fi
         return 0
         ;;
     esac
 
+  else
+
+    case "${prev}" in
+      set_verbose|unset_verbose)
+        COMPREPLY=()
+        return 0
+        ;;
+      set_file)
+        COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) )
+        return 0
+        ;;
+      *)
+        COMPREPLY=( $(compgen -W 'set_file \
+                                  set_verbose unset_verbose -h' -- $cur ) )
+        return 0
+        ;;
+    esac
+
+  fi
 }
 
 complete -F _Complete ezfio

README.rst

@@ -19,8 +19,8 @@ The following packages are needed:
 
 * `IRPF90 <http://irpf90.ups-tlse.fr>`_
 * `Python <http://www.python.org>`_
+* `GNU make <http://www.python.org>`_ or `Ninja <http://github.com/martine/ninja>`_
 
-The latest version can be downloaded `here <http://qmcchem.ups-tlse.fr/files/scemama/EZFIO.latest.tar.gz>`_.
 
 Tutorial
 ========
@@ -39,15 +39,9 @@ Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file
   $ ls
   EZFIO/
 
-Get into the ``EZFIO`` directory and set up your compiling options: 
+Get into the ``EZFIO`` directory and configure the library to produce the
-
+desired suboutines. Get into the ``config`` directory and create a new file
-.. code-block:: bash
+``test.config``
-
-  $ cp make.config.example make.config
-  $ vim make.config
-
-Now, configure the library to produce the desired suboutines. Get into
-the ``config`` directory and create a new file ``test.config``
 containing::
 
   molecule
@@ -79,19 +73,27 @@ simple operation is written after an = symbol (as for ``mass`` in the
 Once your configuration file is ready, run ``make`` and your library
 will be built.
 
+
 Building the library
 --------------------
 
-Now, go back to the EZFIO root directory, and run:
+Now, go back to the EZFIO root directory. To build with GNU make, run:
 
 .. code-block:: bash
 
   $ make
 
-The ``lib`` directory now contains the shared library
+Or you can use Ninja to build the library:
-(``libezfio.so``), the static library (``libezfio.a``), and a static
+
+.. code-block:: bash
+
+  $ ninja
+
+
+The ``lib`` directory now contains the static library ``libezfio.a``, and a static
 library for use under the IRPF90 environment (``libezfio_irp.a``).
-The ``Python`` directory contains the Python module for the use of the library in Python.
+The ``Python``, ``Ocaml`` and ``Bash`` directories contain the binding for these languages.
+
 
 Using the produced library
 --------------------------
@@ -220,7 +222,7 @@ Create a file named ``create_input.py`` with:
   ezfio.molecule_mass = mass
   ezfio.molecule_coord = coord
   
-  # Check that the total charge and mass is correct:
+  # Check that the total mass is correct:
   print ezfio.properties_mass   # Should give 18.
 
 Execute the script:
@@ -236,10 +238,10 @@ The printed mass is correct, and a new directory (``Water``) was created with ou
 
   $ ls Water/*
   Water/ezfio:
-  creation
+  creation  library  user
 
   Water/molecule:
-  charge.gz  coord.gz  mass.gz  num_atoms
+  coord.gz  mass.gz  num_atoms
 
 In Fortran
 ----------
@@ -307,6 +309,20 @@ the EZFIO file.
   
   end
 
+Compile the fortran program and link it the ``libezfio.a`` library, and run the
+executable.
+
+.. code-block:: bash
+
+  $ gfortran test.f90 EZFIO/lib/libezfio.a -o test.x
+  $ ./test.x
+  Data in the EZFIO file:
+     16.0000000       0.00000000      0.222396001       0.00000000    
+     1.00000000       1.43649399     -0.889660001       0.00000000    
+     1.00000000      -1.43649399     -0.889660001       0.00000000    
+
+
+
 A new directory (``properties``) was created with the center_of_mass
 file:
 
@@ -317,25 +333,64 @@ file:
   creation
 
   Water/molecule:
-  charge.gz  coord.gz  mass.gz  num_atoms
+  coord.gz  mass.gz  num_atoms
 
   Water/properties:
   center_of_mass.gz
 
 
-Compile and run the program using:
+Using Bash
+----------
+
+To use EZFIO in Bash, you need to source the ``ezfio.sh`` file:
 
 .. code-block:: bash
 
-  $ $FC -o test test.F90 EZFIO/lib/libezfio.a
+  $ source EZFIO/Bash/ezfio.sh
-  $ ./test
 
-where ``$FC`` is your fortran compiler, and ``test.F90`` is the file
+The usage of the ``ezfio`` bash command is::
-containing the test example.  If you don't have the EZFIO static
+
-library, you can use the shared library as:
+  ezfio set_file    EZFIO_DIRECTORY
+  ezfio unset_file 
+
+  ezfio has         DIRECTORY   ITEM
+  ezfio get         DIRECTORY   ITEM
+  ezfio set         DIRECTORY   ITEM  VALUE  : Scalar values
+  ezfio set         DIRECTORY   ITEM         : Array values read from stdin
+
+  ezfio set_verbose
+  ezfio unset_verbose
+
+
+Here is the same script as the Python script, but using Bash (``create_input.sh``):
 
 .. code-block:: bash
 
-  $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/EZFIO/lib
+  #!/bin/bash
-  $ $FC -o test -L./EZFIO/lib -lezfio
+  
+  source EZFIO/Bash/ezfio.sh
+  
+  # Select the EZFIO file
+  ezfio set_file Water
+  
+  # Set the number of atoms
+  ezfio set molecule num_atoms 3
+  
+  # Create the mass array
+  mass="[16.0, 1.0, 1.0]"
+  echo $mass | ezfio set molecule mass
+  
+  # Create the coordinates
+  cat << EOF | ezfio set molecule coord
+  [
+  [ 0.000000,  0.222396, 0.0],
+  [ 1.436494, -0.889660, 0.0],
+  [-1.436494, -0.889660, 0.0]
+  ]
+  EOF
+  
+  # Check that the total mass is correct:
+  ezfio get properties mass      # Should print 18.
+
+
 

configure.py

@@ -52,18 +52,18 @@ def create_build_ninja():
     d["irpf90_files"] = [ "src/{0}".format(x) for x in
         """
         IRPF90_temp/build.ninja irpf90.make irpf90_entities
-        tags
+        tags libezfio_groups-gen.py libezfio_util-gen.py
         """.split() ] + \
         """
-        Python/ezfio.py Ocaml/ezfio.ml Bash/ezfio.sh
+        Python/ezfio.py Ocaml/ezfio.ml 
         """.split()
 
     d["irpf90_sources"] = [ "src/{0}".format(x) for x in
         """
         libezfio_error.irp.f create_ocaml.py groups_templates.py
-        libezfio_file.irp.f create_python.py libezfio_groups-gen.py
+        libezfio_file.irp.f create_python.py 
-        libezfio_groups.irp.f ezfio-head.py libezfio_util-gen.py
+        libezfio_groups.irp.f ezfio-head.py  
-        libezfio_util.irp.f ezfio-tail.py read_config.py run.irp.f
+        libezfio_util.irp.f ezfio-tail.py read_config.py 
         f_types.py test.py create_bash.py groups.py 
         """.split() ] + [ "make.config" ]
 
@@ -93,7 +93,7 @@ rule build_libezfio_a
    description = Building libezfio.a
 
 rule build_libezfio_irp_a
-   command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o ; {RANLIB} lib/libezfio_irp.a
+   command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o > /dev/null ; {RANLIB} lib/libezfio_irp.a
    description = Building libezfio_irp.a
 
 

src/ezfio-head.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 #   EZFIO is an automatic generator of I/O libraries
 #   Copyright (C) 2009 Anthony SCEMAMA, CNRS
 #

src/ezfio-tail.py

@@ -24,3 +24,52 @@
 
 ezfio = ezfio_obj()
 
+def main():
+  import pprint
+  import sys
+  import os
+
+  try:
+    EZFIO_FILE = os.environ["EZFIO_FILE"]
+  except KeyError:
+    print "EZFIO_FILE not defined"
+    return 1
+
+  ezfio.set_file(EZFIO_FILE)
+
+  command = '_'.join(sys.argv[1:]).lower()
+
+  try:
+    f = getattr(ezfio,command)
+  except AttributeError:
+    print "{0} not found".format(command)
+    return 1
+
+  if command.startswith('has'):
+      if f(): return 0
+      else  : return 1
+
+  elif command.startswith('get'):
+      result = f()
+      pprint.pprint( result, width=60, depth=3, indent=4 )
+      return 0
+
+  elif command.startswith('set'):
+      try:
+          data = eval(sys.stdin.read())
+      except:
+          print "Syntax Error"
+          return 1
+      f(data)
+      return 0
+
+  else:
+      return 1
+
+
+if __name__ == '__main__':
+  rc = main()
+  sys.exit(rc)
+
+
+

src/groups.py

@@ -144,10 +144,3 @@ for group in groups.keys():
       print >>file_py, attributes_arr_py%d
 
 file_py.close()
-
-import create_ocaml
-create_ocaml.run()
-
-import create_python
-create_python.run()
-

src/libezfio_util.irp.f

@@ -354,6 +354,13 @@ print >>file_py, """
 """%cwd
 
 file_py.close()
+
+import create_ocaml
+create_ocaml.run()
+
+import create_python
+create_python.run()
+
 END_SHELL
 
 BEGIN_PROVIDER [ integer, libezfio_buffer_rank ]

src/run.irp.f

@@ -1,31 +0,0 @@
-!   EZFIO is an automatic generator of I/O libraries
-!   Copyright (C) 2009 Anthony SCEMAMA, CNRS
-!
-!   This program is free software; you can redistribute it and/or modify
-!   it under the terms of the GNU General Public License as published by
-!   the Free Software Foundation; either version 2 of the License, or
-!   (at your option) any later version.
-!
-!   This program is distributed in the hope that it will be useful,
-!   but WITHOUT ANY WARRANTY; without even the implied warranty of
-!   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-!   GNU General Public License for more details.
-!
-!   You should have received a copy of the GNU General Public License along
-!   with this program; if not, write to the Free Software Foundation, Inc.,
-!   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-!
-!   Anthony Scemama
-!   LCPQ - IRSAMC - CNRS
-!   Universite Paul Sabatier
-!   118, route de Narbonne      
-!   31062 Toulouse Cedex 4      
-!   scemama@irsamc.ups-tlse.fr
-
-program run
-  BEGIN_DOC
-! Test run
-  END_DOC
-! Leave this empty
-end
-