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# 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
include version
include make.config
.PHONY: default clean distclean archive configure
default: make.config
- bash -c "[[ -e lib/libezfio.a ]] && rm $$PWD/lib/*"
@echo Compiling library && make -C $$PWD/src static
@echo Building Python module && make -C $$PWD/src python
clean:
- bash -c "[[ -e lib/libezfio.a ]] && rm $$PWD/lib/*"
- bash -c "[[ -e Python/ezfio.py ]] && rm $$PWD/Python/*"
- make -C $$PWD/src veryclean
distclean: clean
- rm -rf autom4te.cache config.status config.log make.config
archive: distclean
git archive --format=tar HEAD > EZFIO.$(VERSION).tar
mkdir EZFIO ; cd EZFIO ; tar -xvf ../EZFIO.$(VERSION).tar
rm EZFIO.$(VERSION).tar
tar -zcvf EZFIO.$(VERSION).tar.gz EZFIO
rm -rf EZFIO
configure: make.config.in configure.ac
autoconf
make.config:
./configure --host=dummy

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======================================================================
EZFIO
======================================================================
Author: A. Scemama, LCPQ-IRSAMC, CNRS-Universite Paul Sabatier
scemama@irsamc.ups-tlse.fr
== About EZFIO ==
EZFIO is the Easy Fortran I/O library. With EZFIO, your data is organized
in a file system inside a main directory. This main directory contains
subdirectories, which contain files. Each file corresponds to a data. For
atomic data the file is a plain text file, and for array data the file is a
gzipped text file.
== Building a library ==
Your EZFIO library is built according to the definitions given in the
files of the 'config' directory. A configuration file can be, for example:
---
system
title character*(128)
num_elec integer = system_num_alpha + system_num_beta
num_alpha integer
num_beta integer
geometry
num_atom integer
nuc_energy double precision
label character*(32) (geometry_num_atom)
atomic_number integer (geometry_num_atom)
charge double precision (geometry_num_atom)
coord double precision (3,geometry_num_atom)
---
A subdirectory is defined by its name at the beginning of a new line. The
data contained in this subdirectory is defined by the triplet
(name,type,dimension), leaving at least one white space at the beginning of the
line.
If the dimension of an array is a data defined in the file, its name can be
used as <name of the subdirectory>_<name of the data>. For example, the
dimension '(geometry_num_atom)' uses the data 'num_atom' of subdirectory
'geometry'.
A data can also be the result of a simple operation. In that case, the
simple operation is written after an '=' symbol (as for 'num_elec'). In
that case, the data is read_only.
Once your configuration file is ready, run 'make' and your library will be
built.
== Using the library ==
In the following, we will call 'EZFIO file' the main directory containing the
EZFIO data.
Only one EZFIO file can be manipulated at a time. To select a file, use:
character*(64) :: filename
call ezfio_set_file(filename)
To get the name of the current used EZFIO file, use
character*(64) :: filename
call ezfio_get_filename(filename)
For each data, 3 subroutines are created.
<dir> is the name of the subdirectory which contains the data and
<data> is the name of the data.
* subroutine ezfio_has_<dir>_<data> (result)
sets result to .True. if the data exists in the EZFIO file, .False. otherwise.
* subroutine ezfio_set_<dir>_<data> (source)
writes the source data to the EZFIO file.
* subroutine ezfio_get_<dir>_<data> (destination)
reads the data from the EZFIO file to the destination.
For safety, a read-only attribute can be set to the file by
call ezfio_set_read_only(.True.)
or inquired by
logical :: is_read_only
call ezfio_is_read_only(is_read_only)

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EZFIO
=====
The Easy Fortran I/O library generator

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EZFIO
=====
EZFIO is the Easy Fortran I/O library generator. It generates
automatically an I/O library from a simple configuration file. The
produced library contains Fortran subroutines to read/write the data
from/to disk, and to check if the data exists.
A Python and an Ocaml API are also provided.
With EZFIO, the data is organized in a file system inside a main
directory. This main directory contains subdirectories, which contain
files. Each file corresponds to a data. For atomic data the file is a
plain text file, and for array data the file is a gzipped text file.
Download
========
The following packages are needed:
* `IRPF90 <http://irpf90.ups-tlse.fr>`_
* `Python <http://www.python.org>`_
The latest version can be downloaded `here <http://qmcchem.ups-tlse.fr/files/scemama/EZFIO.latest.tar.gz>`_.
Tutorial
========
In this example, we will write a Fortran program which computes
properties of a molecule. The molecule is described as point charges in
the 3D space.
Preparation of the library
--------------------------
Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file in this directory. This directory now contains:
.. code-block:: bash
$ ls
EZFIO/
Get into the ``EZFIO`` directory and run:
.. code-block:: bash
$ ./configure
Now, configure the library to produce the desired suboutines. Get into
the ``config`` directory and create a new file ``test.config``
containing::
molecule
num_atoms integer
mass real (molecule_num_atoms)
coord real (3,molecule_num_atoms)
properties
mass real = sum(molecule_mass)
center_of_mass real (3)
In this example, ``molecule`` and ``properties`` are containers of data.
Those are defined in the config file by their name at the beginning of a
new line.
Each data contained inside a container is characterized by a triplet
(name,type,dimension), preceded by at least one white space at the
beginning of the line.
If the dimension of an array is a data, the name of the data can be used
as ``<container>_<data>`` in the definition of the dimension. For
example, the dimension (``molecule_num_atoms``) uses the data
``num_atoms`` of container ``molecule``.
Data can also be the result of a simple operation. In that case, the
simple operation is written after an = symbol (as for ``mass`` in the
``properties`` container). In that case, the data is read-only.
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:
.. code-block:: bash
$ make
The ``lib`` directory now contains the shared library
(``libezfio.so``), 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.
Using the produced library
--------------------------
In the following, we will call 'EZFIO file' the main directory
containing the EZFIO data.
All the produced libraries contain the following subroutines:
subroutine ezfio_set_read_only(ro)
If ``ro`` is .True., the read-only attribute is set. It will be
impossible to write to the EZFIO file.
subroutine ezfio_is_read_only(ro)
Returns the value of the read_only attribute to ``ro``.
subroutine ezfio_set_file(filename)
Only one EZFIO can be manipulated at a time. This subroutine selects
which file will be manipulated.
subroutine ezfio_get_filename(fname)
Returns the name of the EZFIO file which is currently manipulated.
For each data, 3 subroutines are created.
<dir> is the name of the container which contains the data and
<data> is the name of the data.
subroutine ezfio_has_<dir>_<data> (has_it)
``has_it`` is .True. if the data exists in the EZFIO file, .False. otherwise.
subroutine ezfio_set_<dir>_<data> (source)
writes the source data to the EZFIO file.
subroutine ezfio_get_<dir>_<data> (destination)
reads the data from the EZFIO file to the destination.
With our example, the library contains the following subroutines:
.. code-block:: fortran
subroutine ezfio_set_read_only(ro)
subroutine ezfio_is_read_only(ro)
subroutine ezfio_set_file(filename)
subroutine ezfio_get_filename(filename)
subroutine ezfio_set_molecule_num_atoms(num_atoms)
subroutine ezfio_get_molecule_num_atoms(num_atoms)
subroutine ezfio_has_molecule_num_atoms(has_it)
subroutine ezfio_set_molecule_mass(mass)
subroutine ezfio_get_molecule_mass(mass)
subroutine ezfio_has_molecule_mass(has_it)
subroutine ezfio_set_molecule_coord(coord)
subroutine ezfio_get_molecule_coord(coord)
subroutine ezfio_has_molecule_coord(has_it)
subroutine ezfio_get_properties_mass(mass)
subroutine ezfio_set_properties_center_of_mass(center_of_mass)
subroutine ezfio_get_properties_center_of_mass(center_of_mass)
subroutine ezfio_has_properties_center_of_mass(has_it)
subroutine ezfio_set_properties_center_of_charge(center_of_charge)
subroutine ezfio_get_properties_center_of_charge(center_of_charge)
subroutine ezfio_has_properties_center_of_charge(has_it)
Note that ``ezfio_get_properties_mass`` has only the ``get`` subroutine
since it is computed data.
In Python
---------
All the subroutines are also produced for Python in the ezfio.py file in
the Python directory. To use them, in your Python script, use:
.. code-block:: python
import sys
EZFIO = "./EZFIO" # Put here the absolute path to the EZFIO directory
sys.path = [ EZFIO+"/Python" ]+sys.path
from ezfio import ezfio
and all the subroutines will be accessible by replacing the first
underscore character of the name of the subroutine by a dot (``ezfio_``
becomes ``ezfio.``).
Let us create the input of our Fortran program with a Python script.
Create a file named ``create_input.py`` with:
.. code-block:: python
#!/usr/bin/python
import sys
EZFIO = "./EZFIO" # Put here the absolute path to the EZFIO directory
sys.path = [ EZFIO+"/Python" ]+sys.path
from ezfio import ezfio
# Water molecule:
# mass, x, y, z
input = """16. 0.000000 0.222396 0.000000
1. 1.436494 -0.889660 0.000000
1. -1.436494 -0.889660 0.000000 """
Molecule = []
for line in input.splitlines():
new_list = map(eval,line.split())
Molecule.append(new_list)
# Create the mass array
mass = map( lambda x: x[0], Molecule )
# print mass
# [16.0, 1.0, 1.0]
# Create the coord array
coord = map( lambda x: (x[1], x[2], x[3]), Molecule )
# print coord
# [(0.0, 0.222396, 0.0), (1.436494, -0.88966, 0.0), (-1.436494, -0.88966, 0.0)]
# Select the EZFIO file
ezfio.set_file("Water")
# Add the arrays to the file
ezfio.molecule_num_atoms = len(Molecule)
ezfio.molecule_mass = mass
ezfio.molecule_coord = coord
# Check that the total charge and mass is correct:
print ezfio.properties_mass # Should give 18.
Execute the script:
.. code-block:: bash
$ python create_input.py
18.0
The printed mass is correct, and a new directory (``Water``) was created with our data:
.. code-block:: bash
$ ls Water/*
Water/ezfio:
creation
Water/molecule:
charge.gz coord.gz mass.gz num_atoms
In Fortran
----------
We will create here a Fortran program which reads the atomic coordinates
and the atomic masses from an EZFIO file, computes the coordinates of
the center of mass, and writes the coordinates of the center of mass to
the EZFIO file.
.. code-block:: fortran
program test
implicit none
integer :: num_atoms
real, allocatable :: mass(:)
real, allocatable :: coord(:,:)
real :: center_of_mass(3)
real :: total_mass
integer :: i,j
! Set which file is read/written
call ezfio_set_file("Water")
! Read the number of atoms
call ezfio_get_molecule_num_atoms(num_atoms)
! Allocate the mass and coord arrays
allocate(mass(num_atoms), coord(3,num_atoms))
! Read the arrays from the file
call ezfio_get_molecule_mass(mass)
call ezfio_get_molecule_coord(coord)
! Check that the read data is correct
print *, 'Data in the EZFIO file:'
do i=1,num_atoms
print *, mass(i), (coord(j,i),j=1,3)
end do
! prints:
! Data in the EZFIO file:
! 16.00000 0.000000 0.2223960 0.000000
! 1.000000 1.436494 -0.8896600 0.000000
! 1.000000 -1.436494 -0.8896600 0.000000
! Perform the calculation of the center of mass
do j=1,3
center_of_mass(j) = 0.
end do
do i=1,num_atoms
do j=1,3
center_of_mass(j) = center_of_mass(j) + mass(i)*coord(j,i)
end do
end do
call ezfio_get_properties_mass(total_mass)
do j=1,3
center_of_mass(j) = center_of_mass(j)/total_mass
end do
deallocate(mass, coord)
! Write the center of mass to the EZFIO file
call ezfio_set_properties_center_of_mass(center_of_mass)
end
A new directory (``properties``) was created with the center_of_mass
file:
.. code-block:: bash
$ ls Water/*
Water/ezfio:
creation
Water/molecule:
charge.gz coord.gz mass.gz num_atoms
Water/properties:
center_of_mass.gz
Compile and run the program using:
.. code-block:: bash
$ $FC -o test test.F90 EZFIO/lib/libezfio.a
$ ./test
where ``$FC`` is your fortran compiler, and ``test.F90`` is the file
containing the test example. If you don't have the EZFIO static
library, you can use the shared library as:
.. code-block:: bash
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/EZFIO/lib
$ $FC -o test -L./EZFIO/lib -lezfio

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ezfio
creation character*(64)
user character*(64)
library character*(2048)
last_library character*(2048)

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# 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
# -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.
VERSION=[`. version ; echo $VERSION`]
AC_SUBST([VERSION])
AC_REVISION([$Revision: $VERSION $])
AC_PREREQ([2.50])
AC_INIT([EZFIO Library Generator], [], [scemama@irsamc.ups-tlse.fr],[ezfio],[http://ezfio.sourceforge.net])
AC_SYS_LONG_FILE_NAMES
ROOT=`pwd`
AC_SUBST([ROOT])
AC_CONFIG_SRCDIR([src/run.irp.f])
AC_CONFIG_FILES([make.config])
AC_PREFIX_DEFAULT([./])
STATIC_LIB=$ROOT/lib/libezfio.a
AC_PROG_RANLIB
# Test Fortran
# ------------
AC_LANG([Fortran])
AC_PROG_FC([ifort gfortran],[Fortran 90])
AC_PROG_FC_C_O
AC_FC_SRCEXT([F90])
AC_FC_FREEFORM
# Test Python
# ------------
AC_CHECK_PROG([PYTHON],[python],[yes],[no])
if [[ "$PYTHON" = no ]] ; then
AC_MSG_ERROR([Please install Python.])
fi
# Test AR
# -------
if [[ -z "$AR" ]] ; then
AC_CHECK_PROG([AR],[ar],[yes],[no])
if [[ "$AR" = no ]] ; then
AC_MSG_ERROR([ar not found.])
fi
AR=ar
fi
AC_SUBST([AR])
# Test Gzip and zcat
# ------------------
if [[ -z "$HAS_GZIP" ]] ; then
AC_CHECK_PROG([GZIP],[gzip],[yes],[no])
if [[ "$GZIP" = no ]] ; then
HAS_GZIP="-DNO_GZIP"
fi
AC_CHECK_PROG([ZCAT],[zcat],[yes],[no])
if [[ "$ZCAT" = no ]] ; then
HAS_GZIP="-DNO_GZIP"
fi
AC_CHECK_PROG([MKFIFO],[mkfifo],[yes],[no])
if [[ "$MKFIFO" = no ]] ; then
HAS_GZIP="-DNO_GZIP"
fi
fi
AC_SUBST([HAS_GZIP])
# Test IRPF90
# ------------
if [[ -z "$IRPF90" ]] ; then
AC_CHECK_PROG([IRPF90],[irpf90],[yes],[no])
if [[ "$IRPF90" = no ]] ; then
AC_MSG_ERROR([Please install IRPF90:\nhttp://irpf90.ups-tlse.fr])
fi
IRPF90=`which irpf90`
fi
AC_SUBST([IRPF90])
if [[ -z "$FCFLAGS" ]] ; then
case $FC in
ifort*)
FCFLAGS="-O2 -g -ip"
STATIC_FC="-static-intel -static-libgcc -static"
;;
gfortran*)
FCFLAGS="-O2 -g -ffree-line-length-none"
STATIC_FC="-static-libgcc -static"
;;
esac
fi
# Write make.config
LIB="$STATIC_LIB"
FCFLAGS="$FCFLAGS $STATIC_FC"
AC_SUBST([LIB])
# Done
#-----
AC_OUTPUT

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#!/usr/bin/python
import os,sys
ROOT = os.path.dirname(__file__)+'/../../'
file = open(ROOT+'version','r')
lines = file.readlines()
file.close()
file = open(sys.argv[1],'a')
print >>file, 'Version:'+lines[0].split('=')[1]
file.close()

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#!/bin/bash
OLD_DIR=$PWD
cd ../.git/hooks/
for i in commit-msg post-commit
do
rm $i
ln -s $OLD_DIR/$i $PWD/$i
done

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#!/usr/bin/python
import os
ROOT = os.path.dirname(__file__)+'/../../'
file = open(ROOT+'version','r') ;
lines = file.readlines() ;
file.close() ;
v = map(int,lines[0].split('=')[1].split('.'));
v[2] += 1
lines[0] = "VERSION=%d.%d.%d\n"%tuple(v)
file = open(ROOT+'version','w')
file.writelines(lines)
file.close()

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IRPF90 = @IRPF90@ @HAS_GZIP@
FC = @FC@ -fPIC
FCFLAGS= @FCFLAGS@
RANLIB = @RANLIB@
AR = @AR@

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# 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
DEFAULT_TARGET: python
../make.config:
make -C .. make.config
include ../make.config
include irpf90.make
irpf90.make: $(wildcard *.irp.f) ../config/*
$(IRPF90)
include ../version
.PHONY: python static
static: ../lib/libezfio_irp.a ../lib/libezfio.a
../lib/libezfio.a: $(OBJ1)
- bash -c "[[ -e ../libezfio.a ]] && rm ../lib/libezfio.a"
$(AR) cru ../lib/libezfio.a $(OBJ1)
$(RANLIB) ../lib/libezfio.a
../lib/libezfio_irp.a: ../lib/libezfio.a
cp ../lib/libezfio.a ../lib/libezfio_irp.a
$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o
$(RANLIB) ../lib/libezfio_irp.a
test: static
ifort -o $@ IRPF90_temp/run.irp.F90 -L../lib/ -lezfio
python: static
cat ezfio-head.py libezfio_groups-gen.py libezfio_util-gen.py ezfio-tail.py > ../Python/ezfio.py
ezfio.py: python

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#!/usr/bin/env python
# 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
import re
from read_config import groups
from groups_templates import *
from f_types import t_short, f2ocaml
import os
import sys
def run():
head = []
tail = []
file = open("../version","r")
v = file.readline()
file.close()
v = v.split('=')[1].strip()
l = os.getcwd().replace('/src','')
head += ["""let version = "%s";;"""%(v),
"""let library = "%s";;"""%(l)]
for group in groups.keys():
for var,type,dims,command in groups[group]:
if command is not "":
continue
dims_py = str(dims)
for g in groups.keys():
dims_py = dims_py.replace(g,'self.'+g)
var = var.lower()
group = group.lower()
strdims = tuple(map(lambda x: '('+str(x)+')',dims))
strdims = str(strdims).replace("'","")
if len(dims) == 1:
strdims = strdims[:-2]+")"
dim_max = strdims[1:-1].replace(',','*')
type_set = type
if type.lower().startswith('character'):
type_set = 'character*(*)'
d = { 'type_short': f2ocaml[t_short(type)],
'type': type,
'type_set': type_set,
'var': var,
'group': group,
'dims': strdims}
if dims == ():
tail += ['let get_%(group)s_%(var)s () = read_%(type_short)s "%(group)s" "%(var)s";;' %(d),
'let set_%(group)s_%(var)s = write_%(type_short)s "%(group)s" "%(var)s" ;;' %(d) ,
'let has_%(group)s_%(var)s () = has "%(group)s" "%(var)s" ;;' %(d) ]
else:
tail += ['let get_%(group)s_%(var)s () = read_%(type_short)s_array "%(group)s" "%(var)s";;' %(d),
'let set_%(group)s_%(var)s = write_%(type_short)s_array "%(group)s" "%(var)s";;' %(d) ,
'let has_%(group)s_%(var)s () = has_array "%(group)s" "%(var)s" ;;' %(d) ]
file = open('ezfio.ml','r')
template = file.read()
file.close()
template = template.replace("(*$HEAD*)",'\n'.join(head))
template = template.replace("(*$TAIL*)",'\n'.join(tail))
file = open('../Ocaml/ezfio.ml','w')
file.write(template)
file.close()

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# 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
import os, sys
import time
import cStringIO as StringIO
from gzip import GzipFile
import tempfile
import threading
def version(x):
b = [int(i) for i in x.split('.')]
return b[2] + b[1]*100 + b[0]*10000
def size(x):
return len(x)
def flatten(l):
res = []
for i in l:
if hasattr(i, "__iter__") and not isinstance(i, basestring):
res.extend(flatten(i))
else:
res.append(i)
return res
def maxval(l):
return reduce(max, l, l[0])
def minval(l):
return reduce(min, l, l[0])
def reshape(l,shape):
l = flatten(l)
for d in shape[:-1]:
buffer = []
buffer2 = []
i=0
while i<len(l):
buffer2.append(l[i])
if len(buffer2) == d:
buffer.append(buffer2)
buffer2 = []
i+=1
l = list(buffer)
return l
def at(array,index):
return array[index-1]
def n_count_ch(array,isize,val):
result = 0
for i in array:
if i == val:
result +=1
return result
n_count_in = n_count_ch
n_count_do = n_count_ch
n_count_lo = n_count_ch
def get_conv(type):
if type in ["do","re"]:
conv = float
elif type in ["in","i8"]:
conv = int
elif type == "lo":
def conv(a):
if a == True:
return 'T'
elif a == False:
return 'F'
elif a.lower() == 't':
return True
elif a.lower() == 'f':
return False
else:
raise TypeError
elif type == "ch":
conv = lambda x: x.strip()
else:
raise TypeError
return conv
class ezfio_obj(object):
def __init__(self,read_only=False):
self._filename = "EZFIO_File"
self.buffer_rank = -1
self.read_only = read_only
self.locks = {}
def acquire_lock(self,var):
locks = self.locks
try:
locks[var].acquire()
except:
locks[var] = threading.Lock()
locks[var].acquire()
def release_lock(self,var):
self.locks[var].release()
def set_read_only(self,v):
self.read_only = v
def get_read_only(self):
return self.read_only
def exists(self,path):
if os.access(path+'/.version',os.F_OK) == 1:
file = open(path+'/.version',"r")
v = file.readline().strip()
file.close()
else:
return False
def mkdir(self,path):
if self.read_only:
self.error('Read-only file.')
if self.exists(path):
self.error('mkdir','Group '+path+' exists')
try:
os.mkdir(path.strip())
except OSError:
pass
file = open(path.strip()+'/.version','w')
print >>file,self.version
file.close()
def error(self,where,txt):
print '------------------------------------------------------------'
print 'EZFIO File : '+self.filename
print 'EZFIO Error in : '+where.strip()
print '------------------------------------------------------------'
print ''
print txt.strip()
print ''
print '------------------------------------------------------------'
raise IOError
def get_filename(self):
if not self.exists(self._filename):
self.mkdir(self._filename)
return self._filename
def set_filename(self,filename):
self._filename = filename
filename = property(fset=set_filename,fget=get_filename)
def set_file(self,filename):
self.filename = filename
if not self.exists(filename):
self.mkdir(filename)
self.mkdir(filename+"/ezfio")
os.system("""
LANG= date > %s/ezfio/creation
echo $USER > %s/ezfio/user
echo %s > %s/ezfio/library"""%(filename,filename,self.LIBRARY,filename))
def open_write_buffer(self,dir,fil,rank):
if self.read_only:
self.error('Read-only file.')
l_filename=dir.strip()+'/'+fil+'.gz'
if self.buffer_rank != -1:
self.error('open_write_buffer','Another buffered file is already open.')
self.buffer_rank = rank
assert (self.buffer_rank > 0)
try:
self.file = GzipFile(filename=l_filename,mode='wb7')
except IOError:
self.error('open_write_buffer','Unable to open buffered file.')
self.file.write("%2d\n"%(rank,))
def open_read_buffer(self,dir,fil,rank):
l_filename=dir.strip()+'/'+fil+'.gz'
if self.buffer_rank != -1:
self.error('open_read_buffer','Another buffered file is already open.')
try:
self.file = GzipFile(filename=l_filename,mode='rb')
except IOError:
self.error('open_read_buffer','Unable to open buffered file.')
try:
rank = eval(self.file.readline())
except IOError:
self.error('open_read_buffer','Unable to read buffered file.')
self.buffer_rank = rank
assert (self.buffer_rank > 0)
return rank
def close_buffer(self):
assert (self.buffer_rank > 0)
self.buffer_rank = -1
self.file.close()
def read_buffer(self,isize):
if self.buffer_rank == -1:
self.error('read_buffer','No buffered file is open.')
indices = []
values = []
for i in xrange(isize):
try:
line = self.file.readline().split()
except:
return indices, values
if len(line) == 0:
return indices, values
indices.append ( [ int(i) for i in line[:-1] ] )
values.append (eval(line[-1]))
return indices, values
def write_buffer(self,indices,values,isize):
if self.read_only:
self.error('Read-only file.')
if self.buffer_rank == -1:
self.error('write_buffer','No buffered file is open.')
for i in xrange(isize):
for j in indices[i]:
self.file.write("%4d "%(j,))
self.file.write("%24.15e\n"%(values[i],))

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# 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
ezfio = ezfio_obj()

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(*
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
*)
(*$HEAD*)
(*
Exceptions
==========
*)
exception Read_only of string;;
(*
State variables
===============
*)
let read_only = ref false;;
let ezfio_filename = ref "EZFIO_File";;
(*
Helper functions
=================
*)
let check_readonly =
if !read_only then
raise (Read_only "Read only attribute is set");
;;
let exists path =
let filename = path^"/.version" in
Sys.file_exists filename
;;
let has group name =
let dirname = !ezfio_filename ^ "/" ^ group in
if (exists dirname) then
(Sys.file_exists (dirname ^ "/" ^ name) )
else
false
;;
let has_array group name = has group (name^".gz");;
let mkdir path =
check_readonly;
if (exists path) then
raise (Failure (path^" already exists"));
Unix.mkdir path 0o777;
let out_channel = open_out (path^"/.version") in
Printf.fprintf out_channel "%s\n" version ;
close_out out_channel;
;;
let create_group group =
let dirname = !ezfio_filename ^ "/" ^ group in
if not (exists dirname) then
mkdir dirname;
;;
let split line s =
let rec do_work lst word = function
| 0 -> word::lst
| i ->
begin
match line.[i-1] with
| a when a == s ->
if word <> "" then
do_work (word::lst) "" (i-1)
else
do_work lst "" (i-1)
| a -> do_work lst ( (Char.escaped a)^word) (i-1)
end
in do_work [] "" (String.length line)
;;
let ltrim s =
let rec do_work s l =
match s.[0] with
| '\n'
| ' ' -> do_work (String.sub s 1 (l-1)) (l-1)
| _ -> s
in
do_work s (String.length s)
;;
let rtrim s =
let rec do_work s l =
let newl = l-1 in
match s.[newl] with
| '\n'
| ' ' -> do_work (String.sub s 0 (newl)) (newl)
| _ -> s
in
do_work s (String.length s)
;;
let trim s = ltrim (rtrim s) ;;
let maxval l =
match l with
| [] -> None
| [a] -> Some a
| hd::tail -> Some (List.fold_left max hd tail)
;;
let minval l =
match l with
| [] -> None
| [a] -> Some a
| hd::tail -> Some (List.fold_left min hd tail)
;;
let at arr idx = arr.(idx);;
let size (_) = 0;;
let n_count_ch (str,_,v) =
let rec do_work accu = function
| 0 -> accu
| i ->
let newaccu =
if str.[i-1] == v then accu+1
else accu
in do_work newaccu (i-1)
in do_work 0 (String.length str)
;;
let n_count (l,_,v) =
let rec do_work accu = function
| [] -> accu
| h::tail ->
let newaccu =
if h == v then accu+1
else accu
in do_work newaccu tail
in do_work 0 l
;;
(*
Scalars
=======
*)
(*
Read
----
*)
let read_scalar type_conversion group name =
let in_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name in
let in_channel = open_in in_filename in
let trimmed_line = trim (input_line in_channel) in
let result = type_conversion trimmed_line in
begin
close_in in_channel ;
result
end
;;
let fortran_bool_of_string = function
| "T" | "t" -> true
| "F" | "f" -> false
| x -> raise (Failure ("fortran_bool_of_string should be T or F: "^x))
;;
let fortran_string_of_bool = function
| true -> "T\n"
| false-> "F\n"
;;
let read_int = read_scalar int_of_string ;;
let read_float = read_scalar float_of_string ;;
let read_string= read_scalar (fun (x:string) -> x);;
let read_bool = read_scalar fortran_bool_of_string;;
(*
Write
-----
*)
let print_int out_channel i = Printf.fprintf out_channel "%16d\n" i
and print_float out_channel f = Printf.fprintf out_channel "%24.15e\n" f
and print_string out_channel s = Printf.fprintf out_channel "%s\n" s
and print_bool out_channel b = Printf.fprintf out_channel "%s\n" (fortran_string_of_bool b);;
let write_scalar print_fun group name s =
check_readonly;
create_group group;
let out_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name in
let out_channel = open_out out_filename in
begin
print_fun out_channel s;
close_out out_channel;
end
;;
let write_int = write_scalar print_int
and write_float = write_scalar print_float
and write_bool = write_scalar print_bool
and write_string = write_scalar print_string
;;
(*
Arrays
======
*)
type 'a ezfio_data =
| Ezfio_item of 'a array
| Ezfio_data of ('a ezfio_data) array
;;
type 'a ezfio_array =
{ rank : int ;
dim : int array;
data : 'a ezfio_data ;
}
;;
let ezfio_get_element { rank=r ; dim=d ; data=data } coord =
(*assert ((List.length coord) == r);*)
let rec do_work buffer = function
| [c] ->
begin match buffer with
| Ezfio_item buffer -> buffer.(c)
| Ezfio_data buffer -> raise (Failure "Error in ezfio_get_element")
end
| c::tail ->
begin match buffer with
| Ezfio_item buffer -> raise (Failure "Error in ezfio_get_element")
| Ezfio_data buffer -> do_work buffer.(c) tail
end
| [] -> raise (Failure "Error in ezfio_get_element")
in
do_work data coord
;;
let flattened_ezfio_data d =
match d with
| Ezfio_item d -> d
| Ezfio_data d ->
let d = Array.to_list d in
let rec do_work accu = function
| [] -> accu
| (Ezfio_item x)::tail -> do_work (Array.append accu x) tail
| (Ezfio_data x)::tail ->
let newaccu = do_work accu (Array.to_list x )
in do_work newaccu tail
in
do_work (Array.of_list []) d
;;
(*
Read
----
*)
let unzipped_filename filename =
if not (Sys.file_exists filename) then
raise (Failure ("file "^filename^" doesn't exist"));
let uz_filename = Filename.temp_file "" ".tmp" ~temp_dir:(Sys.getcwd ()) in
let command = "zcat "^filename^" > "^uz_filename
in
if (Sys.command command) == 0 then
uz_filename
else
begin
Sys.remove uz_filename ;
raise (Failure ("Unable to execute :\n"^command))
end
;;
let read_rank in_channel =
let trimmed_line = trim (input_line in_channel) in
int_of_string trimmed_line
;;
let read_dimensions in_channel =
let trimmed_line = trim (input_line in_channel) in
let list_of_str = split trimmed_line ' ' in
Array.of_list (List.map int_of_string list_of_str)
;;
let read_array type_conversion group name : 'a ezfio_array =
let in_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name ^ ".gz" in
let uz_filename = unzipped_filename in_filename in
let in_channel = open_in uz_filename in
(* Read rank *)
let rank = read_rank in_channel
(* Read dimensions *)
and dimensions = read_dimensions in_channel
in
begin
assert (rank == Array.length dimensions) ;
(* Read one-dimensional arrays *)
let read_1d nmax =
let rec do_work accu = function
| 0 -> Array.of_list (List.rev accu)
| n ->
let trimmed_line = trim (input_line in_channel) in
do_work ( (type_conversion trimmed_line)::accu ) (n-1)
in
Ezfio_item (do_work [] nmax)
in
(* Read multi-dimensional arrays *)
let rec read_nd = function
| m when m<1 -> raise (Failure "dimension should not be <1")
| 1 -> read_1d dimensions.(0)
| m ->
let rec do_work accu = function
| 0 -> Array.of_list (List.rev accu)
| n ->
let newlist = read_nd (m-1) in
do_work (newlist::accu) (n-1)
in
Ezfio_data (do_work [] dimensions.(m-1))
in
let result = {
rank = rank ;
dim = dimensions ;
data = read_nd rank ;
}
in
close_in in_channel ;
Sys.remove uz_filename ;
result;
end
;;
let read_int_array = read_array int_of_string
and read_float_array = read_array float_of_string
and read_bool_array = read_array fortran_bool_of_string
and read_string_array = read_array (fun (x:string) -> x)
;;
(*
Write
-----
*)
let write_array print_fun group name a =
check_readonly;
create_group group;
let out_filename = !ezfio_filename ^ "/" ^ group ^ "/" ^ name ^".gz" in
let uz_filename = Filename.temp_file "" ".tmp" ~temp_dir:(Sys.getcwd ()) in
let out_channel = open_out uz_filename in
let { rank=rank ; dim=dimensions ; data=data } = a in
let data = flattened_ezfio_data data
in
begin
(* Write rank *)
Printf.fprintf out_channel "%4d\n" rank;
(* Write dimensions *)
Array.iter (Printf.fprintf out_channel " %8d") dimensions;
Printf.fprintf out_channel "\n";
Array.iter (print_fun out_channel) data;
close_out out_channel ;
let command = "gzip -c < "^uz_filename^" > "^out_filename
in
if (Sys.command command == 0) then (Sys.remove uz_filename )
else raise (Failure ("command failed:\n"^command))
end
;;
let write_int_array = write_array print_int
and write_float_array = write_array print_float
and write_string_array = write_array print_string
and write_bool_array = write_array print_bool;;
(*
Library routines
*)
let set_file filename =
if not (exists filename) then
begin
mkdir filename;
mkdir (filename^"/ezfio");
let command = Printf.sprintf "
LANG= date > %s/ezfio/creation
echo $USER > %s/ezfio/user
echo %s > %s/ezfio/library" filename filename library filename
in
if (Sys.command command <> 0) then
raise (Failure ("Unable to create new ezfio file:\n"^filename))
end ;
ezfio_filename := filename
;;
(*$TAIL*)

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# 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
format= {
'integer*8' : ["'(I20)'", "%20d"],
'integer' : ["'(I20)'", "%20d"],
'real' : ["'(E24.15)'","%24.15E"],
'double precision': ["'(E24.15)'","%24.15E"],
'logical' : ["'(L)'","%c"],
'character*(*)' : ["'(A)'","%s"]
}
def t_short(x):
x = x.lower()
if x == 'integer*8':
return 'i8'
elif x == 'integer':
return 'in'
elif x == 'real':
return 're'
elif x.startswith('double'):
return 'do'
elif x == 'logical':
return 'lo'
elif x.startswith('character'):
return 'ch'
f2c = {
'in' : 'int',
're' : 'float',
'i8' : 'long int',
'do' : 'double',
'ch' : 'char',
'lo' : 'int'
}
f2ocaml = {
'in' : 'int',
're' : 'float',
'i8' : 'int',
'do' : 'float',
'ch' : 'string',
'lo' : 'bool'
}

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#!/usr/bin/python
# 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
import re
from read_config import groups
from groups_templates import *
from f_types import t_short, f2c
file_py = open("libezfio_groups-gen.py","w")
file = open("../version","r")
v = file.readline()
file.close()
v = v.split('=')[1].strip()
print >>file_py, """
def get_version(self):
return '%s'
version = property(fset=None,fget=get_version)
"""%(v)
import sys
for group in groups.keys():
print path%{ 'group' : group }
print >>file_py, path_py%{ 'group' : group }
for var,type,dims,command in groups[group]:
command_py = command
dims_py = str(dims)
for g in groups.keys():
command_py = command_py.replace(g,'self.'+g)
dims_py = dims_py.replace(g,'self.'+g)
var = var.lower()
group = group.lower()
strdims = tuple(map(lambda x: '('+str(x)+')',dims))
strdims = str(strdims).replace("'","")
if len(dims) == 1:
strdims = strdims[:-2]+")"
dim_max = strdims[1:-1].replace(',','*')
type_set = type
cstring = ""
cstring2 = ""
if type.lower().startswith('character'):
type_set = 'character*(*)'
cstring = ',long size_'+var+'_string'
cstring2 = ',strlen(size_'+var+'_string)'
if dims == ():
if command == "":
d = { 'type_short': t_short(type),
'type': type,
'ctype': f2c[t_short(type)],
'cstring': cstring,
'cstring2': cstring2,
'type_set': type_set,
'var': var,
'group': group,
'dims': strdims}
print attributes%d
print >>file_py, attributes_py%d
else:
d = { 'type': type,
'var': var,
'ctype': f2c[t_short(type)]+"*",
'cstring': cstring,
'group': group,
'expr': command,
'expr_py': command_py}
buffer = calculated%d
buffer = re.sub(r"at\((.*),(.*)\)",r'\1(\2)',buffer)
print buffer
print >>file_py, calculated_py%d
elif type == "buffered":
d = { 'group': group,
'var': var,
'dims_py': dims_py,
'dims': dims }
print buffered%d
print >>file_py, buffered_py%d
else:
dims_loop = ''
copy_loop = ''
dims_loop_py = ''
declar_loop = ' integer :: '
for k,d in enumerate(dims):
declar_loop += "i"+str(k+1)+","
declar_loop = declar_loop[:-1]
for k,d in enumerate(dims):
dims_loop += " dims("+str(k+1)+") = "+str(d)+"\n"
dims_loop_py += " dims["+str(k)+"] = "+str(d)+"\n"
for k,d in enumerate(dims):
copy_loop += k*" "+" do i"+str(k+1)+"=1,"+str(d)+'\n'
copy_loop += (k+1)*" "+" %(var)s ("
for k,d in enumerate(dims):
copy_loop += "i"+str(k+1)+","
copy_loop = copy_loop[:-1] + ") = %(group)s_%(var)s ("
for k,d in enumerate(dims):
copy_loop += "i"+str(k+1)+","
copy_loop = copy_loop[:-1]%{'var': var,'group': group} + ")\n"
for k,d in enumerate(dims):
copy_loop += (len(dims)-k-1)*" "+" enddo\n"
for g in groups.keys():
dims_loop_py = dims_loop_py.replace(" "+g,' self.'+g)
dims_loop_py = dims_loop_py.replace("*"+g,'*self.'+g)
dims_loop_py = dims_loop_py.replace("/"+g,'/self.'+g)
dims_loop_py = dims_loop_py.replace("+"+g,'+self.'+g)
dims_loop_py = dims_loop_py.replace("-"+g,'-self.'+g)
dims_loop_py = dims_loop_py.replace("("+g,'(self.'+g)
d = { 'type_short': t_short(type),
'type': type,
'type_set': type_set,
'var': var,
'ctype': f2c[t_short(type)]+"*",
'cstring': cstring,
'group': group,
'rank' : str(len(dims)),
'dims': strdims,
'dim_max': str(dim_max),
'dims_loop': dims_loop,
'dims_loop_py': dims_loop_py,
'copy_loop': copy_loop,
'declar_loop' : declar_loop}
print attributes_arr%d
print >>file_py, attributes_arr_py%d
file_py.close()
import create_ocaml
create_ocaml.run()

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#!/usr/bin/python
# 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
#--------
# Fortran
#--------
path = """
BEGIN_PROVIDER [ character*(128), path_%(group)s ]
BEGIN_DOC
! Path to the %(group)s group
END_DOC
logical :: ezfio_exists
path_%(group)s = trim(libezfio_filename)//'/%(group)s'
if (.not.ezfio_exists(path_%(group)s)) then
if (.not.libezfio_read_only) then
call ezfio_mkdir(path_%(group)s)
endif
endif
END_PROVIDER
"""
attributes = """
BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
BEGIN_DOC
! %(var)s attribute of group %(group)s
END_DOC
call ezfio_read_%(type_short)s(path_%(group)s,'%(var)s',%(group)s_%(var)s)
END_PROVIDER
subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
%(type_set)s :: %(var)s
call ezfio_write_%(type_short)s(path_%(group)s,'%(var)s',%(var)s)
FREE %(group)s_%(var)s
end subroutine
subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
%(type)s :: %(var)s
%(var)s = %(group)s_%(var)s
end subroutine
subroutine ezfio_has_%(group)s_%(var)s(result)
logical :: result
inquire(file=trim(path_%(group)s)//'/%(var)s',exist=result)
end subroutine
subroutine ezfio_free_%(group)s_%(var)s()
FREE %(group)s_%(var)s
end
"""
attributes_arr = """
BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s, %(dims)s ]
BEGIN_DOC
! %(var)s attribute of group %(group)s
END_DOC
integer :: rank, dim_max, i
integer :: dims(10)
rank = %(rank)s
%(dims_loop)s
dim_max = %(dim_max)s
call ezfio_read_array_%(type_short)s(path_%(group)s,'%(var)s', &
rank,dims,dim_max,%(group)s_%(var)s)
END_PROVIDER
subroutine ezfio_set_%(group)s_%(var)s(%(var)s)
%(type_set)s :: %(var)s (*)
integer :: rank, dim_max, i
integer :: dims(10)
rank = %(rank)s
character*(1024) :: message
%(dims_loop)s
call ezfio_write_array_%(type_short)s(path_%(group)s,'%(var)s', &
rank,dims,%(dim_max)s,%(var)s)
FREE %(group)s_%(var)s
end subroutine
subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
%(type)s, intent(out) :: %(var)s (*)
character*(1024) :: message
%(var)s(1: %(dim_max)s ) = reshape ( %(group)s_%(var)s, (/ %(dim_max)s /) )
end subroutine
subroutine ezfio_has_%(group)s_%(var)s(result)
logical :: result
inquire(file=trim(path_%(group)s)//'/%(var)s.gz',exist=result)
end subroutine
subroutine ezfio_free_%(group)s_%(var)s()
FREE %(group)s_%(var)s
end
"""
calculated="""
BEGIN_PROVIDER [ %(type)s, %(group)s_%(var)s ]
BEGIN_DOC
! Calculated as %(expr)s
END_DOC
%(group)s_%(var)s = %(expr)s
END_PROVIDER
subroutine ezfio_get_%(group)s_%(var)s(%(var)s)
%(type)s, intent(out) :: %(var)s
%(var)s = %(group)s_%(var)s
end
subroutine ezfio_free_%(group)s_%(var)s()
FREE %(group)s_%(var)s
end
"""
buffered="""
subroutine ezfio_open_read_%(group)s_%(var)s()
call ezfio_open_read_buffer(path_%(group)s,'%(var)s',%(dims)s)
end
subroutine ezfio_open_write_%(group)s_%(var)s()
call ezfio_open_write_buffer(path_%(group)s,'%(var)s',%(dims)s)
end
subroutine ezfio_close_read_%(group)s_%(var)s()
call ezfio_close_read_buffer(path_%(group)s,'%(var)s')
end
subroutine ezfio_close_write_%(group)s_%(var)s()
call ezfio_close_write_buffer(path_%(group)s,'%(var)s')
end
subroutine ezfio_has_%(group)s_%(var)s(result)
logical :: result
inquire(file=trim(path_%(group)s)//'/%(var)s.gz',exist=result)
end subroutine
subroutine ezfio_free_%(group)s_%(var)s()
FREE %(group)s_%(var)s
end
"""
#---------
# C
#---------
attributes_c = """
void ezfio_set_%(group)s_%(var)s(%(type)s %(var)s)
{
ezfio_set_%(group)s_%(var)s_(&%(var)s);
}
"""
c_header = """
#ifndef EZFIO_H
#define EZFIO_H
#ifdef __cplusplus
extern "C" {
#endif
"""
c_footer = """
#ifdef __cplusplus
}
#endif
#endif
"""
file_h = [c_header]
file_h +=[ """
void ezfio_set_file_(char* filename, long filename_size);
void ezfio_read_buffer_(int* indices,double* values, int* isize);
void ezfio_write_buffer_(int* indices,double* values, int* isize);
"""]
file_c = [ """
typedef struct
{
int* indices;
double* values;
} sparse;
void ezfio_set_file(char* filename)
{
long len;
len = strlen(filename);
ezfio_set_file_(filename,mlen);
}
sparse ezfio_read_buffer(int isize)
{
sparse result;
ezfio_read_buffer_(result.indices,result.values,&isize);
return result;
}
void ezfio_write_buffer(sparse data, int isize)
{
ezfio_write_buffer_(data.indices,data.values,&isize);
}
""" ]
#--------
# Python
#--------
path_py = """
def get_path_%(group)s(self):
result = self.filename.strip()+'/%(group)s'
self.acquire_lock('%(group)s')
try:
if not self.exists(result):
self.mkdir(result)
finally:
self.release_lock('%(group)s')
return result
path_%(group)s = property(fget=get_path_%(group)s)
"""
attributes_py = """
def get_%(group)s_%(var)s(self):
self.acquire_lock('%(group)s_%(var)s')
try:
result = self.read_%(type_short)s(self.path_%(group)s,'%(var)s')
finally:
self.release_lock('%(group)s_%(var)s')
return result
def set_%(group)s_%(var)s(self,%(var)s):
self.acquire_lock('%(group)s_%(var)s')
try:
self.write_%(type_short)s(self.path_%(group)s,'%(var)s',%(var)s)
finally:
self.release_lock('%(group)s_%(var)s')
%(group)s_%(var)s = property(fset=set_%(group)s_%(var)s, \
fget=get_%(group)s_%(var)s)
def has_%(group)s_%(var)s(self):
return (os.access(self.path_%(group)s+'/%(var)s',os.F_OK) == 1)
"""
attributes_arr_py = """
def get_%(group)s_%(var)s(self):
rank = %(rank)s
dims = range(rank)
%(dims_loop_py)s
dim_max = 1
for d in dims:
dim_max *= d
self.acquire_lock('%(group)s_%(var)s')
try:
result = self.read_array_%(type_short)s(self.path_%(group)s,'%(var)s', rank,dims,dim_max)
finally:
self.release_lock('%(group)s_%(var)s')
return result
def set_%(group)s_%(var)s(self,%(var)s):
rank = %(rank)s
dims = range(rank)
%(dims_loop_py)s
dim_max = 1
for d in dims:
dim_max *= d
self.acquire_lock('%(group)s_%(var)s')
try:
self.write_array_%(type_short)s(self.path_%(group)s,'%(var)s', rank,dims,dim_max,%(var)s)
finally:
self.release_lock('%(group)s_%(var)s')
%(group)s_%(var)s = property(fset=set_%(group)s_%(var)s,fget=get_%(group)s_%(var)s)
def has_%(group)s_%(var)s(self):
return (os.access(self.path_%(group)s+'/%(var)s.gz',os.F_OK) == 1)
"""
calculated_py="""
def get_%(group)s_%(var)s(self):
return %(expr_py)s
%(group)s_%(var)s = property(fget=get_%(group)s_%(var)s)
"""
buffered_py="""
def open_read_%(group)s_%(var)s(self):
self.open_read_buffer(self.path_%(group)s,'%(var)s',%(dims_py)s)
def open_write_%(group)s_%(var)s(self):
self.open_write_buffer(self.path_%(group)s,'%(var)s',%(dims_py)s)
def close_read_%(group)s_%(var)s(self):
self.close_buffer()
def close_write_%(group)s_%(var)s(self):
self.close_buffer()
def has_%(group)s_%(var)s(self):
return (os.access(self.path_%(group)s+'/%(var)s.gz',os.F_OK) == 1)
"""

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! 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
subroutine ezfio_error(where,txt)
implicit none
character*(*) :: where
character*(*) :: txt
character*(128) :: fname
fname = libezfio_filename
print *, '------------------------------------------------------------'
print *, 'EZFIO File : '//trim(fname)
print *, 'EZFIO Error in : '//trim(where)
print *, '------------------------------------------------------------'
print *, ''
print *, trim(txt)
print *, ''
print *, '------------------------------------------------------------'
stop
end subroutine

162
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! 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
BEGIN_PROVIDER [ logical, libezfio_read_only ]
BEGIN_DOC
! If true, the EZFIO file is read-only
END_DOC
libezfio_read_only = .False.
END_PROVIDER
subroutine ezfio_set_read_only(v)
logical :: v
libezfio_read_only = v
TOUCH libezfio_read_only
end subroutine ezfio_set_read_only
subroutine ezfio_is_read_only(v)
logical :: v
v = libezfio_read_only
end subroutine ezfio_is_read_only
integer function char_to_version(v)
implicit none
character*(32), intent(in) :: v
character*(32) :: vnew
integer :: i, j, k
vnew=v
do i=1,32
if (vnew(i:i) == '.') then
vnew(i:i) = ' '
endif
enddo
read(vnew,*) i,j,k
char_to_version = j*1000 + i*1000000
end
BEGIN_PROVIDER [ character*(32), libezfio_version ]
implicit none
BEGIN_DOC
! Version of the library
END_DOC
BEGIN_SHELL [/bin/sh]
echo libezfio_version = \"`cat ../version | cut -d '=' -f 2` \"
END_SHELL
END_PROVIDER
BEGIN_PROVIDER [ character*(128), libezfio_filename ]
implicit none
BEGIN_DOC
! Name of the EZFIO filesystem
END_DOC
libezfio_filename = 'EZFIO_File'
END_PROVIDER
subroutine ezfio_get_filename(fname)
implicit none
character*(*) :: fname
fname = libezfio_filename
end subroutine
BEGIN_PROVIDER [ integer, libezfio_iunit ]
implicit none
BEGIN_DOC
! Unit number for I/O access
END_DOC
logical :: is_open
is_open = .True.
libezfio_iunit = 99
do while (is_open)
inquire(unit=libezfio_iunit,opened=is_open)
if (is_open) then
libezfio_iunit = libezfio_iunit-1
endif
if (libezfio_iunit == 9) then
call ezfio_error(irp_here,'No more free file units!')
endif
enddo
if ( (libezfio_iunit < 10).or.(libezfio_iunit > 99) ) then
call ezfio_error(irp_here,'No more free units for files.')
endif
END_PROVIDER
logical function exists(path)
implicit none
character*(*) :: path
character*(32) :: V
inquire(file=trim(path)//'/.version',exist=exists)
if (exists) then
open(libezfio_iunit,file=trim(path)//'/.version')
read(libezfio_iunit,*) V
close(libezfio_iunit)
! integer :: char_to_version
! if (char_to_version(V) > char_to_version(libezfio_version)) then
! call ezfio_error(irp_here, 'This file was generated with version '//trim(V)//&
! ' but the current installed version is '//trim(libezfio_version)//'')
! endif
endif
end function
subroutine ezfio_set_file(filename_in)
implicit none
character*(*) :: filename_in
if (filename_in == '') then
call ezfio_error(irp_here,'EZFIO file name is empty.')
endif
libezfio_filename = filename_in
logical :: exists
if (.not.exists(libezfio_filename)) then
call ezfio_mkdir(libezfio_filename)
call ezfio_mkdir(trim(libezfio_filename)//'/ezfio')
call system('LANG= date > '//trim(libezfio_filename)//'/ezfio/creation')
call system('echo $USER > '//trim(libezfio_filename)//'/ezfio/user')
BEGIN_SHELL [ /usr/bin/python ]
import os
command = "'echo %s > '//trim(libezfio_filename)//'/ezfio/library'"
cwd = os.getcwd()
cwd = cwd.split('src')[:-1]
cwd = '/'.join(cwd)
print "call system("+command%cwd+")"
END_SHELL
endif
TOUCH libezfio_filename
end subroutine
subroutine ezfio_finish()
implicit none
close(libezfio_iunit)
BEGIN_SHELL [ /usr/bin/python ]
import os
from zlib import crc32
print ' call irp_finalize_%s'%(str(abs(crc32(os.getcwd()))))
END_SHELL
end

28
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! 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
BEGIN_SHELL [ /usr/bin/python ]
import groups
END_SHELL

473
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! 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
BEGIN_PROVIDER [ integer, PID ]
&BEGIN_PROVIDER [ character*(8), PID_str ]
implicit none
BEGIN_DOC
! Current process ID
END_DOC
integer :: getpid
PID = getpid()
write(PID_str,'(I8.8)') PID
END_PROVIDER
logical function ezfio_exists(path)
implicit none
character*(*) :: path
inquire(file=trim(path)//'/.version',exist=ezfio_exists)
if (ezfio_exists) then
open(unit=libezfio_iunit,file=trim(path)//'/.version')
character*(32) :: V
read(libezfio_iunit,*) V
close(libezfio_iunit)
! integer :: char_to_version
! if (char_to_version(V) > char_to_version(libezfio_version)) then
! call ezfio_error(irp_here, "This file was generated with version "//trim(V)//&
! " but the current installed version is "//trim(libezfio_version)//".")
! endif
endif
end function
subroutine ezfio_mkdir(path)
implicit none
character*(*) :: path
logical :: ezfio_exists
if (libezfio_read_only) then
call ezfio_error(irp_here,'Read-only file.')
endif
if (.not.ezfio_exists(path)) then
call system('mkdir '//trim(path))
open(unit=libezfio_iunit,file=trim(path)//'/.version')
write(libezfio_iunit,'(A)') libezfio_version
close(libezfio_iunit)
endif
end subroutine
subroutine libezfio_openz(filename,mode,err)
implicit none
character*(*) :: filename, mode
character*(1024) :: fifo
integer :: err
fifo = trim(filename)//'.'//PID_str
err=1
if (mode(1:1) == 'r') then
call system('zcat '//trim(filename)//' > '//trim(fifo))
open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='READ')
err=0
else if (mode(1:1) == 'w') then
open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='WRITE')
err=0
else
call ezfio_error(irp_here,'Mode '//trim(mode)//' is not implemented.')
endif
end
subroutine libezfio_closez(filename,mode)
implicit none
character*(*) :: filename, mode
character*(1024) :: fifo
fifo = trim(filename)//'.'//PID_str
if (mode(1:1) == 'w') then
close(unit=libezfio_iunit)
call system('gzip -c < '//trim(fifo)//' > '//trim(filename))
open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='WRITE')
endif
close(unit=libezfio_iunit,status='DELETE')
end
BEGIN_SHELL [ /usr/bin/python ]
from f_types import format, t_short
template = """
subroutine ezfio_read_%(type_short)s(dir,fil,dat)
implicit none
character*(*), intent(in) :: dir, fil
%(type)s, intent(out) :: dat
character*(1024) :: l_filename
l_filename=trim(dir)//'/'//fil
open(unit=libezfio_iunit,file=l_filename,form='FORMATTED', &
action='READ',err=9)
read(libezfio_iunit,%(fmt)s,end=9,err=9) dat
close(libezfio_iunit)
return
9 continue
call ezfio_error(irp_here,'Attribute '//trim(dir)//'/'//trim(fil)//' is not set')
end
subroutine ezfio_write_%(type_short)s(dir,fil,dat)
implicit none
character*(*), intent(in) :: dir, fil
%(type)s, intent(in) :: dat
character*(1024) :: l_filename(2)
if (libezfio_read_only) then
call ezfio_error(irp_here,'Read-only file.')
endif
l_filename(1)=trim(dir)//'/.'//fil//'.'//PID_str
l_filename(2)=trim(dir)//'/'//fil
open(unit=libezfio_iunit,file=l_filename(1),form='FORMATTED',action='WRITE')
write(libezfio_iunit,%(fmt)s) dat
close(libezfio_iunit)
call system( 'mv -f '//trim(l_filename(1))//' '//trim(l_filename(2)) )
end
subroutine ezfio_read_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
implicit none
character*(*), intent(in) :: dir, fil
integer :: rank
integer :: dims(rank)
integer :: dim_max
%(type)s :: dat(dim_max)
integer :: err
character*(1024) :: l_filename
l_filename=trim(dir)//'/'//fil//'.gz'
err = 0
call libezfio_openz(trim(l_filename),'rb',err)
if (err == 0) then
integer :: rank_read
integer :: dims_read(rank), i
read(libezfio_iunit,'(I3)') rank_read
if (rank_read /= rank) then
call ezfio_error(irp_here,'Rank of data '//trim(l_filename)//&
' different from array.')
endif
if (err /= 0) then
call ezfio_error(irp_here,'Error reading data in '//trim(l_filename)//&
'.')
endif
read(libezfio_iunit,'(30(I20,X))') dims_read(1:rank)
do i=1,rank
if (dims_read(i) /= dims(i)) then
call ezfio_error(irp_here,'Dimensions of data '//trim(l_filename)//&
' different from array.')
endif
enddo
do i=1,dim_max
if (err /= 0) then
call ezfio_error(irp_here,'Error reading data in '//trim(l_filename)//&
'.')
endif
read(libezfio_iunit,%(fmt)s) dat(i)
enddo
call libezfio_closez(trim(l_filename),'r')
return
else
call ezfio_error(irp_here,'Attribute '//trim(l_filename)//' is not set')
endif
end
subroutine ezfio_write_array_%(type_short)s(dir,fil,rank,dims,dim_max,dat)
implicit none
character*(*), intent(in) :: dir, fil
integer, intent(in) :: rank
integer, intent(in) :: dims(rank)
integer, intent(in) :: dim_max
%(type)s, intent(in) :: dat(dim_max)
integer :: err
character*(1024) :: l_filename(2)
if (libezfio_read_only) then
call ezfio_error(irp_here,'Read-only file.')
endif
l_filename(1)=trim(dir)//'/.'//fil//PID_str//'.gz'
l_filename(2)=trim(dir)//'/'//fil//'.gz'
err = 0
call libezfio_openz(trim(l_filename(1)),'wb',err)
if (err == 0) then
write(libezfio_iunit,'(I3)') rank
write(libezfio_iunit,'(30(I20,X))') dims(1:rank)
integer :: i
do i=1,dim_max
write(libezfio_iunit,%(fmt)s) dat(i)
enddo
call libezfio_closez(trim(l_filename(1)),'w')
endif
call system( 'mv -f '//trim(l_filename(1))//' '//trim(l_filename(2)) )
end
"""
template_no_logical = """
integer function n_count_%(type_short)s(array,isize,val)
%(type)s, intent(in) :: array(*)
integer, intent(in) :: isize
%(type)s, intent(in) :: val
integer :: i
n_count_%(type_short)s = 0
do i=1,isize
if (array(i) == val) then
n_count_%(type_short)s = n_count_%(type_short)s +1
endif
enddo
end function
! Build Python functions
"""
for t in format.keys():
print template%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
if t != "logical":
print template_no_logical%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
template_py = """
def read_%(type_short)s(self,dir,fil):
conv = get_conv("%(type_short)s")
l_filename=dir.strip()+'/'+fil
try:
file = open(l_filename,"r")
except IOError:
self.error('read_%(type_short)s',\
'Attribute '+dir.strip()+'/'+fil+' is not set')
dat = file.readline().strip()
try:
dat = conv(dat)
except SyntaxError:
pass
file.close()
return dat
def write_%(type_short)s(self,dir,fil,dat):
if self.read_only:
self.error('Read-only file.')
conv = get_conv("%(type_short)s")
l_filename= [ dir.strip()+'/.'+fil ]
l_filename += [ dir.strip()+'/'+fil ]
dat = conv(dat)
file = open(l_filename[0],'w')
print >>file,'%(fmt)s'%%(dat,)
file.close()
os.rename(l_filename[0],l_filename[1])
def read_array_%(type_short)s(self,dir,fil,rank,dims,dim_max):
l_filename=dir.strip()+'/'+fil+'.gz'
conv = get_conv("%(type_short)s")
try:
file = GzipFile(filename=l_filename,mode='rb')
lines = file.read().splitlines()
rank_read = int(lines[0])
assert (rank_read == rank)
dims_read = map(int,lines[1].split())
for i,j in zip(dims_read,dims):
assert i == j
lines.pop(0)
lines.pop(0)
dat = map(conv,lines)
file.close()
return reshape(dat,dims)
except IOError:
self.error('read_array_%(type_short)s', 'Attribute '+l_filename+' is not set')
def write_array_%(type_short)s(self,dir,fil,rank,dims,dim_max,dat):
if self.read_only:
self.error('Read-only file.')
l_filename = [ tempfile.mktemp(dir=dir.strip()), dir.strip()+'/'+fil+'.gz' ]
try:
file = StringIO.StringIO()
file.write("%%3d\\n"%%(rank,))
for d in dims:
file.write("%%20d "%%(d,))
file.write("\\n")
dat = flatten(dat)
for i in xrange(dim_max):
file.write("%(fmt)s\\n"%%(dat[i],))
file.flush()
buffer = file.getvalue()
file.close()
file = GzipFile(filename=l_filename[0],mode='wb')
file.write(buffer)
file.close()
os.rename(l_filename[0],l_filename[1])
except:
self.error("write_array_%(type_short)s",
"Unable to write "+l_filename[1])
"""
file_py = open("libezfio_util-gen.py","w")
for t in format.keys():
print >>file_py, template_py%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][1] }
import os
command = "'echo %s > '//libezfio_filename//'/ezfio/last_library'"
cwd = os.getcwd()
cwd = cwd.split('src')[:-1]
cwd = '/'.join(cwd)
print >>file_py, """
LIBRARY = "%s"
"""%cwd
file_py.close()
END_SHELL
BEGIN_PROVIDER [ integer, libezfio_buffer_rank ]
BEGIN_DOC
! Rank of the buffer ready for reading
END_DOC
libezfio_buffer_rank = -1
END_PROVIDER
subroutine ezfio_open_write_buffer(dir,fil,rank)
implicit none
character*(*),intent(in) :: dir
character*(*),intent(in) :: fil
integer,intent(in) :: rank
character*(1024) :: l_filename
if (libezfio_read_only) then
call ezfio_error(irp_here,'Read-only file.')
endif
l_filename=trim(dir)//'/'//fil//'.gz'
if (libezfio_buffer_rank /= -1) then
call ezfio_error(irp_here,'Another buffered file is already open.')
endif
libezfio_buffer_rank = rank
if (libezfio_buffer_rank <= 0) then
call ezfio_error(irp_here,'In file '//trim(l_filename)//': rank <= 0.')
endif
TOUCH libezfio_buffer_rank
integer :: err
call libezfio_openz(trim(l_filename),'wb',err)
if (err /= 0) then
call ezfio_error(irp_here,'Unable to open buffered file '//trim(l_filename)//'.')
endif
write(libezfio_iunit,'(I2)') rank
end
subroutine ezfio_open_read_buffer(dir,fil,rank)
implicit none
character*(*),intent(in) :: dir
character*(*),intent(in) :: fil
integer,intent(in) :: rank
character*(1024) :: l_filename
l_filename=trim(dir)//'/'//fil//'.gz'
if (libezfio_buffer_rank /= -1) then
call ezfio_error(irp_here,'Another buffered file is already open.')
endif
integer :: err
call libezfio_openz(trim(l_filename),'rb',err)
if (err /= 0) then
print *, err, l_filename
call ezfio_error(irp_here,'Unable to open buffered file '//trim(l_filename)//'.')
endif
if (err /= 0) then
print *, err, l_filename
call ezfio_error(irp_here,'Unable to read buffered file '//trim(l_filename)//'.')
endif
read(libezfio_iunit,'(I2)') libezfio_buffer_rank
if (libezfio_buffer_rank /= rank) then
call ezfio_error(irp_here,'In file '//trim(l_filename)//': Rank is not correct')
endif
TOUCH libezfio_buffer_rank
end
subroutine ezfio_close_read_buffer(dir,fil,rank)
implicit none
character*(*),intent(in) :: dir
character*(*),intent(in) :: fil
integer,intent(in) :: rank
character*(1024) :: l_filename
l_filename=trim(dir)//'/'//fil//'.gz'
ASSERT (libezfio_buffer_rank > 0)
call libezfio_closez(l_filename,'r')
FREE libezfio_buffer_rank
end
subroutine ezfio_close_write_buffer(dir,fil,rank)
implicit none
character*(*),intent(in) :: dir
character*(*),intent(in) :: fil
integer,intent(in) :: rank
character*(1024) :: l_filename
l_filename=trim(dir)//'/'//fil//'.gz'
ASSERT (libezfio_buffer_rank > 0)
call libezfio_closez(l_filename,'w')
FREE libezfio_buffer_rank
end
subroutine ezfio_read_buffer(indices,values,isize)
implicit none
integer, intent(inout) :: isize
integer, intent(out) :: indices(*)
double precision, intent(out) :: values(isize)
integer :: i, j
if (libezfio_buffer_rank == -1) then
call ezfio_error(irp_here,'No buffered file is open.')
endif
do i=1,isize
read(libezfio_iunit,err=10) (indices((i-1)*libezfio_buffer_rank+j), j=1,libezfio_buffer_rank), values(i)
enddo
return
10 continue
isize=i-1
end
subroutine ezfio_write_buffer(indices,values,isize)
implicit none
integer, intent(in) :: isize
integer, intent(in) :: indices(*)
double precision, intent(in) :: values(isize)
character*(80) :: cformat
integer :: i, j, k, num, imax, l1, l2
if (libezfio_read_only) then
call ezfio_error(irp_here,'Read-only file.')
endif
if (libezfio_buffer_rank == -1) then
call ezfio_error(irp_here,'No buffered file is open.')
endif
write(cformat,*) '(',num,'(',libezfio_buffer_rank,'(I4,X),E24.15,A1))'
write(libezfio_iunit,cformat) ((indices((i-1)*libezfio_buffer_rank+j), j=1,libezfio_buffer_rank), &
values(i), i=1,isize)
end

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#!/usr/bin/python
# 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
# Read ezfio config file
#----------------------
import os, sys
lines = []
for filename in [ '../config/'+i for i in os.listdir('../config')]:
file = open(filename,'r')
lines += map(lambda x: (x,filename), file.readlines())
try:
if lines[-1] != '':
lines.append( ('', filename) )
except:
pass
file.close()
import re
groups = {}
group = None
my_list = []
for line, filename in lines:
try:
if len(line.strip()) == 0:
groups[group] = my_list
elif line[0] != ' ': # New group
group = line.strip()
if group in groups.keys():
my_list = groups[group]
else:
my_list = []
else:
line = line.replace("double precision","double_precision")
line = line.split('=')
if len(line) == 1:
command = ""
else:
command = line[1].strip()
line = line[0]
buffer = line.split()
if len(buffer) == 2:
buffer += ["()"]
else:
buffer[2] = re.sub(r"\)",r',)',buffer[2])
if buffer[1] == "double_precision":
buffer[1] = "double precision"
buffer[2] = re.sub(r"([a-zA-Z0-9_\-\+*/]+)",r'"\1"',buffer[2])
buffer[2] = eval(buffer[2])
buffer.append(command)
my_list.append(tuple(buffer))
except:
import sys, time
print >>sys.stderr, ''
print >>sys.stderr, '*'*80
print >>sys.stderr, 'Error in EZFIO config file '+filename+' :'
print >>sys.stderr, line
print >>sys.stderr, '*'*80
print >>sys.stderr, ''
time.sleep(3)
sys.exit(1)

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src/run.irp.f Normal file
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! 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
! Leave this empty
end

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#!/usr/bin/python
# 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
from ezfio import ezfio
EZFIO=ezfio
EZFIO.set_file('icule')
EZFIO.set_system_num_alpha(4)
EZFIO.set_geometry_num_atom(5)
x = [ "label"+str(i) for i in range(5) ]
indices = [ [ 1, 2, 3, 4 ], [ 5, 6, 7, 8] ]
values = [ 10., 20.]
isize = len(indices)
EZFIO.open_write_ao_two_int()
EZFIO.write_buffer(indices,values,isize)
EZFIO.write_buffer(indices,values,isize)
EZFIO.close_write_ao_two_int()
indices = []
values = []
isize = 5
EZFIO.open_read_ao_two_int()
indices,values = EZFIO.read_buffer(isize)
print indices
print values
EZFIO.close_read_ao_two_int()

1
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VERSION=1.1.5