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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.
Starting with version 2.0, EZFIO produces Python3 files.
The following packages are needed:
* `IRPF90 <http://irpf90.ups-tlse.fr>`_
* `Python <http://www.python.org>`_
* `GNU make <https://www.gnu.org/software/make>`_
* `Zlib <https://www.zlib.net>`_
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
Get into the ``EZFIO`` directory and configure the library to produce the
desired suboutines. Get into the ``config`` directory and create a new
file ``test.config`` containing::
num_atoms integer
mass real (molecule_num_atoms)
coord real (3,molecule_num_atoms)
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. To build with GNU make, run:
.. code-block:: bash
$ make
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``, ``Ocaml`` and ``Bash`` directories
contain the binding for these languages.
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
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 = list(map(eval,line.split()))
# Create the mass array
mass = [ x[0] for x in Molecule ]
# print(mass)
# [16.0, 1.0, 1.0]
# Create the coord array
coord = [ (x[1], x[2], x[3]) for x in 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
# Add the arrays to the file
ezfio.molecule_num_atoms = len(Molecule)
ezfio.molecule_mass = mass
ezfio.molecule_coord = coord
# Check that the total mass is correct:
print(ezfio.properties_mass) # Should give 18.
Execute the script:
.. code-block:: bash
$ python3 create_input.py
The printed mass is correct, and a new directory (``Water``) was created
with our data:
.. code-block:: bash
$ ls Water/*
creation library user
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)
Compile the fortran program and link it the ``libezfio.a`` library and
``zlib``, and run the executable.
.. code-block:: bash
$ gfortran test.f90 EZFIO/lib/libezfio.a -lz -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
.. code-block:: bash
$ ls Water/*
coord.gz mass.gz num_atoms
Using Bash
To use EZFIO in Bash, you need to source the ``ezfio.sh`` file:
.. code-block:: bash
$ source EZFIO/Bash/ezfio.sh
The usage of the ``ezfio`` bash command is::
ezfio set_file EZFIO_DIRECTORY
ezfio unset_file
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
.. code-block:: bash
source EZFIO/Bash/ezfio.sh # Put correct path here
# 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]
# Check that the total mass is correct:
ezfio get properties mass # Should print 18.