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. Starting with version 2.0, EZFIO produces Python3 files. Download ======== The following packages are needed: * `IRPF90 `_ * `Python `_ * `GNU make `_ * `Zlib `_ 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 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 ``_`` 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. is the name of the container which contains the data and is the name of the data. subroutine ezfio_has__ (has_it) ``has_it`` is .True. if the data exists in the EZFIO file, .False. otherwise. subroutine ezfio_set__ (source) writes the source data to the EZFIO file. subroutine ezfio_get__ (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/python3 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())) Molecule.append(new_list) # 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 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 mass is correct: print(ezfio.properties_mass) # Should give 18. Execute the script: .. code-block:: bash $ python3 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 library user Water/molecule: 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 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 file: .. code-block:: bash $ ls Water/* Water/ezfio: creation Water/molecule: coord.gz mass.gz num_atoms Water/properties: center_of_mass.gz 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 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 #!/bin/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] ] EOF # Check that the total mass is correct: ezfio get properties mass # Should print 18.