From 3b97748adcfad05b350bd095ca6c1590d4e9c569 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 2 Jun 2015 12:12:11 +0200 Subject: [PATCH] Bash calls ezfio.py --- Bash/ezfio.sh | 124 ++++++++++++++++++---------------------- README.rst | 107 +++++++++++++++++++++++++--------- configure.py | 12 ++-- src/ezfio-head.py | 1 + src/ezfio-tail.py | 49 ++++++++++++++++ src/groups.py | 7 --- src/libezfio_util.irp.f | 7 +++ src/run.irp.f | 31 ---------- 8 files changed, 201 insertions(+), 137 deletions(-) delete mode 100644 src/run.irp.f diff --git a/Bash/ezfio.sh b/Bash/ezfio.sh index e43c9e4..9d36360 100644 --- a/Bash/ezfio.sh +++ b/Bash/ezfio.sh @@ -1,5 +1,13 @@ #!/bin/bash +EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/.. ; pwd -P ) + +function _ezfio_py() +{ + python ${EZFIO_ROOT}/Python/ezfio.py $@ +} + + function _ezfio_usage() { echo " @@ -78,8 +86,7 @@ function _ezfio_set_file() if [[ ! -d $1 ]] then - echo "No such directory: $1" - return 1 + mkdir -p $1 || return 1 fi export EZFIO_FILE=$1 _ezfio_info "Set file ${EZFIO_FILE}" @@ -109,18 +116,7 @@ function _ezfio_has() return 0 fi - if [[ -f ${EZFIO_FILE}/${1,,}/${2,,} ]] - then - _ezfio_info "EZFIO has $1 / $2" - return 0 - elif [[ -f ${EZFIO_FILE}/${1,,}/${2,,}.gz ]] - then - _ezfio_info "EZFIO has $1 / $2" - return 0 - else - _ezfio_info "EZFIO doesn't have $1 / $2" - return 1 - fi + _ezfio_py has $@ && return 0 || return 1 } function _ezfio_get() @@ -129,29 +125,15 @@ function _ezfio_get() if [[ -z $1 ]] then - ls ${EZFIO_FILE} - return 0 + ls ${EZFIO_FILE} && return 0 || return 1 fi - _ezfio_has $@ || return 1 - if [[ -z $2 ]] then - ls ${EZFIO_FILE}/${1,,} - return 0 + ls ${EZFIO_FILE}/${1,,} && return 0 || return 1 fi - if [[ -f ${EZFIO_FILE}/${1,,}/${2,,} ]] - then - cat ${EZFIO_FILE}/${1,,}/${2,,} - elif [[ -f ${EZFIO_FILE}/${1,,}/${2,,}.gz ]] - then - zcat ${EZFIO_FILE}/${1,,}/${2,,}.gz - else - _ezfio_info "EZFIO doesn't have $1 / $2" - return 1 - fi - return 0 + _ezfio_py get $@ && return 0 || return 1 } function _ezfio_set() @@ -160,15 +142,11 @@ function _ezfio_set() _require_first_argument $@ || return 1 _require_second_argument $@ || return 2 - if [[ ! -d ${EZFIO_FILE}/${1,,} ]] + if [[ -z $3 ]] then - mkdir -p ${EZFIO_FILE}/${1,,} - fi - if [[ ! -z "$3" ]] - then - echo "$3" > ${EZFIO_FILE}/${1,,}/${2,,} + _ezfio_py set $@ || return 1 else - zcat > ${EZFIO_FILE}/${1,,}/${2,,}.gz + echo $3 | _ezfio_py set $1 $2 || return 1 fi return 0 } @@ -234,39 +212,51 @@ _Complete() prev="${COMP_WORDS[COMP_CWORD-1]}" prev2="${COMP_WORDS[COMP_CWORD-2]}" - case "${prev2}" in - set|has|get) - COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE}/${prev} ; ls | sed 's/\.gz//' )" -- $cur ) ) - return 0 - ;; - esac + if [[ -n ${EZFIO_FILE} && -d ${EZFIO_FILE} ]] + then - case "${prev}" in - unset_file|set_verbose|unset_verbose) - COMPREPLY=() - return 0 - ;; - set_file) - COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) ) - return 0 - ;; - set|has|get) - COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) ) - return 0 - ;; - *) - if [[ -z ${EZFIO_FILE} ]] - then - COMPREPLY=( $(compgen -W 'set_file \ - set_verbose unset_verbose -h' -- $cur ) ) - else + case "${prev2}" in + set|has|get) + COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE}/${prev} ; ls | sed 's/\.gz//' )" -- $cur ) ) + return 0 + ;; + esac + + case "${prev}" in + unset_file|set_verbose|unset_verbose) + COMPREPLY=() + return 0 + ;; + set|has|get) + COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) ) + return 0 + ;; + *) COMPREPLY=( $(compgen -W 'has get set unset_file \ set_verbose unset_verbose -h' -- $cur ) ) - fi - return 0 - ;; - esac + return 0 + ;; + esac + else + + case "${prev}" in + set_verbose|unset_verbose) + COMPREPLY=() + return 0 + ;; + set_file) + COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) ) + return 0 + ;; + *) + COMPREPLY=( $(compgen -W 'set_file \ + set_verbose unset_verbose -h' -- $cur ) ) + return 0 + ;; + esac + + fi } complete -F _Complete ezfio diff --git a/README.rst b/README.rst index 95970cb..459f1c8 100644 --- a/README.rst +++ b/README.rst @@ -19,8 +19,8 @@ The following packages are needed: * `IRPF90 `_ * `Python `_ +* `GNU make `_ or `Ninja `_ -The latest version can be downloaded `here `_. Tutorial ======== @@ -39,15 +39,9 @@ Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file $ ls EZFIO/ -Get into the ``EZFIO`` directory and set up your compiling options: - -.. code-block:: bash - - $ cp make.config.example make.config - $ vim make.config - -Now, configure the library to produce the desired suboutines. Get into -the ``config`` directory and create a new file ``test.config`` +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 @@ -79,19 +73,27 @@ simple operation is written after an = symbol (as for ``mass`` in the Once your configuration file is ready, run ``make`` and your library will be built. + Building the library -------------------- -Now, go back to the EZFIO root directory, and run: +Now, go back to the EZFIO root directory. To build with GNU make, run: .. code-block:: bash $ make -The ``lib`` directory now contains the shared library -(``libezfio.so``), the static library (``libezfio.a``), and a static +Or you can use Ninja to build the library: + +.. code-block:: bash + + $ ninja + + +The ``lib`` directory now contains the static library ``libezfio.a``, and a static library for use under the IRPF90 environment (``libezfio_irp.a``). -The ``Python`` directory contains the Python module for the use of the library in Python. +The ``Python``, ``Ocaml`` and ``Bash`` directories contain the binding for these languages. + Using the produced library -------------------------- @@ -220,7 +222,7 @@ Create a file named ``create_input.py`` with: ezfio.molecule_mass = mass ezfio.molecule_coord = coord - # Check that the total charge and mass is correct: + # Check that the total mass is correct: print ezfio.properties_mass # Should give 18. Execute the script: @@ -236,10 +238,10 @@ The printed mass is correct, and a new directory (``Water``) was created with ou $ ls Water/* Water/ezfio: - creation + creation library user Water/molecule: - charge.gz coord.gz mass.gz num_atoms + coord.gz mass.gz num_atoms In Fortran ---------- @@ -307,6 +309,20 @@ the EZFIO file. end +Compile the fortran program and link it the ``libezfio.a`` library, and run the +executable. + +.. code-block:: bash + + $ gfortran test.f90 EZFIO/lib/libezfio.a -o test.x + $ ./test.x + Data in the EZFIO file: + 16.0000000 0.00000000 0.222396001 0.00000000 + 1.00000000 1.43649399 -0.889660001 0.00000000 + 1.00000000 -1.43649399 -0.889660001 0.00000000 + + + A new directory (``properties``) was created with the center_of_mass file: @@ -317,25 +333,64 @@ file: creation Water/molecule: - charge.gz coord.gz mass.gz num_atoms + coord.gz mass.gz num_atoms Water/properties: center_of_mass.gz -Compile and run the program using: +Using Bash +---------- + +To use EZFIO in Bash, you need to source the ``ezfio.sh`` file: .. code-block:: bash - $ $FC -o test test.F90 EZFIO/lib/libezfio.a - $ ./test + $ source EZFIO/Bash/ezfio.sh -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: +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 - $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/EZFIO/lib - $ $FC -o test -L./EZFIO/lib -lezfio + #!/bin/bash + + source EZFIO/Bash/ezfio.sh + + # Select the EZFIO file + ezfio set_file Water + + # Set the number of atoms + ezfio set molecule num_atoms 3 + + # Create the mass array + mass="[16.0, 1.0, 1.0]" + echo $mass | ezfio set molecule mass + + # Create the coordinates + cat << EOF | ezfio set molecule coord + [ + [ 0.000000, 0.222396, 0.0], + [ 1.436494, -0.889660, 0.0], + [-1.436494, -0.889660, 0.0] + ] + EOF + + # Check that the total mass is correct: + ezfio get properties mass # Should print 18. + + diff --git a/configure.py b/configure.py index d6d11cb..3865a77 100755 --- a/configure.py +++ b/configure.py @@ -52,18 +52,18 @@ def create_build_ninja(): d["irpf90_files"] = [ "src/{0}".format(x) for x in """ IRPF90_temp/build.ninja irpf90.make irpf90_entities - tags + tags libezfio_groups-gen.py libezfio_util-gen.py """.split() ] + \ """ - Python/ezfio.py Ocaml/ezfio.ml Bash/ezfio.sh + Python/ezfio.py Ocaml/ezfio.ml """.split() d["irpf90_sources"] = [ "src/{0}".format(x) for x in """ libezfio_error.irp.f create_ocaml.py groups_templates.py - libezfio_file.irp.f create_python.py libezfio_groups-gen.py - libezfio_groups.irp.f ezfio-head.py libezfio_util-gen.py - libezfio_util.irp.f ezfio-tail.py read_config.py run.irp.f + libezfio_file.irp.f create_python.py + libezfio_groups.irp.f ezfio-head.py + libezfio_util.irp.f ezfio-tail.py read_config.py f_types.py test.py create_bash.py groups.py """.split() ] + [ "make.config" ] @@ -93,7 +93,7 @@ rule build_libezfio_a description = Building libezfio.a rule build_libezfio_irp_a - command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o ; {RANLIB} lib/libezfio_irp.a + command = cp lib/libezfio.a lib/libezfio_irp.a ; {AR} dv lib/libezfio_irp.a irp_stack.irp.o > /dev/null ; {RANLIB} lib/libezfio_irp.a description = Building libezfio_irp.a diff --git a/src/ezfio-head.py b/src/ezfio-head.py index 6c64cbb..d38091d 100644 --- a/src/ezfio-head.py +++ b/src/ezfio-head.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python # EZFIO is an automatic generator of I/O libraries # Copyright (C) 2009 Anthony SCEMAMA, CNRS # diff --git a/src/ezfio-tail.py b/src/ezfio-tail.py index e9a090a..63e6e62 100644 --- a/src/ezfio-tail.py +++ b/src/ezfio-tail.py @@ -24,3 +24,52 @@ ezfio = ezfio_obj() +def main(): + import pprint + import sys + import os + + try: + EZFIO_FILE = os.environ["EZFIO_FILE"] + except KeyError: + print "EZFIO_FILE not defined" + return 1 + + ezfio.set_file(EZFIO_FILE) + + command = '_'.join(sys.argv[1:]).lower() + + try: + f = getattr(ezfio,command) + except AttributeError: + print "{0} not found".format(command) + return 1 + + if command.startswith('has'): + if f(): return 0 + else : return 1 + + elif command.startswith('get'): + result = f() + pprint.pprint( result, width=60, depth=3, indent=4 ) + return 0 + + elif command.startswith('set'): + try: + data = eval(sys.stdin.read()) + except: + print "Syntax Error" + return 1 + f(data) + return 0 + + else: + return 1 + + +if __name__ == '__main__': + rc = main() + sys.exit(rc) + + + diff --git a/src/groups.py b/src/groups.py index 8e3ddf1..83dd175 100644 --- a/src/groups.py +++ b/src/groups.py @@ -144,10 +144,3 @@ for group in groups.keys(): print >>file_py, attributes_arr_py%d file_py.close() - -import create_ocaml -create_ocaml.run() - -import create_python -create_python.run() - diff --git a/src/libezfio_util.irp.f b/src/libezfio_util.irp.f index 91887ce..89d4aa6 100644 --- a/src/libezfio_util.irp.f +++ b/src/libezfio_util.irp.f @@ -354,6 +354,13 @@ print >>file_py, """ """%cwd file_py.close() + +import create_ocaml +create_ocaml.run() + +import create_python +create_python.run() + END_SHELL BEGIN_PROVIDER [ integer, libezfio_buffer_rank ] diff --git a/src/run.irp.f b/src/run.irp.f deleted file mode 100644 index 7d78f38..0000000 --- a/src/run.irp.f +++ /dev/null @@ -1,31 +0,0 @@ -! EZFIO is an automatic generator of I/O libraries -! Copyright (C) 2009 Anthony SCEMAMA, CNRS -! -! This program is free software; you can redistribute it and/or modify -! it under the terms of the GNU General Public License as published by -! the Free Software Foundation; either version 2 of the License, or -! (at your option) any later version. -! -! This program is distributed in the hope that it will be useful, -! but WITHOUT ANY WARRANTY; without even the implied warranty of -! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -! GNU General Public License for more details. -! -! You should have received a copy of the GNU General Public License along -! with this program; if not, write to the Free Software Foundation, Inc., -! 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. -! -! Anthony Scemama -! LCPQ - IRSAMC - CNRS -! Universite Paul Sabatier -! 118, route de Narbonne -! 31062 Toulouse Cedex 4 -! scemama@irsamc.ups-tlse.fr - -program run - BEGIN_DOC -! Test run - END_DOC -! Leave this empty -end -