mirror of
https://gitlab.com/scemama/EZFIO.git
synced 2024-12-13 07:53:33 +01:00
Removed Ninja
Version:1.4.0 Version:1.4.0
This commit is contained in:
parent
744cbac511
commit
fa6d40a857
@ -1,4 +1,7 @@
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#!/bin/bash
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#
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# ezfio shell command with completion
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#
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EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/.. ; pwd -P )
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2
LICENSE
2
LICENSE
@ -1,4 +1,4 @@
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GNU GENERAL PUBLIC LICENSE
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GNU GENERAL PUBLIC LICENSE
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Version 2, June 1991
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Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
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6
Makefile
6
Makefile
@ -38,19 +38,15 @@ clean:
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- bash -c "[[ -f Bash/ezfio.sh ]] && rm $$PWD/Bash/*"
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- $(MAKE) -C $$PWD/src veryclean
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archive: distclean
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archive: veryclean
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git archive --format=tar HEAD > EZFIO.$(VERSION).tar
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mkdir EZFIO ; cd EZFIO ; tar -xvf ../EZFIO.$(VERSION).tar
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rm EZFIO.$(VERSION).tar
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tar -zcvf EZFIO.$(VERSION).tar.gz EZFIO
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rm -rf EZFIO
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make.config:
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./configure.py
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veryclean:
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$(MAKE) -C src veryclean
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rm -f make.config
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rm -f Ocaml/ezfio.ml
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rm -f Python/ezfio.py
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rm -f lib/{libezfio.a,libezfio_irp.a}
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56
README.rst
56
README.rst
@ -4,13 +4,13 @@ EZFIO
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EZFIO is the Easy Fortran I/O library generator. It generates
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automatically an I/O library from a simple configuration file. The
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produced library contains Fortran subroutines to read/write the data
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from/to disk, and to check if the data exists.
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A Python and an Ocaml API are also provided.
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from/to disk, and to check if the data exists. A Python and an Ocaml API
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are also provided.
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With EZFIO, the data is organized in a file system inside a main
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directory. This main directory contains subdirectories, which contain
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files. Each file corresponds to a data. For atomic data the file is a
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plain text file, and for array data the file is a gzipped text file.
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plain text file, and for array data the file is a gzipped text file.
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Download
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========
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@ -19,7 +19,8 @@ The following packages are needed:
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* `IRPF90 <http://irpf90.ups-tlse.fr>`_
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* `Python <http://www.python.org>`_
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* `GNU make <http://www.python.org>`_ or `Ninja <http://github.com/martine/ninja>`_
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* `GNU make <https://www.gnu.org/software/make>`_
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* `Zlib <https://www.zlib.net>`_
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Tutorial
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@ -32,7 +33,8 @@ the 3D space.
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Preparation of the library
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--------------------------
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Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file in this directory. This directory now contains:
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Create an empty directory for your project and unpack the
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``EZFIO.tar.gz`` file in this directory. This directory now contains:
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.. code-block:: bash
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@ -40,9 +42,8 @@ Create an empty directory for your project and unpack the ``EZFIO.tar.gz`` file
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EZFIO/
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Get into the ``EZFIO`` directory and configure the library to produce the
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desired suboutines. Get into the ``config`` directory and create a new file
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``test.config``
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containing::
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desired suboutines. Get into the ``config`` directory and create a new
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file ``test.config`` containing::
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molecule
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num_atoms integer
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@ -56,14 +57,13 @@ containing::
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In this example, ``molecule`` and ``properties`` are containers of data.
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Those are defined in the config file by their name at the beginning of a
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new line.
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Each data contained inside a container is characterized by a triplet
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(name,type,dimension), preceded by at least one white space at the
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beginning of the line.
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new line. Each data contained inside a container is characterized by a
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triplet (name,type,dimension), preceded by at least one white space at
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the beginning of the line.
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If the dimension of an array is a data, the name of the data can be used
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as ``<container>_<data>`` in the definition of the dimension. For
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example, the dimension (``molecule_num_atoms``) uses the data
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If the dimension of an array is a data, the name of the data can be
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used as ``<container>_<data>`` in the definition of the dimension.
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For example, the dimension (``molecule_num_atoms``) uses the data
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``num_atoms`` of container ``molecule``.
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Data can also be the result of a simple operation. In that case, the
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@ -83,16 +83,10 @@ Now, go back to the EZFIO root directory. To build with GNU make, run:
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$ make
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Or you can use Ninja to build the library:
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.. code-block:: bash
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$ ninja
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The ``lib`` directory now contains the static library ``libezfio.a``, and a static
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library for use under the IRPF90 environment (``libezfio_irp.a``).
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The ``Python``, ``Ocaml`` and ``Bash`` directories contain the binding for these languages.
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The ``lib`` directory now contains the static library ``libezfio.a``,
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and a static library for use under the IRPF90 environment
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(``libezfio_irp.a``). The ``Python``, ``Ocaml`` and ``Bash`` directories
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contain the binding for these languages.
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Using the produced library
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@ -232,7 +226,8 @@ Execute the script:
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$ python2 create_input.py
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18.0
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The printed mass is correct, and a new directory (``Water``) was created with our data:
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The printed mass is correct, and a new directory (``Water``) was created
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with our data:
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.. code-block:: bash
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@ -309,12 +304,12 @@ the EZFIO file.
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end
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Compile the fortran program and link it the ``libezfio.a`` library, and run the
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executable.
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Compile the fortran program and link it the ``libezfio.a`` library and
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``zlib``, and run the executable.
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.. code-block:: bash
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$ gfortran test.f90 EZFIO/lib/libezfio.a -o test.x
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$ gfortran test.f90 EZFIO/lib/libezfio.a -lz -o test.x
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$ ./test.x
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Data in the EZFIO file:
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16.0000000 0.00000000 0.222396001 0.00000000
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@ -362,7 +357,8 @@ The usage of the ``ezfio`` bash command is::
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ezfio unset_verbose
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Here is the same script as the Python script, but using Bash (``create_input.sh``):
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Here is the same script as the Python script, but using Bash
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(``create_input.sh``):
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.. code-block:: bash
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31
build.ninja
31
build.ninja
@ -1,31 +0,0 @@
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include version
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rule build_generated_ninja
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command = python2 configure.py
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description = Creating generated.ninja
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rule run_ninja
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command = bash -c 'source .make.config.sh ; $$NINJA -f $in'
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description = Building Fortran library
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pool = console
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rule build_archive
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command = git archive --format=tar HEAD > EZFIO.${VERSION}.tar && mkdir -p EZFIO && cd EZFIO && tar -xvf ../EZFIO.${VERSION}.tar && cd .. && rm EZFIO.${VERSION}.tar && tar -zcvf EZFIO.${VERSION}.tar.gz EZFIO && rm -rf EZFIO
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description = Building archive
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rule clean_all
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command = bash -c 'source .make.config.sh ; bash -c "$$NINJA -f $in -t clean ; $$NINJA -t clean" ; rm -rf src/IRPF90_{temp,man} src/*.pyc'
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description = Cleaning directory
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build make.config .make.config.sh generated.ninja impossible_target: build_generated_ninja
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build all: run_ninja generated.ninja
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default all
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build EZFIO.${VERSION}.tar.gz: build_archive
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build archive: phony EZFIO.${VERSION}.tar.gz
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build clean: clean_all generated.ninja
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146
configure.py
146
configure.py
@ -1,146 +0,0 @@
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#!/usr/bin/env python2
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import os,sys
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def write_if_different(filename,s):
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try:
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with open(filename, "r") as f:
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ref = f.read()
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except:
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ref = ""
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if ref == s:
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return
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else:
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with open(filename, "w") as f:
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f.write(s)
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with open("version",'r') as f:
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version = f.read().strip().rsplit('=')[1]
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d_default = {
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"VERSION" : version,
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"IRPF90" : 'irpf90',
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"FC" : 'gfortran -g -ffree-line-length-none -fPIC -fopenmp',
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"FCFLAGS" : '-O2',
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"RANLIB" : 'ranlib',
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"AR" : 'ar',
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"BUILD_SYSTEM" : 'make',
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"NINJA" : 'ninja',
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}
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CONFIG_FILES=' '.join([ os.path.join("config",x) for x in os.listdir('config') if x != '.empty'])
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def create_make_config():
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try:
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d = read_make_config()
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except:
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d = {}
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fmt = { "make.config" :'{0}={1}\n' ,
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".make.config.sh": 'export {0}="{1}"\n' }
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for var,default in d_default.iteritems():
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if var not in d:
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try:
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cur = os.environ[var]
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except KeyError:
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cur = default
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d[var]=cur
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for filename in fmt:
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out = ""
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for var,default in d_default.iteritems():
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cur = d[var]
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out += fmt[filename].format(var,cur)
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write_if_different(filename,out)
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return d
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def read_make_config():
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result = {}
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with open("make.config",'r') as f:
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for line in f.readlines():
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try:
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key, value = line.strip().split('=',1)
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except:
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print "Error in make.config:"
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print line
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sys.exit(1)
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result[key] = value
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return result
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def create_build_ninja():
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d=create_make_config()
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d["irpf90_files"] = [ "src/{0}".format(x) for x in
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"""
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IRPF90_temp/build.ninja irpf90.make irpf90_entities
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tags libezfio_groups-gen.py libezfio_util-gen.py
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""".split() ]
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d["irpf90_sources"] = [ "src/{0}".format(x) for x in
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"""
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libezfio_error.irp.f create_ocaml.py groups_templates.py
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libezfio_file.irp.f create_python.py
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libezfio_groups.irp.f ezfio-head.py
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libezfio_util.irp.f ezfio-tail.py read_config.py
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f_types.py test.py groups.py
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""".split() ] + [ "make.config" ]
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d["irpf90_files"] = ' '.join(d["irpf90_files"])
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d["irpf90_sources"] = ' '.join(d["irpf90_sources"])
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template = """
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rule compile_irpf90
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command = bash -c 'source .make.config.sh ; cd src ; {IRPF90} --ninja'
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description = Compiling IRPF90
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rule build_irpf90_a
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command = {NINJA} -C src/IRPF90_temp && touch $out
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description = Compiling Fortran files
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rule build_libezfio_a
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command = cp src/IRPF90_temp/irpf90.a lib/libezfio.a ; {RANLIB} lib/libezfio.a
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description = Building libezfio.a
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rule build_libezfio_irp_a
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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
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description = Building libezfio_irp.a
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rule build_python
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command = cd src ; python2 create_python.py
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description = Building Python module
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rule build_ocaml
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command = cd src ; python2 create_ocaml.py
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description = Building Ocaml module
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build {irpf90_files}: compile_irpf90 | {irpf90_sources} {CONFIG_FILES}
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build src/IRPF90_temp/irpf90.a: build_irpf90_a | {irpf90_files}
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build lib/libezfio.a: build_libezfio_a | src/IRPF90_temp/irpf90.a
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build lib/libezfio_irp.a: build_libezfio_irp_a | lib/libezfio.a
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build Python/ezfio.py: build_python | lib/libezfio.a
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build Ocaml/ezfio.ml: build_ocaml | lib/libezfio.a
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"""
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d["CONFIG_FILES"] = CONFIG_FILES
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write_if_different('generated.ninja',template.format(**d))
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if __name__ == '__main__':
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create_build_ninja()
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@ -5,6 +5,6 @@ cd ../.git/hooks/
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for i in commit-msg post-commit
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do
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rm $i
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rm --force -- $i
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ln -s $OLD_DIR/$i $PWD/$i
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done
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|
9
make.config
Normal file
9
make.config
Normal file
@ -0,0 +1,9 @@
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VERSION ?= 1.4.0
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RANLIB ?= ranlib
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IRPF90 ?= irpf90
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CC ?= gcc
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FC ?= gfortran -g -ffree-line-length-none -fPIC # -fopenmp
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FCFLAGS ?= -fPIC
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AR ?= ar
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RANLIB ?= ranlib
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PYTHON ?= python2
|
20
src/Makefile
20
src/Makefile
@ -29,7 +29,7 @@ export
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include irpf90.make
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irpf90.make: $(wildcard *.irp.f) ../config/* system.c
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irpf90.make: $(wildcard *.irp.f) ../config/* IRPF90_temp/system.o IRPF90_temp/system_f.o
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$(IRPF90)
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include ../version
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@ -40,28 +40,30 @@ all: static ../Python/ezfio.py ../Ocaml/ezfio.ml
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static: ../lib/libezfio.a ../lib/libezfio_irp.a
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|
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system_c.o: system_c.c
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$(CC) -c system_c -o system_c.o
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IRPF90_temp/system.o: system.c
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mkdir -p IRPF90_temp/
|
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$(CC) -c system.c -o IRPF90_temp/system.o
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system_f.o: system_f.f90
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$(FC) -c system_f.f90 -o system_f.o
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IRPF90_temp/system_f.o: system_f.f90
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mkdir -p IRPF90_temp/
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$(FC) -c system_f.f90 -o IRPF90_temp/system_f.o && cp system.mod IRPF90_temp/
|
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|
||||
../lib/libezfio.a: IRPF90_temp/irpf90.a
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rm -f ../lib/libezfio.a
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$(AR) cru ../lib/libezfio.a system_c.o system_f.o $(OBJ1)
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||||
$(AR) cru ../lib/libezfio.a IRPF90_temp/system_f.o IRPF90_temp/system.o $(OBJ1)
|
||||
$(RANLIB) ../lib/libezfio.a
|
||||
|
||||
../lib/libezfio_irp.a: ../lib/libezfio.a
|
||||
rm -f ../lib/libezfio_irp.a
|
||||
cp ../lib/libezfio.a ../lib/libezfio_irp.a
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||||
$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o system_c.o system_f.o
|
||||
$(AR) dv ../lib/libezfio_irp.a irp_stack.irp.o
|
||||
$(RANLIB) ../lib/libezfio_irp.a
|
||||
|
||||
|
||||
../Python/ezfio.py: ../lib/libezfio.a
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||||
python2 create_python.py
|
||||
$(PYTHON) create_python.py
|
||||
|
||||
../Ocaml/ezfio.ml: ../lib/libezfio.a
|
||||
python2 create_ocaml.py
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$(PYTHON) create_ocaml.py
|
||||
|
||||
|
||||
|
@ -148,7 +148,7 @@ subroutine ezfio_set_file(filename_in)
|
||||
|
||||
character*(*) :: filename_in
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||||
character(8) :: date
|
||||
character(10) :: time
|
||||
character(73) :: time
|
||||
character(32) :: user
|
||||
|
||||
if (filename_in == '') then
|
||||
@ -163,13 +163,13 @@ subroutine ezfio_set_file(filename_in)
|
||||
|
||||
! using keyword arguments
|
||||
call date_and_time(DATE=date,TIME=time)
|
||||
open (unit=10, file=trim(libezfio_filename)//'/ezfio/creation', ACTION='WRITE', STATUS='UNKNOWN')
|
||||
write(10,*), time, ' ', date
|
||||
close(10)
|
||||
open (unit=10, file=trim(libezfio_filename)//'/ezfio/user', ACTION='WRITE', STATUS='UNKNOWN')
|
||||
open (unit=73, file=trim(libezfio_filename)//'/ezfio/creation', ACTION='WRITE', STATUS='UNKNOWN')
|
||||
write(73,*) time, ' ', date
|
||||
close(73)
|
||||
open (unit=73, file=trim(libezfio_filename)//'/ezfio/user', ACTION='WRITE', STATUS='UNKNOWN')
|
||||
call getenv('USER',user)
|
||||
write(10,*) user
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||||
close(10)
|
||||
write(73,*) user
|
||||
close(73)
|
||||
endif
|
||||
|
||||
TOUCH libezfio_filename
|
||||
|
@ -22,6 +22,7 @@
|
||||
! 31062 Toulouse Cedex 4
|
||||
! scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
BEGIN_PROVIDER [ integer, PID ]
|
||||
&BEGIN_PROVIDER [ character*(256), PID_str ]
|
||||
implicit none
|
||||
@ -64,7 +65,7 @@ subroutine ezfio_mkdir(path)
|
||||
call ezfio_error(irp_here,'Read-only file.')
|
||||
endif
|
||||
if (.not.ezfio_exists(path)) then
|
||||
call mkdir(trim(path))
|
||||
call mkdir(trim(path)//char(0))
|
||||
open(unit=libezfio_iunit,file=trim(path)//'/.version')
|
||||
write(libezfio_iunit,'(A)') libezfio_version
|
||||
close(libezfio_iunit)
|
||||
@ -73,6 +74,7 @@ end subroutine
|
||||
|
||||
|
||||
subroutine libezfio_openz(filename,mode,err)
|
||||
use system
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! Opens a compressed file
|
||||
@ -84,7 +86,7 @@ subroutine libezfio_openz(filename,mode,err)
|
||||
err=1
|
||||
|
||||
if (mode(1:1) == 'r') then
|
||||
call system('zcat '//trim(filename)//' > '//trim(fifo))
|
||||
call zcat(trim(filename)//char(0), trim(fifo)//char(0))
|
||||
open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='READ')
|
||||
err=0
|
||||
else if (mode(1:1) == 'w') then
|
||||
@ -118,6 +120,7 @@ subroutine libezfio_reopenz_unformatted(filename,mode,err)
|
||||
end
|
||||
|
||||
subroutine libezfio_closez(filename,mode)
|
||||
use system
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! Closes a compressed file
|
||||
@ -127,7 +130,7 @@ subroutine libezfio_closez(filename,mode)
|
||||
fifo = trim(filename)//'.'//trim(PID_str)
|
||||
if (mode(1:1) == 'w') then
|
||||
close(unit=libezfio_iunit)
|
||||
call system('gzip -c < '//trim(fifo)//' > '//trim(filename))
|
||||
call gzip(trim(fifo)//char(0), trim(filename)//char(0))
|
||||
open(unit=libezfio_iunit,file=trim(fifo),form='FORMATTED',action='WRITE')
|
||||
endif
|
||||
close(unit=libezfio_iunit,status='DELETE')
|
||||
|
45
src/system.c
Normal file
45
src/system.c
Normal file
@ -0,0 +1,45 @@
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include <assert.h>
|
||||
#include "zlib.h"
|
||||
|
||||
#include <sys/stat.h>
|
||||
#include <sys/types.h>
|
||||
#include <errno.h>
|
||||
|
||||
|
||||
|
||||
void fortran_mkdir(char* filename) {
|
||||
if (mkdir (filename, S_IRWXU)) {
|
||||
perror (strerror (errno));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#define BUFSIZE 16384
|
||||
void gzip(char* filename, char* output) {
|
||||
FILE* in = fopen(filename,"r");
|
||||
gzFile out = gzopen(output,"w");
|
||||
char buffer[BUFSIZE];
|
||||
unsigned int size;
|
||||
while (!feof(in)) {
|
||||
size = (unsigned int) fread (buffer, sizeof(char), BUFSIZE, in);
|
||||
gzwrite(out, buffer, size);
|
||||
}
|
||||
fclose(in);
|
||||
gzclose(out);
|
||||
}
|
||||
|
||||
void zcat(char* filename, char* output) {
|
||||
gzFile in = gzopen(filename,"r");
|
||||
FILE* out = fopen(output,"w");
|
||||
char buffer[BUFSIZE];
|
||||
int size;
|
||||
while (!gzeof(in)) {
|
||||
size = gzread (in, buffer, BUFSIZE);
|
||||
fwrite(buffer, sizeof(char), (size_t) size, out);
|
||||
}
|
||||
gzclose(in);
|
||||
fclose(out);
|
||||
}
|
||||
|
@ -1,13 +0,0 @@
|
||||
#include <sys/stat.h>
|
||||
#include <sys/types.h>
|
||||
#include <errno.h>
|
||||
#include <string.h>
|
||||
|
||||
|
||||
void ezfio_mkdir(char* filename) {
|
||||
errno = 0;
|
||||
if (mkdir (filename, S_IRWXU)) {
|
||||
perror (strerror (errno));
|
||||
}
|
||||
}
|
||||
|
@ -1,5 +1,4 @@
|
||||
MODULE system
|
||||
|
||||
module system
|
||||
USE iso_c_binding
|
||||
|
||||
INTERFACE
|
||||
@ -7,6 +6,19 @@ MODULE system
|
||||
USE iso_c_binding
|
||||
CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
|
||||
END SUBROUTINE
|
||||
END INTERFACE
|
||||
|
||||
END MODULE
|
||||
SUBROUTINE gzip(filename,output) BIND(C,name="gzip")
|
||||
USE iso_c_binding
|
||||
CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
|
||||
CHARACTER(kind=C_CHAR),INTENT(in) :: output(*)
|
||||
END SUBROUTINE
|
||||
|
||||
SUBROUTINE zcat(filename,output) BIND(C,name="zcat")
|
||||
USE iso_c_binding
|
||||
CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
|
||||
CHARACTER(kind=C_CHAR),INTENT(in) :: output(*)
|
||||
END SUBROUTINE
|
||||
|
||||
END INTERFACE
|
||||
end module
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user