Port the preprocessing/meshing folder from the SeisSol repository to here

cmake/FindNetCDF.cmake

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+#[==[
+Provides the following variables:
+
+  * `NetCDF_FOUND`: Whether NetCDF was found or not.
+  * `NetCDF_INCLUDE_DIRS`: Include directories necessary to use NetCDF.
+  * `NetCDF_LIBRARIES`: Libraries necessary to use NetCDF.
+  * `NetCDF_VERSION`: The version of NetCDF found.
+  * `NetCDF::NetCDF`: A target to use with `target_link_libraries`.
+#]==]
+
+# Stolen from VTK with some small modifications
+# https://github.com/Kitware/VTK/blob/master/CMake/FindNetCDF.cmake
+# (BSD 3-Clause License)
+
+#[[=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    Copyright.txt
+
+Copyright (c) 1993-2015 Ken Martin, Will Schroeder, Bill Lorensen
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+ * Neither name of Ken Martin, Will Schroeder, or Bill Lorensen nor the names
+   of any contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+=========================================================================]]
+# Note: The version from VTK tries to first find a CMake built version of CMake and then
+# a pkgConf built one. This doesn't work on all systems with custom built versions of
+# CMake + HDF5.
+# Thus, first try to find it manually, then fall back on CMake/PkgConfig
+
+find_path(NetCDF_INCLUDE_DIR
+  NAMES netcdf.h
+  HINTS $ENV{NETCDF_DIR}/include $ENV{NETCDF_INCLUDE_DIR}
+  DOC "netcdf include directories")
+mark_as_advanced(NetCDF_INCLUDE_DIR)
+
+find_library(NetCDF_LIBRARY
+  NAMES netcdf
+  HINTS $ENV{NETCDF_DIR}/lib $ENV{NETCDF_LIB_DIR}
+  DOC "netcdf library")
+mark_as_advanced(NetCDF_LIBRARY)
+
+string(REGEX REPLACE "(.*)libnetcdf\.(so|a)" "\\1" NetCDF_LIBRARY_DIR "${NetCDF_LIBRARY}")
+mark_as_advanced(NetCDF_LIBRARY_DIR)
+
+if (NetCDF_INCLUDE_DIR)
+  file(STRINGS "${NetCDF_INCLUDE_DIR}/netcdf_meta.h" _netcdf_version_lines
+    REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)")
+  string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}")
+  set(NetCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}")
+  unset(_netcdf_version_major)
+  unset(_netcdf_version_minor)
+  unset(_netcdf_version_patch)
+  unset(_netcdf_version_note)
+  unset(_netcdf_version_lines)
+endif ()
+
+if (NetCDF_FOUND)
+  set(NetCDF_INCLUDE_DIRS "${NetCDF_INCLUDE_DIR}")
+  set(NetCDF_LIBRARIES "${NetCDF_LIBRARY}")
+
+  if (NOT TARGET NetCDF::NetCDF)
+    add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
+    set_target_properties(NetCDF::NetCDF PROPERTIES
+      IMPORTED_LOCATION "${NetCDF_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${NetCDF_INCLUDE_DIR}")
+  endif ()
+else()
+  # Try to find a CMake-built NetCDF.
+  find_package(netCDF CONFIG QUIET)
+  if (netCDF_FOUND)
+    # Forward the variables in a consistent way.
+    set(NetCDF_FOUND "${netCDF_FOUND}")
+    set(NetCDF_INCLUDE_DIRS "${netCDF_INCLUDE_DIR}")
+    set(NetCDF_LIBRARIES "${netCDF_LIBRARIES}")
+    set(NetCDF_VERSION "${NetCDFVersion}")
+    if (NOT TARGET NetCDF::NetCDF)
+      add_library(NetCDF::NetCDF INTERFACE IMPORTED)
+      set_target_properties(NetCDF::NetCDF PROPERTIES
+        INTERFACE_LINK_LIBRARIES "${NetCDF_LIBRARIES}")
+    endif ()
+    # Skip the rest of the logic in this file.
+    return ()
+  endif ()
+
+  find_package(PkgConfig QUIET)
+  if (PkgConfig_FOUND)
+    pkg_check_modules(_NetCDF QUIET netcdf IMPORTED_TARGET)
+    if (_NetCDF_FOUND)
+      # Forward the variables in a consistent way.
+      set(NetCDF_FOUND "${_NetCDF_FOUND}")
+      set(NetCDF_INCLUDE_DIRS "${_NetCDF_INCLUDE_DIRS}")
+      set(NetCDF_LIBRARIES "${_NetCDF_LIBRARIES}")
+      set(NetCDF_VERSION "${_NetCDF_VERSION}")
+      if (NOT TARGET NetCDF::NetCDF)
+        add_library(NetCDF::NetCDF INTERFACE IMPORTED)
+        set_target_properties(NetCDF::NetCDF PROPERTIES
+          INTERFACE_LINK_LIBRARIES "PkgConfig::_NetCDF")
+      endif ()
+      # Skip the rest of the logic in this file.
+      return ()
+    endif ()
+  endif ()
+endif ()
+
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(NetCDF
+  REQUIRED_VARS NetCDF_LIBRARY NetCDF_INCLUDE_DIR
+  VERSION_VAR NetCDF_VERSION)
+

cmake/README.md

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+A selective copy of the CMake files from the SeisSol main repository.

cube/cubeGenerator.py

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+#!/usr/bin/python
+##
+# @file
+# This file is part of SeisSol.
+#
+# @author Sebastian Rettenberger (rettenbs AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Sebastian_Rettenberger,_M.Sc.)
+#
+# @section LICENSE
+# Copyright (c) 2013, SeisSol Group
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+from lib.args import Args
+from lib.gambit import GambitWriter
+from lib.mesh import Mesh
+
+import operator
+
+def main():
+    # Parse command line arguements
+    args = Args()
+
+    print 'Generating mesh with size', ', '.join(map(str, args.size()))
+
+    # Create Mesh
+    mesh = Mesh(args.size(), args.boundary())
+
+    print 'Number of elements:', len(mesh.elements())
+
+    # Write mesh
+    if args.netcdf():
+        try:
+            from lib.netcdf import NetcdfWriter
+        except ImportError, e:
+            print 'netcdf4-python could not be loaded:', e
+            return
+        print 'Mesh will contain', ' * '.join(map(str, args.partitions())), '=', reduce(operator.mul, args.partitions(), 1), 'partitions'
+        NetcdfWriter(mesh, args.partitions(), args.outputFile())
+    else:
+        GambitWriter(mesh, args.outputFile())
+
+if __name__ == '__main__':
+    main()

cube/lib/__init__.py

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+#!/usr/bin/python
+##
+# @file
+# This file is part of SeisSol.
+#
+# @author Sebastian Rettenberger (rettenbs AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Sebastian_Rettenberger,_M.Sc.)
+#
+# @section LICENSE
+# Copyright (c) 2013, SeisSol Group
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.

cube/lib/args.py

@@ -0,0 +1,111 @@
+#! /usr/bin/python
+##
+# @file
+# This file is part of SeisSol.
+#
+# @author Sebastian Rettenberger (rettenbs AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Sebastian_Rettenberger,_M.Sc.)
+#
+# @section LICENSE
+# Copyright (c) 2013, SeisSol Group
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+import argparse
+import operator
+import sys
+
+class Args:
+    """Parses the command line arguments using
+    argparse.ArgumentParser"""
+
+    def __init__(self):
+        parser = argparse.ArgumentParser(prog='cubeGenerator')
+        parser.add_argument('-s', '--size', type=int,
+            help='number of cubes in each dimensions')
+        parser.add_argument('-x', '--size-x', type=int,
+            help='number of cubes in x dimension')
+        parser.add_argument('-y', '--size-y', type=int,
+            help='number of cubes in y dimension')
+        parser.add_argument('-z', '--size-z', type=int,
+            help='number of cubes in z dimension')
+        parser.add_argument('--px', type=int,
+            help='number of partitions x dimension')
+        parser.add_argument('--py', type=int,
+            help='number of partitions in y dimension')
+        parser.add_argument('--pz', type=int,
+            help='number of partitions in z dimension')
+        parser.add_argument('-o', '--output', type=argparse.FileType('w'),
+            required=True, help='output file for resulting Gambit or netCDF mesh')
+        parser.add_argument('-n', '--netcdf', action='store_true',
+            help='Create netCDF files'),
+        parser.add_argument('-b', '--boundary', type=int,
+            help='boundary condition (default 106 = periodic)', default=106)
+        parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.1')
+
+        try:
+            # Parse cmd line options
+            self.__options = parser.parse_args(sys.argv[1:])
+            if self.__options.size == None \
+                and (self.__options.size_x == None \
+                     or self.__options.size_y == None \
+                     or self.__options.size_z == None):
+                raise IOError('Either size or x/y/z is required')
+
+            if self.__options.netcdf:                
+                partitions = [getattr(self.__options, 'p'+i) for i in ['x', 'y', 'z']]
+                p = sum(p != None for p in partitions)
+                if p != 3:
+                    raise IOError('Number of partitions is required for netCDF files')
+
+        except IOError, e:
+            parser.error(str(e))
+
+        # Set correct size options
+        self.__options.size = [self.__options.size for _ in range(3)]
+
+        if self.__options.size_x != None:
+            self.__options.size[0] = self.__options.size_x
+        if self.__options.size_y != None:
+            self.__options.size[1] = self.__options.size_y
+        if self.__options.size_z != None:
+            self.__options.size[2] = self.__options.size_z
+
+    def size(self):
+        return self.__options.size
+
+    def outputFile(self):
+        return self.__options.output
+
+    def boundary(self):
+        return self.__options.boundary
+
+    def netcdf(self):
+        return self.__options.netcdf
+
+    def partitions(self):
+        return (self.__options.px, self.__options.py, self.__options.pz)