started SfePy, based on sfe-release-00.35.01.tgz

INSTALL.txt

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+# 19.01.2007
+# last revision: 14.12.2007
+
+This is not for faint of the heart!
+
+Installation prerequisites:
+    latest (SVN) numpy, scipy (with umfpack support), swig
+
+Dependencies:
+    matplotlib, pyparsing, umfpack, pytables
+    eigen.py can use symeig
+
+Not tested on Windows, I don't have them.
+
+Compiling:
+----------
+1. Edit the Makefile.
+  - compiler, swig command
+  - location of python and numpy include files
+2. 'make'
+
+Installation:
+-------------
+None. Run the executable script 'simple.py' in the top-level directory of the
+distribution (TOPDIR).
+
+Testing:
+--------
+
+Run './runTests.py --filter' or './runTests.py --filter-more' in TOPDIR.
+
+Tests that save results save them into TOPDIR/output-tests directory. View the
+results (*.vtk) with a VTK-capable viewer (e.g. paraview, mayavi2).
+
+If all is ok, four failed tests (of 20) should be reported. The failed tests
+cover code not included in the distribution; they are:
+test_input_pfdpm_permeability.py, test_input_stabilized_navier_stokes.py and
+test_boundaryFluxes() of test_laplace_unit_disk.py,
+test_laplace_unit_square.py.
+
+If you get more failures, be sure to verify that you have the latest SVN
+version of Numpy and SciPy installed (should be at least '0.7.0.dev3649' for
+SciPy and '1.0.5.dev4571' for NumPy).
+Verify also your pytables installation (possible test_io.py failures).

Makefile

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+# 14.12.2004, c
+# last revision: 14.12.2007
+VERSION := 00.35.01
+PROJECTNAME := sfe
+
+############### Edit here. #######################################
+
+ARCH	:= linux
+#ARCH	:= cygwin
+
+ifeq ($(ARCH),linux)
+  C++         := gcc
+  CC          := gcc
+  SWIG        := swig
+  DATE        := date +%Y_%m_%d
+
+#  OPTFLAGS     := -g -pg -fPIC -DPIC
+  OPTFLAGS     := -g -O2 -fPIC -DPIC
+  CARCHFLAGS   := -Wall -c
+  CARCHOUT     := -o
+
+  PYTHON_INCL  := -I/usr/include/python2.4 -I/home/share/software/include -I/usr/lib/python2.4/site-packages/numpy/core/include
+#  SWIG_LIB     := -lswigpy
+
+  EXT_INCL     := $(PYTHON_INCL)
+endif
+
+#DEBUG_FLAGS := -DDEBUG_FMF -DDEBUG_MESH
+DEBUG_FLAGS := -DDEBUG_FMF
+#DEBUG_FLAGS :=
+
+################ Do not edit below! ##############################
+
+ISRELEASE := 1
+MODULES := eldesc input sfe sfe/base sfe/fem sfe/fem/extmods sfe/homogenization sfe/solvers sfe/terms sfe/terms/extmods tests
+ifndef ISRELEASE
+  MODULES += sfe/optimize
+else
+  DEBUG_FLAGS :=
+endif
+VERSIONH := sfe/fem/extmods/version.h
+ALLTARGETS := version modules
+
+CUR_DIR := $(shell pwd)
+
+DISTFILES_TOP := btrace_python Makefile DIARY VERSION findSurf.py init_sfe.py shaper.py test.mesh genDocs.py genPerMesh.py homogen.py extractor.py plotPerfusionCoefs.py runTests.py simple.py eigen.py TODO INSTALL.txt README.txt
+RELDISTFILES_TOP := btrace_python Makefile VERSION init_sfe.py extractor.py findSurf.py genDocs.py genPerMesh.py runTests.py simple.py eigen.py INSTALL.txt README.txt RELEASE_NOTES.txt
+SUBDIRS = database doc eldesc input para script sfe tests umfpack
+RELSUBDIRS = database doc eldesc input script sfe tests
+DATADIRS := database
+DATADISTDIR := $(PROJECTNAME)-data-$(shell $(DATE))
+DISTDIR := $(PROJECTNAME)-$(VERSION)
+RELDISTDIR := $(PROJECTNAME)-release-$(VERSION)
+BKUPDIR = 00backup-$(notdir $(PROJECTNAME))
+
+####### Default rule
+
+all:	$(ALLTARGETS)
+	echo $(DATADIR)
+	@echo All done.
+
+##################################################################
+
+INCL         :=
+SRCPYFILES   := 
+SRCCFILES    :=
+HDRCFILES    :=
+CLEANFILES   :=
+SRC_LIBSWIG  :=
+
+# include the description for each module
+include $(patsubst %,%/Makefile.inc,$(MODULES))
+INCL += $(patsubst %,-I%,$(MODULES))
+
+CFLAGS := $(OPTFLAGS) -D__SDIR__='"${LOCDIR}"' ${DEBUG_FLAGS} ${INCL} ${EXT_INCL} $(CARCHFLAGS)
+
+ifdef ISRELEASE
+  CFLAGS += -DISRELEASE
+  SWIGFLAGS := -DISRELEASE
+endif
+
+####### Implicit rules
+
+%_wrap.c: %.i
+#	$(SWIG) -noruntime -python $(INCL)  ${EXT_INCL} -o $@ $<
+	$(SWIG) -python $(INCL)  ${EXT_INCL} $(SWIGFLAGS) -o $@ $<
+
+%_wrap.o: %_wrap.c
+	$(CC) $(CFLAGS) $< $(CARCHOUT) $@
+
+%.o : %.c
+	$(CC) $(CFLAGS) $< $(CARCHOUT) $@
+
+####### Build rules
+
+.PHONY : tags version dist reldist htmldocs save backup clean
+
+modules: sfe/fem/extmods/version.h $(SRC_LIBSWIG)
+	@echo Python modules done.
+	@echo ""
+
+#$(SRC_LIBSWIG): $(SRC_OBJSWIG) $(SRC_OBJC)
+#	@echo $(SRC_SRCSWIG)
+#	@echo $(SRC_OBJSWIGC)
+#	@echo $(SRC_OBJSWIG)
+#	@echo $(SRC_OBJSWIGPY)
+#	@echo $(SRC_LIBSWIG)
+#	@echo $(SRC_OBJC)
+#	$(CC) -shared -fPIC -DPIC $< $(SRC_OBJC) $(SWIG_LIB) -o $@
+#
+$(VERSIONH) : Makefile
+	sed "s|^\(#define VERSION\) \"[0-9.]*\"|\1 \"$(VERSION)\"|;" $(VERSIONH).in > $(VERSIONH)
+
+clean:
+	-rm -f *.o *.bak *~ *% *tgz #*
+	-rm -f $(CLEANFILES)
+
+tags: clear_tags c_tags python_tags
+
+clear_tags:
+	-rm -f TAGS
+
+c_tags:
+	-etags -a $(SRCCFILES) $(HDRCFILES)
+
+python_tags:
+	-etags -a $(SRCPYFILES)
+
+version:
+	echo $(VERSION) > 'VERSION'
+
+dist: version
+	-mkdir $(DISTDIR)
+	rm -rf $(DISTDIR)/*
+	for i in $(DISTFILES_TOP); do cp -fpd $$i $(DISTDIR)/$$i; done
+	@for i in $(SUBDIRS); do \
+          $(MAKE) -C $$i -f Makefile.dist dist DISTDIR=${CUR_DIR}/$(DISTDIR); \
+	done
+	tar cf $(DISTDIR).tar $(DISTDIR)
+	gzip -f --best $(DISTDIR).tar
+	mv $(DISTDIR).tar.gz $(DISTDIR).tgz
+	rm -rf $(DISTDIR)
+
+reldist: version
+	-./genDocs.py --omit="termsAdjointNavierStokes termsHDPM  cachesHDPM  cachesBasic"
+	-cp -fpd tmp/terms.pdf doc/tex/
+	-mkdir $(RELDISTDIR)
+	rm -rf $(RELDISTDIR)/*
+	for i in $(RELDISTFILES_TOP); do cp -fpd $$i $(RELDISTDIR)/$$i; done
+	@for i in $(RELSUBDIRS); do \
+          $(MAKE) -C $$i -f Makefile.dist reldist DISTDIR=${CUR_DIR}/$(RELDISTDIR); \
+	done
+	mkdir $(RELDISTDIR)/output-tests
+	sed "s|ISRELEASE \:\=|ISRELEASE \:\= 1|;" $(RELDISTDIR)/Makefile > $(RELDISTDIR)/Makefile2
+	mv -f $(RELDISTDIR)/Makefile2 $(RELDISTDIR)/Makefile
+	tar cf $(RELDISTDIR).tar $(RELDISTDIR)
+	gzip -f --best $(RELDISTDIR).tar
+	mv -f $(RELDISTDIR).tar.gz $(RELDISTDIR).tgz
+	rm -rf $(RELDISTDIR)
+
+databackup:
+	-mkdir $(DATADISTDIR)
+	rm -rf $(DATADISTDIR)/*
+	for i in $(DATADIRS); do cp -fa $$i $(DATADISTDIR)/$$i; done
+	tar cf $(DATADISTDIR).tar $(DATADISTDIR)
+	gzip -f --best $(DATADISTDIR).tar
+	mv $(DATADISTDIR).tar.gz $(DATADISTDIR).tgz
+	rm -rf $(DATADISTDIR)
+	mv -f $(DATADISTDIR).tgz $(BKUPDIR)/$(DATADISTDIR).tgz
+
+backup: dist
+	-mkdir $(BKUPDIR)
+	mv -f $(DISTDIR).tgz $(BKUPDIR)/$(DISTDIR).tgz
+
+save: backup
+	-mount /mnt/floppy
+	cp -f  $(BKUPDIR)/$(DISTDIR).tgz /mnt/floppy/
+	umount /mnt/floppy
+
+htmldocs:
+	-rm -rf doc/html
+	-rm -f doc/doxygenrc
+	-mkdir doc/aux
+	-pythfilter.py . doc/aux/
+	sed "s|^\(PROJECT_NUMBER         = \)NUMBER|\1$(VERSION)|;"\
+	doc/doxygen.config > doc/doxygenrc
+	doxygen doc/doxygenrc
+	-rm -rf doc/aux

README.txt

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+See INSTALL.txt for installation instructions.

RELEASE_NOTES.txt

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+# created: 20.07.2007 (-1)
+# last revision: 14.12.2007
+
+from 00.31.06 to 00.35.01:
+==========================
+- per term integration, major rewrite of sfe.fem and related:
+    - term.integral.domain( arguments ) syntax
+    - 'integral_*' keyword for input files
+    - each term can use its own quadrature points
+    - 'field' keyword syntax changed
+
+- minor:
+    - genDocs.py: PDF term documentation generator
+
+from 00.26.01 to 00.31.06:
+==========================
+
+- acoustic band gaps determination:
+    - zones of frequencies where elastic waves do not prapagate
+    - based on homogenization of material made of small inclusions periodically
+    embedded in an elastic matrix
+    - run via 'eigen.py'
+- general linear combination boundary conditions - 'lcbc' keyword:
+    - rigid body motion constraint imposed on regions
+- new Solver classes, solver reorganization:
+    - all solvers now configured in a uniform way ('solver_[0-9]+' keywords)
+    - specify solvers using 'options' keyword
+- new terms:
+    - dot product in a volume or on a surface region
+    - vector field mass term
+    - scalar field "mass", fine-coarse scalar "mass" terms:
+        - used for coarse mesh -> fine mesh interpolation of scalar fields
+
+- minor:
+    - added updated findSurf.py into distribution - extract surface from a mesh
+    - script/kill_*
+    - script/writeMesh2D.m
+    - script/writeSparseMatrixHDF5.m
+
+from 00.22.02 to 00.26.01:
+==========================
+
+- testing framework (in the spirit of unit tests):
+    - particularly tests that standard input files work
+    - runTests.py: output filtering
+- linear spring term (kind of a relaxed Dirichlet BC on node displacements)
+- volume term
+- Laplace term in 2D
+- chained periodic boundary conditions resolving
+- new options for simple.py: --save-field-meshes, --solve-not
+- periodic mesh merger (genPerMesh.py)
+
+- minor:
+    - improved region saving
+    - growing term data cache
+    - sparse matrix saving into HDF5
+    - point dof connectivity and geometry
+    - region handling improvements (canCells flag)
+    - nonlinear solver status reporting
+    - distribution: test and example meshes included in the release tarball

VERSION

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+00.35.01

btrace_python

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+#!/bin/sh
+# 15.12.2004, c
+gdb --quiet --core=core --se=/usr/bin/python

database/MANIFEST

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+kostka_big.mesh
+kostka_medium.mesh
+kostka_medium_tetra.mesh
+plackaplacata.mesh
+pul_klikatak.mesh
+pul_klikatak2.mesh
+simple.mesh
+triplacka.mesh
+triplackaquad.mesh
+triplackasmooth.mesh
+tristverec.mesh
+tristverec2.mesh

database/Makefile.dist

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+# 19.07.2007, c
+# last revision: 23.10.2007
+
+CDIR = $(notdir $(CURDIR))
+DESTDIR = $(DISTDIR)/$(CDIR)
+
+DISTFILES := Makefile.dist MANIFEST
+DISTDIRS := tests phono
+
+RELDISTFILES := $(DISTFILES) $(shell cat MANIFEST)
+RELDISTDIRS := $(DISTDIRS)
+
+dist:
+#	echo $(DESTDIR)
+	mkdir $(DESTDIR)
+	cp -fpd $(DISTFILES) $(DESTDIR)
+	@for i in $(DISTDIRS); do \
+	  $(MAKE) -C $$i -f Makefile.dist dist DISTDIR=${DESTDIR}; \
+	done
+
+reldist:
+	mkdir $(DESTDIR)
+	cp -fpd $(RELDISTFILES) $(DESTDIR)
+	@for i in $(RELDISTDIRS); do \
+	  $(MAKE) -C $$i -f Makefile.dist reldist DISTDIR=${DESTDIR}; \
+	done