[xmds2] branch upstream updated (26b3322 -> 81c1c6b)
Rafael Laboissière
rlaboiss-guest at moszumanska.debian.org
Tue Jan 14 00:03:04 UTC 2014
This is an automated email from the git hooks/post-receive script.
rlaboiss-guest pushed a change to branch upstream
in repository xmds2.
from 26b3322 Imported Upstream version 2.1.4
new 81c1c6b Imported Upstream version 2.2.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
ReleaseNotes | 16 +
admin/TODO | 70 -
admin/create_release_version.sh | 49 -
admin/developer-doc-source/FFTW3MPI Design.graffle | Bin 94768 -> 0 bytes
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admin/userdoc-source/xsil2graphics2.rst | 8 -
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admin/xpdeint.tmbundle/info.plist | 15 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 45 -
debian/copyright | 31 -
debian/docs | 3 -
debian/pycompat | 1 -
debian/pyversions | 1 -
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debian/xmds2.manpages | 2 -
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documentation/latex/sphinxmanual.cls | 16 +-
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documentation/latex/xmds2.idx | 196 +
documentation/latex/xmds2.ilg | 8 +-
documentation/latex/xmds2.ind | 257 +
documentation/latex/xmds2.log | 990 ++-
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documentation/latex/xmds2.pdf | Bin 6678016 -> 7331787 bytes
documentation/latex/xmds2.tex | 1803 ++--
documentation/latex/xmds2.toc | 154 +-
documentation/licensing.html | 222 +-
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documentation/searchindex.js | 2 +-
documentation/tutorial.html | 24 +-
documentation/upgrade.html | 20 +-
documentation/worked_examples.html | 84 +-
documentation/xsil2graphics2.html | 24 +-
examples/2DMultistateSE.xmds | 14 +-
examples/bessel_cosine_groundstate.xmds | 2 +-
examples/bessel_cosine_stochastic_groundstate.xmds | 2 +-
...orm2.xmds => bessel_neumann_wave_equation.xmds} | 14 +-
examples/bessel_transform.xmds | 2 +-
examples/bessel_transform2.xmds | 2 +-
examples/cpc_ex_scaling.xmds | 2 +-
examples/cpc_example1.xmds | 2 +-
examples/cpc_example2.xmds | 2 +-
examples/cpc_example3.xmds | 2 +-
examples/cpc_example4.xmds | 17 +-
examples/cpc_example4_3d.xmds | 22 +-
examples/cpc_example5.xmds | 2 +-
examples/cpc_example6.xmds | 2 +-
examples/cpc_ip_scaling.xmds | 2 +-
examples/diffusion.xmds | 2 +-
examples/diffusion_arguments.xmds | 2 +-
examples/diffusion_dst.xmds | 2 +-
examples/diffusion_mpi.xmds | 2 +-
examples/diffusion_openmp.xmds | 2 +-
examples/diffusion_win.xmds | 2 +-
examples/excitedstate_gaussian.xmds | 2 +-
examples/fibre.xmds | 2 +-
examples/fibre_noisevectors.xmds | 2 +-
examples/groundstate_demo2.xmds | 2 +-
examples/groundstate_gaussian.xmds | 2 +-
examples/groundstate_workedexamples.xmds | 2 +-
examples/hermitegauss_groundstate.xmds | 2 +-
examples/hermitegauss_transform.xmds | 2 +-
examples/hermitegauss_transform_2d.xmds | 2 +-
examples/hermitegauss_transform_2d_mpi.xmds | 2 +-
examples/nlse.xmds | 2 +-
examples/schroedinger_gaussian.xmds | 2 +-
examples/sine_cross.xmds | 4 +-
examples/vibstring.xmds | 2 +-
examples/vibstring2.xmds | 2 +-
examples/vibstring3.xmds | 4 +-
examples/vibstring_circle.xmds | 2 +-
examples/vibstring_circle_mpi.xmds | 2 +-
examples/vibstring_circle_spectral.xmds | 4 +-
examples/vibstring_dct.xmds | 2 +-
examples/vibstring_dirichlet_boundary.xmds | 2 +-
examples/vibstring_dirichlet_boundary2.xmds | 2 +-
examples/vibstring_ellipse.xmds | 2 +-
examples/wigner.xmds | 2 +-
examples/wigner_argument_mpi.xmds | 2 +-
examples/wigner_spectral.xmds | 2 +-
man/xsil2graphics2.1 | 15 +-
run_tests.py | 39 +-
setup.py | 4 +-
testsuite/fast/RbGSdipoles.xmds | 6 +-
{examples => testsuite/fast}/cpc_example4.xmds | 41 +-
testsuite/fast/cpc_example4_expected.h5 | Bin 0 -> 84896 bytes
testsuite/fast/cpc_example4_expected.xsil | 127 +
testsuite/features/arguments.xmds | 8 +-
testsuite/features/space in filename.xmds | 8 +-
.../error_scaling/do_not_run_tests_by_default | 0
.../exponential_scaling_10thOrder.xmds | 8064 ++++++++++++++++++
.../exponential_scaling_10thOrder_expected.xsil | 8584 +++++++++++++++++++
.../exponential_scaling_2ndOrder.xmds | 8065 ++++++++++++++++++
.../exponential_scaling_2ndOrder_expected.xsil | 8585 ++++++++++++++++++++
.../exponential_scaling_4thOrder.xmds | 8064 ++++++++++++++++++
.../exponential_scaling_4thOrder_expected.xsil | 8584 +++++++++++++++++++
.../exponential_scaling_6thOrder.xmds | 8064 ++++++++++++++++++
.../exponential_scaling_6thOrder_expected.xsil | 8584 +++++++++++++++++++
.../exponential_scaling_8thOrder.xmds | 8064 ++++++++++++++++++
.../exponential_scaling_8thOrder_expected.xsil | 8584 +++++++++++++++++++
.../error_scaling/logplotall.gp | 58 +
.../error_scaling/plot_error_data.py | 46 +
.../vibstring_mm.xmds} | 10 +-
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.../vibstring_re.xmds} | 12 +-
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.../vibstring_re_expected_mg1.dat | Bin 0 -> 20824 bytes
...mpi_paths.xmds => kubo_adaptive_mpi_paths.xmds} | 10 +-
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...kubo_integer_dimensions_mpi_break_expected.xsil | 29 +-
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testsuite/mpi/kubo_mpi_paths.xmds | 2 +-
...complex_ip.xmds => constant_complex_ip_2d.xmds} | 17 +-
....xmds => constant_complex_separated_ip_2d.xmds} | 29 +-
...ant_double_ip.xmds => constant_real_ip_2d.xmds} | 17 +-
...e_expected.xsil => derivative_2d_expected.xsil} | 46 +-
testsuite/operators/derivative_2d_expected_mg0.dat | Bin 0 -> 205544 bytes
...plex_ip.xmds => nonconstant_complex_ip_2d.xmds} | 15 +-
...ds => nonconstant_complex_separated_ip_2d.xmds} | 27 +-
..._double_ip.xmds => nonconstant_real_ip_2d.xmds} | 15 +-
.../transforms/bessel_neumann_wave_equation.xmds | 18 +-
.../bessel_neumann_wave_equation_expected.h5 | Bin 0 -> 181632 bytes
... => bessel_neumann_wave_equation_expected.xsil} | 53 +-
xpdeint/Features/Arguments.py | 6 +-
xpdeint/Features/AsciiFormat.py | 6 +-
xpdeint/Features/AutoVectorise.py | 6 +-
xpdeint/Features/Benchmark.py | 6 +-
xpdeint/Features/BinaryFormat.py | 36 +-
xpdeint/Features/BinaryFormat.tmpl | 10 +-
xpdeint/Features/Bing.py | 6 +-
xpdeint/Features/CFlags.py | 6 +-
xpdeint/Features/ChunkedOutput.py | 6 +-
xpdeint/Features/Diagnostics.py | 6 +-
xpdeint/Features/ErrorCheck.py | 6 +-
xpdeint/Features/Globals.py | 6 +-
xpdeint/Features/HDF5Format.py | 265 +-
xpdeint/Features/HDF5Format.tmpl | 7 +
xpdeint/Features/HaltNonFinite.py | 6 +-
xpdeint/Features/MaxIterations.py | 6 +-
xpdeint/Features/OpenMP.py | 6 +-
xpdeint/Features/Output.py | 6 +-
xpdeint/Features/OutputFormat.py | 10 +-
xpdeint/Features/Stochastic.py | 6 +-
xpdeint/Features/Transforms/Basis.py | 6 +-
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xpdeint/Features/Transforms/BesselBasis.tmpl | 2 +-
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xpdeint/Features/Transforms/EPBasis.py | 6 +-
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xpdeint/Features/Transforms/HermiteGaussEPBasis.py | 6 +-
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xpdeint/Geometry/DimensionRepresentation.py | 6 +-
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xpdeint/Geometry/UniformDimensionRepresentation.py | 6 +-
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xpdeint/HDF5.py | 28 +-
xpdeint/MomentGroupElement.py | 6 +-
xpdeint/Operators/ConstantEXOperator.py | 6 +-
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xpdeint/Version.py | 2 +-
xpdeint/XMDS2Parser.py | 81 +-
xpdeint/includes/solirte/randpool.h | 8 +-
xpdeint/parser2.py | 2 +-
xpdeint/support/wscript | 2 -
xpdeint/support/xpdeint.rnc | 4 +-
xpdeint/support/xpdeint.rng | 10 +-
xpdeint/version.sh | 4 +-
xpdeint/waf/waflib/Build.pyc | Bin 44551 -> 43675 bytes
xpdeint/waf/waflib/ConfigSet.pyc | Bin 11923 -> 11623 bytes
xpdeint/waf/waflib/Configure.pyc | Bin 19318 -> 19030 bytes
xpdeint/waf/waflib/Context.pyc | Bin 18167 -> 17891 bytes
xpdeint/waf/waflib/Errors.pyc | Bin 3564 -> 3444 bytes
xpdeint/waf/waflib/Logs.pyc | Bin 10070 -> 9818 bytes
xpdeint/waf/waflib/Node.pyc | Bin 26717 -> 26117 bytes
xpdeint/waf/waflib/Options.pyc | Bin 9252 -> 9108 bytes
xpdeint/waf/waflib/Runner.pyc | Bin 10657 -> 10393 bytes
xpdeint/waf/waflib/Scripting.pyc | Bin 18766 -> 18430 bytes
xpdeint/waf/waflib/Task.py | 22 +-
xpdeint/waf/waflib/Task.pyc | Bin 38676 -> 38357 bytes
xpdeint/waf/waflib/TaskGen.pyc | Bin 25319 -> 24899 bytes
xpdeint/waf/waflib/Tools/__init__.pyc | Bin 185 -> 173 bytes
xpdeint/waf/waflib/Tools/c_config.pyc | Bin 40054 -> 39532 bytes
xpdeint/waf/waflib/Tools/c_preproc.pyc | Bin 28226 -> 27926 bytes
xpdeint/waf/waflib/Utils.pyc | Bin 21201 -> 20691 bytes
xpdeint/waf/waflib/__init__.pyc | Bin 179 -> 167 bytes
xpdeint/waf/waflib/ansiterm.pyc | Bin 11852 -> 11492 bytes
xpdeint/waf/waflib/extras/__init__.pyc | Bin 186 -> 174 bytes
xpdeint/waf/waflib/extras/compat15.pyc | Bin 11160 -> 10944 bytes
xpdeint/xsil2graphics2/MathematicaImport.py | 6 +-
xpdeint/xsil2graphics2/MatlabOctaveImport.py | 22 +-
xpdeint/xsil2graphics2/MatlabOctaveImport.tmpl | 8 +-
xpdeint/xsil2graphics2/PythonImport.py | 6 +-
.../BesselBasis.py => xsil2graphics2/RImport.py} | 140 +-
xpdeint/xsil2graphics2/RImport.tmpl | 67 +
xpdeint/xsil2graphicsParser.py | 5 +-
458 files changed, 95653 insertions(+), 16705 deletions(-)
delete mode 100644 admin/TODO
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delete mode 100644 debian/changelog
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delete mode 100644 debian/xmds2.examples
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create mode 100644 documentation/_images/IntroduceNewElement.png
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create mode 100755 documentation/_images/Overall_Flowchart.dia
create mode 100644 documentation/_images/Overall_Flowchart.png
create mode 100755 documentation/_images/Subprocess3_4_11_2_ParseIntegrateElement.dia
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create mode 100755 documentation/_images/Subprocess3_4_11_ParseTopLvlSeqElements.dia
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create mode 100755 documentation/_images/Subprocess3_4_parseXMLDocument.dia
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create mode 100644 documentation/bulirschStoer.html
create mode 100644 documentation/doctrees/bulirschStoer.doctree
create mode 100644 documentation/doctrees/news_content.doctree
create mode 100644 documentation/latex/IntroduceNewElement.png
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create mode 100644 documentation/latex/error_scaling.png
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copy documentation/{news.html => news_content.html} (77%)
copy examples/{bessel_transform2.xmds => bessel_neumann_wave_equation.xmds} (82%)
copy {examples => testsuite/fast}/cpc_example4.xmds (56%)
create mode 100644 testsuite/fast/cpc_example4_expected.h5
create mode 100644 testsuite/fast/cpc_example4_expected.xsil
copy documentation/latex/xmds2.idx => testsuite/integrators/richardson_extrapolation/error_scaling/do_not_run_tests_by_default (100%)
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_10thOrder.xmds
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_10thOrder_expected.xsil
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_2ndOrder.xmds
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_2ndOrder_expected.xsil
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_4thOrder.xmds
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_4thOrder_expected.xsil
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_6thOrder.xmds
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_6thOrder_expected.xsil
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_8thOrder.xmds
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/exponential_scaling_8thOrder_expected.xsil
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/logplotall.gp
create mode 100644 testsuite/integrators/richardson_extrapolation/error_scaling/plot_error_data.py
copy testsuite/integrators/{vibstring_ark89.xmds => richardson_extrapolation/vibstring_mm.xmds} (90%)
copy testsuite/{transforms/bessel_transform_rectangular_expected.xsil => integrators/richardson_extrapolation/vibstring_mm_expected.xsil} (58%)
create mode 100755 testsuite/integrators/richardson_extrapolation/vibstring_mm_expected_mg0.dat
create mode 100755 testsuite/integrators/richardson_extrapolation/vibstring_mm_expected_mg1.dat
copy testsuite/integrators/{vibstring_ark89.xmds => richardson_extrapolation/vibstring_re.xmds} (87%)
copy testsuite/{transforms/bessel_transform_rectangular_expected.xsil => integrators/richardson_extrapolation/vibstring_re_expected.xsil} (62%)
create mode 100644 testsuite/integrators/richardson_extrapolation/vibstring_re_expected_mg0.dat
create mode 100644 testsuite/integrators/richardson_extrapolation/vibstring_re_expected_mg1.dat
copy testsuite/mpi/{kubo_mpi_paths.xmds => kubo_adaptive_mpi_paths.xmds} (77%)
copy testsuite/operators/{constant_complex_ip.xmds => constant_complex_ip_2d.xmds} (67%)
copy testsuite/operators/{nonconstant_complex_ip.xmds => constant_complex_separated_ip_2d.xmds} (52%)
copy testsuite/operators/{constant_double_ip.xmds => constant_real_ip_2d.xmds} (67%)
copy testsuite/operators/{derivative_expected.xsil => derivative_2d_expected.xsil} (57%)
create mode 100644 testsuite/operators/derivative_2d_expected_mg0.dat
copy testsuite/operators/{nonconstant_complex_ip.xmds => nonconstant_complex_ip_2d.xmds} (71%)
copy testsuite/operators/{nonconstant_complex_ip.xmds => nonconstant_complex_separated_ip_2d.xmds} (56%)
copy testsuite/operators/{nonconstant_double_ip.xmds => nonconstant_real_ip_2d.xmds} (71%)
copy examples/bessel_transform2.xmds => testsuite/transforms/bessel_neumann_wave_equation.xmds (76%)
create mode 100644 testsuite/transforms/bessel_neumann_wave_equation_expected.h5
copy testsuite/transforms/{bessel_transform_rectangular_expected.xsil => bessel_neumann_wave_equation_expected.xsil} (59%)
copy xpdeint/Features/{Globals.py => Transforms/BesselNeumannTransform.py} (69%)
copy xpdeint/Features/{AutoVectorise.tmpl => Transforms/BesselNeumannTransform.tmpl} (58%)
copy xpdeint/{Geometry/GeometryElement.py => Features/Transforms/BesselTransform.py} (69%)
copy xpdeint/Features/{AutoVectorise.tmpl => Transforms/BesselTransform.tmpl} (57%)
copy xpdeint/{Stochastic/RandomVariables/UniformRandomVariable.py => Features/Transforms/HermiteGaussTransform.py} (69%)
copy xpdeint/Features/{AutoVectorise.tmpl => Transforms/HermiteGaussTransform.tmpl} (60%)
create mode 100755 xpdeint/Features/Transforms/_BesselTransform.py
create mode 100755 xpdeint/Features/Transforms/_HermiteGaussTransform.py
copy xpdeint/Geometry/{SphericalBesselDimensionRepresentation.py => BesselNeumannDimensionRepresentation.py} (61%)
copy xpdeint/Geometry/{SphericalBesselDimensionRepresentation.tmpl => BesselNeumannDimensionRepresentation.tmpl} (54%)
create mode 100644 xpdeint/Operators/OperatorContainer.tmpl
copy xpdeint/Operators/{OperatorContainer.py => _OperatorContainer.py} (83%)
create mode 100644 xpdeint/Segments/Integrators/MMStepper.py
create mode 100644 xpdeint/Segments/Integrators/MMStepper.tmpl
create mode 100644 xpdeint/Segments/Integrators/RichardsonFixedStep.py
create mode 100644 xpdeint/Segments/Integrators/RichardsonFixedStep.tmpl
copy xpdeint/Segments/{_FilterSegment.py => Integrators/_RichardsonFixedStep.py} (58%)
create mode 100644 xpdeint/SimulationDrivers/AdaptiveMPIMultiPathDriver.py
create mode 100644 xpdeint/SimulationDrivers/AdaptiveMPIMultiPathDriver.tmpl
copy xpdeint/{Features/Transforms/BesselBasis.py => xsil2graphics2/RImport.py} (59%)
create mode 100644 xpdeint/xsil2graphics2/RImport.tmpl
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