force using rectangular mesh
Paraview cannot handle large number of polyvertices using xdmf, forcing a meshed structure to by pass the problem.
This commit is contained in:
chen
parent
7310c53f73
commit
c311ac47ca
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@ -1,5 +1,6 @@
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<?xml version="1.0"?>
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<h5ds>
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<!--Top level attributes-->
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<history>
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<type>attr</type>
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<h5path>/</h5path>
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@ -12,174 +13,186 @@
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<h5path>/</h5path>
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<category></category>
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<description></description>
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<log></log>
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</inc>
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<!--Geometry section-->
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<Vx>
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<type>Scalar</type>
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<h5path>/Geometry/Vx</h5path>
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<category>Geometry</category>
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<description>Vector along x define the spectral mesh</description>
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</Vx>
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<Vy>
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<type>Scalar</type>
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<h5path>/Geometry/Vy</h5path>
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<category>Geometry</category>
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<description>Vector along y defines the spectral mesh</description>
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</Vy>
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<Vz>
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<type>Scalar</type>
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<h5path>/Geometry/Vz</h5path>
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<category>Geometry</category>
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<description>Vector along z defines the spectral mesh</description>
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</Vz>
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<ip>
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<type>scalar</type>
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<h5path>/ip</h5path>
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<category></category>
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<type>Scalar</type>
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<h5path>/Geometry/ip</h5path>
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<category>Geometry</category>
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<description></description>
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<log></log>
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</ip>
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<node>
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<type>scalar</type>
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<h5path>/node</h5path>
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<category></category>
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<type>Scalar</type>
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<h5path>/Geometry/node</h5path>
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<category>Geometry</category>
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<description></description>
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<log></log>
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</node>
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<grain>
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<type>vector</type>
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<h5path>/grain</h5path>
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<category></category>
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<type>Scalar</type>
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<h5path>/Geometry/grain</h5path>
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<category>Geometry</category>
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<description></description>
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<log></log>
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</grain>
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<pos>
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<type>vector</type>
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<h5path>/pos</h5path>
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<category></category>
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<type>Vector</type>
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<h5path>/Geometry/pos</h5path>
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<category>Geometry</category>
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<description></description>
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<log></log>
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</pos>
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<elem>
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<type>integer</type>
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<h5path>/elem</h5path>
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<category></category>
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<type>Scalar</type>
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<h5path>/Geometry/elem</h5path>
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<category>Geometry</category>
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<description></description>
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<log></log>
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</elem>
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<!--Crystallite section-->
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<phase>
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<type>integer</type>
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<h5path>/phase</h5path>
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<type>Scalar</type>
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<h5path>/Crystallite/phase</h5path>
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<category>Crystallite</category>
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<description></description>
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<log></log>
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</phase>
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<texture>
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<type>integer</type>
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<h5path>/texture</h5path>
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<type>Scalar</type>
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<h5path>/Crystallite/texture</h5path>
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<category>Crystallite</category>
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<description></description>
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<log></log>
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</texture>
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<volume>
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<type>scalar</type>
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<h5path>/volume</h5path>
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<type>Scalar</type>
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<h5path>/Crystallite/volume</h5path>
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<category>Crystallite</category>
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<description></description>
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<log></log>
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</volume>
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<orientation>
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<type>vector</type>
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<h5path>/orientation</h5path>
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<type>Vector</type>
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<h5path>/Crystallite/orientation</h5path>
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<category>Crystallite</category>
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<description></description>
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<log></log>
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</orientation>
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<eulerangles>
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<type>vector</type>
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<h5path>/eulerangles</h5path>
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<type>Vector</type>
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<h5path>/Crystallite/eulerangles</h5path>
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<category>Crystallite</category>
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<description>Bunnge Euler angles in degrees</description>
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<log></log>
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</eulerangles>
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<grainrotation>
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<type>vector</type>
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<h5path>/grainrotation</h5path>
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<type>Vector</type>
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<h5path>/Crystallite/grainrotation</h5path>
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<category>Crystallite</category>
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<description></description>
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<log></log>
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</grainrotation>
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<f>
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<type>tensor</type>
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<h5path>/f</h5path>
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<type>Tensor</type>
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<h5path>/Crystallite/f</h5path>
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<category>Crystallite</category>
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<description>deformation gradient (F)</description>
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<log></log>
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</f>
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<p>
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<type>tensor</type>
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<h5path>/p</h5path>
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<type>Tensor</type>
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<h5path>/Crystallite/p</h5path>
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<category>Crystallite</category>
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<description>Pikola Kirkhoff stress</description>
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<log></log>
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</p>
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<Cauchy>
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<type>Tensor</type>
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<h5path>/Crystallite/Cauchy</h5path>
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<category>Crystallite</category>
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<description>Cauchy stress tensor</description>
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</Cauchy>
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<lnV>
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<type>Tensor</type>
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<h5path>/Crystallite/lnV</h5path>
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<category>Crystallite</category>
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<description></description>
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</lnV>
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<MisesCauchy>
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<type>Scalar</type>
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<h5path>/Crystallite/MisesCauchy</h5path>
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<category>Crystallite</category>
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<description>von Mises equivalent of Cauchy stress</description>
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</MisesCauchy>
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<MiseslnV>
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<type>Scalar</type>
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<h5path>/Crystallite/MiseslnV</h5path>
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<category>Crystallite</category>
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<description>left von Mises strain</description>
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</MiseslnV>
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<!--Constitutive section-->
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<resistance_slip>
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<type>vector</type>
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<h5path>/resistance_slip</h5path>
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<type>Vector</type>
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<h5path>/Constitutive/resistance_slip</h5path>
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<category>Constitutive</category>
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<description></description>
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</resistance_slip>
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<shearrate_slip>
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<type>vector</type>
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<h5path>/shearrate_slip</h5path>
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<type>Vector</type>
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<h5path>/Constitutive/shearrate_slip</h5path>
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<category>Constitutive</category>
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<description></description>
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</shearrate_slip>
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<resolvedstress_slip>
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<type>vector</type>
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<h5path>/resolvedstress_slip</h5path>
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<type>Vector</type>
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<h5path>/Constitutive/resolvedstress_slip</h5path>
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<category>Constitutive</category>
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<description></description>
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</resolvedstress_slip>
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<totalshear>
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<type>scalar</type>
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<h5path>/totalshear</h5path>
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<type>Scalar</type>
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<h5path>/Constitutive/totalshear</h5path>
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<category>Constitutive</category>
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<description></description>
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</totalshear>
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<accumulatedshear_slip>
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<type>vector</type>
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<h5path>/accumulatedshear_slip</h5path>
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<type>Matrix</type>
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<h5path>/Constitutive/accumulatedshear_slip</h5path>
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<category>Constitutive</category>
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<description>vector contains accumulated shear per slip system</description>
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</accumulatedshear_slip>
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<Cauchy>
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<type>tensor</type>
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<h5path>/Cauchy</h5path>
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<category>Derived</category>
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<description>Cauchy stress tensor</description>
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</Cauchy>
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<lnV>
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<type>tensor</type>
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<h5path>/lnV</h5path>
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<category>Derived</category>
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<description></description>
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</lnV>
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<MisesCauchy>
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<type>scalar</type>
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<h5path>/MisesCauchy</h5path>
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<category>Derived</category>
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<description>von Mises equivalent of Cauchy stress</description>
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</MisesCauchy>
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<MiseslnV>
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<type>scalar</type>
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<h5path>/MiseslnV</h5path>
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<category>Derived</category>
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<description>left von Mises strain</description>
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</MiseslnV>
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<!--Derived section-->
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</h5ds>
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@ -23,12 +23,6 @@ except(NameError):
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unicode=str
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# ------------------------------------------------------- #
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# Singleton class for converting feature name to H5F path #
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# ------------------------------------------------------- #
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# NOTE:
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# use simple function to mimic the singleton class in
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# C++/Java
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def lables_to_path(label, dsXMLPath=None):
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"""read the xml definition file and return the path."""
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if dsXMLPath is None:
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@ -41,23 +35,26 @@ def lables_to_path(label, dsXMLPath=None):
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"DS_HDF5.xml")
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# This current implementation requires that all variables
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# stay under the root node, the nesting is defined through the
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# h5path. This could be improved easily with more advanced parsing
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# using ET interface, but for now I can not see the benefits in doing
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# so.
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# h5path.
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# Allow new derived data to be put under the root
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tree = ET.parse(dsXMLPath)
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try:
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dataType = tree.find('{}/type'.format(label)).text
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h5path = tree.find('{}/h5path'.format(label)).text
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except:
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dataType = "Scalar"
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h5path = "/{}".format(label) # just put it under root
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return (dataType, h5path)
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class H5Table(object):
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"""Interface class for h5py
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"""light weight interface class for h5py
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DESCRIPTION
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-----------
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Interface/wrapper class for manipulating data in HDF5 with DAMASK
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specialized data structure.
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-->Minimal API design.
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-->try to maintain a minimal API design.
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PARAMETERS
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----------
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h5f_path: str
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@ -114,7 +111,8 @@ class H5Table(object):
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dsXMLPath=self.dsXMLFile)
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with h5py.File(self.h5f_path, 'a') as h5f:
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h5f_dst = h5f[h5f_path] # get the handle for target dataset(table)
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rst_data = h5f_dst.read_direct(np.zeros(h5f_dst.shape))
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rst_data = np.zeros(h5f_dst.shape)
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h5f_dst.read_direct(rst_data)
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return rst_data
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def add_data(self, feature_name, dataset, cmd_log=None):
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@ -7,6 +7,11 @@
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# new one to the system wide definition file #
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# <DAMASK_ROOT>/lib/damask/DS_HDF5.xml #
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# or specify your own when initializing HDF5 class #
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# 2. Somehow the point cloud structure cannot be properly handled #
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# by Xdmf, which is a descriptive wrapper for visualizing HDF5 #
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# using Paraview. The current solution is using cell structured #
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# HDF5 so that Xdmf can describe the data shape as a rectangular #
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# mesh rather than polyvertex. #
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# ------------------------------------------------------------------- #
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import os
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@ -14,13 +19,24 @@ import damask
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import numpy as np
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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# ----- helper function ----- #
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def get_rectMshVectors(xyz_array, posNum):
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"""take in a xyz array from rectangular mesh and figure out Vx, Vy, Vz"""
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# need some improvement, and only works for rectangular grid
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v = sorted(list(set(xyz_array[:, posNum])))
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v_interval = (v[2]+v[1])/2.0 - (v[1]+v[0])/2.0
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v_start = (v[1]+v[0])/2.0 - v_interval
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v_end = (v[-1]+v[-2])/2.0 + v_interval
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V = np.linspace(v_start, v_end, len(v)+1)
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return V
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# ----- MAIN ---- #
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desp_msg = "Convert DAMASK ascii table to HDF5 file"
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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@ -31,8 +47,14 @@ parser.add_option('-D', '--DefinitionFile',
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type = 'string',
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metavar = 'string',
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help = 'definition file for H5 data storage')
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parser.add_option('-p',
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'--pos', '--position',
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dest = 'pos',
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type = 'string', metavar = 'string',
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help = 'label of coordinates [%default]')
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parser.set_defaults(DefinitionFile='default')
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parser.set_defaults(DefinitionFile='default',
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pos='pos')
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(options,filenames) = parser.parse_args()
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@ -54,17 +76,31 @@ labels_idx = [asciiTable.label_index(label) for label in labels]
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featuresDim = [labels_idx[i+1] - labels_idx[i] for i in xrange(len(labels)-1)]
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featuresDim.append(fullTable.shape[1] - labels_idx[-1])
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# ----- figure out size and grid ----- #
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pos_idx = asciiTable.label_index('pos')
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xyz_array = asciiTable.data[:, pos_idx:pos_idx+3]
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Vx = get_rectMshVectors(xyz_array, 0)
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Vy = get_rectMshVectors(xyz_array, 1)
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Vz = get_rectMshVectors(xyz_array, 2)
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# use the dimension of the rectangular grid to reshape all other data
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mshGridDim = (len(Vx)-1, len(Vy)-1, len(Vz)-1)
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# ----- create a new HDF5 file and save the data -----#
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# Will overwrite existing HDF5 file with the same name
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h5f = damask.H5Table(filename.replace(".txt", ".h5"),
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new_file=True,
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dsXMLFile=defFile)
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# adding increment number as root level attributes
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h5f.add_attr('inc', incNum)
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# add the mesh grid data now
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h5f.add_data("Vx", Vx)
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h5f.add_data("Vy", Vy)
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h5f.add_data("Vz", Vz)
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# add the rest of data from table
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for fi in xrange(len(labels)):
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featureName = labels[fi]
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if featureName == 'inc': continue
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if 'inc' in featureName: continue
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# remove trouble maker "("" and ")"
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if "(" in featureName: featureName = featureName.replace("(", "")
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if ")" in featureName: featureName = featureName.replace(")", "")
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@ -72,8 +108,8 @@ for fi in xrange(len(labels)):
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featureDim = featuresDim[fi]
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# grab the data hook
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dataset = fullTable[:, featureIdx:featureIdx+featureDim]
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# reshape tensor to 3x3 --> just make life slightly easier
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if dataset.shape[1] == 9:
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dataset = dataset.reshape((dataset.shape[0], 3, 3))
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# mapping 2D data onto a 3D rectangular mesh to get 4D data
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dataset = dataset.reshape((mshGridDim[0], mshGridDim[1], mshGridDim[2],
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dataset.shape[1]))
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# write out data
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h5f.add_data(featureName, dataset)
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