I have two Jacobian plots and they have conflicting data from what I can tell. The Jacobian reading from the mesh toolbox gives an all green while the element contour option gives bad elements almost equal to a jacobian of 1. Which one is correct, and how do I fix the hex elements that are bad without messing up the entire mesh?
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I am happy you are worried for Jacobian mesh quality, in general people do not check mesh quality at all, and is very important to produce quality mesh form the point of view of getting accurate results, more when we have in FEMAP powerful tools to check quality mesh, then let's use it, no excuse!!.
Well, first at all you must understand the diference between the various quality checks tools we have in FEMAP:
Regarding your question of how to solve your issue with Jacobian check "without meshing again", well, FEMAP don't have a magic wang, this is the typical problem when creating 3-D solid mesh using horrible WEDGE CPENTA five-sided elements (ie, extruding 2-D 3-nodes triangles to form 3-D six-nodes Wedge solid mesh), simply avoid to have triangles in your 2-D mesh, work the geometry to have regular regions to mesh with perfect QUAD-only elements and you will arrive to 3-D solid CHEXA quality mesh for sure, OK?.