[CIG-SHORT] The pylith_benchmarks reports errors

Thu Mar 15 16:52:14 PDT 2018

On Thu, Mar 15, 2018 at 6:31 AM, tu xiang <tuxiang2016 at outlook.com> wrote:

> Dear Matt,
> The version I am running is Trelis V16.0.3 Linux.X64 .
>
> According to the examples provided by Pylith, I find that there two kinds
> of methods for setting vertex spacing with increasing spacing away from
> fault. I wonder which method will be better for a three-dimensional
> non-planar fault?
>

I do not know the answer. I would try both and look at the condition of the
cells produced.

  Thanks,

    Matt

> One is that you can export the fault surface into Exodus file and then add
> the  variable  of cellsize which specifies the distance between vertices
> of a cell edge into the Exodus file.
> For example
> playback 'geometry.jou'
> # ----------------------------------------------------------------------
> # Create tet4 mesh with resolution dictated by 'cell_size_fn'.
> # ----------------------------------------------------------------------
> volume all scheme tetmesh
> import sizing function  "mesh_cellsize.exo" block all variable
> "cell_size_fn" time 0.0000000
> volume all sizing function type exodus
> surface all sizing function type exodus
> curve all scheme stride
> # ----------------------------------------------------------------------
> # Generate the mesh
> # ----------------------------------------------------------------------
> mesh surface all
> surface all smooth scheme condition number beta 1.2 cpu 10
> smooth surface all
> mesh volume all
> # ----------------------------------------------------------------------
> # Smooth mesh to improve quality
> # ----------------------------------------------------------------------
> ${condnum=2.0}
> ${loop(4)}
> volume all smooth scheme condition number beta {condnum} cpu 2
> smooth volume all
> ${condnum=condnum-0.1}
> ${endloop}
>
> The other is you can specify the function for computing discretization
> size at end of curve with bias.
>
> For example:
> playback 'geometry.jou'
> # ----------------------------------------------------------------------
> # Set discretization size and scheme
> # ----------------------------------------------------------------------
> #{dx=200*m}
> surface all scheme trimesh
> volume all scheme tetmesh
> #{bias_factor=1.02}
>
> # Function for computing discretization size at end of curve with bias
> #{fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_
> factor))/ln(bias_factor))'}
>
> # ----------------------------------------------------------------------
> # Compute sizes at curve endpoints
> # ----------------------------------------------------------------------
> # dxA - size at vertex 32 34
> #{dxStart=dx}{curveL=Length(39)}{execute("dxA="//fun_dx)}
>
> # dxB - size at vertex 63 66
> #{dxStart=dx}{curveL=Length(85)}{execute("dxB="//fun_dx)}
>
> # dxC - size at vertex 31 33
> #{dxStart=dx}{curveL=Length(49)}{execute("dxC="//fun_dx)}
>
> # dxD - size at vertex 17 18
> #{dxStart=dxC}{curveL=Length(38)}{execute("dxD="//fun_dx)}
>
> # dxE - size at vertex 1 2
> #{dxStart=dxA}{curveL=Length(25)}{execute("dxE="//fun_dx)}
>
> # dxF - size at vertex 3 4
> #{dxStart=dxA}{curveL=Length(36)}{execute("dxF="//fun_dx)}
>
> # dxG - size at vertex  64 65
> #{dxStart=dxB}{curveL=Length(84)}{execute("dxG="//fun_dx)}
>
> # dxH - size at vertex 75 76
> #{dxStart=dxB}{curveL=Length(105)}{execute("dxH="//fun_dx)}
>
> # dxI - size at vertex 5 6
> #{dxStart=dxG}{curveL=Length(99)}{execute("dxI="//fun_dx)}
>
> # dxJ - size at vertex 7 8
> #{dxStart=dxD}{curveL=Length(35)}{execute("dxJ="//fun_dx)}
>
> # ----------------------------------------------------------------------
> # Reset sizes
> # ----------------------------------------------------------------------
> curve all scheme default
> surface all sizing function none
> surface fault_surface fault_surface at A fault_surface at B size {dx}
>
> # Set bias on curves extending from faults
>
> curve 39 scheme bias fine size {dx} factor {bias_factor} start vertex 32
> curve 45 scheme bias fine size {dx} factor {bias_factor} start vertex 34
>
> curve 85 scheme bias fine size {dx} factor {bias_factor} start vertex 62
> curve 81 scheme bias fine size {dx} factor {bias_factor} start vertex 61
>
> curve 49 scheme bias fine size {dx} factor {bias_factor} start vertex 36
> curve 48 scheme bias fine size {dx} factor {bias_factor} start vertex 35
>
> # ----------------------------------------------------------------------
> # bias starting at A
> curve 25 scheme bias fine size {dxA} factor {bias_factor} start vertex 19
> curve 36 scheme bias fine size {dxA} factor {bias_factor} start vertex 19
>
> curve 26 scheme bias fine size {dxA} factor {bias_factor} start vertex 20
> curve 34 scheme bias fine size {dxA} factor {bias_factor} start vertex 20
>
> # bias starting at B
> curve 84 scheme bias fine size {dxB} factor {bias_factor} start vertex 66
> curve 105 scheme bias fine size {dxB} factor {bias_factor} start vertex 66
>
> curve 82 scheme bias fine size {dxB} factor {bias_factor} start vertex 63
> curve 107 scheme bias fine size {dxB} factor {bias_factor} start vertex 63
>
> # ----------------------------------------------------------------------
> # C to C
> curve 43 size {dxC}
>
> # bias starting at C
> curve 38 scheme bias fine size {dxC} factor {bias_factor} start vertex 31
> curve 46 scheme bias fine size {dxC} factor {bias_factor} start vertex 33
>
> # bias starting at D
> curve 35 scheme bias fine size {dxD} factor {bias_factor} start vertex 17
> curve 33 scheme bias fine size {dxD} factor {bias_factor} start vertex 18
>
> # bias E to E
> curve 1 size {dxE}
>
> # bias F to F
> curve 3 size {dxF}
>
> # bias G to G
> curve 83 size {dxG}
>
> # bias H to H
> curve 106 size {dxH}
>
> # bias I to I
> curve 5 size {dxI}
>
> # bias J to J
> curve 7 size {dxJ}
>
>
> # bias A to B
> curve 91 scheme bias fine size {dxA} coarse size {dxB} start vertex 19
> curve 88 scheme bias fine size {dxA} coarse size {dxB} start vertex 20
>
> # bias B to D
> curve 98 scheme bias fine size {dxB} coarse size {dxD} start vertex 66
> curve 102 scheme bias fine size {dxB} coarse size {dxD} start vertex 63
>
> # bias D to I
> curve 27 scheme bias fine size {dxD} coarse size {dxI} start vertex 17
> curve 28 scheme bias fine size {dxD} coarse size {dxI} start vertex 18
>
> # bias E to G
> curve 87 scheme bias fine size {dxE} coarse size {dxG} start vertex 1
> curve 86 scheme bias fine size {dxE} coarse size {dxG} start vertex 2
>
> # bias F to H
> curve 108 scheme bias fine size {dxF} coarse size {dxH} start vertex 4
> curve 109 scheme bias fine size {dxF} coarse size {dxH} start vertex 3
>
> # bias G to I
> curve 99 scheme bias fine size {dxG} coarse size {dxI} start vertex 65
> curve 103 scheme bias fine size {dxG} coarse size {dxI} start vertex 64
>
> # bias H to J
> curve 119 scheme bias fine size {dxD} coarse size {dxI} start vertex 75
> curve 117 scheme bias fine size {dxD} coarse size {dxI} start vertex 76
>
> # Set bias on surfaces
> surface fault_body sizing function type bias start curve 90 factor
> {bias_factor}
> surface fault_body at B sizing function type bias start curve 89 factor
> {bias_factor}
> surface fault_body at A sizing function type bias start curve 47 factor
> {bias_factor}
> surface fault_body at C sizing function type bias start curve 100 factor
> {bias_factor}
> surface fault_body at D sizing function type bias start curve 101 factor
> {bias_factor}
> surface 34 sizing function type bias start curve 80 factor {bias_factor}
> surface 48 sizing function type bias start curve 80 factor {bias_factor}
> # ----------------------------------------------------------------------
> # Generate the mesh
> # ----------------------------------------------------------------------
> mesh surface all
> surface all smooth scheme condition number beta 1.3 cpu 10
> smooth surface all
> mesh volume all
>
> Best regards,
> Tu Xiang
>
>
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