Error element face midpoint distance

SPECFEM
1

Hello
I am trying to run specfem3D for a mesh (2layer model) of 5kmx5kmx5km and element size 120m. I am using the stacey absorbing condition. when the database generation is running, I got the following message.

running database generation…

error element face midpoint distance: 0.250000000 - edge length: 899.995422 tolerance: 8.99995416E-02
error corner: 1 xyz: 1040620.06 6291391.00 -191.233078
error corner: 2 xyz: 1040620.06 6291391.00 -161.232971
error corner: 3 xyz: 1040721.06 6291418.50 -159.854706
error corner: 4 xyz: 1040721.06 6291418.50 -189.854630
reference : 1 xyz: 1040721.06 6291418.50 -189.854630
reference : 2 xyz: 1040721.06 6291418.50 -159.854706
reference : 3 xyz: 1040620.06 6291391.00 -161.232971
reference : 4 xyz: 1040620.06 6291391.00 -191.233078
error element face midpoint distance: 0.250000000 - edge length: 900.000000 tolerance: 8.99999961E-02
error corner: 1 xyz: 1037963.50 6292375.00 -164.766586
error corner: 2 xyz: 1037963.50 6292490.00 -166.629639
error corner: 3 xyz: 1037963.50 6292486.50 -106.794266
error corner: 4 xyz: 1037963.50 6292375.00 -134.766586
reference : 1 xyz: 1037963.50 6292375.00 -164.766586
reference : 2 xyz: 1037963.50 6292375.00 -134.766586
reference : 3 xyz: 1037963.50 6292486.50 -106.794266
reference : 4 xyz: 1037963.50 6292490.00 -166.629639
error element face midpoint distance: 0.253906250 - edge length: 900.045349 tolerance: 9.00045335E-02
error corner: 1 xyz: 1041508.19 6294986.50 -98.7428589
error corner: 2 xyz: 1041508.25 6294986.50 -68.7457809
error corner: 3 xyz: 1041431.06 6295078.00 -58.3097878
error corner: 4 xyz: 1041431.12 6295078.00 -88.3104782
reference : 1 xyz: 1041431.12 6295078.00 -88.3104782
reference : 2 xyz: 1041431.06 6295078.00 -58.3097878
reference : 3 xyz: 1041508.25 6294986.50 -68.7457809
reference : 4 xyz: 1041508.19 6294986.50 -98.7428589
error element face midpoint distance: 0.250000000 - edge length: 1841.46899 tolerance: 0.184146896
error corner: 1 xyz: 1037963.50 6294120.00 -22.6280594
error corner: 2 xyz: 1037963.50 6294119.00 19.5043087
error corner: 3 xyz: 1037963.50 6293996.50 19.3953953
error corner: 4 xyz: 1037963.50 6293997.50 -23.5052948
reference : 1 xyz: 1037963.50 6293997.50 -23.5052948
reference : 2 xyz: 1037963.50 6293996.50 19.3953953
reference : 3 xyz: 1037963.50 6294119.00 19.5043087
reference : 4 xyz: 1037963.50 6294120.00 -22.6280594
STOP error element face midpoint
STOP error element face midpoint
STOP error element face midpoint
STOP error element face midpoint

any suggestions?
Thanks

2

looks like your mesh coordinates are a bit large (e.g. y-coordinates around 6,294,120 m) which makes the numerical precision less sensitive, thus the default tolerance value for these face detections becomes too small.

as a quick check to see if things would go round, you could modify the tolerance value in file src/shared/get_element_face.f90 (around line 57):
…
! distance tolerance (relative to coordinate range)
real(kind=CUSTOM_REAL), parameter :: TOL_DIST = 1.e-4
…

to something like:
real(kind=CUSTOM_REAL), parameter :: TOL_DIST = 1.e-3

which would be enough for the values given in your output log.