[CIG-SHORT] Spherical 3d gravity initial stress
Brad Aagaard
baagaard at usgs.gov
Wed Nov 9 10:21:01 PST 2016
Demian,
The information in the spatial database should be in the coordinate
system of the model (mesh).
The spatial databases are generic containers that don't know anything
more than the unit for each value. In other words, the containers don't
know if the values are scalars, vectors, or tensors, so it won't
transform the values. It only transforms the coordinates of the points.
Brad
On 11/09/2016 10:11 AM, Demian Gomez wrote:
> Brad,
>
> Using the SimpleGridDB with a geographic (lon,lat,dep) coordinate system
> seems to have worked fine. Thanks very much. Even though the spatialdb
> files are large (1e6 points) Pylith loads them in a few seconds.
>
> The last question I have is: The stress field in the db should be
> expressed in the coordinate system of the db, right? In other words,
> stress_xx = stress_yy = stress_zz = rho*g*depth and stress_xy =
> stress_yz = stress_xz = 0 and Pylith will transform this into stress_xx,
> stress_yy, stress_zz, stress_xy, stress_yz and stress_xz in the ECEF
> coordinate system, where stress_xy, stress_yz and stress_xz are not
> equal to zero. Or should I write the stress field in the ECEF coord sys?
>
> Demián
>
> --
> *Dr. Demián D. Gómez*
> Postdoctoral Researcher
> The Ohio State University - School of Earth Sciences
> 275 Mendenhall Laboratory
> 125 South Oval Mall
> Columbus, Ohio 43210
> Cell: +1 (901) 900-7324
> email: gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
>
>
> On Wed, Nov 9, 2016 at 12:20 PM, Brad Aagaard <baagaard at usgs.gov
> <mailto:baagaard at usgs.gov>> wrote:
>
> On 11/09/2016 09:13 AM, Demian Gomez wrote:
>
> I didn't realize that there had to be one data point at each
> intersection of the grid. I was only leaving the points that I
> actually
> need to make the file smaller. Is it possible to use a
> transformation so
> that I can specify the points in lat lon depth and let Pylith
> transform
> them into X,Y,Z (ECEF)? Say, something like is-geocentric = false?
>
>
> It *is* possible to use geographic coordinates with a SimpleGridDB
> because it searches each coordinate independently to locate the
> points in the grid.
>
> With a SimpleDB the algorithm assumes the points are located
> arbitrarily within the data dimension. To find nearby points it
> computes distances, so the spatial database needs to use a Cartesian
> coordinate.
>
> Brad
>
>
>
> Thanks for your help,
>
> Demián
>
> --
> *Dr. Demián D. Gómez*
> Postdoctoral Researcher
> The Ohio State University - School of Earth Sciences
> 275 Mendenhall Laboratory
> 125 South Oval Mall
> Columbus, Ohio 43210
> Cell: +1 (901) 900-7324 <tel:%2B1%20%28901%29%20900-7324>
> email: gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>
>
>
> On Wed, Nov 9, 2016 at 12:04 PM, Brad Aagaard <baagaard at usgs.gov
> <mailto:baagaard at usgs.gov>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>>> wrote:
>
> Demian,
>
> Your header shows the grid is
> num-x = 33
> num-y = 21
> num-z = 28
>
> so the total number of points should be 33*21*28, but I only
> see 592
> points in the file.
>
> Brad
>
>
> On 11/09/2016 08:55 AM, Demian Gomez wrote:
>
> Brad,
>
> I'm analyzing the far-field (> 800 km from a thrust fault)
> co-seismic
> displacements and the effect of the asthenospheric
> stiffness in
> the lithospheric stress guide. It's mostly a "theory"
> analysis and I
> cannot neglect the effect of sphericity since this would
> be highly
> criticized by reviewers.
>
> I am trying to implement a spatial grid db as you
> suggested, but
> I am
> having a few problems. First for all, for some reason
> Pylith is
> crashing
> with my spatial grid with the following error:
>
> RuntimeError: Error occurred while reading spatial
> database file
> 'spatialdb/initial_stress-layer1.spatialdb'
> I/O error while reading SimpleGridDB data.
>
> I thought the problem could be the size of the spatialdb
> so I
> reduced
> the number of
> points but the problem persisted.
>
> I then downloaded a traction db example from a benchmark
>
> (https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102>
>
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102>>
>
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102>
>
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102
> <https://github.com/geodynamics/pylith_benchmarks/tree/master/dynamic/scecdynrup/tpv102>>>)
> to compare it against my file. I couldn't see any remarkable
> differences
> (except the coordinate system, number of points, etc) so
> I used my
> header (modifying num-x, num-y and num-z) with the data
> portion
> of the
> benchmark spatial db. Even though the number of values
> (columns)
> in this
> spatial db do not agree with the 6 stress components
> that I need
> (the
> benchmark uses 7 values) and the values itself are
> completely
> meaningless in terms of stress, Pylith does now pass the
> material
> initialization. It then crashes with the second layer
> where I
> left the
> spatial db unmodified.
>
> There seems to be some kind of problem with my data
> portion of the
> spatial db, but I can't find it. I looked for CRLF/LF
> problems,
> field
> sizes, etc just in case, but found no differences.
> Attached you will
> find the spatial grid db that crashes Pylith. I'd
> appreciate if you
> could take a look at it to see if there is anything
> obviously wrong.
>
> Demián
>
> --
> *Dr. Demián D. Gómez*
> Postdoctoral Researcher
> The Ohio State University - School of Earth Sciences
> 275 Mendenhall Laboratory
> 125 South Oval Mall
> Columbus, Ohio 43210
> Cell: +1 (901) 900-7324
> <tel:%2B1%20%28901%29%20900-7324> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> email: gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>>
>
>
> On Wed, Nov 9, 2016 at 9:50 AM, Brad Aagaard
> <baagaard at usgs.gov <mailto:baagaard at usgs.gov>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>>>> wrote:
>
> Demian,
>
> The code for initializing the initial stress and strain
> fields is in
> the method
> ElasticMaterial::_initializeInitialStress() in
> libsrc/pylith/materials/ElasticMaterial.cc.
>
> Before you head in that direction, I would seriously
> consider the
> size of the approximation in using a flat domain
> compared to a
> spherical domain relative to the other assumptions
> in your
> problem.
> In other words, do your have sufficient resolution
> in all
> of your
> other parameters that you know you need to use a
> domain with a
> spherical cap?
>
> Regards,
> Brad
>
>
>
> On 11/08/2016 04:08 PM, Demian Gomez wrote:
>
> Hi Brad,
>
> Thanks for your answer.
>
> Would it be possible to modify Pylith's code to
> calculate the
> initial
> tractions during runtime without having to
> specify them
> through a
> spatial database? I can try to do it if you can
> provide
> me with some
> orientation on where I should start looking. It
> seems
> that for a
> model
> constructed in ECEF coordinates, calculating
> stress_xx,
> stress_yy and
> stress_zz should be trivial if I have access to
> the cell
> centroids and
> the material density.
>
> Thanks again,
> Demián
>
> --
> *Dr. Demián D. Gómez*
> Postdoctoral Researcher
> The Ohio State University - School of Earth Sciences
> 275 Mendenhall Laboratory
> 125 South Oval Mall
> Columbus, Ohio 43210
> Cell: +1 (901) 900-7324
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> email: gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu> <mailto:gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu>>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>>
> <mailto:gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu> <mailto:gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu>>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>>>
>
>
>
> On Mon, Nov 7, 2016 at 12:42 PM, Brad Aagaard
> <baagaard at usgs.gov <mailto:baagaard at usgs.gov>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>>
> <mailto:baagaard at usgs.gov
> <mailto:baagaard at usgs.gov> <mailto:baagaard at usgs.gov
> <mailto:baagaard at usgs.gov>>>
> <mailto:baagaard at usgs.gov
> <mailto:baagaard at usgs.gov> <mailto:baagaard at usgs.gov
> <mailto:baagaard at usgs.gov>>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>
> <mailto:baagaard at usgs.gov <mailto:baagaard at usgs.gov>>>>> wrote:
>
> Demian,
>
> I think you can get things to work with a
> 1-D spatial
> database with
> some minor changes.
>
> WARNING: This will only work if stress_xx =
> stress_yy =
> stress_zz
> and stress_xy = stress_yz = stress_xz = 0.
> This is
> due to
> the fact
> that the orientation of the gravity vector is
> different in the
> projected coordinate system than it is in
> the geocentric
> coordinate
> system.
>
> You should construct your model in a geocentric
> local Cartesian
> coordinate system. This is a geocentric
> coordinate
> system
> with the
> origin at the surface.
>
> The initial tractions should be in a projected
> (flat) geographic
> coordinate system, so that stress(z) =
> integral of rho*g
> from 0 to z.
>
> As an aside, the SimpleGridDB provides much
> faster
> interpolation
> than SimpleDB for a logically Cartesian grid
> because
> it can
> find the
> relevant points without a global search. The
> points
> need to
> conform
> to a grid, but the x, y, and z coordinates
> do not
> have to be
> spaced
> uniformly.
>
> Regards,
> Brad
>
>
>
> On 11/06/2016 01:16 PM, Demian Gomez wrote:
>
> Dear all,
>
> I am trying to turn on gravity in a
> quasi-static
> problem
> that
> uses a 3D
> spherical cap model with layers (see
> attached
> figure for
> geometry and
> displacement field without gravity). The
> coordinate
> system of
> the mesh
> is ECEF and in pylithapp.cfg I've
> defined coordsys =
> spatialdata.geocoords.CSGeo. My spatial
> databases for
> material
> properties, etc are defined using:
>
> num-locs = 1
> data-dim = 0
> space-dim = 3
> cs-data = geographic {
> to-meters = 1.0
> space-dim = 3
> ellipsoid = sphere
> datum-vert = ellipsoid
> is-geocentric = true
> } // cs-data
>
> Since the layers are uniform, I use
> db_properties.query_type =
> nearest.
>
> To turn on gravity, I need to set the
> initial
> lithostatic stress =
> g*rho*h for each element (I can't use a
> uniform
> database
> anymore), but
> because this is a large model (~15e6
> elements), the
> sizes of the
> initial
> stress databases are > 300 MB which
> makes Pylith
> take a very
> long time
> to initialize the materials (so far I've
> waited
> almost
> 12 hours and
> Pylith was still initializing the first
> layer!).
>
> Following this thread:
>
>
>
> http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>>
>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>>>
>
>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>>
>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>
>
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html
> <http://lists.geodynamics.org/pipermail/cig-short/2014-July/001818.html>>>>
>
> I have now attempted to create an
> initial stress
> spatial
> database that
> is only 1D as follows:
>
> #SPATIAL.ascii 1
> SimpleDB {
> num-values = 6
> value-names = stress-xx stress-yy
> stress-zz
> stress-xy
> stress-yz stress-xz
> value-units = Pa Pa Pa Pa Pa Pa // units
> num-locs = 2
> data-dim = 1
> space-dim = 3
> cs-data = geo-local-cartesian {
> origin-lon = -72.6425
> origin-lat = -35.6331
> origin-elev = 0
> to-meters = 1.0
> ellipsoid = sphere
> datum-vert = ellipsoid
> } // cs-data
> }
> 0.0000 0.0000 0.0000
> 0.000
> 0.000
> 0.000 0.00 0.00 0.00
> 0.0000 0.0000 -104911.1753
> -2674950661 <tel:2674950661>.887
> -2674950661 <tel:2674950661>
> <tel:2674950661 <tel:2674950661>> <tel:2674950661 <tel:2674950661>
> <tel:2674950661 <tel:2674950661>>>.887
> -2674950661 <tel:2674950661>
> <tel:2674950661 <tel:2674950661>> <tel:2674950661 <tel:2674950661>
> <tel:2674950661 <tel:2674950661>>> <tel:2674950661
> <tel:2674950661> <tel:2674950661 <tel:2674950661>>
>
> <tel:2674950661 <tel:2674950661> <tel:2674950661
> <tel:2674950661>>>>.887 0.00 0.00 0.00
>
>
>
> and setting db_initial_stress.query_type
> = linear.
>
> My idea was that Pylith would map the
> geo-local-cartesian from the
> spatial database to ECEF coordinates in
> geocoords.CSGeo.
> However, I got
> the following error during execution:
>
> mpinemesis:
> spatialdb/SimpleDBQuery.cc:352: void
>
>
>
> spatialdata::spatialdb::SimpleDBQuery::_findLinePt(std::vector<spatialdata::spatialdb::SimpleDBQuery::WtStruct>*):
> Assertion `locIndexA >= 0' failed.
>
> My questions are:
>
> 1) Is it possible to mix coordinate
> systems the
> way I did?
> 2) Is there another way to tell Pylith
> that the
> initial
> stresses
> in my
> model vary linearly with depth, even
> when I have
> an ECEF
> coordinate
> system? I would like to avoid having to
> assign the
> initial stress to
> every element one by one (which leads to
> a very long
> initialization time).
>
> Any suggestions will be greatly
> appreciated. Let
> me know
> if you need
> more information.
>
> Cheers,
> Demián
>
> --
> *Dr. Demián D. Gómez*
> Postdoctoral Researcher
> The Ohio State University - School of
> Earth Sciences
> 275 Mendenhall Laboratory
> 125 South Oval Mall
> Columbus, Ohio 43210
> Cell: +1 (901) 900-7324
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> <tel:%2B1%20%28901%29%20900-7324>
> email: gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>
> <mailto:gomez.124 at osu.edu <mailto:gomez.124 at osu.edu>>>
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> <mailto:gomez.124 at osu.edu> <mailto:gomez.124 at osu.edu
> <mailto:gomez.124 at osu.edu>>
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