[CIG-SHORT] Spherical 3d gravity initial stress
Demian Gomez
demiang at gmail.com
Thu Nov 10 08:42:17 PST 2016
Brad,
Sorry to bother again, but I am still having some issues with the
simplegriddb. I created 3 spatialdbs (one for each layer) and first tried
to use them with query_type = nearest. Everything worked fine, but as I
expected, the solution shows large displacements because the grid is not
fine enough to approximate linearly increasing stress as a function of
depth using the nearest interpolation scheme. I therefore changed
query_type to linear which should produce better results. Pylith loads
layer1 in just a few seconds but when it starts with layer2 it freezes. The
CPUs are still doing something (12 cores @ 100% each), but I left it for 12
hours and nothing happened. Moreover, thinking that there could be a
problem with the spatialdb for layer2, I used the spatialdb for layer1 in
layer2, which should produce an error because the cells are outside of the
grid. However, again Pylith freezes at:
-- Initializing integrator for material 'layer2'.
If I put in layer1 query_type = linear and layer2 and layer3 as nearest it
works fine (but large displacements, ~250 m).
I've attached my .cfg files. I debuged then to see if I was unintentionally
changing the spatialdb somewhere else in the files back to simpledb (using
pylith stress_guide.cfg
--timedependent.materials.layer2.db_initial_stress.help-properties) but
that seems to be ok. Maybe there's something you can recommend I can test
to try to figure out what is going on.
Thank you,
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
On Wed, Nov 9, 2016 at 1:21 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> 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/maste
>> r/dynamic/scecdynrup/tpv102
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102>
>>
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102>>
>>
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102>
>>
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/dynamic/scecdynrup/tpv102
>> <https://github.com/geodynamics/pylith_benchmarks/tree/maste
>> r/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%20900-73
>> 24>
>> <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/0
>> 01818.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::vect
>> or<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>>>
>> <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 <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>>>>>
>>
>>
>>
>>
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>> >>
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>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
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>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>>
>>
>>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>>>
>>
>>
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