[CIG-SHORT] Problem setting initial conditions

Oliver Boyd olboyd at usgs.gov
Wed Feb 12 12:21:18 PST 2014


When I attempt to add initial_strain to the cell_info_field, Pylith tells
me for the elastic material that the acceptable values are 'mu' 'lambda'
'density' 'stable_dt_implicit' 'stable_dt_explicit' and for the
viscoelastic material, 'mu' 'lambda' 'density' 'stable_dt_implicit'
'stable_dt_explicit' 'maxwell_time'. But with respect to your comments, I
can see why I would get zero total_strain in the output of problem 2 if
it's only outputting the gradients in the displacements. And I expect then
that If I added initial_strain to total_strain from problem 2, it would
equal total_strain from problem 1. I guess then that the only thing that's
different between the two problems is displacement, which it doesn't
appear that I'll be able to fix if I want to change the boundary condition
on the fault.

Thanks again for your help,
Oliver

On 2/11/14 3:51 PM, "Brad Aagaard" <baagaard at usgs.gov> wrote:

>On 02/11/2014 01:52 PM, Oliver Boyd wrote:
>> If I turn off the elastic prestep phase and keep total_time = 0, I
>> get no stress or strain written to the hdf5 material files. If I
>> increase total_time to 1 yr, I get essentially the same results as
>> using the elastic prestep and total_time = 0, which is to say that I
>> can match the stress in the material and tractions on the fault, but
>> I can't match the strain in the material.
>>
>> I'm not sure I understand your question regarding output.
>>
>> If you mean adding initial strain to what I get from running problem
>> 2, then yes, the strain resulting from problem 1 is the same as
>> adding the initial strain to the output of problem 2. That's because
>> in every case I've tried, the strain output from problem 2 is close
>> to zero.
>
>In the output, we are are currently dumping the strains computed from
>the gradients in the displacement field. We are not dumping
>initial_strain + gradient in the displacement field (what you want to
>use in your comparison when you run the full problem without breaking it
>into pieces).
>
>> If you mean including initial strain in the hdf5 output, I'm not
>> sure how to add initial strains to the output. I thought my options
>> were cell_data_fields = [total_strain,stress] for elastic materials
>> and cell_data_fields = [total_strain,viscous_strain,stress] for
>> viscoelastic.
>
>Note that this is the *info* fields (for parameters, initial conditions,
>etc), not the *data* fields (for solution stuff).
>
>cell_info_fields = [initial_strain]
>
>Brad
>
>>
>>
>>
>> On 2/11/14 2:05 PM, "Brad Aagaard" <baagaard at usgs.gov> wrote:
>>
>>> Oliver,
>>>
>>> Did you try turning off the elastic prestep phase?
>>>
>>> [pylithapp.timedependent] elastic_prestep = False
>>>
>>> Are the strains the same if you add the initial strain to the
>>> output strains? It might be an output issue rather than a setup
>>> issue.
>>>
>>> Brad
>>>
>>> On 02/11/2014 01:01 PM, Oliver Boyd wrote:
>>>> Hi Brad, Yes, that's exactly what I was trying to do, i.e. make
>>>> the solution the same at the first time step, but I haven't been
>>>> able to match the strains between problem 1 and 2, maybe because
>>>> of the elastic prestep phase. I guess I'll have to solve my
>>>> problem some other way.
>>>>
>>>> Thanks again, Brad and Charles, for your help. Oliver
>>>>
>>>> On 2/10/14 5:05 PM, "Brad Aagaard" <baagaard at usgs.gov> wrote:
>>>>
>>>>> Oliver,
>>>>>
>>>>> If you use the same boundary conditions in problems 1 and 2
>>>>> and get the same answer in both problems, then your setup with
>>>>> initial stress and strain is working properly for problem 2.
>>>>> If you want to break up a simulation into pieces so that you
>>>>> can solve something different, then your starting point for the
>>>>> new simulations should be consistent with where you left off.
>>>>> In other words, you can replace the BC and fault conditions,
>>>>> etc to change the problem but you need to make sure the
>>>>> solution is the same at the first time step.
>>>>>
>>>>> With a purely elastic material, the stress and strain in the
>>>>> domain are irrelevant so you only need to transfer the fault
>>>>> tractions (as in examples/2d/subduction/step04). For any bulk
>>>>> rheologies with state variables (viscous strain), you may be
>>>>> out of luck for right now as we have not implemented a way to
>>>>> specify initial state variables for bulk constitutive models.
>>>>>
>>>>> We recognize that we are getting greater interest in setting
>>>>> up these types of complicated simulations, where a user wants
>>>>> to take the output of one simulation and use pieces from it as
>>>>> input to another simulation. Implementing this right now
>>>>> doesn't make sense, because we are about to reorganize a bunch
>>>>> of top-level stuff to support multi-physics stuff. As we
>>>>> reorganize things it will make sense to set things up so that
>>>>> we can swap out the "elastic prestep" phase with an "initial
>>>>> condition" phase or a "restart phase" to support this feature.
>>>>> The new functionality probably wouldn't be implemented right
>>>>> away but we will be able to add it or someone else could add
>>>>> it relatively easily.
>>>>>
>>>>> Regards, Brad
>>>>>
>>>>>
>>>>> On 02/10/2014 08:29 AM, Oliver Boyd wrote:
>>>>>> Hi Charles, If I do as you suggest and apply identical
>>>>>> boundary conditions in problem 2 as in problem 1 and apply
>>>>>> both the initial stresses and strains from problem 1, I get
>>>>>> the same output (from visual inspection) from problem 2 as
>>>>>> from problem 1. Now I'd like to change the boundary
>>>>>> conditions on the fault in problem 2. I want to lock the
>>>>>> upper part of the fault and allow the lower to continue to
>>>>>> slip in response to the stresses induced by the earthquake
>>>>>> in problem 1. At this point, it seems to me that in order to
>>>>>> be able to change the boundary conditions on the fault (and
>>>>>> perhaps outer boundaries), I'd have to specify both
>>>>>> initial_stress and initial displacements within the
>>>>>> material? Alternatively, if I have to do this in a single
>>>>>> simulation, I could use rate-and-state friction and an
>>>>>> earthquake cycle. Ultimately, I might do this, but it could
>>>>>> take a complex model a while to run.
>>>>>>
>>>>>> Oliver
>>>>>>
>>>>>> On 2/9/14 3:57 PM, "Charles Williams" <willic3 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Oliver,
>>>>>>>
>>>>>>> If you look in the material section of the manual it
>>>>>>> explains how initial stresses and strains work.  In a
>>>>>>> generic way, the stress is generally computed as:
>>>>>>>
>>>>>>> stress = material_matrix * (strain - initial_strain) +
>>>>>>> initial_stress
>>>>>>>
>>>>>>> That means that if you have identical boundary conditions
>>>>>>> for the two problems, if all of the stress were purely
>>>>>>> elastic, your computed stress would just be equal to the
>>>>>>> initial stress (the strain would cancel with the initial
>>>>>>> strain and not generate any stress).  Since you have some
>>>>>>> viscous strain, this won't be quite the case, but I'm
>>>>>>> guessing it won't be too far off.  Unfortunately, we don't
>>>>>>> yet make use of the other state variables (e.g., viscous
>>>>>>> strain), or we could also take that into account.
>>>>>>>
>>>>>>> Have you tried the following:
>>>>>>>
>>>>>>> 1.  Apply identical BC for the two problems. 2.  Use both
>>>>>>> initial stress and initial strain from problem 1 for
>>>>>>> problem 2.
>>>>>>>
>>>>>>> You should end up with stresses that are pretty much the
>>>>>>> same as what you had in problem 1.  The strains will also
>>>>>>> look very similar at the beginning, because the computed
>>>>>>> strains don't include initial strains. Strains are
>>>>>>> computed purely from displacements, and are independent of
>>>>>>> the material model.
>>>>>>>
>>>>>>> Let me know if this helps.  In the meantime, I think I'll
>>>>>>> have a look at including all the initial state variables.
>>>>>>>
>>>>>>> Cheers, Charles
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 10/02/2014, at 11:10 am, Oliver Boyd <olboyd at usgs.gov>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Charles, Thanks for the suggestion. Yes, the initial
>>>>>>>> conditions are different between the two problems. In
>>>>>>>> the first, everything is driven by the boundaries. In
>>>>>>>> the second, I wanted everything driven internally. The
>>>>>>>> initial material stresses and strains in the second
>>>>>>>> simulation result from the first simulation. If I keep
>>>>>>>> the surficial driving boundary conditions and add
>>>>>>>> internal stresses, the resulting material stresses
>>>>>>>> double. I tried your suggestion of leaving one of the
>>>>>>>> side boundaries free, but it produces very similar
>>>>>>>> results.
>>>>>>>>
>>>>>>>> It also appears that strains are determined by surficial
>>>>>>>> boundary conditions while initial stresses are
>>>>>>>> determined by db_initial_stresses and db_initial_strains.
>>>>>>>> When I specify db_initial_strain, it appears that it's
>>>>>>>> converted to stress and then added to db_initial_stress.
>>>>>>>> So I'm not sure I'll be able to pass the state from one
>>>>>>>> simulation to another.
>>>>>>>>
>>>>>>>> Do you know where in the code it reads in
>>>>>>>> db_initial_strain and where it might convert it to
>>>>>>>> stress. Do you think I'd be able to get it to assign
>>>>>>>> db_initial_strain to the strain field?
>>>>>>>>
>>>>>>>> Thanks for your help, Oliver
>>>>>>>>
>>>>>>>>
>>>>>>>> On 2/9/14 1:30 PM, "Charles Williams"
>>>>>>>> <willic3 at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Sorry for being slow to respond to this, Oliver.  I
>>>>>>>>> haven't gone through everything in detail, but one
>>>>>>>>> thing I noticed is that your boundary conditions on
>>>>>>>>> the external boundaries are different for the two
>>>>>>>>> problems, which means that you won't be able to get
>>>>>>>>> the same stress/strain state for the two cases.  One
>>>>>>>>> possible solution would be to leave one boundary free.
>>>>>>>>> I'm not sure if this will work or not, but it's
>>>>>>>>> probably worth a shot.
>>>>>>>>>
>>>>>>>>> Cheers, Charles
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 8/02/2014, at 6:50 am, Oliver Boyd
>>>>>>>>> <olboyd at usgs.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Brad, Attached are some figures illustrating what
>>>>>>>>>> I mean. In step1Kin, I use Dirichlet boundary
>>>>>>>>>> conditions on the domain edges and specified 100 cm
>>>>>>>>>> of fault slip on the fault. This generates stresses
>>>>>>>>>> and strains in the materials and tractions on the
>>>>>>>>>> fault as depicted in the figure step1Kin.png. If I
>>>>>>>>>> let this simulation run, the viscoelastic layer will
>>>>>>>>>>  relax. But I'd like to change the conditions on the
>>>>>>>>>> fault surface. So as a first step, I wanted to
>>>>>>>>>> transfer the stresses and strains to step2Kin and
>>>>>>>>>> let them relax. In step2Kin, domain boundaries and
>>>>>>>>>> fault surface initial displacement is zero. I am
>>>>>>>>>> hoping to get step1Kin and step2Kin to show the same
>>>>>>>>>> results after 200 years. But they don't. There is the
>>>>>>>>>>  expected relaxation in step1Kin, but there is no
>>>>>>>>>> relaxation in step2Kin. When I first transferred
>>>>>>>>>> just the stress through db_initial_stress and looked
>>>>>>>>>> at the stresses, strains, and tractions,
>>>>>>>>>> step2Kin_stressini.png, I figured I only needed to
>>>>>>>>>> transfer over the strains to make it look like
>>>>>>>>>> step1Kin and everything would proceed as expected.
>>>>>>>>>> But I haven't figured out how to transfer the
>>>>>>>>>> strains properly. When I attempt to transfer both the
>>>>>>>>>>  stresses and strains, They appear to be working
>>>>>>>>>> against each other.
>>>>>>>>>> (step2Kin_stress_strain_ini.png).
>>>>>>>>>>
>>>>>>>>>> Oliver
>>>>>>>>>>
>>>>>>>>>> On 2/6/14 4:45 PM, "Brad Aagaard"
>>>>>>>>>> <baagaard at usgs.gov> wrote:
>>>>>>>>>>
>>>>>>>>>>> Oliver,
>>>>>>>>>>>
>>>>>>>>>>> For the db_initial_strain, you are correct in that
>>>>>>>>>>> the values in the spatial database are strain-xx,
>>>>>>>>>>> etc.
>>>>>>>>>>>
>>>>>>>>>>> I don't know what you mean by "seeing the initial
>>>>>>>>>>> strain field being set". You can ask for the
>>>>>>>>>>> "initial_strain" field to be written as one of the
>>>>>>>>>>> cell info fields to check to make sure it is read
>>>>>>>>>>> in and matches what you expect the spatial
>>>>>>>>>>> database to produce. It does look like we may not
>>>>>>>>>>> be including the initial strain in the
>>>>>>>>>>> "total_strain" output field. Is this what you mean
>>>>>>>>>>> by "not seeing the initial strain field being set"
>>>>>>>>>>> or are you seeing the initial strain field not
>>>>>>>>>>> affecting the solution in the way you expect?
>>>>>>>>>>>
>>>>>>>>>>> Brad
>>>>>>>>>>>
>>>>>>>>>>> On 02/03/2014 09:04 AM, Oliver Boyd wrote:
>>>>>>>>>>>> Hi Brad, Thanks for your help. I had initially
>>>>>>>>>>>> tried using db_initial_strain as well as several
>>>>>>>>>>>> of other things. I did as you suggested below,
>>>>>>>>>>>> but do not see the initial strain field being
>>>>>>>>>>>> set after running step2Kin. Thanks for reminding
>>>>>>>>>>>> me of the use of --component.help. I was trying
>>>>>>>>>>>> to figure out what variables I needed to set in
>>>>>>>>>>>> db_initial_strain. Based on the manual I thought
>>>>>>>>>>>> it was strain-xx Š, but I wasn't sure. I thought
>>>>>>>>>>>> I might be able to get to it with
>>>>>>>>>>>> help-properties, but I still haven't figured that
>>>>>>>>>>>> out. In any case, I'm still doing something
>>>>>>>>>>>> wrong.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks again for your help, Oliver
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/2/14 11:07 AM, "Brad Aagaard"
>>>>>>>>>>>> <baagaard at usgs.gov> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Oliver,
>>>>>>>>>>>>>
>>>>>>>>>>>>> There are separate spatial databases for
>>>>>>>>>>>>> initial stress and initial strain.
>>>>>>>>>>>>>
>>>>>>>>>>>>> [pylithapp.timedependent.materials.upper_crust]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>db_initial_stress = spatialdata.spatialdb.SimpleDB
>>>>>>>>>>>>> db_initial_stress.label = Initial stress in
>>>>>>>>>>>>> upper crust
>>>>>>>>>>>>> db_initial_stress.iohandler.filename =
>>>>>>>>>>>>> spatialdb/afterslip_stress_uppercrust.spatialdb
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>db_initial_stress.query_type = nearest
>>>>>>>>>>>>>
>>>>>>>>>>>>> # ADD db_initial_strain db_initial_strain =
>>>>>>>>>>>>> spatialdata.spatialdb.SimpleDB
>>>>>>>>>>>>> db_initial_strain.label = Initial strain in
>>>>>>>>>>>>> upper crust
>>>>>>>>>>>>> db_initial_strain.iohandler.filename =
>>>>>>>>>>>>> spatialdb/afterslip_strain_uppercrust.spatialdb
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>db_initial_strain.query_type = nearest
>>>>>>>>>>>>>
>>>>>>>>>>>>> Remember you can use pylith --COMPONENT.help
>>>>>>>>>>>>> and --COMPONENT.help-properties and
>>>>>>>>>>>>> --COMPONENT.help-components to interrogate
>>>>>>>>>>>>> what properties and components are available.
>>>>>>>>>>>>> In this case COMPONENT would be
>>>>>>>>>>>>> timedependent.materials.upper_crust.
>>>>>>>>>>>>>
>>>>>>>>>>>>> pylith step1Kin.cfg
>>>>>>>>>>>>> --timedependent.materials.upper_crust.help-components
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>facilities of 'elasticisotropic3d':
>>>>>>>>>>>>> db_initial_state=<component name>: Database
>>>>>>>>>>>>> for initial state variables. current value:
>>>>>>>>>>>>> 'nullcomponent', from {default} configurable
>>>>>>>>>>>>> as: nullcomponent, db_initial_state
>>>>>>>>>>>>> db_initial_strain=<component name>: Database
>>>>>>>>>>>>> for initial strain. current value:
>>>>>>>>>>>>> 'nullcomponent', from {default} configurable
>>>>>>>>>>>>> as: nullcomponent, db_initial_strain
>>>>>>>>>>>>> db_initial_stress=<component name>: Database
>>>>>>>>>>>>> for initial stress. current value:
>>>>>>>>>>>>> 'nullcomponent', from {default} configurable
>>>>>>>>>>>>> as: nullcomponent, db_initial_stress
>>>>>>>>>>>>> db_properties=<component name>: Database for
>>>>>>>>>>>>> physical property parameters. current value:
>>>>>>>>>>>>> 'simpledb', from {default} configurable as:
>>>>>>>>>>>>> simpledb, db_properties output=<component
>>>>>>>>>>>>> name>: Output manager for elastic material
>>>>>>>>>>>>> information. current value:
>>>>>>>>>>>>> 'outputmatelastic', from {default} configurable
>>>>>>>>>>>>> as: outputmatelastic, output
>>>>>>>>>>>>> perf_logger=<component name>: Performance and
>>>>>>>>>>>>> memory logging. current value: 'memory_logger',
>>>>>>>>>>>>> from {default} configurable as: memory_logger,
>>>>>>>>>>>>> perf_logger quadrature=<component name>:
>>>>>>>>>>>>> Quadrature object for numerical integration.
>>>>>>>>>>>>> current value: 'quadrature', from {default}
>>>>>>>>>>>>> configurable as: quadrature
>>>>>>>>>>>>>
>>>>>>>>>>>>> Brad
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 1/31/14 11:26 AM, Oliver Boyd wrote:
>>>>>>>>>>>>>> Hello, I'm trying to generate a set of
>>>>>>>>>>>>>> initial conditions in one problem and then
>>>>>>>>>>>>>> use them in another. The first problem
>>>>>>>>>>>>>> calculates the stress changes due to an
>>>>>>>>>>>>>> earthquake. Currently, the second problem
>>>>>>>>>>>>>> only looks at the viscoelastic response
>>>>>>>>>>>>>> (which of course can be done in the first
>>>>>>>>>>>>>> problem). Once I get the viscoelastic
>>>>>>>>>>>>>> response in the second problem to equal the
>>>>>>>>>>>>>> first (if I let the first progress through
>>>>>>>>>>>>>> time), I will change the fault interface
>>>>>>>>>>>>>> model, but this is not yet implemented.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I'm able to transfer over the initial stress
>>>>>>>>>>>>>> through db_initial_stress but I don't know
>>>>>>>>>>>>>> how to transfer the initial strain. I've
>>>>>>>>>>>>>> tried putting the initial strain in the
>>>>>>>>>>>>>> db_initial_stress.iohandler.filename file
>>>>>>>>>>>>>> with the components given by p71 of the
>>>>>>>>>>>>>> manual, but they don't appear to have an
>>>>>>>>>>>>>> effect when I run the simulation. Attached
>>>>>>>>>>>>>> are the files needed for the simulation.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks for your assistance, Oliver
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Flow pylith step1Kin.cfg python
>>>>>>>>>>>>>> afterslip_initial_parms.py pylith
>>>>>>>>>>>>>> step2Kin.cfg
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>CIG-SHORT mailing list
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
><step2Kin_stress_strain_ini.png><step2Kin_stressini.png><step1Kin.p
>>>>>>>>>> ng
>>>>>>>>>>> <
>>>>>>>>>> st
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 
>>>>>>>>>>ep2Kin.cfg><step1Kin.cfg>________________________________________
>>>>>>>>>>__
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>__
>>>>>>>>>> __ _ CIG-SHORT mailing list CIG-SHORT at geodynamics.org
>>>>>>>>>>
>>>>>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>Charles A. Williams
>>>>>>>>> Scientist GNS Science 1 Fairway Drive, Avalon PO Box
>>>>>>>>> 30368 Lower Hutt  5040 New Zealand ph (office):
>>>>>>>>> 0064-4570-4566 fax (office): 0064-4570-4600
>>>>>>>>> C.Williams at gns.cri.nz
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> CIG-SHORT mailing list CIG-SHORT at geodynamics.org
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>_______________________________________________
>>>>>>>> CIG-SHORT mailing list CIG-SHORT at geodynamics.org
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>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>>
>Charles A. Williams
>>>>>>> Scientist GNS Science 1 Fairway Drive, Avalon PO Box 30368
>>>>>>>  Lower Hutt  5040 New Zealand ph (office): 0064-4570-4566
>>>>>>> fax (office): 0064-4570-4600 C.Williams at gns.cri.nz
>>>>>>>
>>>>>>> _______________________________________________ CIG-SHORT
>>>>>>> mailing list CIG-SHORT at geodynamics.org
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>>>>>>
>>>>>>
>>>>>> _______________________________________________ CIG-SHORT
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>>>>>>
>>>>>
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>>>>
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