[CIG-SHORT] Problem setting initial conditions
Oliver Boyd
olboyd at usgs.gov
Tue Feb 11 13:52:42 PST 2014
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.
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.
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
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> CIG-SHORT mailing list
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> CIG-SHORT mailing list
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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
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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
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>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
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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
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>>>>
>>>>
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