Rework Material Data Structures #109

rrsettgast · 2018-08-11T01:26:37Z

No description provided.

… arbitrary ManagedGroup. Allocated material data off of CellBlockSubRegions.

…directly to a ManagedGroup

… at the top level constitutive relation level

…accessor for constitutive models

… of an array

…Manager::ApplyBC functions with a single function

… old unused files

rrsettgast · 2018-08-20T20:32:58Z

@klevzoff can you update the single phase flow solver to use the auto-generated fields from the materials, and update single phase flow solver inputs to evaluate?

klevzoff · 2018-08-21T06:48:30Z

src/components/core/src/mesh/ElementRegionManager.hpp

+      {
+        dataRepository::ManagedGroup const * const
+        constitutiveRelation = constitutiveGroup->GetGroup(matIndex);
+        accessor[kReg][kSubReg][matIndex].set(constitutiveRelation->getReference<VIEWTYPE>(viewName));


Here matIndex is determined by relative ordering of constitutive models in a (sub)region. Does that mean the material index for the same model (e.g. water) can be different between (sub)regions? If so, I can't use this accessor in a solver, since I can't reliably figure out the material index of interest (or I'd have to search for it in every (sub)region whenever I use it). I'd rather grab the field view wrapper directly by its name using the defined naming convention modelName + "_" + fieldName, since modelName is something the solver will know (provided via input).

@klevzoff good point. i can fix the accessor to enforce constant index across all regions.

@rrsettgast I also just realized, the accessor will likely carry a lot of null pointers wrapped as references. E.g. if I have a fluid model with "fluidDensity" field and a solid model with a "porosity" field, and I request a material accessor for "fluidDensity", which the second model does not have, but it will still be extracted as a nullptr. I'm not going to access that null reference, but the very fact that it exists seems like a trouble waiting to happen. Or technically it's UB i guess.

As I suspected, in debug mode this throws SIGSEGV when trying to dereference a nullptr, even though I'm never using the returned reference

@klevzoff for what problem does this SIGSEGV?

@rrsettgast this was before your commit 3451419
I was working on some changes in parallel (which are now merged with yours and pushed), this particular line was segfaulting on any 2-material test. I don't know if still does, because since today's updates I'm getting errors from ChaiVector (munmap_chunk(): invalid pointer and SIGABRT) during ManagedGroup::Initialize(), so I can't run anything atm. I'll try to debug and document it separately.

…the entire problem to enforce consistent indexing across regions

…imple pore compressibility model from single phase fluid model.

…what material is the fluid

…onManager

…eature/multiMaterial

rrsettgast · 2018-08-22T06:23:43Z

@klevzoff It looks like you are doing some rework of the actual constitutive hierarchy...not that there is much of a hierarchy to start with. We should do the actual rework of the constitutive class hierarchy in another PR after this. This really became a PR centered around the interface to the material data, and the application of boundary conditions.

…alViewAccessor. fixed test file

rrsettgast · 2018-08-22T07:07:44Z

@klevzoff when you move or rename a file, please do a "git mv".

https://stackoverflow.com/questions/2641146/handling-file-renames-in-git

klevzoff · 2018-08-22T18:50:32Z

@rrsettgast The hierarchy change was just a way to test having two meaningful constitutive models (i.e. such that both are actually used by the solver). The main change was about how the solver interacts with the models: it's now actually making use of the state update function, rather than just extracting the state data and operating it manually.

klevzoff · 2018-08-22T18:52:16Z

@rrsettgast noted. The IDE is supposed to take care of using appropriate git commands when I do automated refactoring (such as renaming a class), but it seems to miss sometimes.

rrsettgast · 2018-08-23T02:01:39Z

@klevzoff
The SinglePhaseFlowSolver doesn't appear work anymore. I am trying to finish up the silo output for mixed material zones but I can't verify that I am doing things correct. I noticed that you reworked the set of variables that are used to perform the calculation. I don't really agree with the removal of the delta's in favor of copying the fields at the beginning of the step, so we should have a discussion about that sort of decision. Additionally I think that this sort of thing needs to be done it its own pull request. Unless you have a major objection, I am going to make a branch for these commits off of this branch, rebase them out of this branch, and rebase the commits out the commits that were kept in this branch out of the other branch.

…ize mixed zones properly

rrsettgast · 2018-08-23T06:13:04Z

@klevzoff never mind about the rebase. I can't do it. The histories are too divergent to get a successful rebase.

klevzoff · 2018-08-24T22:35:44Z

@rrsettgast I'm getting SIGESGV from here (when running 1D_10_compressible_2material.xml):

__strlen_avx2 0x00007f6f6bcb85a1
DBStringArrayToStringList 0x00007f6f6e00f1be
db_hdf5_PutMultivar 0x00007f6f6e0a81e6
DBPutMultivar 0x00007f6f6dff8678
geosx::SiloFile::WriteMultiXXXX<int (*)(DBfile*, char const*, int, char const* const*, int const*, DBoptlist_ const*)> SiloFile.hpp:1030
geosx::SiloFile::WriteMaterialDataField<double, double> SiloFile.hpp:968
geosx::SiloFile::WriteMaterialMapsFullStorage SiloFile.cpp:1135
geosx::SiloFile::WriteMeshLevel SiloFile.cpp:1649
geosx::SiloFile::WriteDomainPartition SiloFile.cpp:1468
geosx::SiloOutput::Execute SiloOutput.cpp:96
...

At a first glance, seems to be nothing wrong with data that goes in. I can't see into silo functions though.
Maybe I did something wrong (I had to locally merge bugfix/noChaiString and replace a few more array1d<string> to be able to run).

Anyway, if you merge develop into this PR and it works for you, it's good to go (can't approve while conflicting changes exist). Or I can push mine.

…l namespace

…into feature/multiMaterial

rrsettgast · 2018-08-27T18:25:00Z

resolves #63

rrsettgast · 2018-08-27T18:25:36Z

resolves #80

modified material structures to allow hanging of material data off of…

0bf1890

… arbitrary ManagedGroup. Allocated material data off of CellBlockSubRegions.

rrsettgast force-pushed the feature/multiMaterial branch from 8502a99 to 0bf1890 Compare August 11, 2018 01:31

rrsettgast added 5 commits August 12, 2018 23:49

added cloning feature to ViewWrapper and ablity to add a ViewWrapper …

c537910

…directly to a ManagedGroup

removed StateData and ParameterData groups and are storing everything…

0e92fe4

… at the top level constitutive relation level

Merge branch 'develop' into feature/multiMaterial

937475e

added ElementRegionManager::MaterialViewAccessor

6db4c83

apply uncrustify to constitutive target

a47736e

rrsettgast requested a review from klevzoff August 15, 2018 17:58

rrsettgast added 11 commits August 15, 2018 11:34

added allocation of some field data in constitutive relations. added …

8fa00f2

…accessor for constitutive models

modify and test user defined conversion operators to reduce dimension…

fa9dd91

… of an array

removed USE_ATK from error checks in ViewWrapper::cast() functions

7deb4fd

Merge branch 'develop' into feature/multiMaterial

a5d94d5

merge changes from branch in former submodule into this branch

1199562

added density scalar and field variables

46b2229

quite a bit of boundary condition cleanup. replaced BoundaryCondition…

a15c4a8

…Manager::ApplyBC functions with a single function

further condensation of boundary condition functionality

42417d7

some formatting changes to boundary conditions files. and deletion of…

e61a59a

… old unused files

Merge branch 'develop' into feature/multiMaterial

7a38acc

mainly documentation for the boundary condition classes

28491d3

rrsettgast requested a review from joshua-white August 20, 2018 20:31

klevzoff reviewed Aug 21, 2018

View reviewed changes

rrsettgast and others added 8 commits August 21, 2018 17:56

added more comments to boundary condition classes

c0a50fd

changed material view accessor to have an entry for each material in …

3451419

…the entire problem to enforce consistent indexing across regions

Update SinglePhaseFlow solver to use new constitutive fields. Split s…

20fdb84

…imple pore compressibility model from single phase fluid model.

Merge updates from upstream

e26868d

added specification of fluidName in SinglePhaseFlowSolver to specify …

2371515

…what material is the fluid

Update single phase test inputs

c199753

Merge from upstream

74d725a

Add file somehow lost in previous commit

ffacb3a

rrsettgast added 2 commits August 21, 2018 23:04

fix bug in boundary condition application function in BoundaryConditi…

a47f43e

…onManager

Merge branch 'feature/multiMaterial' of github.com:GEOSX/GEOSX into f…

b390cb2

…eature/multiMaterial

addedadditional protections against nullptr access in ConstructMateri…

7f4702a

…alViewAccessor. fixed test file

removed original material allocations. modified silo output to visual…

f262de5

…ize mixed zones properly

rrsettgast added 2 commits August 23, 2018 00:44

fixed problems in SinglePhaseFlowSolver and CompressibleFluid

75dec8d

changes to silo files to properly handle mixed materials

7d48a0d

rrsettgast and others added 8 commits August 24, 2018 17:07

added the ghost flags into silo file

75f4db7

Merge branch 'develop' into feature/multiMaterial

85a1f67

Merge branch 'develop' into feature/multiMaterial

7b3f0c9

updated solid mechanics solver to conform to new material treatment

81bb5aa

fixed namespace in calls to geosx::raja::for... to refer to the globa…

7621296

…l namespace

Enabled OpenMP on travis

b0ef8be

Merge branch 'feature/multiMaterial' of https://github.com/GEOSX/GEOSX …

4b09ecd

…into feature/multiMaterial

added guards for when Openmp is not found

9df923c

rrsettgast merged commit eac11f3 into develop Aug 27, 2018

klevzoff mentioned this pull request Aug 28, 2018

Update docker and travis #135

Merged

rrsettgast deleted the feature/multiMaterial branch August 31, 2018 04:13

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Rework Material Data Structures #109

Rework Material Data Structures #109

rrsettgast commented Aug 11, 2018

rrsettgast commented Aug 20, 2018

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Rework Material Data Structures #109

Rework Material Data Structures #109

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