Creating 3D Cylinder Mesh for Porous Flow Simulation

[ColinMG2]

Check these boxes if you have followed the posting rules.

• Q&A General is the most appropriate section for my question
• I have consulted the posting Guidelines on the Discussions front page
• I have searched the Discussions forum and my question has not been asked before
• I have searched the MOOSE website and the documentation does not answer my question
• I have formatted my post following the posting guidelines (screenshots as a last resort, triple back quotes around pasted text)

Question

Hello. I am a new user to MOOSE and I am a little confused on how to test whether the functions I am using are creating a cylindrical mesh. I want to simulate Fick's second law of diffusion for a 1D case where diffusion only occurs in the z-direction:

My current code is as follows:

[Mesh]
    [cross_section]
        type = ConcentricCircleMeshGenerator
        has_outer_square = off
        num_sectors = 4
        preserve_volumes = off
        radii = 1
        rings = 1
    []
    [Extrusion]
        type = AdvancedExtruderGenerator
        direction = '0 0 1'
        heights = '1 2 3'
        input = cross_section
        num_layers = '1 2 3'
    []
[]

I am not quite sure how to test this as when I tried to run just the mesh I got this error:
(moose) colinmoose@ColinG14:~/projects/moosecmg$ ./moosecmg-opt -i porous_flow/step1.i --mesh-only

*** ERROR ***
The following error occurred in the Action '' of type SetupMeshCompleteAction.

No mesh file was supplied and no generation block was provided

How would you recommend starting with the mesh for this problem?

[GiudGiud]

Hello

This syntax should be fine. Maybe something else in the input is really breaking the parser
Can you please pase the rest of the input?

[ColinMG2]

This is what it says when I run it in my app name:
(moose) colinmoose@ColinG14:~/projects/moosecmg$ git show
fatal: your current branch 'master' does not have any commits yet

[GiudGiud]

let's try in your moose directory not in your app

[ColinMG2]

It worked in my moose directory. Got the same output as you:
(moose) colinmoose@ColinG14:~/projects/moose/test$ ./moose_test-opt -i test.i --mesh-only
Mesh Information:
elem_dimensions()={3}
spatial_dimension()=3
n_nodes()=287
n_local_nodes()=287
n_elem()=192
n_local_elem()=192
n_active_elem()=192
n_subdomains()=1
n_elemsets()=0
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
is_prepared()=true
is_replicated()=true

Mesh Bounding Box:
Minimum: (x,y,z)=( -1, -1, 0)
Maximum: (x,y,z)=( 1, 1, 6)
Delta: (x,y,z)=( 2, 2, 6)

Mesh Element Type(s):
HEX8

Mesh Nodesets:
Nodeset 0, 41 nodes
Bounding box minimum: (x,y,z)=( -1, -1, 0)
Bounding box maximum: (x,y,z)=( 1, 1, 0)
Bounding box delta: (x,y,z)=( 2, 2, 0)
Nodeset 1, 41 nodes
Bounding box minimum: (x,y,z)=( -1, -1, 6)
Bounding box maximum: (x,y,z)=( 1, 1, 6)
Bounding box delta: (x,y,z)=( 2, 2, 0)

Mesh Sidesets:
Sideset 0, 32 sides (QUAD4), 32 elems (HEX8), 41 nodes
Side volume: 3.06147
Bounding box minimum: (x,y,z)=( -1, -1, 0)
Bounding box maximum: (x,y,z)=( 1, 1, 0)
Bounding box delta: (x,y,z)=( 2, 2, 0)
Sideset 1, 32 sides (QUAD4), 32 elems (HEX8), 41 nodes
Side volume: 3.06147
Bounding box minimum: (x,y,z)=( -1, -1, 6)
Bounding box maximum: (x,y,z)=( 1, 1, 6)
Bounding box delta: (x,y,z)=( 2, 2, 0)

Mesh Edgesets:
None

Mesh Subdomains:
Subdomain 1: 192 elems (HEX8, 192 active), 287 active nodes
Volume: 18.3688
Bounding box minimum: (x,y,z)=( -1, -1, 0)
Bounding box maximum: (x,y,z)=( 1, 1, 6)
Bounding box delta: (x,y,z)=( 2, 2, 6)
Global mesh volume = 18.3688

How do I properly set up git for my app so that it will work in that directory?

[GiudGiud]

If you want git show to show something in your folder you need to make a commit first.

For fixing your app I would recommend recompiling, possibly after cleaning the repository

[ColinMG2]

Okay perfect thank you! That worked! I am now having trouble understanding how to properly apply boundary conditions for the problem since I don't know how to name them correctly. Here is my moose file now:
[Mesh]
[cross_section]
type = ConcentricCircleMeshGenerator
has_outer_square = off
num_sectors = 6
preserve_volumes = on
radii = 1
rings = 1
[]
[Extrusion]
type = AdvancedExtruderGenerator
direction = '0 0 1'
heights = '0.5 0.5 0.5 0.5 0.5 0.5'
input = cross_section
num_layers = '1 1 1 1 1 1'
[]
[]

[Variables]
[concentration]
[]
[]

[Kernels]
[diffusion]
type = ADDiffusion
variable = concentration
[]
[]

[BCs]
[bottom]
type = DirichletBC
boundary = bottom
value = 536
variable = concentration
[]
[sides]
type = NeumannBC
boundary = sides
variable = concentration
[]
[top]
type = NeumannBC
boundary = top
variable = concentration
[]
[]

[Executioner]
type = Transient
[]

[Outputs]
exodus = true
[]

It says that the following node sets (ids) do not exist on the mesh: bottom