Segmentation fault when using displaced mesh with NS kernels

[mlesueur]

Hi,
I'm working on a Navier-Stokes simulation in a granular rock matrix that looks at the effects of grain's dilation on permeability (calculated with Darcy's Law).

I use the variables disp_x and disp_y to make my grains swell but Navier Stokes flow is not affected by the swelling!


Although the velocity should increase in the channels that are tightening.

I figured out that I have to put in my Mesh block: displacements = 'disp_x disp_y'
and put in everything that operates spatially: use_displaced_mesh = true
In my input file, it means BC, Kernels and Postprocessors.

But when I turn everything on, I got a segmentation fault.
So I tried to localise the problem and realise that the only things that are not working with use_displaced_mesh = true are the Navier Stokes kernels.

For an example of usage, you can follow my post on the mailing list:
https://groups.google.com/forum/#!topic/moose-users/KvJZvdritew

Cheers,

Martin Lesueur

[friedmud]

I'm not sure what's going on here... I just wanted to report that the whole team is REALLY busy right now so don't be discouraged if we are a bit slow to respond!

This looks like a really cool application, and I'll take a look into this soon (if someone else doesn't get to it first).

[aeslaughter]

I just downloaded your mesh and executed "with_ns_displacement.i" and did not receive a seg. fault:

~/projects/moose/modules/navier_stokes/navier_stokes-oprof -i with_ns_displacement.i Outputs/print_linear_residuals=false

Framework Information:
MOOSE version:           git commit 3f801dd on 2015-11-23
PETSc Version:           3.6.1
Current Time:            Mon Nov 23 09:59:24 2015
Executable Timestamp:    Mon Nov 23 09:50:33 2015

Parallelism:
  Num Processors:          1
  Num Threads:             1

Mesh: 
  Distribution:            serial
  Mesh Dimension:          2
  Spatial Dimension:       3
  Nodes:                   
    Total:                 1789
    Local:                 1789
  Elems:                   
    Total:                 854
    Local:                 854
  Num Subdomains:          2
  Num Partitions:          1

Nonlinear System:
  Num DOFs:                4246
  Num Local DOFs:          4246
  Variables:               { "vel_x" "vel_y" } "p" { "disp_x" "disp_y" } "fake" 
  Finite Element Types:    "LAGRANGE" "LAGRANGE" "LAGRANGE" "LAGRANGE" 
  Approximation Orders:    "SECOND" "FIRST" "FIRST" "FIRST" 

Execution Information:
  Executioner:             Transient
  TimeStepper:             ConstantDT
  Solver Mode:             Preconditioned JFNK




Time Step  0, time = 0
                dt = 0

Postprocessor Values:
+----------------+----------------+----------------+----------------+
| time           | p_multiapp     | permeability   | v_right        |
+----------------+----------------+----------------+----------------+
|   0.000000e+00 |   1.000000e+00 |   0.000000e+00 |   0.000000e+00 |
+----------------+----------------+----------------+----------------+


Time Step  1, time = 10
                dt = 10
 0 Nonlinear |R| = 3.875486e+00
 1 Nonlinear |R| = 2.638056e-06
 2 Nonlinear |R| = 5.405136e-13
 Solve Converged!
WARNING: At least one element took more than 10 iterations to converge in inverse_map()...
Rerun in devel/dbg mode for more details.

Outlier Variable Residual Norms:
  vel_x: 4.758999e-13

Postprocessor Values:
+----------------+----------------+----------------+----------------+
| time           | p_multiapp     | permeability   | v_right        |
+----------------+----------------+----------------+----------------+
|   0.000000e+00 |   1.000000e+00 |   0.000000e+00 |   0.000000e+00 |
|   1.000000e+01 |   1.000000e+00 |   2.720808e-03 |   2.720808e-03 |
+----------------+----------------+----------------+----------------+

[mlesueur]

Sorry Andrew,
The file had the displacement set up, but not activated.
This following file should fail. It is the same file than before but I activated use_displaced_mesh=true on the NS kernels.

[GlobalParams]

Dummy parameters

gravity = '0 0 0'
rho = 1
mu = 1
[]

[Mesh]
type = FileMesh
file = mesh_navier-meca.msh
dim = 2
boundary_name = 'top grain_edges right bottom left'
block_name = 'pore grains'
boundary_id = '4 1 5 6 7'
block_id = '2 3'
displacements = 'disp_x disp_y'
[]

[Variables]

x-velocity

y-velocity

Pressure

[./vel_x]
order = SECOND
block = pore
[../]
[./vel_y]
order = SECOND
block = pore
[../]
[./p]
order = FIRST
family = LAGRANGE
initial_condition = 1
block = pore
[../]
[./disp_x]
initial_condition = 0
[../]
[./disp_y]
[../]
[./fake]
block = grains
[../]
[]

[Functions]
[./perm_f]
type = ParsedFunction
value = v/p
vals = 'v_right p_multiapp'
vars = 'v p'
[../]
[./displ]
type = ParsedFunction
value = -0.6_y_sin(y_3.14)_max(0,x-0.2)
[../]
[]

[Kernels]

mass

x-momentum, time

x-momentum, space

y-momentum, time

y-momentum, space

active = 'y_momentum_space tdy x_momentum_space tdx mass td'
[./mass]
type = INSMass
variable = p
u = vel_x
v = vel_y
p = p
block = pore
use_displaced_mesh = true
[../]
[./x_momentum_time]
type = INSMomentumTimeDerivative
variable = vel_x
block = pore
use_displaced_mesh = true
[../]
[./x_momentum_space]
type = INSMomentum
variable = vel_x
u = vel_x
v = vel_y
p = p
component = 0
block = pore
use_displaced_mesh = true
[../]
[./y_momentum_time]
type = INSMomentumTimeDerivative
variable = vel_y
block = pore
use_displaced_mesh = true
[../]
[./y_momentum_space]
type = INSMomentum
variable = vel_y
u = vel_x
v = vel_y
p = p
component = 1
block = pore
use_displaced_mesh = true
[../]
[./td]
type = TimeDerivative
variable = fake
block = grains
use_displaced_mesh = true
[../]
[./tdx]
type = TimeDerivative
variable = disp_x
use_displaced_mesh = true
[../]
[./tdy]
type = TimeDerivative
variable = disp_y
use_displaced_mesh = true
[../]
[]

[BCs]
active = 'highp x_no_slip lowp y_no_slip test'
[./x_no_slip]
type = DirichletBC
variable = vel_x
boundary = 'top bottom grain_edges'
value = 0.0
use_displaced_mesh = true
[../]
[./y_no_slip]
type = DirichletBC
variable = vel_y
boundary = 'top bottom grain_edges'
value = 0.0
use_displaced_mesh = true
[../]
[./highp]
type = PostprocessorDirichletBC
variable = p
boundary = left
postprocessor = p_multiapp
use_displaced_mesh = true
[../]
[./lowp]
type = DirichletBC
variable = p
boundary = right
value = 0
use_displaced_mesh = true
[../]
[./inlet]
type = DirichletBC
variable = vel_x
boundary = left
value = 0
use_displaced_mesh = true
[../]
[./test]
type = NSImposedVelocityBC
variable = vel_x
boundary = left
desired_velocity = 0
use_displaced_mesh = true
[../]
[]

[Postprocessors]
[./p_multiapp]
type = Receiver
default = 1
use_displaced_mesh = true
[../]
[./v_right]
type = SideAverageValue
variable = vel_x
boundary = right
use_displaced_mesh = true
[../]
[./permeability]
type = FunctionValuePostprocessor
function = perm_f
use_displaced_mesh = true
[../]
[]

[Preconditioning]
[./SMP_PJFNK]
# Preconditioned JFNK (default)
type = SMP
full = true
solve_type = PJFNK
[../]
[]

[Executioner]

type = Steady

type = Transient
petsc_options_iname = '-ksp_gmres_restart '
petsc_options_value = '300 '
line_search = none
nl_rel_tol = 1e-8
nl_max_its = 6
l_tol = 1e-8
l_max_its = 300
num_steps = 1 # 200
end_time = 10
[]

[Outputs]
file_base = sub1
csv = true
exodus = true
[]

[ICs]
[./disp_y_ic]
function = displ
variable = disp_y
type = FunctionIC
[../]
[]