Hexahedron Element

Asked by li12242 on 2015-03-14

Hi all,

I am using fluidity with a simple case of hexahedron element, unfortunately I got an error at the beginning of the program.
I have tried the same case with tetrahedron element, it works fine.

Could anyone tell me where is the fault?
The error log, mesh file and fluidity options is post back, if you need any information please tell me.

*** FLUIDITY ERROR ***
Source location: (Element_Numbering.F90, 1369)
Error message: Node is not part of an element in vertex_num.
Backtrace will follow if it is available:
Use addr2line -e <binary> <address> to decipher.
Error is terminal.
fluidity(2110,0x7fff74594310) malloc: *** error for object 0x7ff8b15e7ee8: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
[li12242:02110] *** Process received signal ***
[li12242:02110] Signal: Abort trap: 6 (6)
[li12242:02110] Signal code: (0)
[li12242:02110] *** End of error message ***

mesh_3.geo
```
Point(1) = {0, 0, 0, 0.4};
Point(2) = {1.0, 0, 0, 0.4};
Point(3) = {1.0, 1.0, 0, 0.4};
Point(4) = {0.0, 1.0, 0, 0.4};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 1};
Line Loop(5) = {4, 1, 2, 3};
Plane Surface(6) = {5};

Recombine Surface{6};

Extrude {0, 0, -0.5} {
  Surface{6}; Layers{8}; Recombine;
}

Physical Surface(1) = {15};
Physical Surface(2) = {6};
Physical Surface(3) = {28};
Physical Volume(1) = {1};
Physical Surface(29) = {19, 23, 27};
```

fluidity options:
```
<?xml version='1.0' encoding='utf-8'?>
<fluidity_options>
  <simulation_name>
    <string_value lines="1">test_3</string_value>
  </simulation_name>
  <problem_type>
    <string_value lines="1">fluids</string_value>
  </problem_type>
  <geometry>
    <dimension>
      <integer_value rank="0">3</integer_value>
    </dimension>
    <mesh name="CoordinateMesh">
      <from_mesh>
        <mesh name="Basic"/>
        <stat>
          <exclude_from_stat/>
        </stat>
      </from_mesh>
    </mesh>
    <mesh name="VelocityMesh">
      <from_mesh>
        <mesh name="Basic"/>
        <mesh_shape>
          <polynomial_degree>
            <integer_value rank="0">1</integer_value>
          </polynomial_degree>
        </mesh_shape>
        <mesh_continuity>
          <string_value>discontinuous</string_value>
        </mesh_continuity>
        <stat>
          <exclude_from_stat/>
        </stat>
      </from_mesh>
    </mesh>
    <mesh name="PressureMesh">
      <from_mesh>
        <mesh name="Basic"/>
        <mesh_shape>
          <polynomial_degree>
            <integer_value rank="0">2</integer_value>
          </polynomial_degree>
        </mesh_shape>
        <mesh_continuity>
          <string_value>continuous</string_value>
        </mesh_continuity>
        <stat>
          <exclude_from_stat/>
        </stat>
      </from_mesh>
    </mesh>
    <mesh name="Basic">
      <from_file file_name="mesh_Hex/mesh_3">
        <format name="triangle"/>
        <stat>
          <include_in_stat/>
        </stat>
      </from_file>
    </mesh>
    <quadrature>
      <degree>
        <integer_value rank="0">4</integer_value>
      </degree>
    </quadrature>
  </geometry>
  <io>
    <dump_format>
      <string_value>vtk</string_value>
    </dump_format>
    <dump_period>
      <constant>
        <real_value rank="0">1.0</real_value>
      </constant>
    </dump_period>
    <output_mesh name="VelocityMesh"/>
    <stat/>
  </io>
  <timestepping>
    <current_time>
      <real_value rank="0">0.0</real_value>
    </current_time>
    <timestep>
      <real_value rank="0">0.5</real_value>
    </timestep>
    <finish_time>
      <real_value rank="0">5.0</real_value>
    </finish_time>
    <nonlinear_iterations>
      <integer_value rank="0">2</integer_value>
    </nonlinear_iterations>
    <adaptive_timestep>
      <requested_cfl>
        <real_value rank="0">5</real_value>
      </requested_cfl>
      <courant_number name="CFLNumber">
        <mesh name="VelocityMesh"/>
      </courant_number>
    </adaptive_timestep>
  </timestepping>
  <material_phase name="Fiuids">
    <equation_of_state>
      <fluids>
        <linear>
          <reference_density>
            <real_value rank="0">1.0</real_value>
          </reference_density>
        </linear>
      </fluids>
    </equation_of_state>
    <scalar_field name="Pressure" rank="0">
      <prognostic>
        <mesh name="PressureMesh"/>
        <spatial_discretisation>
          <continuous_galerkin>
            <integrate_continuity_by_parts/>
          </continuous_galerkin>
        </spatial_discretisation>
        <scheme>
          <poisson_pressure_solution>
            <string_value lines="1">only first timestep</string_value>
          </poisson_pressure_solution>
          <use_projection_method/>
        </scheme>
        <solver>
          <iterative_method name="cg"/>
          <preconditioner name="sor"/>
          <relative_error>
            <real_value rank="0">1.0e-7</real_value>
          </relative_error>
          <max_iterations>
            <integer_value rank="0">1000</integer_value>
          </max_iterations>
          <never_ignore_solver_failures/>
          <diagnostics>
            <monitors/>
          </diagnostics>
        </solver>
        <output/>
        <stat/>
        <convergence>
          <include_in_convergence/>
        </convergence>
        <detectors>
          <exclude_from_detectors/>
        </detectors>
        <steady_state>
          <include_in_steady_state/>
        </steady_state>
        <no_interpolation/>
      </prognostic>
    </scalar_field>
    <vector_field name="Velocity" rank="1">
      <prognostic>
        <mesh name="VelocityMesh"/>
        <equation name="Boussinesq"/>
        <spatial_discretisation>
          <discontinuous_galerkin>
            <viscosity_scheme>
              <compact_discontinuous_galerkin/>
            </viscosity_scheme>
            <advection_scheme>
              <upwind/>
              <integrate_advection_by_parts>
                <twice/>
              </integrate_advection_by_parts>
            </advection_scheme>
          </discontinuous_galerkin>
          <conservative_advection>
            <real_value rank="0">0.5</real_value>
          </conservative_advection>
        </spatial_discretisation>
        <temporal_discretisation>
          <theta>
            <real_value rank="0">0.5</real_value>
          </theta>
          <relaxation>
            <real_value rank="0">1.0</real_value>
          </relaxation>
        </temporal_discretisation>
        <solver>
          <iterative_method name="gmres">
            <restart>
              <integer_value rank="0">30</integer_value>
            </restart>
          </iterative_method>
          <preconditioner name="sor"/>
          <relative_error>
            <real_value rank="0">1.0e-7</real_value>
          </relative_error>
          <max_iterations>
            <integer_value rank="0">10000</integer_value>
          </max_iterations>
          <never_ignore_solver_failures/>
          <diagnostics>
            <monitors/>
          </diagnostics>
        </solver>
        <initial_condition name="WholeMesh">
          <constant>
            <real_value shape="3" dim1="dim" rank="1">1.0 0.0 0.0</real_value>
          </constant>
        </initial_condition>
        <boundary_conditions name="inflow">
          <surface_ids>
            <integer_value shape="1" rank="1">1</integer_value>
          </surface_ids>
          <type name="dirichlet">
            <align_bc_with_cartesian>
              <x_component>
                <constant>
                  <real_value rank="0">1.0</real_value>
                </constant>
              </x_component>
            </align_bc_with_cartesian>
          </type>
        </boundary_conditions>
        <boundary_conditions name="bottom">
          <surface_ids>
            <integer_value shape="1" rank="1">3</integer_value>
          </surface_ids>
          <type name="no_normal_flow"/>
        </boundary_conditions>
        <output/>
        <stat>
          <include_in_stat/>
          <previous_time_step>
            <exclude_from_stat/>
          </previous_time_step>
          <nonlinear_field>
            <exclude_from_stat/>
          </nonlinear_field>
        </stat>
        <convergence>
          <include_in_convergence/>
        </convergence>
        <detectors>
          <include_in_detectors/>
        </detectors>
        <steady_state>
          <include_in_steady_state/>
        </steady_state>
        <consistent_interpolation/>
      </prognostic>
    </vector_field>
  </material_phase>
</fluidity_options>
```

Question information

Language:
English Edit question
Status:
Solved
For:
Fluidity Edit question
Assignee:
No assignee Edit question
Solved by:
li12242
Solved:
2015-03-15
Last query:
2015-03-15
Last reply:
Tim Greaves (tim-greaves) said : #1

Hello! And thanks for your question. This launchpad page is no longer active for Fluidity; we've moved to GitHub (see title for the new URL) and encourage questions to be asked on the Fluidity mailing list at:

https://mailman.ic.ac.uk/mailman/listinfo/fluidity

Please could you direct your question to the list?

Thanks!

Tim

li12242 (li12242) said : #2

Thanks Tim