Thanks a lot Jakub for your suggestions.
I tried to define fixed (homogeneneous) boundary conditions in step 1 which propagated to step 2, but because of op=New flag, calculix doesn’t seem to recognize the *base motion command in the second step, so the output is zero for displacement and stresses.
Alternatively, I tried to apply inhomoneneous boundary as follows, and in the second step, I applied non-zero boundary for the given axis. This seems to generate some solution, but I have yet to verify the solution accuracy. I am a bit concerned with the statement made below in the calculix manual that the *boundary should be pre-defined in the previous step otherwise unexpected effects may occur.
The following is the shortened set-up that generated some outcome:
**
** Heading +++++++++++++++++++++++++++++++++++++++++++++++++
**
*Heading
Hash: LgKQJrsQ, Date: 07/13/2025, Unit system: MM_TON_S_C
**
** Nodes +++++++++++++++++++++++++++++++++++++++++++++++++++
**
*Node
... hidden data ...
**
** Elements ++++++++++++++++++++++++++++++++++++++++++++++++
**
*Element, Type=C3D20, Elset=Solid_part-1
... hidden data ...
**
** Additional elements +++++++++++++++++++++++++++++++++++++
**
... hidden data ...
**
** Node sets +++++++++++++++++++++++++++++++++++++++++++++++
**
*Nset, Nset=tipNodes
... hidden data ...
*Nset, Nset=Internal_Selection-1_Rigid_Body-1
... hidden data ...
*Nset, Nset=Internal_Selection-1_Displacement_Rotation-1
... hidden data ...
*Nset, Nset=Internal_Selection-1_NODE_SELECTION-1
... hidden data ...
**
** Additional node sets ++++++++++++++++++++++++++++++++++++
**
... hidden data ...
**
** Element sets ++++++++++++++++++++++++++++++++++++++++++++
**
*Elset, Elset=Volume1
... hidden data ...
*Elset, Elset=VolOnly
... hidden data ...
*Elset, Elset=Internal_Selection-1_Solid_Section-1
... hidden data ...
*Elset, Elset=Internal_Selection-1_ELEMENT_SELECTION-1
... hidden data ...
**
** Surfaces ++++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Physical constants ++++++++++++++++++++++++++++++++++++++
**
**
** Coordinate systems ++++++++++++++++++++++++++++++++++++++
**
**
** Materials +++++++++++++++++++++++++++++++++++++++++++++++
**
*Material, Name=steal
*Elastic
210000, 0.3
*Density
1E-09
**
** Sections ++++++++++++++++++++++++++++++++++++++++++++++++
**
*Solid section, Elset=Internal_Selection-1_Solid_Section-1, Material=steal
**
** Additional sections +++++++++++++++++++++++++++++++++++++
**
... hidden data ...
**
** Pre-tension sections ++++++++++++++++++++++++++++++++++++
**
**
** Constraints +++++++++++++++++++++++++++++++++++++++++++++
**
*Rigid body, Nset=Internal_Selection-1_Rigid_Body-1, Ref node=2901, Rot node=2902
**
** Surface interactions ++++++++++++++++++++++++++++++++++++
**
**
** Contact pairs +++++++++++++++++++++++++++++++++++++++++++
**
**
** Amplitudes ++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Initial conditions ++++++++++++++++++++++++++++++++++++++
**
**
** Steps +++++++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Step-1 ++++++++++++++++++++++++++++++++++++++++++++++++++
**
*Step
*Frequency, Solver=Pardiso, Storage=Yes
5
**
** Controls ++++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Output frequency ++++++++++++++++++++++++++++++++++++++++
**
*Output, Frequency=1
**
** Boundary conditions +++++++++++++++++++++++++++++++++++++
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*Boundary, op=New
** Name: Displacement_Rotation-1
*Boundary
Internal_Selection-1_Displacement_Rotation-1, 1, 1, 0
Internal_Selection-1_Displacement_Rotation-1, 2, 2, 0
Internal_Selection-1_Displacement_Rotation-1, 3, 3, 0
**
** Loads +++++++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Defined fields ++++++++++++++++++++++++++++++++++++++++++
**
**
** History outputs +++++++++++++++++++++++++++++++++++++++++
**
**
** Field outputs +++++++++++++++++++++++++++++++++++++++++++
**
*Node file
RF, U
*El file
S, E, NOE
**
** End step ++++++++++++++++++++++++++++++++++++++++++++++++
**
*End step
**
** Step-2 ++++++++++++++++++++++++++++++++++++++++++++++++++
**
*Step
*Steady state dynamics, Solver=Pardiso
0, 300, 30, 3
**
** Damping +++++++++++++++++++++++++++++++++++++++++++++++++
**
*Modal damping
1, 1000000, 0.05
**
** Controls ++++++++++++++++++++++++++++++++++++++++++++++++
**
**
** Output frequency ++++++++++++++++++++++++++++++++++++++++
**
*Output, Frequency=1
**
** Boundary conditions +++++++++++++++++++++++++++++++++++++
**
*Boundary, op=New
** Name: Displacement_Rotation-1
*Boundary, Load case=1
Internal_Selection-1_Displacement_Rotation-1, 1, 1, 0
Internal_Selection-1_Displacement_Rotation-1, 2, 2, 0
Internal_Selection-1_Displacement_Rotation-1, 3, 3, 0
Internal_Selection-1_Displacement_Rotation-1, 2, 2, 0.01
**
** Loads +++++++++++++++++++++++++++++++++++++++++++++++++++
**
*Cload, op=New
*Dload, op=New
**
** Defined fields ++++++++++++++++++++++++++++++++++++++++++
**
**
** History outputs +++++++++++++++++++++++++++++++++++++++++
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*Node print, Nset=Internal_Selection-1_NODE_SELECTION-1, Global=Yes
U
*El print, Elset=Internal_Selection-1_ELEMENT_SELECTION-1, Global=Yes
S
**
** Field outputs +++++++++++++++++++++++++++++++++++++++++++
**
*Node file
RF, U
*El file
S, E, NOE
**
** End step ++++++++++++++++++++++++++++++++++++++++++++++++
**
*End step