Some redundant commas here:
*STEP, NLGEOM,INC=1000,
*STATIC,
1.0000e-04,1.0000e+00,1.0000e-06,1.0000e-04
but I guess CalculiX ignores them.
To attach GAPUNI elements to the model, you may need to use *EQUATION constraints. I would try with a very simple test model first. For example:
*Node
1, 0.00000000E+000, 0.00000000E+000, 0.00000000E+000
2, 0.00000000E+000, 1.00000000E+001, 0.00000000E+000
3, 1.00000000E+001, 0.00000000E+000, 0.00000000E+000
4, 1.00000000E+001, 1.00000000E+001, 0.00000000E+000
5, 0.00000000E+000, 5.00000000E+000, 0.00000000E+000
6, 5.00000000E+000, 0.00000000E+000, 0.00000000E+000
7, 1.00000000E+001, 5.00000000E+000, 0.00000000E+000
8, 5.00000000E+000, 1.00000000E+001, 0.00000000E+000
9, 5.00000000E+000, 5.00000000E+000, 0.00000000E+000
10, 0.00000000E+000, 0.00000000E+000, 0.00000000E+000
11, 0.00000000E+000, 0.00000000E+000, 0.00000000E+000
12, 5.00000000E+000, 0.00000000E+000, 0.00000000E+000
13, 5.00000000E+000, 0.00000000E+000, 0.00000000E+000
14, 5.00000000E+000, 5.00000000E+000, 0.00000000E+000
15, 5.00000000E+000, 5.00000000E+000, 0.00000000E+000
16, 0.00000000E+000, 5.00000000E+000, 0.00000000E+000
17, 0.00000000E+000, 5.00000000E+000, 0.00000000E+000
18, 1.00000000E+001, 0.00000000E+000, 0.00000000E+000
19, 1.00000000E+001, 0.00000000E+000, 0.00000000E+000
20, 1.00000000E+001, 5.00000000E+000, 0.00000000E+000
21, 1.00000000E+001, 5.00000000E+000, 0.00000000E+000
22, 5.00000000E+000, 1.00000000E+001, 0.00000000E+000
23, 5.00000000E+000, 1.00000000E+001, 0.00000000E+000
24, 0.00000000E+000, 1.00000000E+001, 0.00000000E+000
25, 0.00000000E+000, 1.00000000E+001, 0.00000000E+000
26, 1.00000000E+001, 1.00000000E+001, 0.00000000E+000
27, 1.00000000E+001, 1.00000000E+001, 0.00000000E+000
*Element, Type=S4, Elset=Shell_part-1
1, 1, 6, 9, 5
2, 6, 3, 7, 9
3, 5, 9, 8, 2
4, 9, 7, 4, 8
*Element, Type=GAPUNI
5, 10, 11
6, 12, 13
7, 14, 15
8, 16, 17
9, 18, 19
10, 20, 21
11, 22, 23
12, 24, 25
13, 26, 27
*Nset, Nset=Internal_Selection-1_Fixed-1
1, 2, 3, 4, 6, 8
*Nset, Nset=Internal-1_Internal_Selection-1_Compression_Only-1_Master
1, 2, 3, 4, 5, 6, 7, 8, 9
*Nset, Nset=Internal_All_Compression_Only_Constraints_NodeSet
10, 12, 14, 16, 18, 20, 22, 24, 26
*Elset, Elset=Internal-1_Internal_Selection-1_Compression_Only-1_Master_S2
1, 2, 3, 4
*Elset, Elset=Internal_Selection-1_Shell_Section-1
1, 2, 3, 4
*Elset, Elset=Compression_Only-1_ElementSet-1
5
*Elset, Elset=Compression_Only-1_ElementSet-2
6
*Elset, Elset=Compression_Only-1_ElementSet-3
7
*Elset, Elset=Compression_Only-1_ElementSet-4
8
*Elset, Elset=Compression_Only-1_ElementSet-5
9
*Elset, Elset=Compression_Only-1_ElementSet-6
10
*Elset, Elset=Compression_Only-1_ElementSet-7
11
*Elset, Elset=Compression_Only-1_ElementSet-8
12
*Elset, Elset=Compression_Only-1_ElementSet-9
13
*Surface, Name=Internal_Selection-1_Compression_Only-1_Master, Type=Element
Internal-1_Internal_Selection-1_Compression_Only-1_Master_S2, S2
*Material, Name=Material-1
*Elastic
210000, 0.3
*Shell section, Elset=Internal_Selection-1_Shell_Section-1, Material=Material-1, Offset=0
1
*Gap, Elset=Compression_Only-1_ElementSet-1
0, 0, 0, -1, , 62500000000, 6.25E-05
*Gap, Elset=Compression_Only-1_ElementSet-2
0, 0, 0, -1, , 125000000000, 0.000125
*Gap, Elset=Compression_Only-1_ElementSet-3
0, 0, 0, -1, , 250000000000, 0.00025
*Gap, Elset=Compression_Only-1_ElementSet-4
0, 0, 0, -1, , 125000000000, 0.000125
*Gap, Elset=Compression_Only-1_ElementSet-5
0, 0, 0, -1, , 62500000000, 6.25E-05
*Gap, Elset=Compression_Only-1_ElementSet-6
0, 0, 0, -1, , 125000000000, 0.000125
*Gap, Elset=Compression_Only-1_ElementSet-7
0, 0, 0, -1, , 125000000000, 0.000125
*Gap, Elset=Compression_Only-1_ElementSet-8
0, 0, 0, -1, , 62500000000, 6.25E-05
*Gap, Elset=Compression_Only-1_ElementSet-9
0, 0, 0, -1, , 62500000000, 6.25E-05
*Equation
2
11, 1, 1, 1, 1, -1
*Equation
2
11, 2, 1, 1, 2, -1
*Equation
2
11, 3, 1, 1, 3, -1
*Equation
2
13, 1, 1, 6, 1, -1
*Equation
2
13, 2, 1, 6, 2, -1
*Equation
2
13, 3, 1, 6, 3, -1
*Equation
2
15, 1, 1, 9, 1, -1
*Equation
2
15, 2, 1, 9, 2, -1
*Equation
2
15, 3, 1, 9, 3, -1
*Equation
2
17, 1, 1, 5, 1, -1
*Equation
2
17, 2, 1, 5, 2, -1
*Equation
2
17, 3, 1, 5, 3, -1
*Equation
2
19, 1, 1, 3, 1, -1
*Equation
2
19, 2, 1, 3, 2, -1
*Equation
2
19, 3, 1, 3, 3, -1
*Equation
2
21, 1, 1, 7, 1, -1
*Equation
2
21, 2, 1, 7, 2, -1
*Equation
2
21, 3, 1, 7, 3, -1
*Equation
2
23, 1, 1, 8, 1, -1
*Equation
2
23, 2, 1, 8, 2, -1
*Equation
2
23, 3, 1, 8, 3, -1
*Equation
2
25, 1, 1, 2, 1, -1
*Equation
2
25, 2, 1, 2, 2, -1
*Equation
2
25, 3, 1, 2, 3, -1
*Equation
2
27, 1, 1, 4, 1, -1
*Equation
2
27, 2, 1, 4, 2, -1
*Equation
2
27, 3, 1, 4, 3, -1
*Step, Nlgeom
*Static
*Boundary
Internal_Selection-1_Fixed-1, 1, 6, 0
*Boundary
Internal_All_Compression_Only_Constraints_NodeSet, 1, 1, 0
Internal_All_Compression_Only_Constraints_NodeSet, 2, 2, 0
Internal_All_Compression_Only_Constraints_NodeSet, 3, 3, -1
*Node file
RF, U
*El file
S, E, NOE
*End step