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Add an option to loosen the criteria for symmetry from GAMESS input file #52

Open shoubhikraj opened 3 years ago

shoubhikraj commented 3 years ago

Make sure these boxes are checked before submitting your issue - thank you!

C 6.0 0.70621 0.97202 -1.79688 H 1.0 1.33771 1.84120 -1.85824 Fe 26.0 -0.00000 0.00000 0.00000 $END

- [x] Summary of the issue and expected results:

I am trying to build an input file for a ferrocene molecule with D5d symmetry. For creating the structure, I started from a structure provided by another software, and then used wxMacMolPlt to detect point group, and then impose D5d point group on the molecule. The input file was generated by wxMacMolPlt.

However, on running the input file with GAMESS, it shows an error because the atoms generated by the symmetry operations are less than 0.1 Angstrom apart, which means that GAMESS is producing extra atoms that are not supposed to be there. The output:
 RUN TITLE
 ---------

Title

THE POINT GROUP OF THE MOLECULE IS DND
THE ORDER OF THE PRINCIPAL AXIS IS 5

ATOM ATOMIC COORDINATES (BOHR) CHARGE X Y Z C 6.0 -1.3345529582 1.8368445027 -3.3956108328 C 6.0 -2.1593424777 -0.7016191198 -3.3956108328 C 6.0 0.0000059136 -2.2704689660 -3.3956108328 C 6.0 2.1593461325 -0.7016078715 -3.3956108328 C 6.0 1.3345433898 -1.8368514546 3.3956108328 C 6.0 2.1593461325 0.7016078715 3.3956108328 C 6.0 0.0000059136 2.2704689660 3.3956108328 C 6.0 -2.1593424777 0.7016191198 3.3956108328 C 6.0 -1.3345529582 -1.8368445027 3.3956108328 C 6.0 2.1593424777 -0.7016191198 -3.3956108328 C 6.0 1.3345529582 1.8368445027 -3.3956108328 C 6.0 -1.3345433898 1.8368514546 -3.3956108328 C 6.0 -2.1593461325 -0.7016078715 -3.3956108328 C 6.0 -0.0000059136 -2.2704689660 -3.3956108328 C 6.0 2.1593424777 0.7016191198 3.3956108328 C 6.0 -0.0000059136 2.2704689660 3.3956108328 C 6.0 -2.1593461325 0.7016078715 3.3956108328 C 6.0 -1.3345433898 -1.8368514546 3.3956108328 C 6.0 1.3345529582 -1.8368445027 3.3956108328 C 6.0 1.3345433898 1.8368514546 -3.3956108328 H 1.0 -2.5279056047 3.4793633043 -3.5115644194 H 1.0 -4.0902369351 -1.3289987074 -3.5115644194 H 1.0 0.0000001568 -4.3007296764 -3.5115644194 H 1.0 4.0902370320 -1.3289984091 -3.5115644194 H 1.0 2.5279053510 -3.4793634886 3.5115644194 H 1.0 4.0902370320 1.3289984091 3.5115644194 H 1.0 0.0000001568 4.3007296764 3.5115644194 H 1.0 -4.0902369351 1.3289987074 3.5115644194 H 1.0 -2.5279056047 -3.4793633043 3.5115644194 H 1.0 2.5279053510 3.4793634886 -3.5115644194 FE 26.0 0.0000000000 0.0000000000 0.0000000000

      INTERNUCLEAR DISTANCES (ANGS.)
      ------------------------------

            1 C          2 C          3 C          4 C          5 C

1 C 0.0000000 1.4124251 2.2853518 2.2853518 4.3231161
2 C 1.4124251 0.0000000 1.4124251 2.2853518 4.0858749
3 C 2.2853518 1.4124251 0.0000000 1.4124251 3.6696718
4 C 2.2853518 2.2853518 1.4124251 0.0000000 3.6696742
5 C 4.3231161 4.0858749 3.6696718 3.6696742 0.0000000
6 C 4.0858784 4.3231161 4.0858749 3.6696718 1.4124251 7 C 3.6696742 4.0858784 4.3231161 4.0858749 2.2853518 8 C 3.6696718 3.6696742 4.0858784 4.3231161 2.2853518 9 C 4.0858749 3.6696718 3.6696742 4.0858784 1.4124251 10 C 2.2853537 2.2853498 1.4124200 0.0000063 3.6696730
11 C 1.4124301 2.2853537 2.2853498 1.4124200 4.0858767
12 C 0.0000063 1.4124301 2.2853537 2.2853498 4.3231161
13 C 1.4124200 0.0000063 1.4124301 2.2853537 4.0858767
14 C 2.2853498 1.4124200 0.0000063 1.4124301 3.6696730
15 C 4.0858767 4.3231161 4.0858767 3.6696730 1.4124301 16 C 3.6696730 4.0858767 4.3231161 4.0858767 2.2853537 17 C 3.6696730 3.6696730 4.0858767 4.3231161 2.2853498 18 C 4.0858767 3.6696730 3.6696730 4.0858767 1.4124200 19 C 4.3231161 4.0858767 3.6696730 3.6696730 0.0000063 20 C 1.4124251 2.2853518 2.2853518 1.4124251 4.0858784
21 H 1.0761186 2.2219080 3.3243264 3.3243239 5.0449696
22 H 2.2219019 1.0761186 2.2219080 3.3243264 4.6554134
23 H 3.3243239 2.2219019 1.0761186 2.2219080 3.9444395
24 H 3.3243264 3.3243239 2.2219019 1.0761186 3.9444416
25 H 5.0449696 4.6554134 3.9444395 3.9444416 1.0761186 26 H 4.6554163 5.0449696 4.6554134 3.9444395 2.2219080 27 H 3.9444416 4.6554163 5.0449696 4.6554134 3.3243264
28 H 3.9444395 3.9444416 4.6554163 5.0449696 3.3243239
29 H 4.6554134 3.9444395 3.9444416 4.6554163 2.2219019 30 H 2.2219080 3.3243264 3.3243239 2.2219019 4.6554163
31 FE 2.1615580 2.1615580 2.1615580 2.1615580 2.1615580 *

            6 C          7 C          8 C          9 C         10 C

1 C 4.0858784 3.6696742 3.6696718 4.0858749 2.2853537 2 C 4.3231161 4.0858784 3.6696742 3.6696718 2.2853498 3 C 4.0858749 4.3231161 4.0858784 3.6696742 1.4124200 4 C 3.6696718 4.0858749 4.3231161 4.0858784 0.0000063 5 C 1.4124251 2.2853518 2.2853518 1.4124251 3.6696730
6 C 0.0000000 1.4124251 2.2853518 2.2853518 3.6696730
7 C 1.4124251 0.0000000 1.4124251 2.2853518 4.0858767
8 C 2.2853518 1.4124251 0.0000000 1.4124251 4.3231161
9 C 2.2853518 2.2853518 1.4124251 0.0000000 4.0858767
10 C 3.6696730 4.0858767 4.3231161 4.0858767 0.0000000
11 C 3.6696730 3.6696730 4.0858767 4.3231161 1.4124251 12 C 4.0858767 3.6696730 3.6696730 4.0858767 2.2853518 13 C 4.3231161 4.0858767 3.6696730 3.6696730 2.2853518 14 C 4.0858767 4.3231161 4.0858767 3.6696730 1.4124251 15 C 0.0000063 1.4124200 2.2853498 2.2853537 3.6696742
16 C 1.4124301 0.0000063 1.4124200 2.2853498 4.0858784
17 C 2.2853537 1.4124301 0.0000063 1.4124200 4.3231161
18 C 2.2853498 2.2853537 1.4124301 0.0000063 4.0858749
19 C 1.4124200 2.2853498 2.2853537 1.4124301 3.6696718
20 C 3.6696742 3.6696718 4.0858749 4.3231161 1.4124301 21 H 4.6554163 3.9444416 3.9444395 4.6554134 3.3243264
22 H 5.0449696 4.6554163 3.9444416 3.9444395 3.3243239
23 H 4.6554134 5.0449696 4.6554163 3.9444416 2.2219019 24 H 3.9444395 4.6554134 5.0449696 4.6554163 1.0761186 25 H 2.2219019 3.3243239 3.3243264 2.2219080 3.9444395
26 H 1.0761186 2.2219019 3.3243239 3.3243264 3.9444416
27 H 2.2219080 1.0761186 2.2219019 3.3243239 4.6554163
28 H 3.3243264 2.2219080 1.0761186 2.2219019 5.0449696
29 H 3.3243239 3.3243264 2.2219080 1.0761186 4.6554134
30 H 3.9444416 3.9444395 4.6554134 5.0449696 2.2219080 31 FE 2.1615580 2.1615580 2.1615580 2.1615580 2.1615580 *

           11 C         12 C         13 C         14 C         15 C

1 C 1.4124301 0.0000063 1.4124200 2.2853498 4.0858767
2 C 2.2853537 1.4124301 0.0000063 1.4124200 4.3231161
3 C 2.2853498 2.2853537 1.4124301 0.0000063 4.0858767
4 C 1.4124200 2.2853498 2.2853537 1.4124301 3.6696730
5 C 4.0858767 4.3231161 4.0858767 3.6696730 1.4124301 6 C 3.6696730 4.0858767 4.3231161 4.0858767 0.0000063 7 C 3.6696730 3.6696730 4.0858767 4.3231161 1.4124200 8 C 4.0858767 3.6696730 3.6696730 4.0858767 2.2853498 9 C 4.3231161 4.0858767 3.6696730 3.6696730 2.2853537 10 C 1.4124251 2.2853518 2.2853518 1.4124251 3.6696742
11 C 0.0000000 1.4124251 2.2853518 2.2853518 3.6696718
12 C 1.4124251 0.0000000 1.4124251 2.2853518 4.0858749
13 C 2.2853518 1.4124251 0.0000000 1.4124251 4.3231161
14 C 2.2853518 2.2853518 1.4124251 0.0000000 4.0858784
15 C 3.6696718 4.0858749 4.3231161 4.0858784 0.0000000
16 C 3.6696742 3.6696718 4.0858749 4.3231161 1.4124251 17 C 4.0858784 3.6696742 3.6696718 4.0858749 2.2853518 18 C 4.3231161 4.0858784 3.6696742 3.6696718 2.2853518 19 C 4.0858749 4.3231161 4.0858784 3.6696742 1.4124251 20 C 0.0000063 1.4124200 2.2853498 2.2853537 3.6696730
21 H 2.2219080 1.0761186 2.2219019 3.3243239 4.6554134
22 H 3.3243264 2.2219080 1.0761186 2.2219019 5.0449696
23 H 3.3243239 3.3243264 2.2219080 1.0761186 4.6554163
24 H 2.2219019 3.3243239 3.3243264 2.2219080 3.9444416
25 H 4.6554134 5.0449696 4.6554163 3.9444416 2.2219080 26 H 3.9444395 4.6554134 5.0449696 4.6554163 1.0761186 27 H 3.9444416 3.9444395 4.6554134 5.0449696 2.2219019 28 H 4.6554163 3.9444416 3.9444395 4.6554134 3.3243239
29 H 5.0449696 4.6554163 3.9444416 3.9444395 3.3243264
30 H 1.0761186 2.2219019 3.3243239 3.3243264 3.9444395
31 FE 2.1615580 2.1615580 2.1615580 2.1615580 2.1615580 *

           16 C         17 C         18 C         19 C         20 C

1 C 3.6696730 3.6696730 4.0858767 4.3231161 1.4124251 2 C 4.0858767 3.6696730 3.6696730 4.0858767 2.2853518 3 C 4.3231161 4.0858767 3.6696730 3.6696730 2.2853518 4 C 4.0858767 4.3231161 4.0858767 3.6696730 1.4124251 5 C 2.2853537 2.2853498 1.4124200 0.0000063 4.0858784
6 C 1.4124301 2.2853537 2.2853498 1.4124200 3.6696742
7 C 0.0000063 1.4124301 2.2853537 2.2853498 3.6696718
8 C 1.4124200 0.0000063 1.4124301 2.2853537 4.0858749
9 C 2.2853498 1.4124200 0.0000063 1.4124301 4.3231161
10 C 4.0858784 4.3231161 4.0858749 3.6696718 1.4124301 11 C 3.6696742 4.0858784 4.3231161 4.0858749 0.0000063 12 C 3.6696718 3.6696742 4.0858784 4.3231161 1.4124200 13 C 4.0858749 3.6696718 3.6696742 4.0858784 2.2853498 14 C 4.3231161 4.0858749 3.6696718 3.6696742 2.2853537 15 C 1.4124251 2.2853518 2.2853518 1.4124251 3.6696730
16 C 0.0000000 1.4124251 2.2853518 2.2853518 3.6696730
17 C 1.4124251 0.0000000 1.4124251 2.2853518 4.0858767
18 C 2.2853518 1.4124251 0.0000000 1.4124251 4.3231161
19 C 2.2853518 2.2853518 1.4124251 0.0000000 4.0858767
20 C 3.6696730 4.0858767 4.3231161 4.0858767 0.0000000
21 H 3.9444395 3.9444416 4.6554163 5.0449696 2.2219019 22 H 4.6554134 3.9444395 3.9444416 4.6554163 3.3243239
23 H 5.0449696 4.6554134 3.9444395 3.9444416 3.3243264
24 H 4.6554163 5.0449696 4.6554134 3.9444395 2.2219080 25 H 3.3243264 3.3243239 2.2219019 1.0761186 4.6554163
26 H 2.2219080 3.3243264 3.3243239 2.2219019 3.9444416
27 H 1.0761186 2.2219080 3.3243264 3.3243239 3.9444395
28 H 2.2219019 1.0761186 2.2219080 3.3243264 4.6554134
29 H 3.3243239 2.2219019 1.0761186 2.2219080 5.0449696
30 H 3.9444416 4.6554163 5.0449696 4.6554134 1.0761186 31 FE 2.1615580 2.1615580 2.1615580 2.1615580 2.1615580 *

           21 H         22 H         23 H         24 H         25 H

1 C 1.0761186 2.2219019 3.3243239 3.3243264 5.0449696
2 C 2.2219080 1.0761186 2.2219019 3.3243239 4.6554134
3 C 3.3243264 2.2219080 1.0761186 2.2219019 3.9444395
4 C 3.3243239 3.3243264 2.2219080 1.0761186 3.9444416
5 C 5.0449696 4.6554134 3.9444395 3.9444416 1.0761186 6 C 4.6554163 5.0449696 4.6554134 3.9444395 2.2219019 7 C 3.9444416 4.6554163 5.0449696 4.6554134 3.3243239
8 C 3.9444395 3.9444416 4.6554163 5.0449696 3.3243264
9 C 4.6554134 3.9444395 3.9444416 4.6554163 2.2219080 10 C 3.3243264 3.3243239 2.2219019 1.0761186 3.9444395
11 C 2.2219080 3.3243264 3.3243239 2.2219019 4.6554134
12 C 1.0761186 2.2219080 3.3243264 3.3243239 5.0449696
13 C 2.2219019 1.0761186 2.2219080 3.3243264 4.6554163
14 C 3.3243239 2.2219019 1.0761186 2.2219080 3.9444416
15 C 4.6554134 5.0449696 4.6554163 3.9444416 2.2219080 16 C 3.9444395 4.6554134 5.0449696 4.6554163 3.3243264
17 C 3.9444416 3.9444395 4.6554134 5.0449696 3.3243239
18 C 4.6554163 3.9444416 3.9444395 4.6554134 2.2219019 19 C 5.0449696 4.6554163 3.9444416 3.9444395 1.0761186 20 C 2.2219019 3.3243239 3.3243264 2.2219080 4.6554163
21 H 0.0000000 2.6754201 4.3289207 4.3289207 5.8762374
22 H 2.6754201 0.0000000 2.6754201 4.3289207 5.2318536
23 H 4.3289207 2.6754201 0.0000000 2.6754201 3.9737401
24 H 4.3289207 4.3289207 2.6754201 0.0000000 3.9737402
25 H 5.8762374 5.2318536 3.9737401 3.9737402 0.0000000
26 H 5.2318537 5.8762374 5.2318536 3.9737401 2.6754201 27 H 3.9737402 5.2318537 5.8762374 5.2318536 4.3289207
28 H 3.9737401 3.9737402 5.2318537 5.8762374 4.3289207
29 H 5.2318536 3.9737401 3.9737402 5.2318537 2.6754201 30 H 2.6754201 4.3289207 4.3289207 2.6754201 5.2318537
31 FE 2.9381187 2.9381187 2.9381187 2.9381187 2.9381187 *

           26 H         27 H         28 H         29 H         30 H

1 C 4.6554163 3.9444416 3.9444395 4.6554134 2.2219080 2 C 5.0449696 4.6554163 3.9444416 3.9444395 3.3243264
3 C 4.6554134 5.0449696 4.6554163 3.9444416 3.3243239
4 C 3.9444395 4.6554134 5.0449696 4.6554163 2.2219019 5 C 2.2219080 3.3243264 3.3243239 2.2219019 4.6554163
6 C 1.0761186 2.2219080 3.3243264 3.3243239 3.9444416
7 C 2.2219019 1.0761186 2.2219080 3.3243264 3.9444395
8 C 3.3243239 2.2219019 1.0761186 2.2219080 4.6554134
9 C 3.3243264 3.3243239 2.2219019 1.0761186 5.0449696
10 C 3.9444416 4.6554163 5.0449696 4.6554134 2.2219080 11 C 3.9444395 3.9444416 4.6554163 5.0449696 1.0761186 12 C 4.6554134 3.9444395 3.9444416 4.6554163 2.2219019 13 C 5.0449696 4.6554134 3.9444395 3.9444416 3.3243239
14 C 4.6554163 5.0449696 4.6554134 3.9444395 3.3243264
15 C 1.0761186 2.2219019 3.3243239 3.3243264 3.9444395
16 C 2.2219080 1.0761186 2.2219019 3.3243239 3.9444416
17 C 3.3243264 2.2219080 1.0761186 2.2219019 4.6554163
18 C 3.3243239 3.3243264 2.2219080 1.0761186 5.0449696
19 C 2.2219019 3.3243239 3.3243264 2.2219080 4.6554134
20 C 3.9444416 3.9444395 4.6554134 5.0449696 1.0761186 21 H 5.2318537 3.9737402 3.9737401 5.2318536 2.6754201 22 H 5.8762374 5.2318537 3.9737402 3.9737401 4.3289207
23 H 5.2318536 5.8762374 5.2318537 3.9737402 4.3289207
24 H 3.9737401 5.2318536 5.8762374 5.2318537 2.6754201 25 H 2.6754201 4.3289207 4.3289207 2.6754201 5.2318537
26 H 0.0000000 2.6754201 4.3289207 4.3289207 3.9737402
27 H 2.6754201 0.0000000 2.6754201 4.3289207 3.9737401
28 H 4.3289207 2.6754201 0.0000000 2.6754201 5.2318536
29 H 4.3289207 4.3289207 2.6754201 0.0000000 5.8762374
30 H 3.9737402 3.9737401 5.2318536 5.8762374 0.0000000
31 FE 2.9381187 2.9381187 2.9381187 2.9381187 2.9381187 *

           31 FE

1 C 2.1615580 2 C 2.1615580 3 C 2.1615580 4 C 2.1615580 5 C 2.1615580 6 C 2.1615580 7 C 2.1615580 8 C 2.1615580 9 C 2.1615580 10 C 2.1615580 11 C 2.1615580 12 C 2.1615580 13 C 2.1615580 14 C 2.1615580 15 C 2.1615580 16 C 2.1615580 17 C 2.1615580 18 C 2.1615580 19 C 2.1615580 20 C 2.1615580 21 H 2.9381187 22 H 2.9381187 23 H 2.9381187 24 H 2.9381187 25 H 2.9381187 26 H 2.9381187 27 H 2.9381187 28 H 2.9381187 29 H 2.9381187 30 H 2.9381187 31 FE 0.0000000

job aborted: [ranks] message

[0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 911, comm rank 0

[1-7] terminated



As you can see, GAMESS is producing 20 carbon atoms whereas ferrocene should have 10 carbon atoms. Looking closely at the cartesian coordinates of the atoms generated by the symmetry operations, there are several pairs of atoms which are essentially the same but are treated as different atoms by GAMESS. For example, C1 and C12 are apart by 0.0000063 Angstrom (from the internuclear distance matrix), but they are treated as different atoms. The requirement for this level of precision seems unnecessary, particularly as input builder softwares (like wxMacMolPlt) cannot impose symmetry constraints with that amount of precision.

I have also tried using WebMO to impose symmetry and write input file for GAMESS, but it still runs into the same problem. Therefore, I think there should be an option available through a keyword in the input file, which simply sets the tolerance for identifying unique atoms (by their distance perhaps).

This problem seems to appear more often for point groups with higher symmetry like D5d, D5h, Td etc. than for lower symmetry point groups. It also breaks the usability of the symmetry feature of GAMESS.

- [x] Description of the run environment:
  * operating system - Windows 10
  * compiler - Intel C++/Fortran v2021
  * math library - Intel MKL
  * communication library - MS-MPI
serguei-patchkovskii commented 3 years ago

I am not a GAMESS-US developer; however, if there is a problem here, it is with wxMacMolPlt, not GAMESS. In the nutshell: in ferrocene, the carbon and hydrogen atoms fall exactly on the symmetry planes, so that these sites have non-unit multiplicity. The input file produced by wxMacMolPlt does not generate these positions with a sufficiently high accuracy, so that GAMESS (correctly) treats them as general points.

Basically, you want GAMESS to recognize approximate symmetries, and to symmetrize the user-supplied data to match what the user intended, rather than that the user specified. That is a very, very long and slippery slope.

If one gives more significant digits on input:

 $CONTRL SCFTYP=RHF RUNTYP=ENERGY MULT=1 COORD=UNIQUE $END
 $SYSTEM TIMLIM=525600 MEMORY=1000000 $END
 $BASIS GBASIS=MINI $END
 $SCF DIRSCF=.TRUE. $END
 $DATA
Title
DND 5

C     6.0     0.70621253168819 0.972018160625 -1.79688
H     1.0     1.33771006712866 1.841199951228 -1.85824
Fe    26.0    -0.00000     0.00000     0.00000
 $END

your example runs just fine. Alternatively, if one places the generating atoms at a position where sigma-d planes coincide with the Cartesian planes, one can user fewer significant digits:

 $CONTRL SCFTYP=RHF RUNTYP=ENERGY MULT=1 COORD=UNIQUE $END
 $SYSTEM TIMLIM=525600 MEMORY=1000000 $END
 $BASIS GBASIS=MINI $END
 $SCF DIRSCF=.TRUE. $END
 $DATA 
Title
DND 5

C     6.0     0.0 1.2014805218978   -1.79688
H     1.0     0.0 2.2758482998873   -1.85824
Fe    26.0    -0.00000     0.00000     0.00000
 $END

If it is any consolation, generating high-symmetry inputs with atoms occupying high-multiplicity positions is a hard problem - regardless of whether one does it by hand or with the aid of a GUI.

shoubhikraj commented 3 years ago

@serguei-patchkovskii

Thanks for the reply. May I ask which program you used to generate the symmetrized coordinates with higher number of significant figures?

I understand that the problem is due to MacMolPlt not writing the coordinates with a high enough precision. I tried the WebMO symmetrizer and I still ran into the same problem. If the common GUI editors cannot write coordinates with that high number of decimal places, then what is the point of GAMESS enforcing such a strict criteria?

I had also posted the problem on the repository for wxMacMolPlt here.

But I think GAMESS should have an option to change the threshold for symmetry detection from the input file. It is not a slippery slope at all because most other QM codes including Orca, Gaussian, NWChem have an option to change the tolerance. GAMESS is the only program I have come across so far that doesn't. (I suspect the option is there inside the GAMESS code, it's just not modifiable from the input)

serguei-patchkovskii commented 3 years ago

Thanks for the reply. May I ask which program you used to generate the symmetrized coordinates with higher number of significant figures?

I used a calculator and a piece of paper. The X/Y ratio in your input should have been equal to the tangent of 36 degrees.

As far as implementing the feature you requested, only the GAMESS developers can give you a definite answer. However, please consider the following: Let's assume the feature you want has been implemented (which would be rather easy to do: as far as I can see, all one has to do is to make the constant 1.0D-12 in inputa.src an input parameter):

2394                IF ((QMCHKA.EQV.QMCHKB).AND.(TEST.LE.1.0D-12)) THEN
2395                   GO TO 820
2396                END IF
2397             ELSE
2398                IF(TEST .LE. 1.0D-12) GO TO 820
2399             END IF

What happens now? All you have done is to force GAMESS to treat a broken-symmetry Hamiltonian as if it was actually symmetric. At best, this will cause mis-classification of orbital- and state-symmetry labels. At worst, it will make calculations which do rely on the Hamiltonian symmetry (e.g. finite-difference Hessian calculation) produce wrong results. Therefore, by itself, this is not a particularly attractive solution.

The obvious way to make it somewhat sensible would be to notice that the symmetry is (slightly) broken, and automatically set NOSYM=1 flag after generating the geometry. This would would at least have the advantage of not silently producing incorrect results for some inputs. The downside is the loss of symmetry labels and (potentially enormous) decrease in efficiency.

Another approach would be to recognize that the molecule is approximately-symmetric, and forcibly symmetrize it (as far as I remember, this was the approach taken by Gaussian some 20 years ago, when I last used it). This will necessarily cause a change in the molecular geometry and/or orientation relative to that was specified on input. This may be OK in some cases, but in the others.

Given that there is no obviously "correct" way of handling this situation, I would rather have the code detect an error in my input, and stop - rather than trying to guess what was it I actually wanted. However, this is simply my personal preference. Again, only the GAMESS developers can give you a definite answer.