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brettbode / wxmacmolplt

wxMacMolPlt is a graphical user interface principally for the GAMESS program
https://brettbode.github.io/wxmacmolplt/
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Issue with generating input file with symmetry (point group) #123

Open shoubhikraj opened 3 years ago

shoubhikraj commented 3 years ago

Hi,

I am trying to build an input file for a ferrocene molecule with D5d point group. I build the structure by hand, optimised it with semi-empirical xTB, and then opened the .xyz file with wxMacMolPlt.

After that, I used the "Determine Point Group" option from the "Molecule" menu. Setting the tolerance to low gave D5d as an option, so I selected it and pressed "Set Point Group". Then I wrote the input file with unique Cartesian coordinates for GAMESS.

The input file is:

!   File created by MacMolPlt 7.7
 $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     0.70621     0.97202    -1.79688
H     1.0     1.33771     1.84120    -1.85824
Fe    26.0    -0.00000     0.00000     0.00000
 $END

The input file when opened with wxMacMolPlt, shows the correct structure of ferrocene.

On running the input file, GAMESS runs into error. It seems that imposing the symmetry has some kind of bug/issue, so that GAMESS is generating extra carbon atoms than there is in the actual molecule. The error message is:


     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  

  * ... LESS THAN  3.000

 **** THERE ARE ATOMS LESS THAN   0.100 APART, QUITTING... ****
 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT 14:21:37 08-JUN-2021    
                580000  WORDS OF DYNAMIC MEMORY USED
 CPU     0: STEP CPU TIME=     0.06 TOTAL CPU TIME=          0.1 (      0.0 MIN)
 TOTAL WALL CLOCK TIME=          0.1 SECONDS, CPU UTILIZATION IS    89.29%
 DDI Process 0: error code 911

job aborted:
[ranks] message

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

[1-7] terminated

So as can be seen, GAMESS is generating 20 carbon atoms by symmetry operations, whereas there should be 10 carbon atoms.

This problem appears most often for point groups with higher symmetry like D4h, D4d, Td, Oh etc.

Version: wxMacMolPlt v7.7 OS: Windows 10, 64 bit

brettbode commented 3 years ago

Hello, You are struggling with an acknowledged difficult part of GAMESS input. GAMESS tolerance for generating symmetry dependent atoms is very tight so coordinates have to be nearly perfect to be accepted. I will take a look to see if increasing the number of digits in the coordinates helps. Otherwise the recommended way to get around the issue with GAMESS is to choose a lower order point group. In the Determine Point group dialog you can adjust the slider to the left which will lower the number of groups that match. I thought the default was similar to GAMESS, but will have to verify.