I experience problems with the detected molecular symmetry when I copy the optimized geometry from an output to a new input. I would like to ask for a recommendation on how to get the symmetry treated consistently.
I believe that it has to do with the numerical symmetry thresholds, but perhaps someone has worked through this problem before and can suggest an elegant solution? Thanks
Here is an example.
I’ve used the following input to optimize the geometry of cis-stilbene
$comment
Cis stilbene. Geometry from iqmol with C2 symmetry.
$end
$molecule
0 1
C -0.4190145 -0.0922729 -3.8979208
C -0.4754862 0.9208250 -2.9360428
C 0.1766046 -1.3163405 -3.5907810
C 0.7262371 -1.5242673 -2.3249681
C 0.6696862 -0.5141326 -1.3596938
C 0.0465242 0.7175941 -1.6452713
C -0.0173085 1.8497835 -0.6769613
C 0.0173085 1.8497835 0.6769613
C -0.0465242 0.7175941 1.6452713
C -0.6696862 -0.5141326 1.3596938
C -0.7262371 -1.5242673 2.3249681
C -0.1766046 -1.3163405 3.5907810
C 0.4190145 -0.0922729 3.8979208
C 0.4754862 0.9208250 2.9360428
H -0.8346660 0.0739444 -4.8833946
H -0.9387768 1.8644392 -3.1981689
H 0.2233616 -2.0987777 -4.3371525
H 1.2059237 -2.4665597 -2.0933879
H 1.1385598 -0.6985533 -0.4053548
H -1.1385598 -0.6985533 0.4053548
H -1.2059237 -2.4665597 2.0933879
H 0.8346660 0.0739444 4.8833946
H 0.9387768 1.8644392 3.1981689
H -0.2233616 -2.0987777 4.3371525
H -0.0688410 2.8346816 -1.1355815
H 0.0688410 2.8346816 1.1355815
$end
$rem
jobtype = opt
method = ccsd
basis = cc-pVDZ
$end
At the end of the output I’ve got the converged geometry:
******************************
** OPTIMIZATION CONVERGED **
******************************
----------------------------------------------------------------
Standard Nuclear Orientation (Angstroms)
I Atom X Y Z
----------------------------------------------------------------
1 C 3.6830124699 -0.5321219659 0.3038669860
2 C 2.7932773117 -0.6120636883 -0.7803043433
3 C 3.3882282498 0.3018387672 1.3953693572
4 C 2.2008151800 1.0555490456 1.3923019562
5 C 1.3093558446 0.9691814434 0.3120044808
6 C 1.5880795495 0.1220617780 -0.7831753057
7 C 0.6769577259 0.0318385110 -1.9606167618
8 C -0.6769568813 -0.0318507675 -1.9606169051
9 C -1.5880808903 -0.1220661696 -0.7831765953
10 C -1.3093621202 -0.9691893883 0.3120001002
11 C -2.2008213977 -1.0555538572 1.3922972831
12 C -3.3882275446 -0.3018331421 1.3953696544
13 C -3.6830064966 0.5321346956 0.3038705587
14 C -2.7932730179 0.6120702226 -0.7803029396
15 H 4.6097095144 -1.1170770155 0.2926563133
16 H 3.0302470147 -1.2593434261 -1.6335115280
17 H 4.0830274953 0.3710504984 2.2398501301
18 H 1.9708411986 1.7200643627 2.2329551514
19 H 0.3912326653 1.5656835844 0.3117133703
20 H -0.3912432890 -1.5656986670 0.3117044398
21 H -1.9708529709 -1.7200748708 2.2329474381
22 H -4.6096979555 1.1170987501 0.2926659829
23 H -3.0302362934 1.2593555233 -1.6335077118
24 H -4.0830252763 -0.3710427639 2.2398521034
25 H 1.1775620674 0.0246198036 -2.9394698711
26 H -1.1775621534 -0.0246312639 -2.9394695316
----------------------------------------------------------------
Molecular Point Group C2 NOp = 2
Largest Abelian Subgroup C2 NOp = 2
Nuclear Repulsion Energy = 764.66494428 hartrees
There are 48 alpha and 48 beta electrons
Z-matrix Print:
$molecule
0 1
C
C 1 1.411188
H 2 1.096854 1 119.335281
C 2 1.404794 1 120.855292 3 -179.438256 0
H 4 1.095931 2 119.820627 1 179.410559 0
C 4 1.404908 2 120.032175 1 -0.962355 0
H 6 1.095757 4 120.212501 2 -179.631336 0
C 6 1.406427 4 119.575567 2 -0.142400 0
H 8 1.095977 6 120.027481 4 -179.072651 0
C 8 1.403282 6 120.333823 4 0.493696 0
H 10 1.094882 8 119.959271 6 -179.434297 0
C 1 1.491527 2 119.461452 3 -1.585024 0
H 12 1.099459 1 115.155782 2 -40.472256 0
C 12 1.355412 1 127.809211 2 140.021933 0
H 14 1.099459 12 117.033232 1 175.901054 0
C 14 1.491527 12 127.809133 1 -4.601567 0
C 16 1.411187 14 119.461301 12 140.022641 0
H 17 1.096854 16 119.335311 14 -1.584883 0
C 17 1.404794 16 120.855335 14 178.976628 0
H 19 1.095931 17 119.820506 16 179.410725 0
C 19 1.404908 17 120.032214 16 -0.962181 0
H 21 1.095757 19 120.212439 17 -179.631453 0
C 21 1.406428 19 119.575563 17 -0.142512 0
H 23 1.095977 21 120.027522 19 -179.072709 0
C 23 1.403282 21 120.333787 19 0.493611 0
H 25 1.094881 23 119.959171 21 -179.434240 0
$end
The problem appears when I copy the output geometry and use it with other calculations, e.g., when I try to find the excited states with the following input file:
$comment
Cis stilbene. C2-symmetry optimized with CCSD/cc-pVDZ.
$end
$molecule
0 1
C 3.6830124699 -0.5321219659 0.3038669860
C 2.7932773117 -0.6120636883 -0.7803043433
C 3.3882282498 0.3018387672 1.3953693572
C 2.2008151800 1.0555490456 1.3923019562
C 1.3093558446 0.9691814434 0.3120044808
C 1.5880795495 0.1220617780 -0.7831753057
C 0.6769577259 0.0318385110 -1.9606167618
C -0.6769568813 -0.0318507675 -1.9606169051
C -1.5880808903 -0.1220661696 -0.7831765953
C -1.3093621202 -0.9691893883 0.3120001002
C -2.2008213977 -1.0555538572 1.3922972831
C -3.3882275446 -0.3018331421 1.3953696544
C -3.6830064966 0.5321346956 0.3038705587
C -2.7932730179 0.6120702226 -0.7803029396
H 4.6097095144 -1.1170770155 0.2926563133
H 3.0302470147 -1.2593434261 -1.6335115280
H 4.0830274953 0.3710504984 2.2398501301
H 1.9708411986 1.7200643627 2.2329551514
H 0.3912326653 1.5656835844 0.3117133703
H -0.3912432890 -1.5656986670 0.3117044398
H -1.9708529709 -1.7200748708 2.2329474381
H -4.6096979555 1.1170987501 0.2926659829
H -3.0302362934 1.2593555233 -1.6335077118
H -4.0830252763 -0.3710427639 2.2398521034
H 1.1775620674 0.0246198036 -2.9394698711
H -1.1775621534 -0.0246312639 -2.9394695316
$end
$rem
method = eom-ccsd
ee_states = [7, 7] ! C2 [A, B]
basis = cc-pVDZ
$end
Q-Chem detects it as a C1 molecule and reports that the input uses inconsistent number of irreps. The same happens if I use the z-matrix.