I am trying to optimize the Cs symmetry geometry of the benzoic acid and triethylamine complex but I get the following error. The initial geometry is fully optimized using Gaussian (wB97X-D/aDZ). The input file is also appended.
====== last few lines of the output file ==============================
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.0750
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.1125
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.1688
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.2531
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.3797
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.5695
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 0.8543
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 1.2814
ERROR: Symmetry operation 1 did not map atom 1 to another atom:
attempted to find atom at 6.296341 2.199168 -0.689321
atom_map() throwing PsiException
Unable to symmetrize geometry.
Increasing symmetry tolerance to 1.9222
ERROR: Symmetry operation 1 did not map atom 2 to another atom:
attempted to find atom at 5.729294 2.867505 -2.658083
atom_map() throwing PsiException
Unable to symmetrize geometry.
**** Optimization has failed! (in 1 steps) ****
--------------------------
OPTKING Finished Execution
--------------------------
Removing binary optimization data file.
Cleaning optimization helper files.
PsiException: Could not converge geometry optimization in 0 iterations.
Traceback (most recent call last):
File "/mnt/home/kakeshpo/anaconda3/bin/psi4", line 269, in <module>
exec(content)
File "<string>", line 66, in <module>
File "/mnt/home/kakeshpo/anaconda3/lib//python3.6/site-packages/psi4/driver/driver.py", line 1220, in optimize
raise OptimizationConvergenceError("""geometry optimization""", n - 1, wfn)
OptimizationConvergenceError: Could not converge geometry optimization in 0 iterations.
Psi4 stopped on: Friday, 18 January 2019 01:55AM
Psi4 wall time for execution: 0:08:59.58
*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at github.com/psi4/psi4.
====== end of output file ============================
molecule {
0 1
C 3.21688113 1.15174036 0.00000000
H 2.92869003 1.74850938 0.87371200
H 2.92869003 1.74850938 -0.87371200
N 2.38500072 -0.05936026 0.00000000
C 4.72833918 0.92738468 0.00000000
H 5.05878731 0.37491737 -0.88927900
H 5.05878731 0.37491737 0.88927900
H 5.24276530 1.89689042 0.00000000
C 2.53800152 -0.89618441 -1.20087800
H 1.79768853 -1.69943379 -1.10018700
H 3.53587423 -1.37075354 -1.22212200
C 2.53800152 -0.89618441 1.20087800
H 1.79768853 -1.69943379 1.10018700
H 3.53587423 -1.37075354 1.22212200
C 2.28578921 -0.14932674 2.50359900
H 2.23254080 -0.87093862 3.32808900
H 1.33177849 0.39281482 2.46491100
H 3.08478055 0.56454553 2.74249300
C 2.28578921 -0.14932674 -2.50359900
H 1.33177849 0.39281482 -2.46491100
H 2.23254080 -0.87093862 -3.32808900
H 3.08478055 0.56454553 -2.74249300
O -0.15805335 0.68773704 0.00000000
H 0.82616689 0.38854021 0.00000000
C -0.94154401 -0.37928711 0.00000000
O -0.52146693 -1.52491092 0.00000000
C -2.40325702 -0.05775038 0.00000000
C -5.14373328 0.46823462 0.00000000
C -3.31998328 -1.11310970 0.00000000
C -2.86282721 1.26273104 0.00000000
C -4.23138203 1.52350341 0.00000000
C -4.68684583 -0.85059427 0.00000000
H -2.94184553 -2.13429164 0.00000000
H -2.14358229 2.07932838 0.00000000
H -4.58802597 2.55348371 0.00000000
H -5.39944287 -1.67535684 0.00000000
H -6.21453295 0.67401418 0.00000000
}
memory 60 GB
set basis aug-cc-pvdz
set scf_type df
set freeze_core True
optimize('mp2')
freq('mp2')
===== end of input file =============================
when I include “symmetry Cs” in molecule specifications, then i get this error:
====last a few lines of output ====================
Fatal Error: User specified point group (Cs(X)) is not a subgroup of the highest detected point group (C1). If this is because the symmetry increased, try to start the calculation again from the last geometry, after checking any symmetry-dependent input, such as DOCC.
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1532493090788/work/psi4/src/psi4/libmints/molecule.cc on line: 2625
The most recent 5 function calls were:
psi::Molecule::find_point_group(double) const
psi::Molecule::update_geometry()
Traceback (most recent call last):
File "/mnt/home/kakeshpo/anaconda3/bin/psi4", line 269, in <module>
exec(content)
File "<string>", line 67, in <module>
File "/mnt/home/kakeshpo/anaconda3/lib//python3.6/site-packages/psi4/driver/driver.py", line 1167, in optimize
moleculeclone.update_geometry()
RuntimeError:
Fatal Error: User specified point group (Cs(X)) is not a subgroup of the highest detected point group (C1). If this is because the symmetry increased, try to start the calculation again from the last geometry, after checking any symmetry-dependent input, such as DOCC.
Error occurred in file: /scratch/psilocaluser/conda-builds/psi4-multiout_1532493090788/work/psi4/src/psi4/libmints/molecule.cc on line: 2625
The most recent 5 function calls were:
psi::Molecule::find_point_group(double) const
psi::Molecule::update_geometry()
Psi4 stopped on: Friday, 18 January 2019 02:34AM
Psi4 wall time for execution: 0:01:34.06
*** Psi4 encountered an error. Buy a developer more coffee!
*** Resources and help at github.com/psi4/psi4.
===== end of output file =============================
I made a couple edits to your posts. I’ve enclosed all your sample code in triple backticks (`) so that the forum formats it correctly, and I’ve changed the topic title to be more specific.
I can reproduce your error on a recent version of Psi. It looks like something is wrong with the gradient. Here’s the HF gradient I get:
Many components that should be zero or positive/negative pairs are not. The deviation is slight, but it’s enough to cost you symmetry. It looks to me like this gradient was never adapted to point group symmetry, but somebody more familiar with the code should check me on this.
Not yet. We need to accept the fix (which should be soon) and we need to update the nightly channel of conda. Then on your end, it’s a simple matter of switching to the nightly version if necessary and updating the package.
We’ll post here when both of those things on the dev end are finished.
It’s taken a while, but we have the developer version of Psi4 on conda!
Follow the instructions for Linux -> Conda -> Nightly here. If those work, mark a post here as closing the issue, so we know the problem is solved. If not, let us know what the new problem is.
but before doing that I have a question: Does installing the nightly version affect my stable version? and can I use them in parallel on the same system?
newenv is just a name. You can change to whatever you want. The important part is that the command will now install the developer version of Psi to a new conda environment, separate from your other installs. When you want to use stable Psi, just use it as normal. When you want to use developer Psi, activate the conda environment newenv and run Psi as normal to. When you want to use normal Psi again, deactivate the environment. (See here.)
Thank you! I was able to optimize my geometry successfully. I am running frequencies and so far I have not seen any error.
--------------------------------------------------------------------------------------------- ~
Step Total Energy Delta E MAX Force RMS Force MAX Disp RMS Disp ~
--------------------------------------------------------------------------------------------- ~
Convergence Criteria 1.00e-06 * 3.00e-04 * o 1.20e-03 * o ~
--------------------------------------------------------------------------------------------- ~
1 -711.23285635 -7.11e+02 2.29e-02 3.21e-03 o 3.83e-02 8.75e-03 o ~
2 -711.23491866 -2.06e-03 3.37e-03 4.57e-04 o 2.77e-02 5.29e-03 o ~
3 -711.23504772 -1.29e-04 2.56e-03 2.43e-04 o 4.77e-02 7.42e-03 o ~
4 -711.23513030 -8.26e-05 1.71e-03 2.01e-04 o 1.94e-02 4.58e-03 o ~
5 -711.23515698 -2.67e-05 9.91e-04 1.13e-04 o 2.14e-02 3.61e-03 o ~
6 -711.23517191 -1.49e-05 3.08e-04 5.06e-05 o 6.08e-03 1.29e-03 o ~
7 -711.23517408 -2.17e-06 2.19e-04 * 2.31e-05 o 1.95e-03 4.35e-04 o ~
8 -711.23517463 -5.50e-07 * 1.34e-04 * 1.40e-05 o 2.06e-03 2.99e-04 o ~
Glad to hear it! Feel free to post again if any more symmetry-loss problems come up. Seeing as this works for you, I’m going to mark this topic as solved.
Thank you for your help! So far the frequencies are running and there is no error. I will know in a couple of days for sure if the frequencies finish successfully .