Trouble Shooting

• You try to "publish" and an error box comes up. In the first instance please wait 5-10min and try again. It maybe that the system is very busy (there are a lot of you trying to publish jobs at the same time). If it still doesn't work go to the portal profile page and tick "Publish to Dspace" then save. If this doesn't work do as the error message suggests and e-mail m.harvey with your job ID. Check back a little later and then try to publish them again. If the job is still not published within 24hrs then contact one of the demonstrators in the lab next lab session. Do not get hung up on waiting to publish but continue on with the lab. Do not delete the job and do not repeat the job as you will still be able to publish it later, the jobs will stay in your list until you delete them so there is no harm in leaving them a couple of days before publishing.
  
  
• The go to edit point group and you cannot apply the right symmetry (T_d or D_4h) point group. This problem can arise if you are you trying to "correct" the symmetry of a higher level calculation. ONLY correct the symmetry if the calculation is at the 3-21G level. This problem can occur when the coordinates are not accurate enough, so we need to loosen the criteria a bit. In the tolerance click on "loose" and hopefully the symmetry point groups will become active. If not then try "very loose". If that doesn't work there may be something more serious going on and you should ask a demonstrator to have a look at your file.
• Your B3LYP/6-31G(d) vibrational wavenumbers do not match mine by more than 1-2 cm^-1? For example my lowest frequency is 54cm^-1 and your lowest frequency is more like 65 cm^-1. When you check the "Item" part of your frequency file, you find that the molecule is not converged! What is wrong? You have symmetrised your optimised geometry before doing the frequency analysis, this was the wrong thing to do! By doing this you have destroyed the optimisation, and a frequency calculation should only ever be performed on a fully optimised structure. How do you fix it? Find your old B3LYP/6-31G(d) and this time when you set up the frequency job do not symmetrise the geometry. Alternatively use the geometry from your current frequency job to start a new optimisation. (Be careful to check the link0 information as discussed below).
  

          Item               Value     Threshold  Converged?
   Maximum Force            0.002612     0.000450     NO
   RMS     Force            0.001533     0.000300     NO
   Maximum Displacement     0.141613     0.001800     NO
   RMS     Displacement     0.077553     0.001200     NO
   Predicted change in Energy=-1.387744D-03
   GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
  

• Have you have added extra extra words in the additional keywords? Gaussian is very sensitive to the exact text. For example you should be adding "int=ultrafine scf=(conver=9)" your job will fail if you used "int=ultrafine and scf=(conver=9)"! Any other extra text not exactly as stated in the instructions will cause a job to fail.
• Have you used the "opt=z-matrix" on the square planar NiCl₂(PH₃)₂ complex? This option was only to be used on the [NiCl₄]^2- complex because of the D_4h symmetry. NiCl₂(PH₃)₂ is C₁ and so it does not need this option, and your job will take too long and then fail if you use it. Do not use "opt=z-matrix" with NiCl₂(PH₃)₂.
• Do you have one negative frequency for the cis square planar NiCl₂(PH₃)₂ complex? This can occur when the PH₃ groups are staggered. In this complex they prefer to be eclipsed. If you animate the negative frequency does it look like a PH₃ rotation forward and back? If so use the torsion tool to rotate one PH₃ group such that the H-atoms are eclipsed and start the optimisation from this point, you should be able to optimise to a lower energy structure with no negative mode. If you are unsure how to do this ask a demonstrator to help you.
• If you have used a file that has already been submitted to the SCAN queue it will have had some "extra" information added at the head of the file (this controls how many processors are used, the memory allocated and the checkpoint file). If you try to sumbit a job with this extra information a second time it will fail. You have two options (do one OR the other, not both!):
  • 1. For example if you use "view file" you will see something like this at the top of the file:

    %nprocshared=8
    %mem=13000MB
    %NoSave
    %Chk=chk.chk
    %rwf=/tmp/pbs.7098272.cx1b/rwf
    (blank line in the file)
    # opt b3lyp/6-311g(d,p) geom=connectivity int=ultrafine scf=conver=9
    

    edit the input file in word-pad to remove the extra material, that is everything before the line beginning with the hash symbol, be sure to remove any blank lines as well. You should be left with something that starts like this:

    # opt b3lyp/6-311g(d,p) geom=connectivity int=ultrafine scf=conver=9
    

  • 2. when you prepare the input file under "gaussian set-up" click on the link 0 tab. You will see something like the first image below, you need to change these options to reflect those in the second image below:
    
    incorrect file options

    
    correct file options