When you submit an ORCA calculation to the cluster (see Running calculations on Sól), ORCA will run your job on one of the nodes of the cluster (a node is just one of many computers of the clusters) but will immediately write the output of the calculation to a new file, that we call the outputfile. So if you submitted an ORCA inputfile called h2o-exercise1.inp to the cluster, then an outputfile called h2o-exercise1.out will immediately be created in the same directory as the inputfile. This does not mean that the job is over, just that the job started successfully. To check whether the job is over you can use qstat to see if your job is running or not (it may be stuck in the queue) but actually the best way is to check the ORCA outputfile directly for an end message at the end of the file.
To monitor a running ORCA job you can "tail" the outputfile:
tail -f h2o-exercise1.out
This command will write the last 10 lines of the outputfile to the screen and will then continually update the screen when more data gets added to the outputfile. You can thus monitor the status of your ORCA job "live". To exit the tail program, you press the characters Ctrl and C on the keyboard.
You can also look inside the outputfile using the less program:
less h2o-exercise1.out
The less program will show the contents of your outputfile, one page at a time (whatever fits in your window).You can use the Space bar to scroll through the outputfile page-by-page but even better is to jump right to the end of the outputfile by typing: Shift and ">". You then exit less by typing "q".
You can of course also use an SFTP client to copy your outputfile back to your computer (and then open with Notepad(Windows) or TextEdit(Mac) or something) using a GUI or even look inside the file using the GUI SFTP client but this just takes longer. Once you get used to the command line programs like less, tail and nano, this will take you a lot less time.
When the ORCA calculation is done, ORCA signals this by a message in the outputfile ("ORCA TERMINATED NORMALLY"):
Timings for individual modules:
Sum of individual times ... 51.609 sec (= 0.860 min)
GTO integral calculation ... 20.363 sec (= 0.339 min) 39.5 %
SCF iterations ... 5.418 sec (= 0.090 min) 10.5 %
SCF Gradient evaluation ... 18.663 sec (= 0.311 min) 36.2 %
Geometry relaxation ... 2.435 sec (= 0.041 min) 4.7 %
Analytical frequency calculation... 4.730 sec (= 0.079 min) 9.2 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 1 minutes 2 seconds 496 msec
Reading through the whole output
You can learn a lot by reading through the entire outputfile for a simple molecule using e.g. less page-by-page. By doing that you will see what happens in the beginning of an ORCA job and what the calculation spends long time on and there is plenty of data in the outputfile that may be useful to you that you can not quickly find by typing grep keywords like we do below.
Reading through the outputfile every time, however, is time consuming and therefore it is important to learn how to quickly find the relevant information (like energies, geometries etc.). This is shown below.
Checking whether the geometry optimization converged.
If you have checked that the ORCA job terminated normally and you did a geometry optimization job, you might want to first quickly check whether the optimization finished without problems. A line containing OPTIMIZATION RUN DONE should appear towards the end of the output IF your optimization converged (or earlier if frequencies were calculated as well). Also if any of the following lines appear in the output:
***********************HURRAY********************
*** THE OPTIMIZATION HAS CONVERGED ***
FINAL ENERGY EVALUATION AT THE STATIONARY POINT"
*** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
then your optimization converged.
You can quickly check this by using grep , a handy command-line utility that quickly searches for letters or words in text files and prints out the whole line:
For example:
grep 'OPTIMIZATION RUN' h2o-exercise1.out
should reveal the output : *** OPTIMIZATION RUN DONE ***
if the geometry optimization job converged.
grep FINAL h2o-exercise1.out
should reveal the outputline (and other lines) : *** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
if the geometry optimization job converged.
grep HURRAY h2o-exercise1.out
should reveal the outputline : ***********************HURRAY********************
if the geometry optimization job converged.
Chemcraft should also reveal whether the optimization converged or not by showing a field called "Optimized geometry" in the left part of the Chemcraft window.
Getting the optimized geometry from a geometry optimization job
After checking that the job converged you may want check how the optimized geometry looks. You have a few options here:
1. Copy the output to your computer and open in Chemcraft. By doing this you can see the last geometry (the optimized geometry) and also the intermediate geometries that ORCA calculated while trying to find the minimum (the last geometry if ORCA succeeded).
2. Open the ORCA output using less, go to the end of the outputfile (Shift and ">"), typing a question mark and then typing CARTESIAN COORDINATES in the "? field" that appears at the end of the screen. By doing this you search "upwards" for the words CARTESIAN COORDINATES in the file. You will then find a table with the last coordinates (hopefully optimized) in Angstrom.
3. An even better way is to look inside the file called (in this tutorial) h2o-exercise1.xyz which will contain Cartesian coordinates of your optimized geometry.
This file you can copy back or copy/paste the coordinates into Chemcraft.
These coordinates you can then use for other calculations, for example for a separate single-point energy job.
Getting the energies from a geometry optimization or a single-point calculation
You might also be interested in the energies or the final energy (the energy of the opimized geometry) from your geometry optimization job.
Chemcraft will tell you this but an even quicker way is to "grep" the energy from the output. The energy (also called the total energy, potential energy or electronic energy) always appear in a line like that looks like this (several times in a geometry optimization job):
FINAL SINGLE POINT ENERGY -45.098341464012
So you can grep the word FINAL in the output:
grep FINAL h2o-exercise1.out
and it will print the energy of each geometry optimization step or print the energy once if it was a single-point energy job.
The grep output for a geometry optimization will look like this:
grep FINAL h2o-exercise1.out
FINAL SINGLE POINT ENERGY -45.097876040381
FINAL SINGLE POINT ENERGY -45.098052163135
FINAL SINGLE POINT ENERGY -45.098105712344
FINAL SINGLE POINT ENERGY -45.098235415207
FINAL SINGLE POINT ENERGY -45.098305622302
FINAL SINGLE POINT ENERGY -45.098327093679
FINAL SINGLE POINT ENERGY -45.098338421725
FINAL SINGLE POINT ENERGY -45.098340623287
*** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
FINAL SINGLE POINT ENERGY -45.098341464012
This grep command actually quickly tells you that the optimization converged (because of the FINAL ENERGY EVALUTATION... line) and also that the energy (also called the total energy, potential energy or electronic energy) of the optimized geometry is -45.098341464012 hartree.
A single-point energy ORCA job would only show a single line:
grep FINAL h2o-exercise1.out
FINAL SINGLE POINT ENERGY -45.098341464012
This energy is refererred to as the total energy, potential energy or electronic energy (E) at 0 Kelvin. This is not the same as the enthalpy (H) or the free energy (G) at temperature X. See below for thermochemical corrections.
Getting vibrational frequency data and thermochemistry data from the output
If you did a vibrational frequency job (e.g. like this : ! HF-3c opt freq) then the vibrational frequency data will appear after the geometry optimization has converged. A vibrational frequency calculation may take some time. To find the vibrational frequency data you can either use Chemcraft (that should show the vibrational frequencies in cm-1 as well as animate them) or you can quickly find them using less or grep.
Open the outputfile using less: less h2o-exercise1.out and then search downward by typing / and then typing VIBRATIONAL and hit ENTER. This should reveal a table like this:
VIBRATIONAL FREQUENCIES
-----------------------
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 0.00 cm**-1
6: 625.43 cm**-1
7: 1102.23 cm**-1
8: 2181.05 cm**-1
etc.
The first six ( number 0 to 5) vibrational frequencies are always zero, because these are the translational and rotational degrees of freedom of a nonlinear molecule that don't have any vibrational energy. After that the real vibrational frequencies appear. You should check that these vibrational frequencies are real positive numbers. If a negative sign appears (or an imaginary label) then this means that you are not in a proper minimum on the potential energy surface. This might be due to some numerical noise (if the frequencies are low in magnitude) that can sometimes be removed by tightening convergence criteria (or choosing a better grid in a DFT calculation). It can also mean that you have accidentally found a saddlepoint instead of a minimum and if this is the case then you often have to distort the geometry a bit to move away from the saddlepoint.
If you were searching for a saddlepoint, however, and you get 1 imaginary frequency then everything is fine of course.
Later in the output, the IR spectrum is printed (search for "IR SPECTRUM") and after that the thermochemistry output ("THERMOCHEMISTRY AT 298.15K").
Reading the thermochemistry output in detail can be useful but you can also quickly find the relevant data in the following lines like this (obviously with different energies):
Zero point energy ... 0.00890470 Eh 5.59 kcal/mol
Thermal vibrational correction ... 0.00017149 Eh 0.11 kcal/mol
Thermal rotational correction ... 0.00094418 Eh 0.59 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
Total Enthalpy ... -188.66530093 Eh
Final entropy term ... 0.02416130 Eh 15.16 kcal/mol
Final Gibbs free enthalpy ... -188.68946223 Eh
G-E(el) ... -0.01178045 Eh -7.39 kcal/mol