How do I extract the whole Hessian from my chk/output/fchk Gaussian file?
Note: The data in the .out file from a FREQ run is displacement and frequencies, NOT hessian data.
The only think I can find close is by using demofc, with an input file point to "Cartesian Force Constants". But this returns only force constants. These force constants are useless when I want to understand the bond stretch between two atoms in a large molecule because typically these force constants will contain the dynamics of other parts of the molecule.
Hello Anthony,
I think that the solution is: Open the .chk with gaussian as a normal input or output (selecting on type of file .chk). Then it will open a windows with your molecule and if you go to RESULTS>VIEW FILE the program will open it and you will be able to save it. I attach an example of the benzene.
I hope it helps you
Hello Joaquim,
Thanks for that example file. I hadn't thought of opening the .chk in GView. I have however, converted one of my own chk to a fchk, and I still can't find the Hessian matrix data. Do you know where it is in the example file you gave me?
Many thanks
Anthony
What I am hoping to get is the Hessian for the optimised structure. See attached for an example of a very basic Hessian along with the reaction force as a product of the hessian with a displacement vector.
Article Calculation of intramolecular force fields from second-deriv...
Hello Anthnoy,
I have made pictures of the procedure to open the chk. Even so, I do not see clear the matrix in there, but I will continue searching if there are some command, for example, "print" one.
Hi Joaquim,
Thanks for you help. I think there may be an old g03 command which prints out the whole hessian matrix. It is just a question of what it is! I've sent Gaussian Help and email, hopefully they will be able to help.
Hello Anthony,
I have been searching but I could not find a clear command, only the "scf=save". I add the results. I am sorry for do not have a clear answer. For me it has been a surprise that in .chk was not the full Hessian. I think that Gamess do it in thier .dat.
Hello Joaquim,
Thank you for all of you help. When Gaussian respond to my email I will let you know if the full Hessian can be retrieved.
Many thanks
Hello Joaquim, an update.
I think I'm getting a little closer. I do believe the Hessian is being saved as "Cartesian Force Constants" in either the .chk file if iop(7/33=1) is used OR when you convert the .chk to .fchk.
I tried this on H2O. I get 3N-6 normal modes i.e., 3. (twisting, wagging, rocking https://en.wikipedia.org/wiki/Molecular_vibration).
However, the Cartesian Force Constants is a 9x5 matrix. I am now trying to work out:
a) why are there 45 entries?
b) what does each column and each row mean?
c) why is it a 9x5 matrix?
Thanks
Anthony
Hessian is a 3Nx3N symmetrical matrix, so only half of them are written in Gaussian Output.
They are Cartesian coordinates (x, y, z) for each atom. So Hessian of H2O have 9 rows and columns.
Please see under the 9x5 matrix, there is another 9x4 matrix indeed. Hessian are written in a format of every 5 column.
Hi Irtaza,
The Hessian stored in FCHK file has the same sequence as in LOG file. Since the Hessian matrix is symmetric, both of them only stored the lower triangle of the Hessian matrix.
For a 32 atoms system, the Hessian matrix is 96x96 indeed; but the number of elements in the lower triangle is (1+96)*96/2=4656=1164x4.
A lower triangle looks like:
1
2 3
4 5 6
7 8 9 10
and the FCHK file just stores the elements in sequence, that is, [1, 2, 3, 4, 5, 6, 7, 8, 9, 10].
Hi Rui
I was wondering if it is possible to get the hessian in internal coordinates? When I do calculations with small molecules ( which contain about 3-4 atoms), the internal hessian is printed in the log file. But for larger molecules, Gaussian doesn't print the hessian.
Thanks
@Ruixing
Thanks a lot
Using freq=intmodes prints out the internal modes in the log file, is there a way to construct the hessian using this information?
For small molecules, gaussian directly prints out the complete hessian in internal coordinates, I was wondering if there is a way to get that directly?
@salman:
Using freq=intmodes will give the internal Hessian as is, plz search "Internal force constants" in the LOG file, or "Internal Force Constants" in the FCHK file.
The definition of internal coordinates can be found after "Initial Parameters" in the LOG file(search it). You may hope to modify them, and in that case you can use "freq=(intmodes,modredundant)".
@Ruixing
I can not find the internal force constants in either the log or the fchk file. I am attaching my .gjf, .log and .fchk files. I will be grateful if you could help me out with this.
Thanks
@Ruixing
It worked. I was not using the #p tag in the first line, on adding that tag I get the hessian in both the internal and cartesian coordinates.
Thanks a lot for the help.
Dear Ruixing, could you please answer to my question? (https://www.researchgate.net/post/How_to_extract_force_constants_from_the_Gaussian_log_file#5919b1f8ed99e12e1425c2ee) Thank you! Roland
- Badges
- Science topic
- Similar topics
- Filing