Resgrp:comp-photo-calculations
Example input files for different types of calculation, mainly using the development code.
nonstd
This keyword means 'don't use any keywords', and allows you to access the gaussian route generator directly. For more info see here and here. For some types of calculation, we have to use template input files that have non-standard routes and bypass Gaussian's own route generator in 'expert mode'. A route is generated for all Gaussian calculations, and should be at the top of the text .log file. Alternatively, for a calculation that has keywords already available, use the testrt keyword interactively at a terminal to see what route is generated.
ionic states
For ionic states, a 'minimal' active space (e.g. cas(6,6) for benzene) won't give realistic excitation energies, as there's not enough flexibility to properly describe charge redistribution. With conjugated hydrocarbons, using a double active space and a 1-electron basis set with 3p-like functions (scaled from Si basis set) gives much of the necessary flexibility.
#p CASSCF(...)/6-31G* extrabasis Title 0 1 Geometry C 0 P 3 0.5 .1727380000D+01 -.1779510000D-01 .5729220000D+00 .2535390000D+00 .2221920000D+00 .8006690000D+00 P 1 0.5 .7783690000D-01 .1000000000D+01 ****
Calculating and viewing the normal modes and frequencies of the energy difference; the modes of the seam; and the modes of the bilinear coupling
Calculation:
Use the non-standard route described in the section "Computation of Intersection-Space Frequencies" on the page "Seam Calculations of CHD". The only difference in the non-standard route is 7/79. (7/79=1 for energy difference frequencies only, 7/79=2 for the three things, seam, energy difference and bilinear coupling frequencies).
Viewing the modes:
The scripts dffx_modes_g01.sh, seam_modes_g01.sh and eta_modes_g01.sh can be used to create log files that gaussview can read to visualise the normal modes and frequencies of the energy difference, the modes of the seam and/or the modes of the bilinear coupling respectively.
First, you need a directory (on your mac or on the cluster) that we will call /dir/. In here, you put the the scripts (dffx_modes_g01.sh, seam_modes_g01.sh, eta_modes_g01.sh) and a file called template.log, and you create a subdirectory /dir/gaussian_output/ in which you put your log file (say it's called jobname.log). Then you create a subdirectory /dir/data/. Then you execute the script this way: ./dffx_modes_g01.sh jobname and you will get a new file in data that is called jobname_DFFX.log (for energy difference frequencies) or jobname_GV.log (for seam modes) and that can be read by GaussView.
N.B.: ./ might not be needed on the cluster (also this may depend on the type of shell), but it is on my Mac.
Now, there used to be a small printing error in Fabrizio's code that may not have been fixed. It's about the mass-weighting of the branching-space vectors, gradient difference and derivative coupling (the last two modes, given with zero frequencies). The consequence is that the motion of H atoms is exaggerated when you visualise these last two vectors with Gaussview. The other ones are fine.
NB the convention for the energy difference is S0 - S1, so if you want the modes that reduce the energy difference, take those that have a large positive frequency (with respect to the energy difference).
IRC calculations in which the vector to follow is specified by the user
This may be required if the starting point for the IRC is not a transition state (i.e. it has more than one imaginary frequency). In this case, GAUSSIAN will not know which negative frequency to follow so it must be specified explicitly.
Using G03, certain combinations of keywords do not seem to work. Guess=read cannot be used: the orbitals must be specified explicitly in the input file along with the keyword guess=cards. It is also not possible to read in the force constants from a previous .chk file: irc=calcfc must be used. Thus if the calculation requires stateaverage orbitals, the stateaverage keyword must not be used (since, due to a bug in G03, it cannot be used in conjunction with a frequency calculation). Instead, the IOP (5/17=41000200,10/10=700007) should be specified. CAN WE VERIFY IF THIS IS ALL/PARTLY TRUE FOR OTHER VERSIONS OF GAUSSIAN?
A typical route might look like:
# CAS(4,4,nroot=2)/sto-3g IRC=(CalcFC,ReadVector) guess=cards nosymm IOP(5/17=41000200,10/10=700007)
followed by the orbitals and then the vector. The orbitals can be extracted form the .fchk of a previous calculation. Extract the section "Alpha MO coefficients" into a file (named, for example, "mo-file") and then run (on the cluster)
dd_formatmos.out < mo-file > formatted-mos
on "mo-file" to create a file called "formatted-mos" containing the formatted MOs. These can be pasted directly into the input file.
Finally, specify the vector to follow. Find the direction to be followed (in the .log of the frequency calculation). The values may be listed vertically under the desired frequency, in which case these values can be used directly: list these values in rows containing 8 values per row with 10 characters (inc spaces) making up each value. If the direction is specified in cartesian coordinates they will need to be converted to internal coordinates. Do this as described in section "Computation of the Intersection Space Minimum Energy Path (MEP)" on the page "Seam Calculations of CHD". (Essentially this will involve adding the desired cartesian frequency to the cartesian coordinates of the molecule, using GAUSSVIEW to convert this structure to internal coordinates and then subtracting the internal coordinates of the molecule.)