Some minor code snippets that I find useful and might be helpful for others too.
nStates=10
gnuplot> plot for [i=0:nStates-1] "< grep 'STATE.*:' s2.out" every nStates::i using 4 with lp title sprintf("S_{%i}", i+1)
:let t=[] | %s/\[\(\d\+\(-\d\+\)\?,\?\)\+\]/\=add(t,submatch(1))[1:0]/gWhen the document has been searched, the contents of t can be printed with :pu=t
:%s/Excited State \([0-9]\+\) [0-9]\+ \(.*\)/Excited State \1 3 \2/gI encountered the error Internal consistency failure #1 in ROv06.
This error means that there is a problem with the Overlay 6 from the IOps: https://gaussian.com/overlay6/
By looking at what is handled by overlay 6, it is clear that the error has something to do with my population analysis keyword.
In my case, it was the combination of nboread and npa together as pop=(nobread,npa) which does not work.
nboread means that all keywords are redirected to the $NBO $END section beneath the coordinates, where NPA would be placed then.
2*$4*$4 >= 0.08) for a closed shell calculationgrep 'Excited State\|->\|<-' vertical.log | sed 's/://g' |awk '{if ($1 != "Excited" && 2*$4*$4 >= 0.08) print $1," -> ",$3," ", 200*$4*$4; else if ($1 == "Excited") print $0}'grep 'Excited State\|->\|<-' vertical.log | sed 's/://g' |awk '{if ($1 != "Excited" && 2*$4*$4 >= 0.08 && ($1 == 205 || $1 == 206 || $1 == 207) && ($3 == 210 || $3 == 211 || $3 == 213 || $3 == 214 || $3 == 215)) print $1, $2, $3, " ", 200*$4*$4; else if ($1 == "Excited") print $0}'Gaussian is often called a "suite of programs" because it is not a single executable file but consists of many executables, that work together. These executables are called "Links" and can be found on the Gaussian website. To not have to search them on their website, because I think they are a bit hidden, I list them here too.
Details
| 0 |
Initializes program and controls overlaying |
| 1 |
Processes route section, builds list of links to execute, and initializes scratch files |
| 101 |
Reads title and molecule specification |
| 102 |
Fletcher-Powell optimizations |
| 103 |
Berny optimizations to minima and TS, STQN transition state searches |
| 105 |
Murtaugh-Sargent optimizations |
| 106 |
Numerical differentiation of forces/dipoles to obtain polarizability/ hyperpolarizability |
| 107 |
Linear-synchronous-transit (LST) transition state search |
| 108 |
Unrelaxed potential energy surface scan |
| 109 |
Newton-Raphson optimization |
| 110 |
Double numerical differentiation of energies to produce frequencies |
| 111 |
Double numerical differentiation of energies to compute polarizabilities and hyperpolarizabilities |
| 112 |
Performs the Self-Consistent Virial Scaling method (SCVS), T. A. Keith’s extension of [Lowdin59, Magnoli82, Lehd91] |
| 113 |
EF optimization using analytic gradients |
| 114 |
EF numerical optimization (using only energies) |
| 115 |
Follows reaction path using GS3 algorithm |
| 116 |
Numerical self-consistent reaction field (SCRF) |
| 117 |
Performs IPCM solvation calculations. |
| 118 |
BOMD calculations |
| 120 |
Controls ONIOM calculations |
| 121 |
ADMP calculations |
| 122 |
Counterpoise calculations |
| 123 |
Follows reaction path using the HPC algorithm (and others) |
| 124 |
Performs ONIOM with PCM and external-iteration PCM |
| 202 |
Reorients coordinates, calculates symmetry, and checks variables |
| 301 |
Generates basis set information |
| 302 |
Calculates overlap, kinetic, and potential integrals |
| 303 |
Calculates multipole integrals |
| 308 |
Computes dipole velocity and Rx∇ integrals |
| 310 |
Computes spdf 2-electron integrals in a primitive fashion |
| 311 |
Computes sp 2-electron integrals |
| 314 |
Computes spdf 2-electron integrals |
| 316 |
Prints 2-electron integrals |
| 319 |
Computes 1-electron integrals for approximate spin orbital coupling |
| 401 |
Forms the initial MO guess |
| 402 |
Performs semi-empirical and molecular mechanics calculations |
| 405 |
Initializes an MCSCF calculation |
| 502 |
Iteratively solves the SCF equations (conven. UHF & ROHF, all direct methods, SCRF) |
| 503 |
Iteratively solves the SCF equations using direct minimization |
| 506 |
Performs an ROHF or GVB-PP calculation |
| 508 |
Quadratically convergent SCF program |
| 510 |
MC-SCF |
| 601 |
Population and related analyses (including multipole moments) |
| 602 |
1-electron properties (potential, field, and field gradient) |
| 604 |
Evaluates MOs or density over a grid of points |
| 607 |
Performs NBO analyses |
| 608 |
Non-iterative DFT energies |
| 609 |
Atoms in Molecules properties |
| 610 |
Numerical integration (for testing integral codes) |
| 701 |
1-electron integral first or second derivatives |
| 702 |
2-electron integral first or second derivatives (sp) |
| 703 |
2-electron integral first or second derivatives (spdf) |
| 716 |
Processes information for optimizations and frequencies |
| 801 |
Initializes transformation of 2-electron integrals |
| 802 |
Performs integral transformation (N3 in-core) |
| 804 |
Integral transformation |
| 811 |
Transforms integral derivatives & computes their contributions to MP2 2nd derivatives |
| 901 |
Anti-symmetrizes 2-electron integrals |
| 902 |
Determines the stability of the Hartree-Fock wavefunction |
| 903 |
Old in-core MP2 |
| 904 |
Complete basis set (CBS) extrapolation method of Petersson, et. al. |
| 905 |
Complex MP2 |
| 906 |
Semi-direct MP2 |
| 908 |
Electron Propagator Program |
| 909 |
ADC(3) and related electron propagator models |
| 913 |
Calculates post-SCF energies and gradient terms |
| 914 |
CI-Singles, RPA and ZIndo excited states; SCF stability |
| 915 |
Computes fifth order quantities (for MP5, QCISD(TQ) and BD(TQ)) |
| 916 |
Old MP4 and CCSD |
| 918 |
Reoptimizes the wavefunction |
| 923 |
SAC-CI program |
| 925 |
Implements the Excited State Electron Transfer (EET) model |
| 1002 |
Iteratively solves the CPHF equations; computes various properties (including NMR) |
| 1003 |
Iteratively solves the CP-MCSCF equations |
| 1014 |
Computes analytic CI-Singles second derivatives |
| 1101 |
Computes 1-electron integral derivatives |
| 1102 |
Computes dipole derivative integrals |
| 1110 |
2-electron integral derivative contribution to F(x) |
| 1111 |
2 particle density matrix and post-SCF derivatives |
| 1112 |
MP2 second derivatives |
| 9999 |
Finalizes calculation and output |
I am using regular expressions a lot, when extracting or modifying existing data. As a regex can look very confusing, it helps to visualize it. It can be done easily using https://regexper.com where you just have to enter your regex and get a nice ouput on what it is doing.
Let’s take the example from searching for the reference indexes in VIM from above.
There I searched for (\d+(-\d+)?,?)+ which produces the following graph:
Using the website https://regex101.com one can also test the expressions directly and one gets a nice literal description of what one is doing. For the example above, you can have a look here: https://regex101.com/r/BIgwCO/1 .
Another, more complex example, would be the following expression (^(\d+\.|[])) (,(\s?\w\.?-?))(((;|,) (and)?,(\s?\w\.?-?))) \((\d+)\)(\.|,)? (.), (.), (\w+((-|–)\d+)?), (\w+((-|–)\d+)?).
If I remember correctly, this regex is extracting the references as produced by, e.g., JACS.