others
The utils included here were custom made for some users that requested them, thus they have a much more narrow usage scope. Nonetheless we saw no reason to not disclose them.
track
Prints the name of the scanned variable, its value (in Bohrs or radians), derivative, Max Forces convergence Y/N, Cartesian forces value and Geometry index of the geometry in the file. If no variable is provided nor it is a scan calculation it will print the variables that may be tracked and exit.
usage: pyssianutils others track [-h] [-o OFILE] [--scan] ifile [variable]
Positional Arguments
- ifile
Gaussian Output File
- variable
Internal variable name to track
Named Arguments
- -o, --outfile
- File to write the Data. If it exists, the data will
be appended, if not specified it will print to the console
- --scan
- Specify that the gaussian out file is a
a scan automatically detect the coordinate to track
Default:
False
Usage
The development of this tool was focused into inspecting optimizations and relaxed scan calculations in order to find good guesses for transition states or detect at which step the transition state may have changed to converge to a different transition state than the desired one.
Note
The output of the following example has been simplified with respect to the
actual output, and thus the presented results are not realistic. These are
merely used to illustrate how the output from pyssianutils other track
looks like and what it contains.
First we can inspect the gaussian output file by hand to extract the different
internal coordinates definitions and select the one that we find the most
relevant. Or we can instead use track to simplify it a little bit:
$ pyssianutils others track path/to/example.log
Available parameters to track for path/to/example.log
Name Definition
R1 R(1,2)
R2 R(1,3)
R3 R(1,4)
R4 R(2,10)
R5 R(2,11)
A1 A(2,1,4)
A2 A(3,1,4)
A3 A(1,2,10)
A4 A(1,2,11)
D1 D(4,1,2,10)
D2 D(4,1,2,11)
D3 D(4,1,2,17)
Let's say that from those variables, we might think that distance "R3" is the most likely to be related to the TS that we are looking for. Then we can track that variable during the optimization:
$ pyssianutils others track path/to/example.log
Variable Value dE/dX Conver Car Forces Geom Num
R3 4.84074 -0.00268 NO 0.002445317 1
R3 4.82437 -0.00127 NO 0.008095657 2
R3 4.85777 -0.00003 NO 0.004442530 3
R3 4.83914 -0.00210 NO 0.001962615 4
R3 4.79272 -0.00071 NO 0.002282302 5
R3 4.81657 0.00155 NO 0.004568041 6
R3 4.83462 0.00016 NO 0.001937148 7
R3 4.81713 -0.00064 NO 0.001487927 8
R3 4.80367 0.00044 NO 0.000762087 9
R3 4.81339 0.00094 NO 0.001016865 10
R3 4.81620 0.00030 NO 0.000505738 11
R3 4.81584 0.00004 YES 0.000310116 12
R3 4.81533 -0.00002 YES 0.000232864 13
R3 4.81447 -0.00003 YES 0.000098242 14
R3 4.81395 -0.00002 YES 0.000094327 15
R3 4.81378 -0.00000 YES 0.000086698 16
R3 4.81386 0.00001 YES 0.000053593 17
R3 4.81387 0.00000 YES 0.000017043 18
Here we have the value of the variable, (in Bohrs for distances and in radians for angles and dihedrals) de differential of the energy relative to the variable, if the cartesian forces have converged (YES/NO) and their actual value and finally the number of the geometry. In the present example the numbers have been taken from an optimization to minima, therefore it makes sense that the geometry with the highest cartesian forces value is at the initial geometries. However, we may use the value of the cartesian forces or the differencial of the energy relative to the variable to select a new initial geometry for an optimization.
cubes-tddft
Takes a gaussian output file and a gaussian chk file and a list of Excited States (by number) and creates a .in.sub file to generate only the cube files of the orbitals involved in the transitions as well as a python script(s) to generate the appropiate combination of the cubes.
usage: pyssianutils others cubes-tddft [-h] -es EXCITED_STATES
[EXCITED_STATES ...] (-sq | -sum) [-m]
[-n NAME]
[-q {unknown,4,q4,8,12,20,24,28,36}]
ifile chk
Positional Arguments
- ifile
Gaussian Output File
- chk
Gaussian Checkpoint File
Named Arguments
- -es, --excited-states
list of numbers that correspond to the excited states whose output is desired
- -sq, --squarefirst
Calculates the cubes squaring the cubes after the scaling and before summing the donors and/or acceptors
Default:
False- -sum, --sumfirst
Calculates the cubes squaring the cubes after summing the donors, acceptors
Default:
True- -m, --multiple
Generate one .py per each Electronic State selected, otherwise a single .py with all the Electronic states is generated
Default:
False- -n, --name
name of the job for the queue system
Default:
'CubeGenerator'- -q, --queue
Possible choices: unknown, 4, q4, 8, 12, 20, 24, 28, 36
name of the queue that will be used which may be identified by the number of processors. This is HPC specific
Default:
'unknown'
Usage
This is probably the util with the narrowest scope. The original aim of the present tool was to simplify and automate the generation of cubefiles containing the molecular orbitals involved in transitions of excited states. This util outputs two scripts, a shell script that is used to generate the cubefiles with cubegen in individual files and a python script, that using the Cube class of pyssian, simplifies the process of combining the different cube files ( which could potentialy involve a large amount of individual commands as some utils only allow the combination of a maximum of 2 cubefiles at the same time)
Warning
This tool has not been maintained in a long time, thus it is likely to break. If you face troubles trying to use it we heavily recommend that you contact the main developer.