Now updated to Python3.0!
PySOC is a program, library, and interface to calculate spin-orbit coupling (SOC) between singlet ground states/excited states and triplet excited states.
PySOC currently supports excited state calculations with Gaussian and DFTB+.
- Evaluation of spin-orbit coupling elements between singlet and triplet states
- Python scripts + FORTRAN
- Interfaced to third-party quantum chemistry packages, such as Gaussian 09 and DFTB+
- Based on Casida’s wave functions in LR-TDDFT, TDA, TDDFTB
- Breit-Pauli spin-orbit Hamiltonian with effective charge approximation
$ pip install cclib tabulate periodictable scipyThe main pysoc directory should be added to the PYTHONPATH:
export PYTHONPATH="$PYTHONPATH:/path/to/pysoc"The bin folder should be added to the PATH:
export PATH="$PATH:/path/to/pysoc/bin"Before spin-orbit coupling can be calculated, it is first necessary to perform an excited states calculation with either the Gaussian or DFTB+ calculation programs. The next section will briefly cover the necessary options to perform SOC calculations with each, but the reader is expected to be familiar with the basic operation of the QM program of choice.
Note
Shells higher than the f shell are not currently supported by PySOC. The user should ensure that the basis set used in the QM program does not contain g (or higher) shells.
Time-dependant DFT excited states calculations both with and without the Tamm–Dancoff approximation are supported for Gaussian versions 09 and 16. Older versions of Gaussian and alternative calculation methods (CIS etc.) may additionally be supported, but have not been tested.
PySOC requires both the log file (.log/.out) and read/write binary file (.rwf) from the calculation as input. The .rwf file is normally deleted automatically by Gaussian after the calculation finishes. You can prevent this behaviour by adding the following line to the Gaussian input file:
%Rwf="FILE.rwf"
Where FILE can be changed as appropriate.
Additionally, PySOC requires that the basis set be printed in the calculation output. This can be requested with the following options:
6D 10F GFInput
A full example Gaussian input file for formaldehyde would look like this:
%mem=1GB
%chk=formaldehyde.chk
%rwf=formaldehyde.rwf
# TD(50-50,nstates=5) wB97XD/TZVP 6D 10F GFInput
test
0 1
C -0.131829 -0.000001 -0.000286
O 1.065288 0.000001 0.000090
H -0.718439 0.939705 0.000097
H -0.718441 -0.939705 0.000136
Note
This section is under revision.
Note
PySOC requires Gaussian type orbitals (GTOs) to perform the SOC calculation, yet DFTB+ uses Slater-type orbitals (STOs).
Thus the parameter set used for the DFTB+ calculation must be fitted to GTOs for use with PySOC.
PySOC contains a fitted set for the mio-1-1 parameter set which will be used by default, alternative fitted sets can be specified with the --fitted_basis option.
An example dftb_in.hsd file is given below:
Geometry = GenFormat {
<<< "ch2o.gen"
}
Driver = {}
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1e-10 # Very tight for test purposes only
MaxAngularMomentum = {
H = "s"
C = "p"
O = "p"
}
SlaterKosterFiles = Type2FileNames {
Prefix = "/fsnfs/users/xinggao/work/gsh/thiothymine/gtsh/test_python/tddftb/sk/mio-1-1/"
Separator = "-"
Suffix = ".skf"
}
LinearResponse {
NrOfExcitations = 10
StateOfInterest = 0
Symmetry = both
HubbardDerivatives {
H = 0.347100 0.491900
C = 0.341975 0.387425
O = 0.467490 0.523300
}
WriteTransitions = Yes
WriteTransitionDipole = Yes
WriteXplusY = Yes
}
}
Options {
WriteEigenvectors = Yes
WriteHS = No
}
ParserOptions {
ParserVersion = 4
}
After performing the DFTB+ calculation, set WriteHS = Yes and run the calculation a second time.
Once the QC/TB calculation has completed, SOC can be calculated using the pysoc command.
pysoc has only one mandatory argument: the calculation output file. For Gaussian, this is the main calculation .log file, while for DFTB+ this is the .xyz geometry file.
For example, to calculate SOC for a file in the current directory with the name ch2o.log:
$ pysoc formaldehyde.logThe rwf file, which is also required, will be guessed based on the name of the given log file. The rwf file can also be specified explicitly:
$ pysoc formaldehyde.log --rwf-file gaussian.rwfTo calculate SOC from a completed DFTB+ calculation:
$ pysoc formaldehyde.xyzOnce the calculation is complete, the SOC table will be printed:
$ pysoc ch2o.log
Singlet Triplet RSS (cm-1) +1 (cm-1) 0 (cm-1) -1 (cm-1)
--------- --------- ------------ ----------- ---------- -----------
S0 T1 60.7419 42.9510 0.0077 42.9510
S0 T2 0.0194 0.0137 0.0000 0.0137
S0 T3 10.6234 0.0133 10.6234 0.0133
S0 T4 59.8873 42.3467 0.0012 42.3467
S0 T5 11.7332 0.0013 11.7332 0.0013
S1 T1 0.0008 0.0006 0.0000 0.0006
S1 T2 44.3144 31.3350 0.0224 31.3350
S1 T3 8.6280 6.1009 0.0002 6.1009
S1 T4 50.7211 0.0151 50.7211 0.0151
S1 T5 5.5317 3.9115 0.0001 3.9115
S2 T1 7.3854 5.2223 0.0001 5.2223
S2 T2 0.2532 0.0008 0.2531 0.0008
S2 T3 0.0003 0.0002 0.0000 0.0002
S2 T4 0.2432 0.1720 0.0013 0.1720
...Here, each line indicates SOC between one singlet and one triplet state, which are given by the ‘Singlet’ and ‘Triplet’ columns respectively. The last three columns each contain the calculated spin-orbit coupling for the triplet sub-state with quantum number +1, 0, or -1. The root-sum-square for the three triplet sub-states is presented in the RSS column.
Alternatively, a comma-separated values (CSV) format can be requested with the ‘-c’ option, which can be more easily imported into a spreadsheet for analysis:
$ pysoc ch2o.log -c
Singlet,Triplet,RSS (cm-1),+1 (cm-1),0 (cm-1),-1 (cm-1)
S0,T1,60.7419154885397,42.95102,0.00769,42.95102
S0,T2,0.019431296920174937,0.01374,1e-05,0.01374
S0,T3,10.623396701112124,0.01332,10.62338,0.01332
S0,T4,59.887319900989056,42.34673,0.00124,42.34673
S0,T5,11.733160146260683,0.00131,11.73316,0.00131
...To write to a file instead of to the screen, use standard Linux file redirection with the ‘>’ or ‘>>’ characters (to overwrite or append to an existing file respectively):
$ pysoc ch2o.log -c > SOC.csvPySOC generates a number of intermediate files during operation. By default, these are deleted at the end of the calculation and only the final SOC values are displayed.
To override this behaviour and keep these intermediate files, use the -o (output) option with a path to a directory where the intermediate files should be stored.
One may use -o ./ to write the intermediate files to the current directory. The -o option has no effect on the final SOC values:
$ pysoc ch2o.log -o ./
Singlet Triplet RSS (cm-1) +1 (cm-1) 0 (cm-1) -1 (cm-1)
--------- --------- ------------ ----------- ---------- -----------
S0 T1 60.7419 42.9510 0.0077 42.9510
S0 T2 0.0194 0.0137 0.0000 0.0137
S0 T3 10.6234 0.0133 10.6234 0.0133
S0 T4 59.8873 42.3467 0.0012 42.3467
S0 T5 11.7332 0.0013 11.7332 0.0013
...- code: pysoc.tar.gz; short tutorial: doc/pysoc.pdf
- Even more better tutorial written in Chinese by sobereva Lu Tian:http://bbs.keinsci.com/thread-9442-1-1.html
- For Gaussian 16 by ggdh:http://bbs.keinsci.com/thread-19813-1-1.html
Evaluation of Spin-Orbit Couplings with Linear-Response Time-Dependent Density Functional Methods
Xing Gao, Shuming Bai, Daniele Fazzi, Thomas Niehaus, Mario Barbatti, and Walter Thiel
J. Chem. Theory Comput., 2017, 13 (2), pp 515–524
DOI: 10.1021/acs.jctc.6b00915
PySOC was originally written by Xing Gao et al. for python 2.x (J. Chem. Theory Comput. 13 (2017) 515–524).
MolSOC, which is used for the calculation of atomic integrals, was originally written by Sandro Giuseppe Chiodo et al. (Computer Physics Communications 185 (2014) 676–683).
PySOC was re-written for Python 3.x by Oliver S. Lee.