Principal Interacting Orbital
This manual works for the following combinations.
- Python 2.7
- Numpy 1.14.1
- Gaussian 09 & 16
- NBO 6.0 and above are recommended but NBO 3.0 is also compatible (see below for detailed discussions).
For Python 3 users, please see https://github.com/jxzhangcc/PIO-py3.
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Run quantum chemistry calculation
Optmize the structure and calculate the electronic structure using standard quantum chemistry softwares. Gaussian09 is used for following demonstration.
Input
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FILENAME.gjf
# ... pop=nboread ... $nbo archive file=FILENAME $end"
Output
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FILENAME.log
ordinary Gaussian output file
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FILENAME.FChk
FormCheck file is required for the current version of PIO analysis, for the purpose of visualizing orbital using GaussView. It can be generated via keyword formcheck specified in gjf file, or via running external formchk utility
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FILENAME.47
A FILENAME.47 file can be generated in Gaussian calculations via keyword pop=nboread and nbo keyword $NBO archive $end specified in gjf file. As the built-in NBO package in Gaussian 09 is NBO3.0, which is a quite old version of NBO package, an external NBO analysis with more recent version is suggested.
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Run NBO analysis
Run NBO analysis on the system of interest to obtain the NAO basis and corresponding density matrix.
For people who have bought individual NBO programs (such as NBO 6.0 or 7.0), modify the 47 file generated in the last step as following and run the NBO program.
Input
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FILENAME.47
NBO input file, can be generated via running an internal NBO analysis in Gaussian
The following NBO keywords should be specified in the 47 file for NBO analysis:
$NBO AONAO=W49 FNAO=W49 DMNAO=W49 SKIPBO $END
Running the NBO analysis
Run the NBO analysis using the following command (replace FILENAME with your own file name, and note .47 should not be included):
gennbo FILENAMEOutput
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FILENAME.nbo
ordinary NBO output file
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FILENAME.49
extra output required for PIO analysis, containing NAO coefficients, density matrix in NAO basis, and Fock matrix in NAO basis if available; only appear if the above mentioned NBO keywords have been specified properly
For people who do not have an external NBO progam, the NBO 3.0 built in Gaussian is still compatible to complete PIO analysis. Just modify the Gaussian input file as following:
Input
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FILENAME.gjf
# ... pop=nboread ... $nbo archive file=FILENAME AONAO=W49 FNAO=W49 DMNAO=W49 SKIPBO $end
The NBO 3.0 built in Gaussian will read in the keywords and do the same as external NBO programs.
Output
- FILENAME.log
- FILENAME.49
However, the results with NBO 3.0 should be dealed with cautious because it is known that NBO 3.0 may produce weird results such as counter-intuitive negative charge for transition metals in coordination complexes.
No matter you use NBO 3.0 or 6.0, if you want to apply PIO analysis on spin-polarized systems (no matter restricted open-shell or unrestricted calculations), change the NBO keywords from "AONAO=W49 FNAO=W49 DMNAO=W49" to "AONAO=W33 FNAO=W61 DMNAO=W71" and run the following command to produce the required FILENAME.49 file in correct format.
cat FILENAME.33 FILENAME.61 FILENAME.71 > FILENAME.49A bash script "genpionbos" is attached with the code that can perform all these steps for you by automatically modifying the keywords in .47 file and then generating the .49 file by calling the external NBO program. Make sure relevant paths are correctly set if you use this script. This script works for both open-shell and closed-shell species.
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Run PIO analysis
We now run PIO analysis with the following command. Note that FILENAME.49 must exist with the same name as FILENAME.FChk.
python PIO.py FILENAME.FChkThe program will then request for a fragmentation as input to specify two groups of atoms
Input
1-5,8,13 6-7,9-12Two groups of atom IDs should be input here separated by a space. Numbers in each group are separated by a comma. Hyphen is supported for sequential numbers. Atom numbering starts from 1. Complete fragmentation is always recommended (i.e. the specified two groups cover all the atoms present in the system). Incomplete fragmentation will lead to absence of mathematical elegance but is still meaningful if you really want to do it.
Output
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FILENAME_pio.txt
PIO log file, containing basic information of the PIOs of the system subject to the input fragmentation
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FILENAME_pio.FChk
Gaussian FormCheck file containing PIOs labeled as in the txt file, could be visualized by GaussView and other compatable orbital visualization softwares
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FILENAME_pimo.FChk
A similar Gaussian FormCheck file containing PIMOs whose ordering is same as that of PIOs
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FILENAME_pio.raw (discarded in latest PIO version)
numpy-formatted raw data file for debugging or advanced user
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Principal Interacting Spin Orbital (PISO) analysis now available for spin-polarized systems. The usage is the same as above.
Original method of PIO: doi.org/10.1002/chem.201801220
Extension to spin-polarized systems: doi.org/10.1039/D0CP00127A
A recent review on PIO: doi.org/10.1002/wcms.1469
Copyright (c) 2018 jxzhangcc and fksheong
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