Quantum Chemistry Modeling Packages

LModeA-nano can directly read the formatted checkpoint file generated by Gaussian and Q-Chem. Other quantum chemistry modeling packages (e.g. ORCA, xtb) requires the formatted data file generated by UniMoVib.

Note

LModeA-nano can do basic local mode analysis for bond length and bond angles. More advanced analysis including decomposition of normal modes, adiabatic connection scheme and other internal coordinates are supported only by LModeA code.

Gaussian

Tested with Gaussian 16.

Perform an OPT+Freq calculation to do geometry optimization and then vibrational analysis.

%chk=ben.chk
%nproc=36
#p hf/6-31g opt freq  geom=connectivity

Title Card Required

0 1
 C                 -0.54491017    1.16167665    0.00000000
 C                  0.85024983    1.16167665    0.00000000
 C                  1.54778783    2.36942765    0.00000000
 C                  0.85013383    3.57793665   -0.00119900
 C                 -0.54469117    3.57785865   -0.00167800
 C                 -1.24229217    2.36965265   -0.00068200
 H                 -1.09466917    0.20935965    0.00045000
 H                  1.39975783    0.20916365    0.00131500
 H                  2.64746783    2.36950765    0.00063400
 H                  1.40033383    4.53007965   -0.00125800
 H                 -1.09481317    4.53013965   -0.00263100
 H                 -2.34189617    2.36983565   -0.00086200

 1 2 1.5 6 1.5 7 1.0
 2 3 1.5 8 1.0
 3 4 1.5 9 1.0
 4 5 1.5 10 1.0
 5 6 1.5 11 1.0
 6 12 1.0
 7
 8
 9
 10
 11
 12

Please check the vibrational frequencies to make sure that the molecular structure is at a local minimum point.

The %chk is a must to first produce checkpoint file. Convert it to formatted one with

$ formchk ben.chk

The corresponding .fchk file is then generated. Then follow the instructions in quickstart example to do local mode analysis with LModeA-nano.

Q-Chem

Tested with Q-Chem 5.1.0

Given an optimized molecular structure, perform vibrational analysis

$comment
  water freq 
$end

$molecule
0 1
 O     -0.000001   -0.000001   -0.408455
 H      0.758758   -0.000004    0.204225
 H     -0.758756    0.000004    0.204230
$end



$rem
MEM_TOTAL  100000
BASIS cc-pVDZ
METHOD b3lyp
xc_grid 75000302
UNRESTRICTED FALSE
JOBTYPE   freq
THRESH 14
SCF_CONVERGENCE 10
GUI 2
$end

GUI 2 asks Q-Chem to produce the formatted checkpoint file .fchk. Always check the vibrational frequencies before doing local mode analysis. Then follow the instructions in quickstart example to do local mode analysis with LModeA-nano.

Other Packages

To perform local mode analysis based on the calculation results by other quantum chemistry packages, the UniMoVib package should be installed first.

The workflow is

  • Perform vibrational analysis on an optimized molecular structure with a quantum chemistry package (e.g. ORCA, xtb)

  • Run UniMoVib to generate a formatted data file .umv by parsing the output file in the last step

  • Load the .umv file to LModeA-nano for local mode analysis

A complete list of supported quantum chemistry packages by UniMoVib can be found at https://github.com/zorkzou/UniMoVib.

In this tutorial, ORCA 4 is used as an example.

The vibrational analysis of an optimized molecular structure with ORCA 4 produces an .hess file. Compose an input file job.inp for UniMoVib

a test job

 $contrl
   qcprog="orca"
   ifsave=.true.
 $end

 $qcdata
   fchk="h2o.hess"
 $end

ifsave=.true. saves a formatted data file .umv. Running UniMoVib with above input, it produces job.umv.

Compose an input file unimovib.inp for LModeA-nano

@unimovib

UMV = job.umv

Follow these steps to perform local mode analysis with LModeA-nano

  • open a new PyMOL window and launch LModeA-nano by clicking Plugin → LModeA-nano

  • click the … (Browse) button and select the unimovib.inp file

  • change the program drop-down list from VASP to UniMoVib

  • click Load

  • change Dimensions to 0 and click Confirm button

Then local mode analysis can be performed as described in quickstart examples.