Quickstart Examples

The following two examples may familiarize you with the use of LModeA-nano.

Ethane calculated by Gaussian 16

In the LModeA-nano-main/quickstart/ethane directory, a formatted checkpoint file ethane-pbe.fchk was generated by the vibrational analysis (freq) calculation in Gaussian 16 package.

For this type of input data file, it can be directly loaded to LModeA-nano.

Following these steps

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

  • click the … (Browse) button and select the ethane-pbe.fchk file

  • change the program drop-down list from VASP to Gaussian/Q-Chem

  • click Load

  • change Dimensions to 0 and click Confirm button

We will see the following

_images/quick-ethane-1.png

By selecting the CC bond for local mode analysis, the result is

_images/quick-ethane-2.png

2D Graphene calculated by CRYSTAL17

In the LModeA-nano-main/quickstart/graphene directory, two files were generated by the vibrational frequency calculation with CRYSTAL17 program

  • crystal_21991013.out - CRYSTAL output file of vibrational analysis

  • HESSFREQ.DAT - Hessian file generated after vibrational analysis calculation

In the same directory, we compose an input file crystal.inp for LModeA-nano

@crystal

OUTPUT = crystal_21991013.out
HESSFREQ = HESSFREQ.DAT

Following these steps

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

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

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

  • click Load

  • change Dimensions to 2 and click Confirm button

  • change the supercell size percentage from 110% to 140% and click Partial Supercell button

We will see the structure like the following

_images/quick-graphene-1.png

The PyMOL window shows the graphene primitive cell having two carbon atoms (with larger radii) and other carbon atoms belong to neighboring unit cells.

To do local vibrational mode analysis of CC bonds in this structure, click the Bond button in the LModeA-nano window. The interactive wizard may ask for the selection of the first atom of a bond

_images/quick-graphene-2.png

Click the left carbon atom in the primitive cell, the wizard prompts the selection of the second atom of a bond

_images/quick-graphene-3.png

Click the right carbon atom in the primitive cell, the wizard prompts clicking Done button in the wizard menu on the right-hand-side.

_images/quick-graphene-4.png

Afterwards, the local mode analysis result for this CC bond is shown in the table region of the LModeA-nano GUI window.

_images/quick-graphene-5.png

Users are encouraged to try to select a different CC bond in this example for local mode analysis, the result is expected to be the same as for C1-C2 due to symmetry in graphene structure.