VecMap is a convenient and lightweight tool to calculate the atomic displacements in some polarized materials such as perovskite. The tool was written by Dr. Tao Ma. For questions and suggestions, please send a message to matao1984@gmail.com.

The tool requires Python 3 environment. I recommend to install Anaconda which is the most straightforward way. Download and install the Python 3 version of Anaconda from here: https://www.anaconda.com/.

After the Anaconda is installed, open the Anaconda prompt console. Run the following commands:

conda create -n vecmap python=3.8

conda activate vecmap

Navigate to a desired loaction on your hard disk (e.g., C:/Users/xxx/Documents) and download the installation files from the github. Replace the "xxx" with your actual user name.

cd c:/Users/xxx/Documents
git clone "https://github.com/matao1984/vec-map" vecmap

In case you don't have git installed, run the following script:

conda install git -c anaconda

If git raises an error about an existing "vecmap" folder, delete it and retry. Then navigate to the folder that was just downloaded, and run the setup script:

cd c:/Users/xxx/Documents/vecmap
pip install -e ./

If other errors happen in the installation, most likely they are related to hyperSpy or atomap packages which are the main dependencies. It is worth trying in the Anaconda console to install them first: pip install hyperspy atomap.

To run the app from anaconda cmd window:

conda activate vecmap
vecmap

A GUI will pop up.

In the Windows system, you can create a bat file with the following content:

@echo off
CALL  C:\ProgramData\Anaconda3\Scripts\activate.bat C:\ProgramData\Anaconda3\envs\vecmap
vecmap
echo on 

Replace the path and environment name if they are different in your system. Save this bat, e.g., "VecMap App.bat", on your desktop and double-click it to run the app. Note that you can name this bat file in any strings EXCEPT FOR "vecmap.bat", otherwise it will go into an infinite loop when you run it!

VecMap was described in this paper:

Tao Ma, VecMap: A Python-based Graphic User Interface Tool for Atomic Displacement Mapping in Perovskite Structures, Microscopy and Microanalysis, Volume 29, Issue 2, April 2023, Pages 520–528, https://doi.org/10.1093/micmic/ozac038

The measured was originally designed and used in the following papers:

Tao Ma, Zhongming Fan, Bin Xu, Tae-Hoon Kim, Ping Lu, Laurent Bellaiche, Matthew J. Kramer, Xiaoli Tan, and Lin Zhou; Uncompensated Polarization in Incommensurate Modulations of Perovskite Antiferroelectrics. Phys. Rev. Lett. 2019, 123, 217602. https://doi.org/10.1103/PhysRevLett.123.217602

Tao Ma, Zhongming Fan, Xiaoli Tan, Lin Zhou; Atomically resolved domain boundary structure in lead zirconate-based antiferroelectrics. Appl. Phys. Lett. 2019, 16, 115 (12): 122902. https://doi.org/10.1063/1.5115039

• Improved scale bar font size rendering and small bug fixes.
• Added control for oxygen vector color.

• Improved scale bar rendering. Now it uses matplotlib built-in functions. Matplotlib-scalebar no longer needed.
• Correct the wrong unit for displacement data in output csv.

• Improved plotting function

• [001] and [011] radio selection
• ABF couple with HAADF function to calculate O map
• Algorithm to calculate O map on [011] direction
• Bug fixes

• Minor bug fix

• The first versio of VecMap