XtraCrysPy 0.7.8

A Python tool for visualizing atomic systems and properties of condensed matter.

XtraCrysPy

A Python tool for visualizing atomic systems and spatial properties of condensed matter.

Features:

• Plot molecular systems with minimal setup
• Plot systems from DFT or MD input/output files
• Interact with the system to caluclate distances, angles, or receive atomic information
• Display relaxation or MD steps from QE relax output or LAMMPS trajectory files. (CP2K xyz coming soon)
• Display reciprocal space features
• Plot real space iso-surfaces (charge density, etc)
• Plot reciprocal iso-surfaces (Fermi surface, spin-texture, etc)

Supported File Types:

• Quantum ESPRESSO input or output
• POSCAR
• CIF
• XSF
• CP2K
• BXSF (coming soon)
• Any ASE supported format

Requirements:

• python 3.8
• numpy 1.19
• fury 0.8 (Use the latest GitHub commit. The latest release contains a bug with cylinder orientation used for drawing bonds.)
• ase

Installation:

INSTALLATION NOTE: Use FURY master branch from GitHub. The latest release contains a bug causing misaligned cylinder orientation. (only use --user if you do not have permission to install python packages)

• python setup.py install
• python setup.py install --user

Control Inputs:

• 'u' : Toggle UI visibility
• 'a' : Toggle Axis visibility
• 'b' : Toggle Boundary visiblity
• '>' : Step forward in relax or MD
• '<' : Step backward in relax or MD
• CTRL + ('>' or '<') : Step 5% through the relaxation or MD steps
• SHIFT + 'c' : Reset camera to default position
• SHIFT + 's' : Take snapshot
• CTRL + 'w' : Exit
• Arrow Keys : Rotate model
• SHIFT + Arrow Keys : Translate camera
• CTRL + Arrow Keys (+ SHIFT) : Rotate (or Translate) in smaller steps

Display an atomic model from inputfile, with the examples/main.py script:

• python main.py <input_file>
• python main.py <input_file> <bond_distance>

Examples:

Available in the examples directory

From scratch:

• python caffeine.py
• python silicon_fcc.py

From inputfile (with main.py script):

• python main.py <input_file>
• python main.py <input_file> <bond_distance>

From inputfile (programmatic):

• python SnTe_2D.py
• python example_cif.py
• python example_cp2k.py
• python example_qe_in.py
• python example_poscar.py

Relax QE outputfile:

• python example_relax.py

LAMMPS MD trajectory:

• python example_lammps_md.py

Charge Density:

• python example_charge_density.py

Reciprocal Space:

• python example_BZ.py

Fermi Surfaces:

• python example_isosurface1.py
• python example_isosurface2.py
• python example_isosurface_clip.py
• python example_colored_isosurface.py
• python example_textured_isosurface_clip.py