Crystal Shape Control project

The repository for Imperial-BASF research project on multi-scale modelling of molecular crystals.

Topics:

• Ab initio and quasi-harmonic method for thermodynamics of molecular crystals
• Dispersion and BSSE corrected DFT energy for molecular crystals
• Interfacial therodynamics and crystal growth

Software:

Current focus:

• CRYSTAL: A Gaussian orbital periodic DFT code.
• Quantum Espresso: A planar wave periodic DFT code.
• GULP : A classical force field for LD (analytical) and MD (numerical).

Supported:

• ONETEP: A linear-scaling periodic DFT code based on generalized orthogonal Wannier function orbitals.
• LAMMPS: A classical force field MD solver for large systems.
• GROMACS: A composite MD simulation package.

Table of contents

1. QHA-model, Python 3 scripts for quasi-harmonic fittings based on exact phonon frequencies. N.B. Its precursor is thermodynamics script implemented in CRYSTALpytools package, and it is now used for testing ideas. Spica. Vir.
2. ONETEP_conv_test, ONETEP convergence testing scripts in bash. See README for details. Spica. Vir.
3. Dimer-disp.ipynb, a python3 script displacing a molecule in dimer along any vector. Geometry read from CRYSTAL output. CRYSTALpytools package required. Spica. Vir.
4. Surface-Cut, a 'semi-atomic' scheme based on python3 script stacking 2D periodic molecular layers to generate twisted slab surfaces for molecular crystals. Spica. Vir.
5. qe2cif.py, Convert Quantum-Espresso pw.x output file into cif geometry, or convert a cif file into formatted QE input keyword / card. Spica. Vir.
6. get_qe_optgeom.py, Similar to 'qe2cif.py'. Used for substracting geometries from pw.x optimisations only. Formatted QE input keyword / card are printed onto the screen. Spica. Vir.
7. xsd2qe.py, Convert Materials Studio xml formatted geometry file (xsd) into QE input keyword / card. Constraints on atomic coordinates are available. Spica. Vir.
8. xsf-kit, Read XCrySDen real space 3D grid data in xsf format and perform planar-averaged 1D profile analysis along 3 lattice vectors / get 3D differential data / get planar-averaged 1D differential profile. Also as a practice of free format Fortran. See the comment lins of 'main.f' for instructions. Spica. Vir.

Student

H. Zhou 21 PhD, Dept. Chem., GitHub: Spica-Vir

Post Studnets

A. Arber 21 IMSE MRes
K. Tallat-Kelpsa 21 IMSE MRes