Computational notes

Some pages are still on the old "secure" part of the website. These are clearly marked.

Where do I start?

Your molecule

• Naming your molecule, and numbering the atoms Nomenclature & Numbering rules (for molecules)
• Optimising the molecule Gaussian manual
• Selecting conformations - VConf

Existing crystal structure determinations

• Workflow for a lattice energy minimisation (ExpMinExp or ExpMinOpt)
• Info on optimal paste

Minimising a structure

• DMACRYS manual (Former code: DMAREL manual)
• NEIGHCRYS manual (Former code: Neighbours manual)
• Known problems with DMACRYS and NEIGHCRYS
• CrystalOptimizer
• CASTEP (Periodic Electronic Structure calculations)
• DFTB3-D3 minimization
• AutoLD manual (python file is /home/cposs/bin/LatticeDynamics/autold100.py on xenon)
• AutoFree manual (python file is /home/cposs/bin/LatticeDynamics/autofree100.py on xenon)

Generating structures with MOLPAK

• MOLPAK instructions on Xenon
• Input and output files for MOLPAK on Xenon
• Instruction line formats for MOLPAK H. Ammon Aug 2002
• Tables of packing types for MOLPAK and spacegroups H. Ammon Aug 2002

More on crystal structures (relating to MOLPAK searching)

• Space groups and symmetry reduction
• Find LATT and SYMM lines by space group
• Editing crystal structures (including instructions for ISOCIF)

CrystalPredictor searches

• Version 2.4.3

  • CrystalPredictor v2.4.3 Manual
  • Louise's notes
  • Additional notes on torsion group version

• Version 2.2 (obselete)

  • Manual
  • Louise's notes

• Version 1.6 (some useful comments)

  • Creating the grid, running the search and post-processing
  • Troubleshooting, and some comments on output

Python

• Using Python

Conformer Generator searches

• Conformer Generator description and searches

What to do with a search output

• File naming convention (Louise needs to update this page)
• Calculating conformation energy differences
• Notes of morphology and powder pattern calculations
• Notes on definition of elastic tensor axes (this is really old, and is covered in the NEIGHCRYS/DMACRYS manuals)
• RUDOLPh and Symmetry analysis of k=0 phonos (written in 2005, for NEIGHBOURS/DMAREL output)
• Comparing powder patterns (from .res or .pp)
• Clustering

The Database and file storage

• Database info
• Upload to database (form to send to Louise)
• Crystal Structure Navigator (get password from Louise if you do not already have one)

Magnetic Susceptibility Calculations

• Calculating Magnetic Susceptibilities - Tensor Addition Method

Packing Coefficient calculations

• Calculating packing coefficients

Disordered systems

• SOD-ORG calculations

Enter secure pages (For project members only - password required)

© UCL Chemistry Department 2022. This page was last updated on 17 August, 2022. If you have any problems with this page please email the WebMaster