Tutorials

• RMC Execution Tutorial
  • 1. Overview
  • 2. Required Files
  • 3. rmc_init.py
  • 4. rmc_dat.init()
  • 5. Execution
  • 6. Log Directories
  • 7. Ctrl+C
  • 8. CONTINUE_NUMBERED_INIT
  • 9. Typical Parameters to Edit
• VASP Execution Tutorial
  • 1. Overview
  • 2. Required Files
  • 3. rmc_vasp_init.py
    • KPOINTS
    • POTCAR
    • INCAR
  • 4. VaspIncar.init()
  • 5. Execution
  • 6. Postprocessing
  • 7. Log Directories
  • 8. CONTINUE_NUMBERED_INIT
  • 9. General Editing Guidelines
• RMC-DFT Execution Tutorial
  • 1. Basic Operation
  • 2. Shared Sequence Numbers
  • 3. Normal Start
  • 4. Restart
  • 5. Standard Initialization Files
  • 6. Numbered Initialization Files
  • 7. Continuing a Numbered Initialization File
    • False
    • True
  • 8. Initialization Files Are Reloaded Dynamically
  • 9. RMC and VASP Initialization
  • 10. Transferring Structures from RMC to VASP
  • 11. Transferring Structures from VASP to RMC
  • 12. Choosing the Appropriate Initialization Files
• RMC-DFT Manual Sequence Execution Tutorial
  • 1. Purpose of a Sequence
  • 2. Files Used
  • 3. manual_sequence
  • 4. Matching Sequence Numbers
  • 5. Running RMC Multiple Times in Succession
  • 6. Inserting VASP at an Arbitrary Point
  • 7. Initialization Files Are Read Immediately Before Execution
  • 8. continue_rmc_dft
    • False: Execute Only the Sequence
    • True: Switch to Standard RMC-DFT After the Sequence
  • 9. CONTINUE_NUMBERED_INIT and Sequences
  • 10. Dynamic Changes During a Sequence
  • 11. Example: Gradual RMC Convergence Followed by DFT
  • 12. Example: Return to Standard RMC-DFT After a Sequence
  • 13. Choosing Between the Standard Script and a Manual Sequence
• pypackmol (in RMC_DFT)
  • Official Packmol website
  • Linux
  • macOS
  • Official Packmol module
  • Input file (packmol.inp)
  • rmc_dft.packmol.packmol.Packmol
  • rmc_dft.packmol.PackmolInp
• TOP/ITP and FNC in RMC_POT
• 1. RmcPotDatTop
  • 1.1 Supported TOP sections
  • 1.2 Reading and writing files
  • 1.3 Automatic saving
  • 1.4 Low-level line and section operations
  • 1.5 Includes and conditional directives
• 2. Molecular types and atoms in TOP
  • 2.1 [ moleculetype ]
  • 2.2 [ atoms ]
    • Example index mapping for SnI4
  • 2.3 Virtual atoms
• 3. Interactions in TOP
  • 3.1 [ pairs ]
  • 3.2 [ bonds ]
  • 3.3 [ angles ]
  • 3.4 Periodic dihedrals
  • 3.5 Harmonic dihedrals
  • 3.6 Ryckaert–Bellemans dihedral
  • 3.7 Explicit exclusions
• 4. Virtual sites
  • 4.1 Virtual sites defined by two atoms
  • 4.2 Virtual sites defined by three atoms
  • 4.3 Virtual sites defined by four atoms
• 5. [ system ] and [ molecules ]
• 6. High-level TOP generation methods
  • 6.1 add_molecule_template()
    • first_instance_indices and second_instance_indices
    • Entries that can be added together
  • 6.2 validate_rmc_index_progression()
  • 6.3 add_explicit_network_molecule()
• 7. TOP validation
• 8. RmcPotDatFnc
  • 8.1 Information stored in FNC
  • 8.2 Initialization
  • 8.3 File operations
• 9. FNC distance-constraint types
  • 9.1 Setting one type at a time
  • 9.2 Setting multiple types at once
• 10. Operations on FNC atom pairs
  • 10.1 Adding one reciprocal pair
  • 10.2 Adding multiple pairs at once
  • 10.3 Adding a one-way neighbour entry
  • 10.4 Replacing the neighbour list of one atom
  • 10.5 Removing a pair
  • 10.6 Removing all pairs for one atom
• 11. Expanding FNC templates
  • 11.1 Expanding one instance
  • 11.2 Expanding multiple instances
• 12. Complete-graph FNC constraints
• 13. FNC validation and retrieval
  • 13.1 validate()
  • 13.2 Retrieving the pair list
• 14. Basic procedure for creating an FNC file
• 15. Choosing between TOP and FNC
• 16. Implementation notes
  • TOP
  • FNC