Input File

• NOTE: You need to successfully compile the code to continue, if you haven't done so, go here.

Basics

• Look at the flowchart below for general ideas about the input files

  classDiagram
    class Restart{
      * text file
      * configuration of system
    }
  
    class Movies{
      * LAMMPS data file
    }
  
    class OUTPUT{
      * FILES and INFO GENERATED
    }
    class RUN{
      * the actual process of the simulation
    }
  
    class Adsorbate_definition{
      * Critical_Properties
      * Molecule_Size
      * Atom_Positions
      * Conectivity
    }
  
    class CIF{
      * P1 symmetry
      * System size
      * positions
      * partial_charge (optional)
    }
  
    class simulation_input{
      * Does your system have charge?
      * Run Steps or Cycles?
      * Run for how long?
      * Simulation Type?
    }
  
    class FORCEFIELD{
      * dictates general and special interactions
    }
  
    class SPACE{
      * spatial information of the system
    }
  
    FORCEFIELD <|-- force_field_def
    FORCEFIELD <|-- force_field_mixing_rules_def
    FORCEFIELD <|-- pseudo_atoms_def
    simulation_input <|-- FORCEFIELD
    SPACE <|-- CIF
    SPACE <|-- Adsorbate_definition
    simulation_input <|-- SPACE
    RUN <|-- simulation_input
  
    OUTPUT <|-- RUN
  
    Movies <|-- OUTPUT
    Restart <|-- OUTPUT
  
    class force_field_def{
      * tail correction  (optional)
    }
    class force_field_mixing_rules_def{
      * Lennard-Jones
    }
    class pseudo_atoms_def{
      * Mass
      * Charge
      * Element
      * Polarization
    }

• There are FIVE files needed to run the simplist simulation
  1. simulation.input
  2. force_field_mixing_rules.def
  3. pseudo_atoms.def
  4. Crystallographic Information File (CIF)
  5. Adsorbate definition file, for example: methane.def
• There are also OPTIONAL files
  1. force_field.def
  2. Machine Learning models

simulation.input

• gRASPA takes a very similar format as RASPA-2.
• However, to ensure reproducibility and strictness, we have additional requirements.
  1. The code checks for a list of required keywords
     • If a keyword is missing, the code will terminate

force_field_mixing_rules.def

pseudo_atoms.def

CIF File