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LASSI Analysis

Python files to parse and analyze trajectories from the LASSI simulation engine

Contents:

parseToFile.py parses .lammpstrj trajectory file and outputs a dictionary

json schema:

dictionary output from parseToFile.py has 4 keys "id_to_atom-type", "dimensions", "natoms", and "structured-data"

output from function = outdict

outdict["id_to_atom-type"] itself is a dictionary with keys corresponding to the unique id assigned to each atom, and the value of each key corresponds to the type of atom that particular key is assigned


outdict["structured-data"] is itself too a dictionary, however containing much nested information. The keys of the dictionary outdict["structured-data"] are the individual timesteps, for example the first three keys are the integers 0, 25000000, and 50000000.
Keying into and of these individual timesteps returns another dictionary whose keys are unique molecular identifiers which range from 0-N, where N is the number of chains. Each unique molecule dictionary will itself have a dictionary whose keys correspond to the individual atoms in that particular molecule and each molecular will contain n atoms. Each unique can then be accessed to obtain its x, y, and z coordinate by using the string 'x', string 'y' and string 'z' for that unique id to obtain the desired coordinates

Structure of "structured-data" key:

outdict["structured-data"] =
            {
            TIMESTEP(integer value): {
                  MOLECULE_ID(integer value): {
                    ATOM_ID: {
                      "x":(integer value)
                      "y":(integer value)
                      "z":(integer value)
                    }
                  }
                }
             }

outdict["id_to_atom-type"] maps the id of the atom to the type.
e.g., atom id 0 is 2 would mean that id 0 is a particular site corresponding to bead 2 (e.g., a sticker).

Structure of "id_to_atom-type" key:

outdict["id_to_atom-type"] =
            {
            ATOM_ID(integer value): ATOM_TYPE (integer value)
            }

outdict["natoms"] returns the number of atoms in the simulation box. The number is conserved during the simulation.

Structure of "natoms" key:

outdict["natoms"] = NUMBER OF ATOMS (integer value)

outdict["dimensions"] returns the xmin and xmax of the simulation box as a python list, where the first element corresponds to xmin and the second corresponds to xmax.
NOTE: The box is cubic and the size stays the same during the simulation.

Structure of "dimensions" key:

outdict["dimensions"] = LIST(XMIN, XMAX)

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