LammpsFileManipulation 1.0.2

This is a package designed to help streamline the process of preprocessing LAMMPS output files for scientific calculations/manipulations in Python. The class structures are built using pandas DataFrames making it easy to manipulate.

LAMMPS File Manipulation Package

This is a package designed to help streamline the process of preprocessing LAMMPS output files for scientific calculations/manipulations in Python. The class structures are built using pandas DataFrames making it easy to manipulate. Currently this only supports dump files in a text format. Soon to be added are data file capabilities and other file formats. A current assumption is that the operations are done in Cartesian Space and all shapes are square.

Disclaimer

I am in no way associated with sandia labs or the LAMMPS software team this is just something I believe is usefel for the scientific community however niche

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Installing and Importing

Install: pip install LammpsFileManipulation Import: import LammpsFileManipulation as LFM

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Dump Class Features

dumpFile class

This is a class optimized for operations on dump files exported from lammps programs

obj = LFM.dumpFile(timestep:int,numberofatoms:int,boxbounds:pd.DataFrame,atoms:pd.DataFrame,serial=None)

Alternative class construction methods(file_path = path to file): dumpFile.lammps_dump(cls, file_path) #reads in a standard lammps dump dumpFile.pandas_to_dumpfile(cls, file_path) #reads in lammps data from pandas dataframe to new valid property calls: obj.timestep = returns timestep in the file[int] obj.numberofatoms = numbers of atoms in the dump[int] obj.atoms = atomic data[pd.DataFrame] obj.boxbounds = returns the bounds with type,low,high in a pandas datframe[pd.DataFrame] obj.volume = returns cubic shaped volume obj.xy_area = returns square shaped area of xy plane obj.xz_area = returns square shaped area of xz plane obj.yz_area = returns square shaped area of yz plane obj.xlo = low x value in obj.atoms obj.ylo = low y value in obj.atoms obj.zlo = low z value in obj.atoms obj.xhi = high x value in obj.atoms obj.yhi = high y value in obj.atoms obj.zhi = high z value in obj.atoms

Mathmatical Operations Equals obj1 == obj2 returns if the atomic positional distances are identical uses the class variable checking_tolerance for amount of precission in check Addition merged_obj = obj1+obj2 alternative way to merge data of the obj.atoms this will check that the atomic positions are equal and then will add the unique columns of obj2 to the obj1 this means that the obj1 columns are the same and no overwriting occurs

method calls

Translating the atoms positions new_obj = obj.translate(translation_operation,) method to translate atom locations of the instance this will return a new instance of the class in order to preserve data integrety for the class instance translated = class_instance.translate(translation_operation)

The predefined quadrent operations will make sure one boundry is a 0 0 0

Standards Cartesian: quadrent = x y z 0 = centered at 0 0 0 1 = + + + 2 = + + - 3 = + - + 4 = + - - 5 = - + + 6 = - + - 7 = - - + 8 = - - -

Custom Transform: The value is added to the atoms location from the list in order [x_shift, y_shift, z_shift]

Writing a new dump file write_dump_file(self,file_path:str,mode:str = "a") This takes in a file path and writes a dumpFile class to the file path in standard lammps format

write_lammps_dump(file_path:str,dump_class:dumpFile,mode:str = "a")

file_path = path to file [str] mode = overwrite("w") or append("a") **default append [str]

ITEM: TIMESTEP
10000
ITEM: NUMBER OF ATOMS
275184
ITEM: BOX BOUNDS pp pp pp
4.9560543895066389e-01 1.1978325804094933e+02
-1.5869515341562740e+02 1.5869515341562740e+02
4.9786870883599993e-01 1.1978099477096400e+02
ITEM: ATOMS id type x y z c_eng c_csym ...
1 2 2.59722 -158.646 2.91064 -3.27376 10.8937
.
.
.

Writing a new dump file to data file format obj.write_dump_to_data_format(self, file_path:str,mode:str = "a")

writes dumpFile class to a data file format

mode = overwrite("w") or append("a") **default append [str]

**this will only save the positions in data fromatting **primary use to write a initiallization data file for a lammps

# LAMMPS data file written by LammpsFileManipulation.py
275184 atoms
2 atom types
0.4892064609 119.789657019 xlo xhi
-158.7268972078 158.7268972078 ylo yhi
0.4917072972 119.7871561826 zlo zhi

Atoms  # atomic

1 2 2.59911 -158.671 2.89486
.
.
.

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Group dump file operations

Format

dump_files = { id1:dump_class1,id2:dump_class2, ... } The format consists of a dictionary with the id as a key and the dump_class as the element

Importing

Same file with multiple dumps multiple_timestep_singular_file_dumps(file_path:str,ids:list = ["TimestepDefault"])

this opens a multi-timestep lammps dump and converts it to a dictionary of dumpFile classes with the keys set to the timesteps

ids:list = ["TimestepDefault"] ids are set to the dumpclass timestep by default however if there are duplicates this will override the timesteps so you can define the ids for the dictionary

Different files but as a group batch_import_files(file_paths:list,ids:list = ["TimestepDefault"])

this opens several lammps dumps and converts it to a dictionary of dumpFile classes with the keys set to the timesteps

ids:list = ["TimestepDefault"] ids are set to the dumpclass timestep by default however if there are duplicates this will override the timesteps so you can define the ids for the dictionary

Group translation group_translate(dump_files, translation_operation)

This takes in a group of dumps in the dictionary format of class and ####translates them as a group the same amount###

because of the nature of this operation the values must be found first therefore when not using a custom transform the function loops through adding a small amount of time to this practice

proper call: translated = group_translate(dump_files,quadrent)

dump_files = {id:class,...}

The predefined quadrent operations will make sure one boundry is a 0 0 0

quadrent = x y z 0 = centered at 0 0 0 1 = + + + 2 = + + - 3 = + - + 4 = + - - 5 = - + + 6 = - + - 7 = - - + 8 = - - -

Custom Transform: The value is added to the atoms direction from the list in order [x_shift, y_shift, z_shift]

Author List (name, email): Aaron Schwan, [e-mail]