Bin1d class
The postmd.avechunk.Bin1d() class is to process the file generated from fix ave/chunk bin1d command in LAMMPS.
Examples
>>> from postmd.avechunk import Bin1d
>>> filepath = r"tests/data/ave_chunk_bin1d.dat"
>>> bin1d = Bin1d(filepath,dim="z")
You are processing the file: 'D:\Onedrive\Github\MyRepos\PostMD\tests\data\ave_chunk_bin1d.dat'
'D:\Onedrive\Github\MyRepos\PostMD\tests\data\ave_chunk_bin1d.dat' is generated by command 'fix ave/chunk'
The first line is: Chunk-averaged data for fix slab_y_free_ion and group vx
>>> bin1d.read_file()
>>> # We stored the blocks in a list
>>> print(f"The type of bin1d.blocks is {type(bin1d._blocks)}")
The type of bin1d.blocks is <class 'list'>
>>>
>>> # you can use len(bin1d) to get the number of blocks
>>> print(f"{bin1d.path} have {len(bin1d)} blocks")
D:\Onedrive\Github\MyRepos\PostMD\tests\data\ave_chunk_bin1d.dat have 10 blocks
>>>
>>> # you can use bin1d[index] to access index-th block
>>> # in each block, we store the information with dict.
>>> print("The first block is:\n", bin1d[0])
The first block is:
{'step': 1000000, 'nchunk': 800, 'total_count': 1.0, 'data': Chunk Coord1 Ncount density/number vx vy vz
0 1 -39.95 0.0 0.0 0.0 0.0 0.0
1 2 -39.85 0.0 0.0 0.0 0.0 0.0
2 3 -39.75 0.0 0.0 0.0 0.0 0.0
3 4 -39.65 0.0 0.0 0.0 0.0 0.0
4 5 -39.55 0.0 0.0 0.0 0.0 0.0
.. ... ... ... ... ... ... ...
795 796 39.55 0.0 0.0 0.0 0.0 0.0
796 797 39.65 0.0 0.0 0.0 0.0 0.0
797 798 39.75 0.0 0.0 0.0 0.0 0.0
798 799 39.85 0.0 0.0 0.0 0.0 0.0
799 800 39.95 0.0 0.0 0.0 0.0 0.0
[800 rows x 7 columns]}
>>> # you can use key to access the data in each block
>>> print("The data in the first block is:\n", bin1d[0]["data"])
The data in the first block is:
Chunk Coord1 Ncount density/number vx vy vz
0 1 -39.95 0.0 0.0 0.0 0.0 0.0
1 2 -39.85 0.0 0.0 0.0 0.0 0.0
2 3 -39.75 0.0 0.0 0.0 0.0 0.0
3 4 -39.65 0.0 0.0 0.0 0.0 0.0
4 5 -39.55 0.0 0.0 0.0 0.0 0.0
.. ... ... ... ... ... ... ...
795 796 39.55 0.0 0.0 0.0 0.0 0.0
796 797 39.65 0.0 0.0 0.0 0.0 0.0
797 798 39.75 0.0 0.0 0.0 0.0 0.0
798 799 39.85 0.0 0.0 0.0 0.0 0.0
799 800 39.95 0.0 0.0 0.0 0.0 0.0
[800 rows x 7 columns]