golobor

import h5py
import argparse

def copy_dataset(source_file, destination_file, source_dataset, destination_dataset, overwrite):
    with h5py.File(source_file, 'r') as source:
        with h5py.File(destination_file, 'a') as destination:
            if source_dataset not in source:
                print(f"Dataset '{source_dataset}' does not exist in the source file.")
                return
            

golobor

from contextlib import contextmanager
import functools

import numpy as np

import gsd
import gsd.hoomd

import hoomd
import hoomd.md

golobor

golobor

class dotdict(dict):
    '''A dict with dot access and autocompletion.
    
    The idea and most of the code was taken from 
    http://stackoverflow.com/a/23689767,
    http://code.activestate.com/recipes/52308-the-simple-but-handy-collector-of-a-bunch-of-named/
    http://stackoverflow.com/questions/2390827/how-to-properly-subclass-dict-and-override-get-set
    '''
    
    def __init__(self,*a,**kw):

golobor

golobor

golobor

golobor

# from https://stackoverflow.com/questions/22712292/how-to-use-numpy-savez-in-a-loop-for-save-more-than-one-array/22716159#22716159

import numpy as np
import tempfile

class my_savez(object):
    def __init__(self, file, compression=None, compresslevel=None):
        # Import is postponed to here since zipfile depends on gzip, an optional
        # component of the so-called standard library.
        import zipfile

golobor

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