Access to HDF5 file

h5BSE class

The data in HDF5 files should be accessed via class bse.h5bse.h5BSE.

class methods

__init__(filename, groupname=””, compression=”gzip”, compression_opts=None)

open(mode=’r’)

Keep the file open.

close()

Close the file if open method is called.

save(key, data)

Save data to the file. See the available key and data structure below.

get(key) return data(Dict)

Get data from the file.

get_keylist_data(input_output=’input’) return List[(key, path), …]

Get the list of keys in the file.

key argument

key argument is a tuple that contains three elements or less. The maximum case is as follows:

key=(type, w, q)

• type (string): 'beta', 'X_loc', 'chi_q', etc. See the table below.

• w (int): Index for the bosonic frequency.

• q (string): A string to distinguish different q-points.

If w and/or q are not necessary, one can omit them. See Structure of HDF5 file for the list of available type.

Example

This example shows how to access the data (gamma0 in this example) in the HDF5 file.

import numpy as np
from bse.h5bse import h5BSE


def _convert_to_matrix(block_matrix, n_block, n_inner):
    assert isinstance(block_matrix, dict)
    dim = n_inner * n_block
    mat = np.zeros((n_block, n_inner, n_block, n_inner), dtype=complex)
    for block, bmat in block_matrix.items():
        i, j = block
        mat[i, :, j, :] = bmat
    return mat.reshape((dim, dim))


def get_gamma0(h5_file):
    BS = h5BSE(h5_file)
    BS.open('r')

    # get info
    block_name = BS.get(key=('block_name'))
    inner_name = BS.get(key=('inner_name'))
    print(f"block_name: {block_name}")
    print(f"inner_name: {inner_name}")
    n_block = len(block_name)
    n_inner = len(inner_name)
    dim = n_inner * n_block

    # get gamma0
    gamma0_dict = BS.get(key=('gamma0',))

    BS.close()

    # convert dict to ndarray
    gamma0_mat = _convert_to_matrix(gamma0_dict, n_block, n_inner)
    assert gamma0_mat.shape == (dim, dim)

    return gamma0_mat


gamma0 = get_gamma0("dmft_bse.h5")
print(f"\ngamma0 loaded. shape={gamma0.shape}")

Data is obtained using the get method of the bse.h5bse.h5BSE class. The returned data is a dictionary type (block matrix), and should be converted to ndarray.

Standard output of the above script for a six-orbital system with j=5/2:

$ python3 get_gamma0.py
block_name: [b'0-ud-0-ud']
inner_name: [b'0-0', b'0-1', b'0-2', b'0-3', b'0-4', b'0-5', b'1-0', b'1-1', b'1-2', b'1-3', b'1-4', b'1-5', b'2-0', b'2-1', b'2-2', b'2-3', b'2-4', b'2-5', b'3-0', b'3-1', b'3-2', b'3-3', b'3-4', b'3-5', b'4-0', b'4-1', b'4-2', b'4-3', b'4-4', b'4-5', b'5-0', b'5-1', b'5-2', b'5-3', b'5-4', b'5-5']

gamma0 loaded
  dtype = complex128
  shape = (36, 36)