Sherman-Morrison/tools/convert-to-h5.py

48 lines
2.1 KiB
Python
Raw Normal View History

#!/usr/bin/env python
2021-02-16 10:49:15 +01:00
import h5py
import numpy as np
from parse import parse
def rl(rf):
return " ".join(rf.readline().split())
with h5py.File('dataset.hdf5', 'w') as f:
with open('dataset.dat', 'r') as rf:
2021-02-16 10:49:15 +01:00
while(1):
line = rl(rf)
if not line or not line.startswith('#START_PACKET'):
break
cycle_id = parse('#CYCLE_ID: {:d}', rl(rf))[0]
slater_matrix_dim = parse('#SLATER_MATRIX_DIM: {:d}', rl(rf))[0]
nupdates = parse('#NUPDATES: {:d}', rl(rf))[0]
assert(rf.readline().startswith('#SLATER_MATRIX'))
# Read matrices
slater_matrix = np.zeros((slater_matrix_dim,slater_matrix_dim))
slater_inverse = np.zeros((slater_matrix_dim,slater_matrix_dim))
for i in range(slater_matrix_dim*slater_matrix_dim):
res = parse('({i:d},{j:d}) {sla:e} {inv:e}', rl(rf))
slater_matrix[res['i']-1, res['j']-1] = res['sla']
slater_inverse[res['j']-1, res['i']-1] = res['inv']
2021-02-16 10:49:15 +01:00
# Read updates
col_update_index = np.zeros(nupdates, dtype='i')
updates = np.zeros((nupdates, slater_matrix_dim))
for n in range(nupdates):
col_update_index[n] = parse('#COL_UPDATE_INDEX: {:d}', rl(rf))[0]
for i in range(slater_matrix_dim):
res = parse('#COL_UPDATE_COMP_({i:d}): {x:e}', rl(rf))
updates[n][res['i']-1] = res['x']
assert(rf.readline().startswith('#END_PACKET'))
rf.readline()
cycle = f.create_group('cycle_{}'.format(cycle_id))
cycle.create_dataset("slater_matrix_dim", data=slater_matrix_dim)
cycle.create_dataset("nupdates", data=nupdates)
cycle.create_dataset("slater_matrix", data=slater_matrix, compression='gzip')
cycle.create_dataset("slater_inverse", data=slater_inverse, compression='gzip')
cycle.create_dataset("col_update_index", data=col_update_index)
cycle.create_dataset("updates", data=updates, compression='gzip')