mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-12-23 12:56:53 +01:00
175 lines
5.7 KiB
Python
175 lines
5.7 KiB
Python
import os
|
|
import shutil
|
|
import numpy as np
|
|
|
|
from trexio.pytrexio import *
|
|
|
|
# TODO:
|
|
# 1) make a user-friendly more pythonic API that will have to be autogenerated
|
|
# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == 0
|
|
|
|
# automatically download (hopefully the latest version) numpy.i using
|
|
# wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i
|
|
# but also keep the original copy in case if wget fails
|
|
|
|
#=========================================================#
|
|
#======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
|
|
#=========================================================#
|
|
|
|
# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
|
|
TEST_TREXIO_BACKEND = 1
|
|
OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
|
|
OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
|
|
|
|
|
|
if TEST_TREXIO_BACKEND == 0:
|
|
output_filename = OUTPUT_FILENAME_HDF5
|
|
elif TEST_TREXIO_BACKEND == 1:
|
|
output_filename = OUTPUT_FILENAME_TEXT
|
|
else:
|
|
raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
|
|
|
|
|
|
try:
|
|
if TEST_TREXIO_BACKEND == 0:
|
|
os.remove(output_filename)
|
|
elif TEST_TREXIO_BACKEND == 1:
|
|
shutil.rmtree(output_filename)
|
|
except:
|
|
print ('Nothing to remove.')
|
|
|
|
#=========================================================#
|
|
#============ WRITE THE DATA IN THE TEST FILE ============#
|
|
#=========================================================#
|
|
|
|
test_file = trexio_open(output_filename, 'w', TEST_TREXIO_BACKEND)
|
|
|
|
nucleus_num = 12
|
|
|
|
rc = trexio_write_nucleus_num(test_file, nucleus_num)
|
|
assert rc==0
|
|
|
|
# initialize charge arrays as a list and convert it to numpy array
|
|
charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
|
|
charges_np = np.array(charges, dtype=np.float64)
|
|
|
|
# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
|
|
# from the size of the list/array by SWIG using typemaps from numpy.i
|
|
rc = trexio_write_safe_nucleus_charge(test_file, charges_np)
|
|
assert rc==0
|
|
|
|
# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
|
|
#charges = doubleArray(nucleus_num)
|
|
#for i in range(nucleus_num):
|
|
# if i < nucleus_num/2:
|
|
# charges[i] = 6.
|
|
# else:
|
|
# charges[i] = 1.
|
|
#rc = trexio_write_nucleus_charge(test_file, charges)
|
|
|
|
# initialize arrays of nuclear indices as a list and convert it to numpy array
|
|
indices = [i for i in range(nucleus_num)]
|
|
# type cast is important here because by default numpy transforms a list of integers into int64 array
|
|
indices_np = np.array(indices, dtype=np.int32)
|
|
|
|
# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
|
|
# from the size of the list/array by SWIG using typemacs from numpy.i
|
|
rc = trexio_write_safe_basis_nucleus_index(test_file, indices_np)
|
|
assert rc==0
|
|
|
|
point_group = 'B3U'
|
|
|
|
rc = trexio_write_nucleus_point_group(test_file, point_group, 10)
|
|
assert rc==0
|
|
|
|
labels = [
|
|
'C',
|
|
'C',
|
|
'C',
|
|
'C',
|
|
'C',
|
|
'C',
|
|
'H',
|
|
'H',
|
|
'H',
|
|
'H',
|
|
'H',
|
|
'H']
|
|
|
|
rc = trexio_write_nucleus_label(test_file, labels, 10)
|
|
assert rc==0
|
|
|
|
rc = trexio_close(test_file)
|
|
assert rc==0
|
|
|
|
#==========================================================#
|
|
#============ READ THE DATA FROM THE TEST FILE ============#
|
|
#==========================================================#
|
|
|
|
test_file2 = trexio_open(output_filename, 'r', TEST_TREXIO_BACKEND)
|
|
|
|
# TODO: think about adding exception handling if rc != 0 throw an exception but do not return the code itself and then there is less arguments
|
|
# TODO: maybe also for the write
|
|
|
|
result = trexio_read_nucleus_num(test_file2)
|
|
assert result[0]==0
|
|
assert result[1]==nucleus_num
|
|
|
|
# safe call to read_safe array of float values
|
|
rc, rcharges_np = trexio_read_safe_nucleus_charge(test_file2, nucleus_num)
|
|
assert rc==0
|
|
assert rcharges_np.dtype is np.dtype(np.float64)
|
|
np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
|
|
|
|
# unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
|
|
# TODO: it should not return numpy array filled with garbage
|
|
rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5)
|
|
#assert rc==TREXIO_UNSAFE_ARRAY_DIM
|
|
|
|
# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
|
|
#charges2 = doubleArray(nucleus_num)
|
|
#for i in range(nucleus_num):
|
|
# charges2[i] = -1.
|
|
#rc = trexio_read_nucleus_charge(test_file2, charges2)
|
|
#assert rc==0
|
|
#for i in range(nucleus_num):
|
|
# assert charges2[i]==charges[i]
|
|
|
|
# safe call to read_safe array of int values
|
|
rc, rindices_np = trexio_read_safe_basis_nucleus_index(test_file2, nucleus_num)
|
|
assert rc==0
|
|
assert rindices_np.dtype is np.dtype(np.int32)
|
|
for i in range(nucleus_num):
|
|
assert rindices_np[i]==indices_np[i]
|
|
|
|
|
|
# [WIP]: ideally, the list of strings should be returned as below
|
|
#rc, label_2d = trexio_read_nucleus_label(test_file2, 10)
|
|
# [WIP]: currently only low-level routines (return one long string instead of an array of strings) work
|
|
rc, labels_1d = trexio_read_nucleus_label_low(test_file2, 10)
|
|
assert rc==0
|
|
|
|
labels_2d = [label for label in labels_1d.split(TREXIO_DELIM) if label]
|
|
print('Read and parsed nuclear labels:\n', labels_2d)
|
|
for i in range(nucleus_num):
|
|
assert labels_2d[i]==labels[i]
|
|
|
|
rc, rpoint_group = trexio_read_nucleus_point_group(test_file2, 3)
|
|
print(f'Read point group: {rpoint_group}')
|
|
assert rc==0
|
|
assert rpoint_group==point_group
|
|
|
|
rc = trexio_close(test_file2)
|
|
assert rc==0
|
|
|
|
try:
|
|
if TEST_TREXIO_BACKEND == 0:
|
|
os.remove(output_filename)
|
|
elif TEST_TREXIO_BACKEND == 1:
|
|
shutil.rmtree(output_filename)
|
|
except:
|
|
print (f'No output file {output_filename} has been produced')
|
|
|
|
#==========================================================#
|
|
|