mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-11-03 20:54:07 +01:00
235 lines
8.1 KiB
Python
235 lines
8.1 KiB
Python
#!/usr/bin/env python3
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import os
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import shutil
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import numpy as np
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import trexio
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#=========================================================#
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#======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
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#=========================================================#
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# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
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TEST_TREXIO_BACKEND = 0
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OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
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OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
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# define TREXIO file name
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if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
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output_filename = OUTPUT_FILENAME_HDF5
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elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
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output_filename = OUTPUT_FILENAME_TEXT
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else:
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raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
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# remove TREXIO file if exists in the current directory
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try:
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if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
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shutil.rmtree(output_filename)
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except:
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print ('Nothing to remove.')
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#=========================================================#
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#============ WRITE THE DATA IN THE TEST FILE ============#
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#=========================================================#
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# create TREXIO file and open it for writing
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test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
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# Print docstring of the trexio.open function
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#print(trexio.open.__doc__)
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nucleus_num = 12
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try:
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trexio.write_nucleus_num(test_file, -100)
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except trexio.Error:
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print("Raise error for an attempt to write negative nucleus_num: checked.")
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# write nucleus_num in the file
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try:
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trexio.write_nucleus_num(test_file, nucleus_num)
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except:
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raise
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try:
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trexio.write_nucleus_num(test_file, nucleus_num*2)
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except trexio.Error:
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print("Raise error for an attempt to overwrite nucleus_num: checked.")
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# initialize charge arrays as a list and convert it to numpy array
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charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
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#charges_np = np.array(charges, dtype=np.float32)
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charges_np = np.array(charges, dtype=np.int32)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemaps from numpy.i
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trexio.write_nucleus_charge(test_file, charges_np)
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basis_num = 24
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# initialize arrays of nuclear indices as a list and convert it to numpy array
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indices = [i for i in range(basis_num)]
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# type cast is important here because by default numpy transforms a list of integers into int64 array
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indices_np = np.array(indices, dtype=np.int64)
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# first write basis_num because it is needed to check dimensions of basis_nucleus_index in TREXIO >= 2.0.0
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trexio.write_basis_num(test_file, basis_num)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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trexio.write_basis_nucleus_index(test_file, indices_np)
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# initialize a list of nuclear coordinates
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coords = [
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[ 0.00000000 , 1.39250319 , 0.00000000 ],
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[-1.20594314 , 0.69625160 , 0.00000000 ],
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[-1.20594314 , -0.69625160 , 0.00000000 ],
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[ 0.00000000 , -1.39250319 , 0.00000000 ],
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[ 1.20594314 , -0.69625160 , 0.00000000 ],
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[ 1.20594314 , 0.69625160 , 0.00000000 ],
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[-2.14171677 , 1.23652075 , 0.00000000 ],
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[-2.14171677 , -1.23652075 , 0.00000000 ],
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[ 0.00000000 , -2.47304151 , 0.00000000 ],
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[ 2.14171677 , -1.23652075 , 0.00000000 ],
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[ 2.14171677 , 1.23652075 , 0.00000000 ],
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[ 0.00000000 , 2.47304151 , 0.00000000 ],
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]
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# write coordinates in the file
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trexio.write_nucleus_coord(test_file, coords)
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point_group = 'B3U'
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# write nucleus_point_group in the file
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trexio.write_nucleus_point_group(test_file, point_group)
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labels = [
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'C',
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'C',
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'C',
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'C',
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'C',
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'C',
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'H',
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'H',
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'H',
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'H',
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'H',
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'H']
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# write nucleus_label in the file
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trexio.write_nucleus_label(test_file,labels)
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# close TREXIO file
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# this call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file
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#trexio.close(test_file)
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# without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end.
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# This, the user still has to explicitly call destructor on test_file object instead of the trexio.close function.
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# This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook)
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del test_file
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#==========================================================#
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#============ READ THE DATA FROM THE TEST FILE ============#
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#==========================================================#
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# open previously created TREXIO file, now in 'read' mode
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test_file2 = trexio.File(output_filename, 'r', TEST_TREXIO_BACKEND)
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# check for existence of some of the previously written variables
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assert trexio.has_nucleus_num
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assert trexio.has_nucleus_charge
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assert trexio.has_nucleus_coord
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assert trexio.has_nucleus_label
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assert trexio.has_nucleus_point_group
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# read nucleus_num from file
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rnum = trexio.read_nucleus_num(test_file2)
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assert rnum==nucleus_num
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# safe call to read_nucleus_charge array of float values
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rcharges_np = trexio.read_nucleus_charge(test_file2, dim=nucleus_num)
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assert rcharges_np.dtype is np.dtype(np.float64)
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np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
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# unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
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try:
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rcharges_fail = trexio.read_nucleus_charge(test_file2, dim=nucleus_num*5)
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except trexio.Error:
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print("Unsafe call to safe API: checked")
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# safe call to read array of int values (nuclear indices)
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rindices_np_16 = trexio.read_basis_nucleus_index(test_file2, dim=basis_num, dtype=np.int16)
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assert rindices_np_16.dtype is np.dtype(np.int16)
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for i in range(basis_num):
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assert rindices_np_16[i]==indices_np[i]
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rindices_np_32 = trexio.read_basis_nucleus_index(test_file2, dim=basis_num, dtype=np.int32)
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assert rindices_np_32.dtype is np.dtype(np.int32)
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for i in range(basis_num):
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assert rindices_np_32[i]==indices_np[i]
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rindices_np_64 = trexio.read_basis_nucleus_index(test_file2)
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assert rindices_np_64.dtype is np.dtype(np.int64)
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assert rindices_np_64.size==basis_num
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for i in range(basis_num):
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assert rindices_np_64[i]==indices_np[i]
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# read nuclear coordinates without providing optional argument dim
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rcoords_np = trexio.read_nucleus_coord(test_file2)
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assert rcoords_np.size==nucleus_num*3
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np.testing.assert_array_almost_equal(rcoords_np, np.array(coords).reshape(nucleus_num,3), decimal=8)
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# set doReshape to False to get a flat 1D array (e.g. when reading matrices like nuclear coordinates)
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#rcoords_reshaped_2 = trexio.read_nucleus_coord(test_file2, doReshape=False)
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# read array of nuclear labels
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rlabels_2d = trexio.read_nucleus_label(test_file2, dim=nucleus_num)
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print(rlabels_2d)
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for i in range(nucleus_num):
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assert rlabels_2d[i]==labels[i]
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# read a string corresponding to nuclear point group
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rpoint_group = trexio.read_nucleus_point_group(test_file2)
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assert rpoint_group==point_group
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# another way to read only if the variable exists
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if trexio.has_mo_num(test_file2):
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rmo_num = trexio.read_mo_num(test_file2)
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else:
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print("Pass on reading the non-existing variable mo_num: checked")
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# close TREXIO file
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#trexio.close(test_file2)
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# cleaning (remove the TREXIO file)
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try:
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if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
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shutil.rmtree(output_filename)
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except:
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print (f'No output file {output_filename} has been produced')
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#==========================================================#
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#==========================================================#
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#======= OPEN NON-EXISTING FILE TO TEST TREXIO.OPEN =======#
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#==========================================================#
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try:
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void_file = trexio.File('non_existing.file', 'r', TEST_TREXIO_BACKEND)
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except trexio.Error as e:
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if e.error == trexio.TREXIO_OPEN_ERROR:
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print("Opening non-existing file returns TREXIO_OPEN_ERROR: checked")
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else:
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raise ValueError("[DEV]: error handling of trexio_open function has changed; check the consistency")
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#==========================================================#
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