trexio/python/test/test_api.py

#!/usr/bin/env python3

import os
import shutil
import numpy as np

import trexio

#=========================================================#
#======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
#=========================================================#

# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
TEST_TREXIO_BACKEND = 0
OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'


# define TREXIO file name
if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
    output_filename = OUTPUT_FILENAME_HDF5
elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
    output_filename = OUTPUT_FILENAME_TEXT
else:
    raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')


# remove TREXIO file if exists in the current directory
try:
    if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
        os.remove(output_filename)
    elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
        shutil.rmtree(output_filename)
except:
    print ('Nothing to remove.')

#=========================================================#
#============ WRITE THE DATA IN THE TEST FILE ============#
#=========================================================#

trexio.info()

# create TREXIO file and open it for writing
test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
assert test_file.exists

# Print docstring of the trexio.open function
#print(trexio.open.__doc__)

nucleus_num = 12

try:
    trexio.write_nucleus_num(test_file, -100)
except trexio.Error:
    print("Raise error for an attempt to write negative nucleus_num: checked.")

# write nucleus_num in the file
try:
    trexio.write_nucleus_num(test_file, nucleus_num)
except:
    raise

try:
    trexio.write_nucleus_num(test_file, nucleus_num*2)
except trexio.Error:
    print("Raise error for an attempt to overwrite nucleus_num: checked.")

# 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.float32)
charges_np = np.array(charges, 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 typemaps from numpy.i
trexio.write_nucleus_charge(test_file, charges_np)

basis_shell_num = 24
# initialize arrays of nuclear indices as a list and convert it to numpy array
indices = [i for i in range(basis_shell_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.int64)

# first write basis_shell_num because it is needed to check dimensions of basis_nucleus_index in TREXIO >= 2.0.0
trexio.write_basis_shell_num(test_file, basis_shell_num)

# 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
trexio.write_basis_nucleus_index(test_file, indices_np)

# initialize a list of nuclear coordinates
coords = [
 [ 0.00000000 ,  1.39250319 ,  0.00000000 ],
 [-1.20594314 ,  0.69625160 ,  0.00000000 ],
 [-1.20594314 , -0.69625160 ,  0.00000000 ],
 [ 0.00000000 , -1.39250319 ,  0.00000000 ],
 [ 1.20594314 , -0.69625160 ,  0.00000000 ],
 [ 1.20594314 ,  0.69625160 ,  0.00000000 ],
 [-2.14171677 ,  1.23652075 ,  0.00000000 ],
 [-2.14171677 , -1.23652075 ,  0.00000000 ],
 [ 0.00000000 , -2.47304151 ,  0.00000000 ],
 [ 2.14171677 , -1.23652075 ,  0.00000000 ],
 [ 2.14171677 ,  1.23652075 ,  0.00000000 ],
 [ 0.00000000 ,  2.47304151 ,  0.00000000 ],
  ]

# write coordinates in the file
trexio.write_nucleus_coord(test_file, coords)


# write mo_num (needed later to write sparse mo_2e_int_eri integrals)
trexio.write_mo_num(test_file, 600)

# write sparse data in the file
num_integrals = 100
indices = [i for i in range(num_integrals*4)]
values  = [(3.14 + float(i)) for i in range(num_integrals)]

trexio.write_mo_2e_int_eri(test_file, 0, num_integrals, indices, values)


# write nucleus_point_group in the file
point_group = 'B3U'

trexio.write_nucleus_point_group(test_file, point_group)


# write nucleus_label in the file
labels = [
        'C',
        'C',
        'C',
        'C',
        'C',
        'C',
        'H',
        'H',
        'H',
        'H',
        'H',
        'H']

trexio.write_nucleus_label(test_file,labels)

# close TREXIO file
# this call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file
#trexio.close(test_file)
# without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end.
# This, the user still has to explicitly call destructor on test_file object instead of the trexio.close function.
# This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook)
del test_file


#==========================================================#
#========== DELETE THE GROUP FROM THE TEST FILE ===========#
#==========================================================#

unsafe_file = trexio.File(output_filename, 'u', TEST_TREXIO_BACKEND)

# overwrite existing data (only allowed in 'u' - unsafe mode)
trexio.write_nucleus_num(unsafe_file, nucleus_num)
trexio.write_nucleus_charge(unsafe_file, charges_np)
trexio.write_nucleus_coord(unsafe_file, coords)
trexio.write_nucleus_label(unsafe_file,labels)
trexio.write_nucleus_point_group(unsafe_file, point_group)

print("Overwriting the data in UNSAFE mode: checked")

# delete existing group (only allowed in 'u' - unsafe mode)
trexio.delete_nucleus(unsafe_file)

assert not trexio.has_nucleus_num(unsafe_file)
assert not trexio.has_nucleus_charge(unsafe_file)
assert not trexio.has_nucleus_coord(unsafe_file)
assert not trexio.has_nucleus_label(unsafe_file)
assert not trexio.has_nucleus_point_group(unsafe_file)

print("Deleting nucleus group in UNSAFE mode: checked")

# restore the deleted data
trexio.write_nucleus_num(unsafe_file, nucleus_num)
trexio.write_nucleus_charge(unsafe_file, charges_np)
trexio.write_nucleus_coord(unsafe_file, coords)
trexio.write_nucleus_label(unsafe_file,labels)
trexio.write_nucleus_point_group(unsafe_file, point_group)

del unsafe_file

#==========================================================#
#============ READ THE DATA FROM THE TEST FILE ============#
#==========================================================#

# open previously created TREXIO file, now in 'read' mode
test_file2 = trexio.File(output_filename, 'r', trexio.TREXIO_AUTO)
assert test_file2.exists

# check for existence of some of the previously written variables
assert trexio.has_nucleus_num(test_file2)
assert trexio.has_nucleus_charge(test_file2)
assert trexio.has_nucleus_coord(test_file2)
assert trexio.has_nucleus_label(test_file2)
assert trexio.has_nucleus_point_group(test_file2)
assert trexio.has_mo_2e_int_eri(test_file2)

# read nucleus_num from file
rnum = trexio.read_nucleus_num(test_file2)
assert rnum==nucleus_num

# safe call to read_nucleus_charge array of float values
rcharges_np = trexio.read_nucleus_charge(test_file2, dim=nucleus_num)
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 fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
try:
    rcharges_fail = trexio.read_nucleus_charge(test_file2, dim=nucleus_num*5)
except trexio.Error:
    print("Unsafe call to safe API: checked")

# safe call to read array of int values (nuclear indices)
rindices_np_16 = trexio.read_basis_nucleus_index(test_file2, dim=basis_shell_num, dtype=np.int16)
assert rindices_np_16.dtype is np.dtype(np.int16)
for i in range(basis_shell_num):
    assert rindices_np_16[i]==indices_np[i]

rindices_np_32 = trexio.read_basis_nucleus_index(test_file2, dim=basis_shell_num, dtype=np.int32)
assert rindices_np_32.dtype is np.dtype(np.int32)
for i in range(basis_shell_num):
    assert rindices_np_32[i]==indices_np[i]

rindices_np_64 = trexio.read_basis_nucleus_index(test_file2)
assert rindices_np_64.dtype is np.dtype(np.int64)
assert rindices_np_64.size==basis_shell_num
for i in range(basis_shell_num):
    assert rindices_np_64[i]==indices_np[i]

# read nuclear coordinates without providing optional argument dim
rcoords_np = trexio.read_nucleus_coord(test_file2)

assert rcoords_np.size==nucleus_num*3
np.testing.assert_array_almost_equal(rcoords_np, np.array(coords).reshape(nucleus_num,3), decimal=8)

# set doReshape to False to get a flat 1D array (e.g. when reading matrices like nuclear coordinates)
#rcoords_reshaped_2 = trexio.read_nucleus_coord(test_file2, doReshape=False)

# read number of integrals already present in the file
assert trexio.has_mo_2e_int_eri(test_file2)
assert trexio.read_mo_2e_int_eri_size(test_file2)==num_integrals

# read sparse arrays on mo_2e_int_eri integrals
buf_size = 60
offset_file = 0
# read full buf_size (i.e. the one that does not reach EOF)
indices_sparse_np, value_sparse_np, read_buf_size, eof = trexio.read_mo_2e_int_eri(test_file2, offset_file, buf_size)
print(f'First complete sparse read size: {read_buf_size}')
#print(indices_sparse_np)
assert not eof
assert read_buf_size==buf_size
assert indices_sparse_np[0][0]==0
assert indices_sparse_np[read_buf_size-1][3]==read_buf_size*4-1
offset_file += buf_size

# read incomplete buf_size (i.e. the one that does reach EOF)
indices_sparse_np, value_sparse_np, read_buf_size, eof2 = trexio.read_mo_2e_int_eri(test_file2, offset_file, buf_size)
print(f'Second incomplete sparse read size: {read_buf_size}')
#print(indices_sparse_np)
assert eof2
assert read_buf_size==(num_integrals - buf_size)
assert indices_sparse_np[0][0]==offset_file*4
assert indices_sparse_np[read_buf_size-1][3]==(offset_file+read_buf_size)*4-1


# read array of nuclear labels
rlabels_2d = trexio.read_nucleus_label(test_file2, dim=nucleus_num)
print(rlabels_2d)
for i in range(nucleus_num):
    assert rlabels_2d[i]==labels[i]

# read a string corresponding to nuclear point group
rpoint_group = trexio.read_nucleus_point_group(test_file2)
assert rpoint_group==point_group

# another way to read only if the variable exists
if trexio.has_ao_num(test_file2):
    rmo_num = trexio.read_ao_num(test_file2)
else:
    print("Pass on reading the non-existing variable ao_num: checked")

# close TREXIO file
#trexio.close(test_file2)

# cleaning (remove the TREXIO file)
try:
    if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
        os.remove(output_filename)
    elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
        shutil.rmtree(output_filename)
except:
    print (f'No output file {output_filename} has been produced')

#==========================================================#

#==========================================================#
#======= OPEN NON-EXISTING FILE TO TEST TREXIO.OPEN =======#
#==========================================================#

try:
    void_file = trexio.File('non_existing.file', 'r', TEST_TREXIO_BACKEND)
except trexio.Error as e:
    if e.error == trexio.TREXIO_OPEN_ERROR:
        print("Opening non-existing file returns TREXIO_OPEN_ERROR: checked")
    else:
        raise ValueError("[DEV]: error handling of trexio_open function has changed; check the consistency")

#==========================================================#