import os import shutil #import numpy as np from pytrexio import * # TODO: make a user-friendly more pythonic API that will have to be autogenerated # add Exception handling # check of dimensions and call to safe API # conversion to and from numpy arrays # 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 = TREXIO_TEXT OUTPUT_FILENAME_TEXT = 'test_py_swig.dir' OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5' if TEST_TREXIO_BACKEND == TREXIO_HDF5: output_filename = OUTPUT_FILENAME_HDF5 elif TEST_TREXIO_BACKEND == TREXIO_TEXT: output_filename = OUTPUT_FILENAME_TEXT else: raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND') try: if TEST_TREXIO_BACKEND == TREXIO_HDF5: os.remove(output_filename) elif TEST_TREXIO_BACKEND == TREXIO_TEXT: shutil.rmtree(output_filename) except: print (f'Test file {output_filename} does not exist') #=========================================================# #============ 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==TREXIO_SUCCESS 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) assert rc==TREXIO_SUCCESS point_group = 'B3U' rc = trexio_write_nucleus_point_group(test_file, point_group, 10) assert rc==TREXIO_SUCCESS labels = [ 'C', 'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H'] rc = trexio_write_nucleus_label(test_file, labels, 10) assert rc==TREXIO_SUCCESS rc = trexio_close(test_file) assert rc==TREXIO_SUCCESS #==========================================================# #============ 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 != TREXIO_SUCCESS 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]==TREXIO_SUCCESS assert result[1]==nucleus_num #print(result) charges2 = doubleArray(nucleus_num) print(charges2[3]) #for i in range(nucleus_num): # charges2[i] = -1. rc = trexio_read_nucleus_charge(test_file2, charges2) assert rc==TREXIO_SUCCESS for i in range(nucleus_num): assert charges2[i]==charges[i] #charge_numpy = np.zeros(nucleus_num, dtype=np.float64) #print(charge_numpy) rc, charge_numpy = trexio_read_safe_nucleus_charge(test_file2, 12) print(charge_numpy) print(charge_numpy[11]) assert rc==TREXIO_SUCCESS # unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM # but also should not return numpy array filled with garbage rc, charge_numpy = trexio_read_safe_nucleus_charge(test_file2, 12*5) #print(charge_numpy) assert rc==TREXIO_UNSAFE_ARRAY_DIM # [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==TREXIO_SUCCESS labels_2d = [label for label in labels_1d.split(TREXIO_DELIM) if label] print(labels_2d) for i in range(nucleus_num): assert labels_2d[i]==labels[i] rc = trexio_close(test_file2) assert rc==TREXIO_SUCCESS try: if TEST_TREXIO_BACKEND == TREXIO_HDF5: os.remove(output_filename) elif TEST_TREXIO_BACKEND == TREXIO_TEXT: shutil.rmtree(output_filename) except: print (f'No output file {output_filename} has been produced') #==========================================================#