diff --git a/pyqchem/parsers/common/__init__.py b/pyqchem/parsers/common/__init__.py index 72d2eea..e620d4c 100644 --- a/pyqchem/parsers/common/__init__.py +++ b/pyqchem/parsers/common/__init__.py @@ -1,8 +1,8 @@ -import numpy as np -import re from pyqchem.utils import get_occupied_electrons from pyqchem.structure import atom_data from pyqchem.structure import Structure +import numpy as np +import re def read_symmetry_info(output): @@ -56,7 +56,7 @@ def read_input_structure(output): if row[1] == s: n_nucleus += i - charge = n_nucleus - (basic_data['n_alpha'] + basic_data['n_alpha']) + charge = n_nucleus - (basic_data['n_alpha'] + basic_data['n_beta']) multiplicity = abs(basic_data['n_alpha'] - basic_data['n_beta']) + 1 return Structure(coordinates=coordinates, @@ -127,7 +127,6 @@ def search_bars(output, from_position=0, bar_type='---'): def standardize_vector(vector): - import numpy as np if vector[0] != 0: if vector[0] < 0: vector = np.array(vector) * -1 @@ -146,6 +145,7 @@ def standardize_vector(vector): return vector + # handle asterisks and convert them to nan class float_asterisk(float): def __new__(cls, value): diff --git a/pyqchem/qchem_core.py b/pyqchem/qchem_core.py index ade5d44..6d5ffbb 100644 --- a/pyqchem/qchem_core.py +++ b/pyqchem/qchem_core.py @@ -8,6 +8,7 @@ import hashlib import pickle import warnings +import copy if sys.version_info[0] < 3 or sys.platform in ["win32", "cygwin"] or os.getenv('PYQCHEM_CACHE') == '1': @@ -255,6 +256,7 @@ def remote_run(input_file_name, work_dir, fchk_file, remote_params, use_mpi=Fals :return: output, err: Q-Chem standard output and standard error """ import paramiko + remote_params = copy.deepcopy(remote_params) # get precommands commands = remote_params.pop('precommand', []) @@ -584,8 +586,10 @@ def get_output_from_qchem(input_qchem, # Q-Chem calculation if output is None or force_recalculation is True: if remote is None: + print('local:') output, err = local_run(temp_filename, work_dir, fchk_filename, use_mpi=use_mpi, processors=processors) else: + print('Remote:') output, err = remote_run(temp_filename, work_dir, fchk_filename, remote, use_mpi=use_mpi, processors=processors) if not finish_ok(output):