Merge remote-tracking branch 'origin/development' into development

abelcarreras · Jul 12, 2023 · b985139 · b985139
2 parents 2aac86b + 9a8cc5e
commit b985139
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git 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
@@ -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):