diff --git a/parser/parser-lammps/LammpsDataParser.py b/parser/parser-lammps/LammpsDataParser.py index 54eefaaf7f2cf387603dea0fc51beddf29538f2f..6fa738cc023fbfc60b98b4fca47b841e0980b539 100644 --- a/parser/parser-lammps/LammpsDataParser.py +++ b/parser/parser-lammps/LammpsDataParser.py @@ -608,12 +608,12 @@ class LammpsDataParserContext(object): xyz_file.append(xyz_line) atomLabelling.append(xyz_line) - mode = 'w' - if sys.version_info.major < 3: - mode += 'b' - - with open(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(sys.argv[1])), 'generated_from_data_file.xyz')), mode) as xyz: - xyz.writelines(' '.join(str(j) for j in i) + '\n' for i in xyz_file) # WRITE XYZ ATOMIC NUMBER AND COORDINATES + # mode = 'w' + # if sys.version_info.major < 3: + # mode += 'b' + # + # with open(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(sys.argv[1])), 'generated_from_data_file.xyz')), mode) as xyz: + # xyz.writelines(' '.join(str(j) for j in i) + '\n' for i in xyz_file) # WRITE XYZ ATOMIC NUMBER AND COORDINATES #### A SINGLE ATOM TYPE MIGHT HAVE MORE THAN ONE CHARGE (E.G. CARBON IN CH3, CH2, CH, ...) @@ -693,12 +693,12 @@ class LammpsDataParserContext(object): xyz_file.append(xyz_line) atomLabelling.append(xyz_line) - mode = 'w' - if sys.version_info.major < 3: - mode += 'b' - - with open(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(sys.argv[1])), 'generated_from_data_file.xyz')), mode) as xyz: - xyz.writelines(' '.join(str(j) for j in i) + '\n' for i in xyz_file) # WRITE XYZ ATOMIC NUMBER AND COORDINATES + # mode = 'w' + # if sys.version_info.major < 3: + # mode += 'b' + # + # with open(os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(sys.argv[1])), 'generated_from_data_file.xyz')), mode) as xyz: + # xyz.writelines(' '.join(str(j) for j in i) + '\n' for i in xyz_file) # WRITE XYZ ATOMIC NUMBER AND COORDINATES return charge_dict, charge_list, mass_dict, mass_list, mass_xyz, new_mass_list, atomLabelling diff --git a/parser/parser-lammps/LammpsLogParser.py b/parser/parser-lammps/LammpsLogParser.py index 1d10038446c4e8eb700002157a56c3cefba9b419..efd26314a77e6d2d29dc5a830a39b6efc150729f 100644 --- a/parser/parser-lammps/LammpsLogParser.py +++ b/parser/parser-lammps/LammpsLogParser.py @@ -1264,7 +1264,6 @@ class LammpsMainParser(MainHierarchicalParser): ''' line = parser.fIn.readline() - filename = line.split()[1] dir_name = os.path.dirname(os.path.abspath(self.fName)) @@ -1274,7 +1273,7 @@ class LammpsMainParser(MainHierarchicalParser): parser.fIn.fIn.close() # owerwrite and open the file reader of the new log file - parser.fIn = PushbackLineFile(open(f_name,'r')) + parser.fIn = PushbackLineFile(open(f_name, 'r')) return None