From 6ac03252b89ff51d4c4aa3089d80815729380c5b Mon Sep 17 00:00:00 2001
From: Adam Fekete <adam.fekete@kcl.ac.uk>
Date: Mon, 1 Aug 2016 18:31:02 +0100
Subject: [PATCH] remove temporary file generation
---
parser/parser-lammps/LammpsDataParser.py | 24 ++++++++++++------------
parser/parser-lammps/LammpsLogParser.py | 3 +--
2 files changed, 13 insertions(+), 14 deletions(-)
diff --git a/parser/parser-lammps/LammpsDataParser.py b/parser/parser-lammps/LammpsDataParser.py
index 54eefaa..6fa738c 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 1d10038..efd2631 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
--
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