From 35a90bed0cd6cb6f0110203f017221ed9bcfb1a9 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@aalto.fi>
Date: Wed, 18 Oct 2017 18:27:02 +0300
Subject: [PATCH] Started using the new way of giving the input file to the
parser.
---
parser/parser-cp2k/cp2kparser/parser.py | 2 +-
.../cp2kparser/versions/cp2k262/commonparser.py | 4 ++--
.../cp2kparser/versions/cp2k262/geooptparser.py | 4 ++--
.../cp2kparser/versions/cp2k262/inputparser.py | 16 ++++++++--------
.../cp2kparser/versions/cp2k262/mdparser.py | 4 ++--
.../versions/cp2k262/singlepointforceparser.py | 8 ++++----
.../versions/cp2k262/singlepointparser.py | 8 ++++----
regtests/regtests.py | 6 +++---
8 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/parser/parser-cp2k/cp2kparser/parser.py b/parser/parser-cp2k/cp2kparser/parser.py
index 74bf4b5..12c22bf 100644
--- a/parser/parser-cp2k/cp2kparser/parser.py
+++ b/parser/parser-cp2k/cp2kparser/parser.py
@@ -153,4 +153,4 @@ class CP2KParser(ParserInterface):
)
raise
- self.main_parser = parser_class(self.parser_context.main_file, self.parser_context)
+ self.main_parser = parser_class(self.parser_context)
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
index 5b2bd27..a7110a2 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
@@ -445,8 +445,8 @@ class CP2KCommonParser(CommonParser):
# If the input file is available, parse it
filepath = self.file_service.get_file_by_id("input")
if filepath is not None:
- input_parser = CP2KInputParser(filepath, self.parser_context)
- input_parser.parse()
+ input_parser = CP2KInputParser(self.parser_context)
+ input_parser.parse(filepath)
else:
logger.warning("The input file of the calculation could not be found.")
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
index 3c1399d..ead4532 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
@@ -16,10 +16,10 @@ class CP2KGeoOptParser(MainHierarchicalParser):
"""Used to parse the CP2K calculation with run types:
-GEO_OPT/GEOMETRY_OPTIMIZATION
"""
- def __init__(self, file_path, parser_context):
+ def __init__(self, parser_context):
"""
"""
- super(CP2KGeoOptParser, self).__init__(file_path, parser_context)
+ super(CP2KGeoOptParser, self).__init__(parser_context)
self.setup_common_matcher(CP2KCommonParser(parser_context))
self.traj_iterator = None
self.energy_reeval_quickstep = None
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
index 65275a0..5504934 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
@@ -28,7 +28,7 @@ class CP2KInputParser(AbstractBaseParser):
supports variables. This is currently not supported, but may be added at
some point.
"""
- def __init__(self, file_path, parser_context):
+ def __init__(self, parser_context):
"""
Attributes:
input_tree: The input structure for this version of CP2K. The
@@ -38,7 +38,7 @@ class CP2KInputParser(AbstractBaseParser):
variables have been stated explicitly and the additional input files have
been merged.
"""
- super(CP2KInputParser, self).__init__(file_path, parser_context)
+ super(CP2KInputParser, self).__init__(parser_context)
self.input_tree = None
self.input_lines = None
self.unit_mapping = {
@@ -68,16 +68,16 @@ class CP2KInputParser(AbstractBaseParser):
self.cache_service.add("traj_add_last")
# self.cache_service.add("electronic_structure_method")
- def parse(self):
+ def parse(self, filepath):
#=======================================================================
# Preprocess to spell out variables and to include stuff from other
# files
- self.preprocess_input()
+ self.preprocess_input(filepath)
#=======================================================================
# Gather the information from the input file
- self.fill_input_tree(self.file_path)
+ self.fill_input_tree(filepath)
#=======================================================================
# Parse everything in the input to cp2k specific metadata
@@ -459,14 +459,14 @@ class CP2KInputParser(AbstractBaseParser):
input_tree_pickle_file = open(pickle_path, 'rb')
self.input_tree = pickle.load(input_tree_pickle_file)
- def preprocess_input(self):
+ def preprocess_input(self, filepath):
"""Preprocess the input file. Concatenate .inc files into the main
input file and explicitly state all variables.
"""
# Read the input file into memory. It shouldn't be that big so we can
# do this easily
input_lines = []
- with open(self.file_path, "r") as f:
+ with open(filepath, "r") as f:
for line in f:
input_lines.append(line.strip())
@@ -477,7 +477,7 @@ class CP2KInputParser(AbstractBaseParser):
if line.startswith("@INCLUDE") or line.startswith("@include"):
split = line.split(None, 1)
includepath = split[1]
- basedir = os.path.dirname(self.file_path)
+ basedir = os.path.dirname(filepath)
filepath = os.path.join(basedir, includepath)
filepath = os.path.abspath(filepath)
if not os.path.isfile(filepath):
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
index 4e126fc..93b25af 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
@@ -18,10 +18,10 @@ class CP2KMDParser(MainHierarchicalParser):
-MD
-MOLECULAR_DYNAMICS
"""
- def __init__(self, file_path, parser_context):
+ def __init__(self, parser_context):
"""
"""
- super(CP2KMDParser, self).__init__(file_path, parser_context)
+ super(CP2KMDParser, self).__init__(parser_context)
self.setup_common_matcher(CP2KCommonParser(parser_context))
self.traj_iterator = None
self.vel_iterator = None
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
index ba3b529..403f5d2 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
@@ -9,13 +9,13 @@ class CP2KSinglePointForceParser(AbstractBaseParser):
calculation. It is not exactly an ZYX file, so here we define separate
parser.
"""
- def __init__(self, file_path, parser_context):
- super(CP2KSinglePointForceParser, self).__init__(file_path, parser_context)
+ def __init__(self, parser_context):
+ super(CP2KSinglePointForceParser, self).__init__(parser_context)
- def parse(self):
+ def parse(self, filepath):
start = False
forces = []
- with open(self.file_path) as f:
+ with open(filepath) as f:
for line in f:
if line.startswith(" # Atom"):
start = True
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
index 001fc04..1cf169e 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
@@ -13,10 +13,10 @@ class CP2KSinglePointParser(MainHierarchicalParser):
-ENERGY
-ENERGY_FORCE
"""
- def __init__(self, file_path, parser_context):
+ def __init__(self, parser_context):
"""
"""
- super(CP2KSinglePointParser, self).__init__(file_path, parser_context)
+ super(CP2KSinglePointParser, self).__init__(parser_context)
self.setup_common_matcher(CP2KCommonParser(parser_context))
#=======================================================================
@@ -54,8 +54,8 @@ class CP2KSinglePointParser(MainHierarchicalParser):
if section["atom_forces"] is None:
force_file = self.file_service.get_file_by_id("force_file_single_point")
if force_file is not None:
- force_parser = CP2KSinglePointForceParser(force_file, self.parser_context)
- force_parser.parse()
+ force_parser = CP2KSinglePointForceParser(self.parser_context)
+ force_parser.parse(force_file)
else:
logger.warning("The file containing the forces printed by ENERGY_FORCE calculation could not be found.")
diff --git a/regtests/regtests.py b/regtests/regtests.py
index 5da0635..a64149c 100644
--- a/regtests/regtests.py
+++ b/regtests/regtests.py
@@ -17,8 +17,8 @@ def get_result(folder, metaname=None):
"""
dirname = os.path.dirname(__file__)
filename = os.path.join("cp2k_{}".format(VERSION), dirname, folder, "unittest.out")
- parser = CP2KParser(filename, None, debug=True, log_level=logging.CRITICAL)
- results = parser.parse()
+ parser = CP2KParser(None, debug=True, log_level=logging.CRITICAL)
+ results = parser.parse(filename)
if metaname is None:
return results
@@ -32,7 +32,7 @@ class TestErrors(unittest.TestCase):
def test_no_file(self):
"""File is not no present.
"""
- with self.assertRaises(IOError):
+ with self.assertRaises(ValueError):
get_result("errors/no_file", "XC_functional")
def test_invalid_file(self):
--
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