Parser: add the cp2k-output-tools parser (aiidateam#133).

aiida_cp2k/parsers/__init__.py

@@ -102,7 +102,7 @@ def _parse_stdout(self):
 
  fname = self.node.process_class._DEFAULT_OUTPUT_FILE # pylint: disable=protected-access
  if fname not in self.retrieved.list_object_names():
- raise OutputParsingError("Cp2k output file not retrieved")
+ raise OutputParsingError("CP2K output file not retrieved.")
 
  try:
  output_string = self.retrieved.get_object_content(fname)
@@ -151,3 +151,47 @@ def _parse_stdout(self):
 
  self.out("output_parameters", Dict(dict=result_dict))
  return None
+
+
+class Cp2kToolsParser(Cp2kBaseParser):
+ """AiiDA parser class for the output of CP2K based on the cp2k-output-tools project."""
+
+ def _parse_stdout(self):
+ """Very advanced CP2K output file parser."""
+
+ from cp2k_output_tools import parse_iter
+
+ fname = self.node.process_class._DEFAULT_OUTPUT_FILE # pylint: disable=protected-access
+ if fname not in self.retrieved.list_object_names():
+ raise OutputParsingError("CP2K output file not retrieved.")
+
+ try:
+ output_string = self.retrieved.get_object_content(fname)
+ except IOError:
+ return self.exit_codes.ERROR_OUTPUT_STDOUT_READ
+
+ result_dict = {}
+
+ # the CP2K output parser is a block-based parser return blocks of data, each under a block key
+ # merge them into one dict
+ for match in parse_iter(output_string, key_mangling=True):
+ result_dict.update(match)
+
+ # nwarnings is the last thing to be printed in the CP2K output file:
+ # if it is not there, CP2K didn't finish properly most likely
+ if 'nwarnings' not in result_dict:
+ raise OutputParsingError("CP2K did not finish properly")
+
+ if "aborted" in result_dict:
+ return self.exit_codes.ERROR_OUTPUT_CONTAINS_ABORT
+
+ try:
+ # the cp2k-output-tools parser is more hierarchical, be compatible with
+ # the basic parser here and provide the total force eval energy as energy
+ result_dict["energy"] = result_dict["energies"]["total_force_eval"]
+ result_dict["energy_units"] = "a.u."
+ except KeyError:
+ pass
+
+ self.out("output_parameters", Dict(dict=result_dict))
+ return None

setup.json

@@ -21,7 +21,8 @@
  ],
  "aiida.parsers": [
  "cp2k_base_parser = aiida_cp2k.parsers:Cp2kBaseParser",
- "cp2k_advanced_parser = aiida_cp2k.parsers:Cp2kAdvancedParser"
+ "cp2k_advanced_parser = aiida_cp2k.parsers:Cp2kAdvancedParser",
+ "cp2k_tools_parser = aiida_cp2k.parsers:Cp2kToolsParser"
  ],
  "aiida.workflows": [
  "cp2k.base = aiida_cp2k.workchains:Cp2kBaseWorkChain"
@@ -33,7 +34,8 @@
  "pytest>=4.4,<5.0.0",
  "pytest-cov>=2.6.1,<3.0.0",
  "coverage",
- "aiida-gaussian-datatypes"
+ "aiida-gaussian-datatypes",
+ "cp2k-output-tools"
  ],
  "pre-commit":[
  "pre-commit==1.18.3",