mirror of https://github.com/abinit/abipy.git
Minor changes
This commit is contained in:
Matteo Giantomassi
parent
9864141da0
commit
e2adb8d9f7
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@ -62,7 +62,7 @@ jobs:
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cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
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cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
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# FIXME TEMPORARY HACK
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#pip install git+https://github.com/gmatteo/pymatgen.git@master
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pip install git+https://github.com/gmatteo/pymatgen.git@master -U
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- name: Build docs with Sphinx
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run: |
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@ -51,7 +51,7 @@ jobs:
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cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
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cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
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# FIXME TEMPORARY HACK
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#pip install git+https://github.com/gmatteo/pymatgen.git@master
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pip install git+https://github.com/gmatteo/pymatgen.git@master -U
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- name: pytest
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run: |
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@ -40,7 +40,7 @@ __all__ = [
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]
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__yaml = YAML()
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_yaml = YAML()
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def straceback() -> str:
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@ -179,14 +179,14 @@ class AbinitEvent(yaml.YAMLObject):
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return 0
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class AbinitComment(AbinitEvent):
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"""Base class for Comment events"""
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yaml_tag = '!COMMENT'
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color = "blue"
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class AbinitError(AbinitEvent):
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"""Base class for Error events"""
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yaml_tag = '!ERROR'
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@ -200,14 +200,14 @@ class AbinitYamlError(AbinitError):
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"""
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class AbinitBug(AbinitEvent):
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"""Base class for Bug events"""
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yaml_tag = '!BUG'
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color = "red"
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class AbinitWarning(AbinitEvent):
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"""
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Base class for Warning events (the most important class).
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@ -232,19 +232,19 @@ class AbinitYamlWarning(AbinitCriticalWarning):
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###############################
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class ScfConvergenceWarning(AbinitCriticalWarning):
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"""Warning raised when the GS SCF cycle did not converge."""
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yaml_tag = '!ScfConvergenceWarning'
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class NscfConvergenceWarning(AbinitCriticalWarning):
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"""Warning raised when the GS NSCF cycle did not converge."""
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yaml_tag = '!NscfConvergenceWarning'
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class RelaxConvergenceWarning(AbinitCriticalWarning):
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"""Warning raised when the structural relaxation did not converge."""
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yaml_tag = '!RelaxConvergenceWarning'
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@ -256,13 +256,13 @@ class RelaxConvergenceWarning(AbinitCriticalWarning):
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# yaml_tag = u'!PhononConvergenceWarning'
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class QPSConvergenceWarning(AbinitCriticalWarning):
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"""Warning raised when the QPS iteration (GW) did not converge."""
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yaml_tag = '!QPSConvergenceWarning'
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class HaydockConvergenceWarning(AbinitCriticalWarning):
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"""Warning raised when the Haydock method (BSE) did not converge."""
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yaml_tag = '!HaydockConvergenceWarning'
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@ -447,9 +447,9 @@ class EventsParser:
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filename = os.path.abspath(filename)
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report = EventReport(filename)
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w = WildCard("*Error|*Warning|*Comment|*Bug|*ERROR|*WARNING|*COMMENT|*BUG")
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import warnings
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warnings.simplefilter('ignore', yaml.error.UnsafeLoaderWarning)
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#w = WildCard("*Error|*Warning|*Comment|*Bug|*ERROR|*WARNING|*COMMENT|*BUG")
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#import warnings
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#warnings.simplefilter('ignore', yaml.error.UnsafeLoaderWarning)
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with YamlTokenizer(filename) as tokens:
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for doc in tokens:
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@ -780,22 +780,22 @@ class DilatmxErrorHandler(ErrorHandler):
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return self.FIXED
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def handle_input_event(self, abiinput, outdir, event):
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def handle_input_event(self, abi_input, outdir, event):
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try:
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old_abiinput = abiinput.deepcopy()
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old_abiinput = abi_input.deepcopy()
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# Read the last structure dumped by ABINIT before aborting.
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filepath = outdir.has_abiext("DILATMX_STRUCT.nc")
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last_structure = Structure.from_file(filepath)
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abiinput.set_structure(last_structure)
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abi_input.set_structure(last_structure)
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#FIXME restart from DEN files not always working with interpolation
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return Correction(self, self.compare_inputs(abiinput, old_abiinput), event, reset=True)
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# return Correction(self, self.compare_inputs(abiinput, old_abiinput), event, event=False)
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return Correction(self, self.compare_inputs(abi_input, old_abiinput), event, reset=True)
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# return Correction(self, self.compare_inputs(abi_input, old_abiinput), event, event=False)
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except Exception as exc:
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logger.warning('Error while trying to apply the handler {}.'.format(str(self)), exc)
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return None
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class TolSymError(AbinitError):
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"""
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Class of errors raised by Abinit when it cannot detect the symmetries of the system.
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@ -838,19 +838,19 @@ class TolSymErrorHandler(ErrorHandler):
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task.log_correction(event, "Increasing tolsym from %s to %s" % (old_tolsym, new_tolsym))
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return self.FIXED
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def handle_input_event(self, abiinput, outdir, event):
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def handle_input_event(self, abi_input, outdir, event):
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try:
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old_abiinput = abiinput.deepcopy()
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old_tolsym = abiinput["tolsym"]
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old_abiinput = abi_input.deepcopy()
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old_tolsym = abi_input["tolsym"]
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new_tolsym = 1e-6 if old_tolsym is None else old_tolsym * 10
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abiinput.set_vars(tolsym=new_tolsym)
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return Correction(self, self.compare_inputs(abiinput, old_abiinput), event, reset=False)
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abi_input.set_vars(tolsym=new_tolsym)
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return Correction(self, self.compare_inputs(abi_input, old_abiinput), event, reset=False)
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except Exception as exc:
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logger.warning('Error while trying to apply the handler {}.'.format(str(self)), exc)
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return None
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class MemanaError(AbinitError):
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"""
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Class of errors raised by the memory analyzer.
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@ -872,17 +872,17 @@ class MemanaErrorHandler(ErrorHandler):
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task.log_correction(event, "Find MemanaError. Setting mem_test to 0 in input file.")
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return self.FIXED
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def handle_input_event(self, abiinput, outdir, event):
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def handle_input_event(self, abi_input, outdir, event):
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try:
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old_abiinput = abiinput.deepcopy()
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abiinput.set_vars(mem_test=0)
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return Correction(self, self.compare_inputs(abiinput, old_abiinput), event, reset=False)
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old_abiinput = abi_input.deepcopy()
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abi_input.set_vars(mem_test=0)
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return Correction(self, self.compare_inputs(abi_input, old_abiinput), event, reset=False)
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except Exception as exc:
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logger.warning('Error while trying to apply the handler {}.'.format(str(self)), exc)
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return None
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@yaml_object(__yaml)
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@yaml_object(_yaml)
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class MemoryError(AbinitError):
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"""
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This error occurs when a checked allocation fails in Abinit
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@ -903,7 +903,7 @@ class MemoryErrorHandler(ErrorHandler):
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task.manager.increase_resources()
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return self.FIXED
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def handle_input_event(self, abiinput, outdir, event):
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def handle_input_event(self, abi_input, outdir, event):
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"""
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Shouldn't do anything on the input
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"""
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