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public distro 2.1.0

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This commit is contained in:
muntwiler_m
2019-07-19 12:54:54 +02:00
parent acea809e4e
commit fbd2d4fa8c
40 changed files with 2813 additions and 345 deletions
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88
pmsco/dispatch.py
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@ -227,7 +227,7 @@ class CalculationTask(object):
# files generated by the task and their category
#
# dictionary key is the file name,
# value is the file category, e.g. 'cluster', 'phase', etc.
# value is the file category, e.g. 'cluster', 'atomic', etc.
#
# this information is used to automatically clean up unnecessary data files.
@ -374,7 +374,7 @@ class CalculationTask(object):
this information is used to automatically clean up unnecessary data files.
@param name: file name (optionally including a path).
@param category: file category, e.g. 'cluster', 'phase', etc.
@param category: file category, e.g. 'cluster', 'atomic', etc.
@return: None
"""
self.files[name] = category
@ -521,7 +521,8 @@ class MscoProcess(object):
def __init__(self, comm):
self._comm = comm
self._project = None
self._calculator = None
self._atomic_scattering = None
self._multiple_scattering = None
self._running = False
self._finishing = False
self.stop_signal = False
@ -529,7 +530,8 @@ class MscoProcess(object):
def setup(self, project):
self._project = project
self._calculator = project.calculator_class()
self._atomic_scattering = project.atomic_scattering_factory()
self._multiple_scattering = project.multiple_scattering_factory()
self._running = False
self._finishing = False
self.stop_signal = False
@ -596,19 +598,18 @@ class MscoProcess(object):
scan = self._define_scan(task)
output_file = task.format_filename(ext="")
# check parameters and call the msc program
if clu.get_atom_count() < 2:
# check parameters and call the calculators
if clu.get_atom_count() >= 1:
self._calc_atomic(task, par, clu, scan, output_file)
else:
logger.error("empty cluster in calculation %s", s_id)
task.result_valid = False
elif clu.get_emitter_count() < 1:
if clu.get_emitter_count() >= 1:
self._calc_multiple(task, par, clu, scan, output_file)
else:
logger.error("no emitters in cluster of calculation %s.", s_id)
task.result_valid = False
else:
task.result_filename, files = self._calculator.run(par, clu, scan, output_file)
(root, ext) = os.path.splitext(task.result_filename)
task.file_ext = ext
task.result_valid = True
task.files.update(files)
task.time = datetime.datetime.now() - start_time
@ -666,6 +667,8 @@ class MscoProcess(object):
"""
nem = self._project.cluster_generator.count_emitters(task.model, task.id)
clu = self._project.cluster_generator.create_cluster(task.model, task.id)
# overwrite atom classes only if they are at their default value
clu.init_atomclasses(field_or_value='t', default_only=True)
if task.id.region == 0:
file_index = task.id._replace(region=-1)
@ -696,6 +699,59 @@ class MscoProcess(object):
return par
def _calc_atomic(self, task, par, clu, scan, output_file):
"""
calculate the atomic scattering factors if necessary and link them to the cluster.
the method first calls the `before_atomic_scattering` project hook,
the atomic scattering calculator,
and finally the `after_atomic_scattering` hook.
this process updates the par and clu objects to link to the created files.
if any of the functions returns None, the par and clu objects are left unchanged.
@param task: CalculationTask with all attributes set for the calculation.
@param par: pmsco.project.Params object for the calculator.
its phase_files attribute is updated with the created scattering files.
the radial matrix elements are not changed (but may be in a future version).
@param clu: pmsco.cluster.Cluster object for the calculator.
the cluster is overwritten with the one returned by the calculator,
so that atom classes match the phase_files.
@return: None
"""
_par = copy.deepcopy(par)
_clu = copy.deepcopy(clu)
_par, _clu = self._project.before_atomic_scattering(task, _par, _clu)
if _clu is not None:
filename, files = self._atomic_scattering.run(_par, _clu, scan, output_file)
if files:
task.files.update(files)
_par, _clu = self._project.after_atomic_scattering(task, _par, _clu)
if _clu is not None:
par.phase_files = _par.phase_files
clu.copy_from(_clu)
def _calc_multiple(self, task, par, clu, scan, output_file):
"""
calculate the multiple scattering intensity.
@param task: CalculationTask with all attributes set for the calculation.
@param par: pmsco.project.Params object for the calculator.
@param clu: pmsco.cluster.Cluster object for the calculator.
@return: None
"""
task.result_filename, files = self._multiple_scattering.run(par, clu, scan, output_file)
if task.result_filename:
(root, ext) = os.path.splitext(task.result_filename)
task.file_ext = ext
task.result_valid = True
if files:
task.files.update(files)
class MscoMaster(MscoProcess):
"""
@ -1025,19 +1081,19 @@ class MscoMaster(MscoProcess):
@return: self._finishing
"""
if not self._finishing and (self._model_done and not self._pending_tasks and not self._running_tasks):
logger.info("finish: model handler is done")
logger.warning("finish: model handler is done")
self._finishing = True
if not self._finishing and (self._calculations >= self.max_calculations):
logger.warning("finish: max. calculations (%u) exeeded", self.max_calculations)
self._finishing = True
if not self._finishing and self.stop_signal:
logger.info("finish: stop signal received")
logger.warning("finish: stop signal received")
self._finishing = True
if not self._finishing and (datetime.datetime.now() > self.datetime_limit):
logger.warning("finish: time limit exceeded")
self._finishing = True
if not self._finishing and os.path.isfile("finish_pmsco"):
logger.info("finish: finish_pmsco file detected")
logger.warning("finish: finish_pmsco file detected")
self._finishing = True
if self._finishing and not self._running_slaves and not self._running_tasks: