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Add phonon workflow
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@ladinesa
ladinesa committed Feb 12, 2025
1 parent 3e46ccc commit 175b7af
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Showing 5 changed files with 280 additions and 125 deletions.
1 change: 1 addition & 0 deletions src/nomad_simulations/schema_packages/workflow/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,6 @@
from .geometry_optimization import GeometryOptimization
from .gw import DFTGWWorkflow
from .molecular_dynamics import MolecularDynamics
from .phonon import Phonon
from .single_point import SinglePoint
from .thermodynamics import Thermodynamics
164 changes: 67 additions & 97 deletions src/nomad_simulations/schema_packages/workflow/general.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,10 @@
m_package = SchemaPackage()


class SimulationTask(Task):
pass


class SimulationWorkflowModel(ArchiveSection):
"""
Base class for simulation workflow model sub-section definition.
Expand Down Expand Up @@ -66,9 +70,16 @@ def normalize(self, archive: EntryArchive, logger: BoundLogger) -> None:
self.final_outputs = archive.data.outputs[-1]


class SimulationWorkflow(Workflow):
class SimulationTaskReference(TaskReference, SimulationTask):
pass


class SimulationWorkflow(Workflow, SimulationTask):
"""
Base class for simulation workflows.
It contains sub-sections model and results which are included in inputs and
outputs, respectively.
"""

task_label = 'Task'
Expand All @@ -78,126 +89,56 @@ class SimulationWorkflow(Workflow):
results = SubSection(sub_section=SimulationWorkflowResults.m_def)

def map_inputs(self, archive: EntryArchive, logger: BoundLogger) -> None:
if not self.model:
self.model = SimulationWorkflowModel()

self.model.normalize(archive, logger)

# set method as inputs
self.inputs.append(Link(name=self.model.label, section=self.model))
if self.model:
self.model.normalize(archive, logger)
# add method to inputs
self.inputs.append(Link(name=self.model.label, section=self.model))

def map_outputs(self, archive: EntryArchive, logger: BoundLogger) -> None:
if not self.results:
self.results = SimulationWorkflowResults()

self.results.normalize(archive, logger)

# set results as outputs
self.outputs.append(Link(name=self.results.label, section=self.results))
if self.results:
self.results.normalize(archive, logger)
# add results to outputs
self.outputs.append(Link(name=self.results.label, section=self.results))

def map_tasks(self, archive: EntryArchive, logger: BoundLogger) -> None:
"""
Generate tasks from archive data outputs. Tasks are ordered and linked based
on the execution time of the calculation corresponding to the output.
By default, the tasks follow the order of the outputs and are linked sequentially.
"""
if not archive.data or not archive.data.outputs:
return

# default should to serial execution
times: list[tuple[float, float]] = list(
[
(
o.wall_start.magnitude if o.wall_start else n,
o.wall_end.magnitude if o.wall_end else n,
tasks = []
for outputs in archive.data.outputs:
tasks.append(
SimulationTask(
outputs=[
Link(
name='Outputs',
section=outputs,
)
]
)
for n, o in enumerate(archive.data.outputs)
]
)
times.sort(key=lambda x: x[0])
# current index of parent
parent_n = 0
for n, time in enumerate(times):
task = Task(
outputs=[
Link(
name='Outputs',
section=archive.data.outputs[n],
)
],
)
self.tasks.append(task)
# link tasks based on overlap in execution time
if time[0] >= times[parent_n][1]:
# assign as new parent
parent_n = n
# reset outputs
self._grouped_tasks.append([n])
else:
if not self._grouped_tasks:
self._grouped_tasks.append([])
self._grouped_tasks[-1].append(n)

self.tasks.extend(tasks)

def normalize(self, archive: EntryArchive, logger: BoundLogger):
"""
Link tasks based on start and end times.
"""
if not self.name:
self.name = self.m_def.name

if not self.inputs:
self.map_inputs(archive, logger)

if not self.outputs:
self.map_outputs(archive, logger)

# group tasks in parallel
# assume serial workflow
self._grouped_tasks = [[n] for n in range(len(self.tasks))]

if not self.tasks:
self.map_tasks(archive, logger)

# add task inputs/outputs to reference
# TODO do this in TaskReference normalizer
for task in self.tasks:
if isinstance(task, TaskReference):
task.inputs.extend(task.task.inputs)
task.outputs.extend(task.task.outputs)

# link successive task groups, first group adds workflow inputs
for tasks_n, grouped_tasks in enumerate(self._grouped_tasks):
# assign outputs of previous tasks an input to next tasks
if tasks_n:
inputs = [
inp
for task in [
self.tasks[n] for n in self._grouped_tasks[tasks_n - 1]
]
for inp in task.outputs
]
else:
inputs = self.inputs
for n in grouped_tasks:
self.tasks[n].inputs.extend(inputs)
if isinstance(self.tasks[n], TaskReference):
self.tasks[n].task.inputs.extend(inputs)

if self._grouped_tasks:
# add inputs of first group to workflow inputs
self.inputs.extend(
[
inp
for task in [self.tasks[n] for n in self._grouped_tasks[0]]
for inp in task.inputs
if inp not in self.inputs
]
)

# add outputs of last group to workflow outputs
self.outputs.extend(
[
out
for task in [self.tasks[n] for n in self._grouped_tasks[-1]]
for out in task.outputs
if out not in self.outputs
]
)


class SerialWorkflow(SimulationWorkflow):
"""
Expand All @@ -210,6 +151,35 @@ def map_tasks(self, archive: EntryArchive, logger: BoundLogger) -> None:
if not task.name:
task.name = f'{self.task_label} {n}'

def normalize(self, archive: EntryArchive, logger: BoundLogger) -> None:
super().normalize(archive, logger)

if not self.tasks:
logger.error(INCORRECT_N_TASKS)
return

# link tasks sequentially
for n, task in enumerate(self.tasks):
if n == 0:
inputs = self.inputs
else:
previous_task = self.tasks[n - 1]
inputs = [
Link(
name='Linked task',
section=previous_task.task
if isinstance(previous_task, TaskReference)
else previous_task,
)
]

task.inputs.extend([inp for inp in inputs if inp not in task.inputs])

# add oututs of last task to outputs
self.outputs.extend(
[out for out in self.tasks[-1].outputs if out not in self.outputs]
)


class ElectronicStructureResults(SimulationWorkflowResults):
"""
Expand Down
2 changes: 1 addition & 1 deletion src/nomad_simulations/schema_packages/workflow/geometry_optimization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ def map_inputs(self, archive: EntryArchive, logger: BoundLogger) -> None:
self.model = GeometryOptimizationModel()
super().map_inputs(archive, logger)

def map_outputs(self, archive: EntryArchive, logger: BoundLogger):
def map_outputs(self, archive: EntryArchive, logger: BoundLogger) -> None:
if not self.results:
self.results = GeometryOptimizationResults()
super().map_outputs(archive, logger)
Expand Down
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Coverage

Coverage Report
FileStmtsMissCoverMissing
src/nomad_simulations
   __init__.py4250%3–4
   _version.py11282%5–6
src/nomad_simulations/schema_packages
   __init__.py15287%39–41
   atoms_state.py1902189%13–15, 201–204, 228, 283–284, 352–353, 355, 537, 549–550, 611–615, 630–634, 641
   basis_set.py2402888%8–9, 122–133, 172–185, 208, 391–395, 417–418, 462–465, 584, 615, 617
   general.py85891%4–7, 123, 143, 253–254, 264
   model_method.py2697871%10–12, 171–174, 177–184, 276–277, 297, 318–339, 355–381, 384–401, 587, 780, 791, 833–840, 878, 897, 977, 1034, 1109, 1223
   model_system.py3483789%45–51, 235, 254, 258, 261, 264, 290, 376–377, 454–455, 472–473, 686–689, 736–743, 917–918, 1140–1144, 1150–1151, 1159–1160, 1165, 1188
   numerical_settings.py2596176%12–14, 217, 219–220, 223–226, 230–231, 238–241, 250–253, 257–260, 262–265, 270–273, 279–282, 469–496, 571, 606–609, 633, 636, 681, 683–686, 690, 694, 741, 745–766, 821–822, 889
   outputs.py1201092%8–9, 253–256, 296–299, 324, 326, 363, 382
   physical_property.py102793%20–22, 202, 331–333
   variables.py861286%8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
   band_gap.py51590%8–10, 135–136
   band_structure.py1232580%9–11, 232–265, 278, 285, 321–322, 325, 372–373, 378
   energies.py42979%7–9, 36, 57, 82, 103, 119, 134
   fermi_surface.py17476%7–9, 40
   forces.py22673%7–9, 36, 56, 79
   greens_function.py991387%7–9, 210–211, 214, 235–236, 239, 260–261, 264, 400
   hopping_matrix.py29583%7–9, 58, 94
   permittivity.py48883%7–9, 97–105
   spectral_profile.py26012851%9–11, 57–60, 95–98, 199–300, 356–368, 393–396, 416, 421–424, 466–502, 526, 573–576, 592–593, 598–604
   thermodynamics.py752764%7–9, 35, 56, 72, 81, 90, 101, 110, 137, 147, 157, 172–174, 177, 193, 213–215, 218, 234, 254–256, 259
src/nomad_simulations/schema_packages/utils
   utils.py791680%8–11, 65–74, 83–84, 89, 92, 169–170
src/nomad_simulations/schema_packages/workflow
   __init__.py770%1–7
   general.py82820%1–197
   geometry_optimization.py53530%1–205
   gw.py28280%1–61
   molecular_dynamics.py27270%1–145
   phonon.py47470%1–186
   single_point.py28280%1–70
   thermodynamics.py23230%1–63
TOTAL289080972% 

Tests Skipped Failures Errors Time
402 0 💤 0 ❌ 0 🔥 6.500s ⏱️

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