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Add back tensor reporters #175

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Merged
mattwthompson merged 6 commits into from
Sep 28, 2026
Merged

Add back tensor reporters #175

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53ba576
Revamp examples
mattwthompson Sep 25, 2026
42f5fc2
Update `.gitignore` to include VS Code config
mattwthompson Sep 25, 2026
e61c6ee
Add back `TensorReporter` in MD simulations
mattwthompson Sep 25, 2026
de76df2
Merge remote-tracking branch 'upstream/update-examples' into add-back…
mattwthompson Sep 25, 2026
a4c0dbf
Merge remote-tracking branch 'upstream/main' into add-back-tensor-rep…
mattwthompson Sep 28, 2026
5dfff60
Claude-suggested improvements
mattwthompson Sep 28, 2026
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20 changes: 15 additions & 5 deletions tyff/compute/_equilibrate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

from parsl import File

import tyff.mm
from tyff.compute._files import (
EquilibrationFiles,
MinimizationFiles,
Expand Down Expand Up @@ -122,18 +123,27 @@ def _run_equilibration(
)
)

dcd_reporter = openmm.app.DCDReporter(
file=files["dcd_trajectory"].filepath,
reportInterval=1000,
simulation.reporters.append(
openmm.app.DCDReporter(
file=files["dcd_trajectory"].filepath,
reportInterval=1000,
)
)

simulation.reporters.append(dcd_reporter)

simulation.context.setVelocitiesToTemperature(
compute_config["temperature"], # kelvin, but as float
compute_config["replicate_index"] + 1,
)

simulation.reporters.append(
tyff.mm.TensorReporter(
output_file=files["msgpack_trajectory"].filepath,
report_interval=1000,
beta=1.0 / (openmm.unit.MOLAR_GAS_CONSTANT_R * compute_config["temperature"] * openmm.unit.kelvin),
pressure=pressure * openmm.unit.kilopascal,
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)
)

logger.info("Running 10,000 steps of MD")

detected_platform = simulation.context.getPlatform().getName()
Expand Down
28 changes: 19 additions & 9 deletions tyff/compute/_produce.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import openmm.app
from parsl import File

import tyff.mm
from tyff.compute._files import (
EquilibrationFiles,
ProductionFiles,
Expand Down Expand Up @@ -97,6 +98,11 @@ def _run_production(

assert barostat.getDefaultPressure() is not None

pressure = compute_config.get("pressure", None)

if pressure is None:
raise PressureNotDefinedError("Trying to set up NPT simulation but no pressure defined.")

simulation.context.setVelocitiesToTemperature(
compute_config["temperature"], # kelvin, but as float
compute_config["replicate_index"] + 1,
Expand All @@ -117,17 +123,21 @@ def _run_production(
)
)

dcd_reporter = openmm.app.DCDReporter(
file=files["dcd_trajectory"].filepath,
reportInterval=1000,
simulation.reporters.append(
openmm.app.DCDReporter(
file=files["dcd_trajectory"].filepath,
reportInterval=1000,
)
)

simulation.reporters.append(dcd_reporter)

pressure = compute_config.get("pressure", None)

if pressure is None:
raise PressureNotDefinedError("Trying to set up NPT simulation but no pressure defined.")
simulation.reporters.append(
tyff.mm.TensorReporter(
output_file=files["msgpack_trajectory"].filepath,
report_interval=1000,
beta=1.0 / (openmm.unit.MOLAR_GAS_CONSTANT_R * compute_config["temperature"] * openmm.unit.kelvin),
pressure=pressure * openmm.unit.kilopascal,
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mattwthompson marked this conversation as resolved.
)
)

logger.info("Running 100,000 steps of MD")

Expand Down
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