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Use smee.mm.TensorReporter in MD apps #113

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Use smee.mm.TensorReporter in MD apps #113

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7d71b3f
Use `smee` reporter
mattwthompson Jul 21, 2026
aee259b
Fix beta definition
mattwthompson Jul 22, 2026
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38 changes: 34 additions & 4 deletions dimsim/compute/apps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,7 @@ def run_equilibration(
import openmm
import openmm.app
import openmm.unit
from smee.mm import TensorReporter

logging.basicConfig(
filename=f"{job_dir}/simulation.log",
Expand Down Expand Up @@ -247,6 +248,7 @@ def run_equilibration(
File(f"{job_dir}/production_system.xml"), # probably don't need to carry this through ...
File(f"{job_dir}/equilibration_integrator.xml"),
File(f"{job_dir}/equilibration_checkpoint.chk"),
File(f"{job_dir}/equilibration_trajectory.msgpack"),
]

simulation.reporters.append(
Expand All @@ -264,10 +266,23 @@ def run_equilibration(
)
)

simulation.reporters.append(openmm.app.DCDReporter(simulation_files[1].filepath, 1000))
dcd_reporter = openmm.app.DCDReporter(
file=simulation_files[1].filepath,
reportInterval=1000,
)

smee_reporter = TensorReporter(
output_file=open(simulation_files[6].filepath, "wb"),
report_interval=1000,
beta=1.0 / openmm.unit.kilocalories_per_mole,
pressure=compute_config["pressure"] * openmm.unit.kilopascal,
)

simulation.reporters.append(dcd_reporter)
simulation.reporters.append(smee_reporter)

logging.info("Running 10,000 steps of MD")
# simulation.step(equilibration_config["steps_per_iteration"])

simulation.step(10_000)

with open(simulation_files[0].filepath, "w") as f:
Expand Down Expand Up @@ -298,9 +313,10 @@ def run_production(
equilibration_future: dict[str, tuple[File, ...]],
job_dir: str,
) -> dict[str, tuple[File, ...]]:

import logging

from smee.mm import TensorReporter

logging.basicConfig(
filename=f"{job_dir}/simulation.log",
level=logging.INFO,
Expand Down Expand Up @@ -332,6 +348,7 @@ def run_production(
File(f"{job_dir}/production_system.xml"),
File(f"{job_dir}/production_integrator.xml"),
File(f"{job_dir}/production_checkpoint.chk"),
File(f"{job_dir}/production_trajectory.msgpack"),
]

simulation.reporters.append(
Expand All @@ -349,7 +366,20 @@ def run_production(
)
)

simulation.reporters.append(openmm.app.DCDReporter(simulation_files[1].filepath, 1000))
dcd_reporter = openmm.app.DCDReporter(
file=simulation_files[1].filepath,
reportInterval=1000,
)

smee_reporter = TensorReporter(
output_file=open(simulation_files[6].filepath, "wb"),
report_interval=1000,
beta=1.0 / openmm.unit.kilocalories_per_mole,
pressure=compute_config["pressure"] * openmm.unit.kilopascal,
)

simulation.reporters.append(dcd_reporter)
simulation.reporters.append(smee_reporter)

logging.info("Running 100,000 steps of MD")
# simulation.step(equilibration_config["steps_per_iteration"])
Expand Down
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