From 7d71b3f97ba011c631b517dbe43988b2e862db85 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 21 Jul 2026 16:03:16 -0500 Subject: [PATCH 1/2] Use `smee` reporter --- dimsim/compute/apps.py | 38 +++++++++++++++-- pixi.lock | 93 ++++++++++++++++++++---------------------- 2 files changed, 79 insertions(+), 52 deletions(-) diff --git a/dimsim/compute/apps.py b/dimsim/compute/apps.py index 0b9545c..948a08d 100644 --- a/dimsim/compute/apps.py +++ b/dimsim/compute/apps.py @@ -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", @@ -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( @@ -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 / (compute_config["temperature"] * openmm.unit.kelvin), + 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: @@ -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, @@ -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( @@ -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 / (compute_config["temperature"] * openmm.unit.kelvin), + 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"]) diff --git a/pixi.lock b/pixi.lock index d31d771..ba0c546 100644 --- a/pixi.lock +++ b/pixi.lock @@ -63,7 +63,7 @@ environments: - 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size: 26412 - timestamp: 1784376970393 + size: 26632 + timestamp: 1784661349391 - conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.6.0-pyhf9edf01_1.conda sha256: e14aafa63efa0528ca99ba568eaf506eb55a0371d12e6250aaaa61718d2eb62e md5: d7585b6550ad04c8c5e21097ada2888e @@ -10732,10 +10730,10 @@ packages: - hdf5 >=2.1.0,<3.0a0 size: 3418702 timestamp: 1775244340092 -- conda: https://conda.anaconda.org/conda-forge/osx-arm64/hf-xet-1.5.2-py310he76dbf2_0.conda +- conda: https://conda.anaconda.org/conda-forge/osx-arm64/hf-xet-1.5.2-py310he76dbf2_1.conda noarch: python - sha256: 3725755944a9a5d8a5d5192d9d0afa717677589497990603b78bb3a8c5cf5608 - md5: a7b5d80ac05814897cc4380b51d01055 + sha256: ae3cc87087670a3135475858ba0c5105fba318a84e23076b44a88602a35f09fd + md5: 76a1ca3ee8ac40988e882ed297299caf depends: - python - __osx >=11.0 @@ -10745,12 +10743,11 @@ packages: constrains: - __osx >=11.0 license: Apache-2.0 - license_family: APACHE purls: - pkg:pypi/hf-xet?source=hash-mapping run_exports: {} - size: 3348052 - timestamp: 1784270234484 + size: 3347116 + timestamp: 1784661242375 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/icu-75.1-hfee45f7_0.conda sha256: 9ba12c93406f3df5ab0a43db8a4b4ef67a5871dfd401010fbe29b218b2cbe620 md5: 5eb22c1d7b3fc4abb50d92d621583137 From aee259b6f2c2b0e587acf2189d49a45cb9e2b816 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 21 Jul 2026 21:39:02 -0500 Subject: [PATCH 2/2] Fix beta definition --- dimsim/compute/apps.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dimsim/compute/apps.py b/dimsim/compute/apps.py index 948a08d..b5d6803 100644 --- a/dimsim/compute/apps.py +++ b/dimsim/compute/apps.py @@ -274,7 +274,7 @@ def run_equilibration( smee_reporter = TensorReporter( output_file=open(simulation_files[6].filepath, "wb"), report_interval=1000, - beta=1 / (compute_config["temperature"] * openmm.unit.kelvin), + beta=1.0 / openmm.unit.kilocalories_per_mole, pressure=compute_config["pressure"] * openmm.unit.kilopascal, ) @@ -374,7 +374,7 @@ def run_production( smee_reporter = TensorReporter( output_file=open(simulation_files[6].filepath, "wb"), report_interval=1000, - beta=1 / (compute_config["temperature"] * openmm.unit.kelvin), + beta=1.0 / openmm.unit.kilocalories_per_mole, pressure=compute_config["pressure"] * openmm.unit.kilopascal, )