def test_calibration_class_multisite(self):
"""Test the multisite SAMS sampling approach."""
old_log_level = log.getEffectiveLevel()
pep = self.setup_peptide_implicit("yeah", createsim=True)
pep.drive.enable_calibration(SAMSApproach.MULTISITE)
sampler = SAMSCalibrationEngine(pep.drive)
total_iterations = 1500
for x in range(total_iterations):
if x == total_iterations - 1:
log.setLevel(logging.DEBUG)
pep.simulation.step(1)
pep.simulation.update(1)
sampler.adapt_zetas(UpdateRule.BINARY, b=0.51, stage=Stage.NODECAY)
log.setLevel(old_log_level)
return
def test_onesite_sams_sampling_global(self):
"""Test the one site sams sampling approach with global updates"""
old_log_level = log.getEffectiveLevel()
pep = self.setup_peptide_implicit("yeah")
pep.drive.enable_calibration(SAMSApproach.ONESITE, group_index=1)
sampler = SAMSCalibrationEngine(pep.drive)
total_iterations = 1500
for x in range(total_iterations):
if x == total_iterations - 1:
log.setLevel(logging.DEBUG)
pep.simulation.step(1)
pep.simulation.update(1)
sampler.adapt_zetas(UpdateRule.GLOBAL, b=0.51, stage=Stage.NODECAY)
log.setLevel(old_log_level)
def test_onesite_sams_sampling_binary_all_stages(self):
"""Test the one site sams sampling approach with binary updates through all 4 stages of the algorithm"""
old_log_level = log.getEffectiveLevel()
log.setLevel(logging.INFO)
pep = self.setup_peptide_implicit("yeah", createsim=False)
pep.drive.enable_calibration(
SAMSApproach.ONESITE,
group_index=0,
min_burn=200,
min_fast=100,
min_slow=100,
flatness_criterion=0.15,
)
pep.simulation = app.ConstantPHSimulation(
pep.topology,
pep.system,
pep.integrator,
pep.drive,
platform=TestSAMS.platform,
)
pep.simulation.context.setPositions(pep.positions)
pep.context = pep.simulation.context
pep.simulation.minimizeEnergy()
total_iterations = 1000
for x in range(total_iterations):
if x == total_iterations - 1:
log.setLevel(logging.DEBUG)
pep.simulation.step(1)
pep.simulation.update(1)
pep.simulation.adapt()
# log.info(pep.drive.calibration_state.observed_counts)
log.setLevel(old_log_level)
def test_onesite_sams_sampling_binary_all_stages_serialization(self):
"""Test the one site sams sampling approach with binary updates through all 4 stages of the algorithm
and after serialization."""
old_log_level = log.getEffectiveLevel()
log.setLevel(logging.INFO)
pep = self.setup_peptide_implicit("yeah", createsim=False)
pep.drive.enable_calibration(
SAMSApproach.ONESITE,
group_index=0,
min_burn=200,
min_fast=200,
min_slow=200,
flatness_criterion=0.15,
)
pep.simulation = app.ConstantPHSimulation(
pep.topology,
pep.system,
pep.integrator,
pep.drive,
platform=TestSAMS.platform,
)
pep.simulation.context.setPositions(pep.positions)
pep.context = pep.simulation.context
pep.simulation.minimizeEnergy()
total_iterations = 1000
for x in range(total_iterations):
pep.simulation.step(1)
pep.simulation.update(1)
pep.simulation.adapt()
pep.drive: NCMCProtonDrive
drive_state = pep.drive.state_to_xml()
new_drive = NCMCProtonDrive(
pep.temperature,
pep.topology,
pep.system,
pressure=None,
perturbations_per_trial=pep.perturbations_per_trial,
propagations_per_step=pep.propagations_per_step,
)
new_drive.state_from_xml_tree(etree.fromstring(drive_state))
new_simulation = app.ConstantPHSimulation(
pep.topology,
pep.system,
create_compound_gbaoab_integrator(pep),
new_drive,
platform=TestSAMS.platform,
)
old_state: app.State = pep.simulation.context.getState(
getPositions=True, getVelocities=True
)
new_simulation.context.setPositions(old_state.getPositions())
new_simulation.context.setVelocities(old_state.getVelocities())
total_iterations = 1000
for x in range(total_iterations):
if x == total_iterations - 1:
log.setLevel(logging.DEBUG)
new_simulation.step(1)
new_simulation.update(1)
new_simulation.adapt()
log.debug("Last deviation: %f", new_simulation.last_dev)
log.info(
"Observed counts: %s", str(pep.drive.calibration_state.observed_counts)
)
log.setLevel(old_log_level)
import numpy as np
from protons.app import AmberProtonDrive, ForceFieldProtonDrive, NCMCProtonDrive
from protons.app import ForceField
from protons.app import UniformProposal
from protons.app.calibration import SAMSCalibrationEngine
from protons.app.driver import SAMSApproach, Stage, UpdateRule
from protons.app import log
import logging
from protons.tests.utilities import (
SystemSetup,
create_compound_gbaoab_integrator,
hasCUDA,
)
log.setLevel(logging.INFO)
class TestSAMS:
"""Test the functionality of the ``app.calibration.WeighsTable`` class."""
if hasCUDA:
default_platform_name = "CUDA"
else:
default_platform_name = "CPU"
platform = mm.Platform.getPlatformByName(default_platform_name)
@staticmethod
def setup_peptide_implicit(name: str, minimize=True, createsim=True):
"""
from protons.app import ForceField
from protons.app import UniformProposal
from protons.app.template_patches import patch_cooh
from protons.app.proposals import UniformSwapProposal, COOHDummyMover
from protons.tests import get_test_data
from protons.tests.utilities import (
SystemSetup,
create_compound_gbaoab_integrator,
hasCUDA,
)
import logging
from random import choice, uniform, sample
from protons.app import log
from math import exp
log.setLevel(logging.INFO)
class TestCarboxylicAcid:
if hasCUDA:
default_platform_name = "CUDA"
else:
default_platform_name = "CPU"
platform = openmm.Platform.getPlatformByName(default_platform_name)
@staticmethod
def setup_viologen_vacuum():
"""
Set up viologen in vacuum
"""