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test_deepmd_dp_region.py
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import os
import time
import numpy as np
try:
import openmm as mm
from openmm import unit as u
from openmm.app import PDBFile, StateDataReporter, DCDReporter, Simulation
except:
import simtk.openmm as mm
from simtk import unit as u
from simtk.openmm.app import PDBFile, StateDataReporter, DCDReporter, Simulation
from OpenMMDeepmdPlugin import DeepPotentialModel
def test_deepmd_fixed_dp_particles_reference(nsteps = 1000, time_step = 0.2, Lambda = 1.0, platform_name = "Reference", output_temp_dir = "/tmp/openmm_deepmd_plugin_test_fixed_dp_particles_output", energy_std_tol = 25):
if not os.path.exists(output_temp_dir):
os.mkdir(output_temp_dir)
pdb_file = os.path.join(os.path.dirname(__file__), "../OpenMMDeepmdPlugin/data", "lw_256_test.pdb")
dp_model = os.path.join(os.path.dirname(__file__), "../OpenMMDeepmdPlugin/data", "water.pb")
output_dcd = os.path.join(output_temp_dir, f"lw_256_test.fixed.dp.region.reference.{Lambda}.dcd")
output_log = os.path.join(output_temp_dir, f"lw_256_test.fixed.dp.region.reference.{Lambda}.log")
# Set up the simulation parameters.
nsteps = nsteps
time_step = time_step # unit is femtosecond.
temperature = 300 # Kelvin
report_frequency = 100 # Save trajectory every report_frequency steps.
box = [19.807884, 0, 0, 0, 19.807884, 0, 0, 0, 19.807884]
box = [mm.Vec3(box[0], box[1], box[2]), mm.Vec3(box[3], box[4], box[5]), mm.Vec3(box[6], box[7], box[8])] * u.angstroms
liquid_water = PDBFile(pdb_file)
topology = liquid_water.topology
positions = liquid_water.getPositions()
# Create a mm system from scratch.
# In practice for DP/MM simulation with fixed DP region, the mm system can be created from a force field. Such as:
# forcefield = ForceField('amber99sbildn.xml', 'tip3p.xml')
# mm_system = forcefield.createSystem(topology, nonbondedMethod=PME, nonbondedCutoff=1.0*nanometers, constraints=HBonds)
mm_system = mm.System()
for atom in topology.atoms():
mm_system.addParticle(atom.element.mass)
# Set up the dp_system with the dp_model.
dp_model = DeepPotentialModel(dp_model, Lambda = Lambda)
dp_model.setUnitTransformCoefficients(10.0, 964.8792534459, 96.48792534459)
# Append the selected DP particles to DP region
dp_particles = []
for atom in topology.atoms():
# Assume the water molecules with residue.id = 1 will be selected as DP particles.
if int(atom.residue.id) == 1 or int(atom.residue.id) == 47 or int(atom.residue.id) == 17 or int(atom.residue.id) == 184:
dp_particles.append(atom.index)
dp_force = dp_model.addParticlesToDPRegion(dp_particles=dp_particles, topology = topology)
mm_system.addForce(dp_force)
integrator = mm.VerletIntegrator(time_step*u.femtoseconds)
platform = mm.Platform.getPlatformByName(platform_name)
# Build up the simulation object.
sim = Simulation(topology, mm_system, integrator, platform)
# In practice for DP/MM simulation with fixed DP region.
# The bonded forces within the DP region should be removed from the mm system.
# num_forces = mm_system.getNumForces()
# for force in mm_system.getForces():
# if isinstance(force, mm.HarmonicBondForce):
# num_bonds = force.getNumBonds()
# for bond_index in range(num_bonds):
# atom1, atom2, length, k = force.getBondParameters(bond_index)
# if atom1 in dp_particles and atom2 in dp_particles:
# # Remove the bond forces within the DP region.
# force.setBondParameters(bond_index, atom1, atom2, length, 0.0)
# force.updateParametersInContext(sim.context)
sim.context.setPeriodicBoxVectors(box[0], box[1], box[2])
sim.context.setPositions(positions)
# Add state reporters
sim.reporters.append(DCDReporter(output_dcd, report_frequency, enforcePeriodicBox=False))
sim.reporters.append(
StateDataReporter(output_log, report_frequency, step=True, time=True, totalEnergy=True, kineticEnergy=True, potentialEnergy=True, temperature=True, progress=True,
remainingTime=True, speed=True, density=True,totalSteps=nsteps, separator='\t')
)
# Run dynamics
print("Running dynamics")
start_time = time.time()
sim.step(nsteps)
end_time = time.time()
cost_time = end_time - start_time
print("Running on %s platform, time cost: %.4f s"%(platform_name, cost_time))
# Fetch the temperature info from the log file.
energy_trajectory = []
energy_index = -5
with open(output_log, "r") as f:
log_content = f.readlines()
for ii , line in enumerate(log_content):
if ii == 0:
continue
tmp = line.split()
energy_trajectory.append(float(tmp[energy_index]))
energy_trajectory = np.array(energy_trajectory)
assert (np.std(energy_trajectory) < energy_std_tol)
assert (np.std(energy_trajectory) > 0.0001)
def test_deepmd_fixed_dp_particles_cuda(nsteps = 1000, time_step = 0.2, Lambda = 1.0, platform_name = "CUDA", output_temp_dir = "/tmp/openmm_deepmd_plugin_test_fixed_dp_particles_output", energy_std_tol = 1):
if not os.path.exists(output_temp_dir):
os.mkdir(output_temp_dir)
pdb_file = os.path.join(os.path.dirname(__file__), "../OpenMMDeepmdPlugin/data", "lw_256_test.pdb")
dp_model = os.path.join(os.path.dirname(__file__), "../OpenMMDeepmdPlugin/data", "water.pb")
output_dcd = os.path.join(output_temp_dir, f"lw_256_test.fixed.dp.region.cuda.{Lambda}.dcd")
output_log = os.path.join(output_temp_dir, f"lw_256_test.fixed.dp.region.cuda.{Lambda}.log")
# Set up the simulation parameters.
nsteps = nsteps
time_step = time_step # unit is femtosecond.
report_frequency = 100 # Save trajectory every report_frequency steps.
box = [19.807884, 0, 0, 0, 19.807884, 0, 0, 0, 19.807884]
box = [mm.Vec3(box[0], box[1], box[2]), mm.Vec3(box[3], box[4], box[5]), mm.Vec3(box[6], box[7], box[8])] * u.angstroms
liquid_water = PDBFile(pdb_file)
topology = liquid_water.topology
positions = liquid_water.getPositions()
# Create a mm system from scratch.
# In practice for DP/MM simulation with fixed DP region, the mm system can be created from a force field. Such as:
# forcefield = ForceField('amber99sbildn.xml', 'tip3p.xml')
# mm_system = forcefield.createSystem(topology, nonbondedMethod=PME, nonbondedCutoff=1.0*nanometers, constraints=HBonds)
mm_system = mm.System()
for atom in topology.atoms():
mm_system.addParticle(atom.element.mass)
# Set up the dp_system with the dp_model.
dp_model = DeepPotentialModel(dp_model, Lambda = Lambda)
dp_model.setUnitTransformCoefficients(10.0, 964.8792534459, 96.48792534459)
# Append the selected DP particles to DP region
dp_particles = []
for atom in topology.atoms():
# Assume the water molecules with residue.id = 1 will be selected as DP particles.
if int(atom.residue.id) == 1 or int(atom.residue.id) == 47 or int(atom.residue.id) == 17 or int(atom.residue.id) == 184:
dp_particles.append(atom.index)
dp_force = dp_model.addParticlesToDPRegion(dp_particles=dp_particles, topology = topology)
mm_system.addForce(dp_force)
integrator = mm.VerletIntegrator(time_step*u.femtoseconds)
platform = mm.Platform.getPlatformByName(platform_name)
# Build up the simulation object.
sim = Simulation(topology, mm_system, integrator, platform)
# In practice for DP/MM simulation with fixed DP region.
# The bonded forces within the DP region should be removed from the mm system.
# num_forces = mm_system.getNumForces()
# for force in mm_system.getForces():
# if isinstance(force, mm.HarmonicBondForce):
# num_bonds = force.getNumBonds()
# for bond_index in range(num_bonds):
# atom1, atom2, length, k = force.getBondParameters(bond_index)
# if atom1 in dp_particles and atom2 in dp_particles:
# # Remove the bond forces within the DP region.
# force.setBondParameters(bond_index, atom1, atom2, length, 0.0)
# force.updateParametersInContext(sim.context)
sim.context.setPeriodicBoxVectors(box[0], box[1], box[2])
sim.context.setPositions(positions)
# Add state reporters
sim.reporters.append(DCDReporter(output_dcd, report_frequency, enforcePeriodicBox=False))
sim.reporters.append(
StateDataReporter(output_log, report_frequency, step=True, time=True, totalEnergy=True, kineticEnergy=True, potentialEnergy=True, temperature=True, progress=True,
remainingTime=True, speed=True, density=True,totalSteps=nsteps, separator='\t')
)
# Run dynamics
print("Running dynamics")
start_time = time.time()
sim.step(nsteps)
end_time = time.time()
cost_time = end_time - start_time
print("Running on %s platform, time cost: %.4f s"%(platform_name, cost_time))
# Fetch the temperature info from the log file.
energy_trajectory = []
energy_index = -5
with open(output_log, "r") as f:
log_content = f.readlines()
for ii , line in enumerate(log_content):
if ii == 0:
continue
tmp = line.split()
energy_trajectory.append(float(tmp[energy_index]))
energy_trajectory = np.array(energy_trajectory)
assert (np.std(energy_trajectory) < energy_std_tol)
assert (np.std(energy_trajectory) > 0.0001)
if __name__ == "__main__":
test_deepmd_fixed_dp_particles_reference(nsteps = 5000, Lambda= 0.0)
test_deepmd_fixed_dp_particles_cuda(nsteps = 5000, Lambda= 0.0)