import numpy as np
import os
import tqdm
from openeye import oechem, oeiupac
from openmmtools import integrators, states, mcmc, constants
from openmoltools import forcefield_generators
from perses.rjmc.topology_proposal import TopologyProposal, SystemGenerator
from perses.rjmc.geometry import FFAllAngleGeometryEngine
from perses.annihilation.ncmc_switching import NCMCEngine
from perses.tests.utils import extractPositionsFromOEMOL
from simtk import openmm, unit
from io import StringIO
from simtk.openmm import app
import copy
from perses.dispersed.feptasks import compute_reduced_potential
import mdtraj as md

def run_equilibrium(system, topology, configuration, n_steps, report_interval, equilibration_steps, filename):
    from mdtraj.reporters import HDF5Reporter
    integrator = integrators.LangevinIntegrator()
    simulation = app.Simulation(topology, system, integrator)
    simulation.context.setPositions(configuration)
    openmm.LocalEnergyMinimizer.minimize(simulation.context)

    #equilibrate:
    integrator.step(equilibration_steps)

    reporter = HDF5Reporter(filename, report_interval)
    simulation.reporters.append(reporter)
    simulation.step(n_steps)

if __name__=="__main__":
    import yaml
    import sys
    import os

    yaml_filename = sys.argv[1]
    index = int(sys.argv[2])

    with open(yaml_filename, "r") as yamlfile:
        options = yaml.load(yamlfile)

    setup_options = options['setup']
    equilibrium_options = options['equilibrium']

    project_prefix = setup_options['project_prefix']
    setup_directory = setup_options['setup_directory']

    file_to_read = os.path.join(setup_directory, "{}_{}_initial.npy".format(project_prefix, index))

    positions, topology, system = np.load(file_to_read).item()

    omm_topology = topology.to_openmm()

    equilibration_steps = equilibrium_options['n_equilibration_steps'] * 1000 # value was in ps
    equilibrium_steps = equilibrium_options['n_equilibrium_steps'] * 1000 # also in ps
    output_directory = equilibrium_options['output_directory']
    report_interval = equilibrium_options['report_interval'] * 1000 # also in ps

    output_file = os.path.join(output_directory, "{}_{}.h5".format(project_prefix, index))

    run_equilibrium(system, topology, positions, equilibrium_steps, report_interval, equilibration_steps, output_file)
import numpy as np
import os
import tqdm
from openeye import oechem, oeiupac
from openmmtools import integrators, states, mcmc, constants
from openmoltools import forcefield_generators
from perses.rjmc.topology_proposal import TopologyProposal, SystemGenerator
from perses.rjmc.geometry import FFAllAngleGeometryEngine
from perses.annihilation.ncmc_switching import NCMCEngine
from perses.tests.utils import extractPositionsFromOEMOL
from simtk import openmm, unit
from io import StringIO
from simtk.openmm import app
import copy
from perses.dispersed.feptasks import compute_reduced_potential
import mdtraj as md

def run_equilibrium(system, topology, configuration, n_steps, report_interval, equilibration_steps, filename):
    from mdtraj.reporters import HDF5Reporter
    integrator = integrators.LangevinIntegrator()
    simulation = app.Simulation(topology, system, integrator)
    simulation.context.setPositions(configuration)
    openmm.LocalEnergyMinimizer.minimize(simulation.context)

    #equilibrate:
    integrator.step(equilibration_steps)

    print("equilibration complete")

    reporter = HDF5Reporter(filename, report_interval)
    simulation.reporters.append(reporter)
    simulation.step(n_steps)

if __name__=="__main__":
    import yaml
    import sys
    import os

    yaml_filename = sys.argv[1]
    index = int(sys.argv[2])

    with open(yaml_filename, "r") as yamlfile:
        options = yaml.load(yamlfile)

    setup_options = options['setup']
    equilibrium_options = options['equilibrium']

    project_prefix = setup_options['project_prefix']
    setup_directory = setup_options['setup_directory']

    file_to_read = os.path.join(setup_directory, "{}_{}_initial.npy".format(project_prefix, index))

    positions, topology, system = np.load(file_to_read).item()

    omm_topology = topology.to_openmm()

    equilibration_steps = equilibrium_options['n_equilibration_steps'] * 1000 # value was in ps
    equilibrium_steps = equilibrium_options['n_equilibrium_steps'] * 1000 # also in ps
    output_directory = equilibrium_options['output_directory']
    report_interval = equilibrium_options['report_interval'] * 1000 # also in ps

    output_file = os.path.join(output_directory, "{}_{}.h5".format(project_prefix, index))

    run_equilibrium(system, topology, positions, equilibrium_steps, report_interval, equilibration_steps, output_file)
Add print statement for completion of equilibration