def setopts(self, **kwargs):
""" Called by __init__ ; Set AMBER-specific options. """
## The directory containing TINKER executables (e.g. dynamic)
if 'amberhome' in kwargs:
self.amberhome = kwargs['amberhome']
if not os.path.exists(os.path.join(self.amberhome,"sander")):
warn_press_key("The 'sander' executable indicated by %s doesn't exist! (Check amberhome)" \
% os.path.join(self.amberhome,"sander"))
else:
warn_once("The 'amberhome' option was not specified; using default.")
if which('sander') == '':
warn_press_key("Please add AMBER executables to the PATH or specify amberhome.")
self.amberhome = os.path.split(which('sander'))[0]
with wopen('.quit.leap') as f:
print >> f, 'quit'
# AMBER search path
self.spath = []
for line in self.callamber('tleap -f .quit.leap'):
if 'Adding' in line and 'to search path' in line:
self.spath.append(line.split('Adding')[1].split()[0])
os.remove('.quit.leap')
def __init__(self, options, tgt_opts, forcefield):
if not recharge_import_success:
warn_once("Note: Failed to import the OpenFF Recharge package - FB Recharge_SMIRNOFF target will not work. ")
if not toolkit_import_success:
warn_once("Note: Failed to import the OpenFF Toolkit - FB Recharge_SMIRNOFF target will not work. ")
super(Recharge_SMIRNOFF, self).__init__(options, tgt_opts, forcefield)
# Store a mapping between the FB pval parameters and the expected recharge
# ordering.
self._parameter_to_bcc_map = None
# Pre-calculate the expensive portion of the objective function.
self._design_matrix = None
self._target_residuals = None
# Store a copy of the objective function details from the previous
# optimisation cycle.
self._molecule_residual_ranges = {}
self._per_molecule_residuals = {}
# Get the filename for the database which contains the ESP data
# to train against.
self.set_option(tgt_opts, "recharge_esp_store", forceprint=True)
self.set_option(tgt_opts, "recharge_property", forceprint=True)
assert self.recharge_property in ["esp", "electric-field"]
# Initialize the target.
self._initialize()
def setopts(self, **kwargs):
""" Called by __init__ ; Set AMBER-specific options. """
## The directory containing TINKER executables (e.g. dynamic)
if 'amberhome' in kwargs:
self.amberhome = kwargs['amberhome']
if not os.path.exists(os.path.join(self.amberhome, "sander")):
warn_press_key("The 'sander' executable indicated by %s doesn't exist! (Check amberhome)" \
% os.path.join(self.amberhome,"sander"))
else:
warn_once(
"The 'amberhome' option was not specified; using default.")
if which('sander') == '':
warn_press_key(
"Please add AMBER executables to the PATH or specify amberhome."
)
self.amberhome = os.path.split(which('sander'))[0]
with wopen('.quit.leap') as f:
print >> f, 'quit'
# AMBER search path
self.spath = []
for line in self.callamber('tleap -f .quit.leap'):
if 'Adding' in line and 'to search path' in line:
self.spath.append(line.split('Adding')[1].split()[0])
os.remove('.quit.leap')
def normal_modes(self, shot=0, optimize=True):
logger.error('Normal modes are not yet implemented in AMBER interface')
raise NotImplementedError
# Copied from tinkerio.py
if optimize:
self.optimize(shot, crit=1e-6)
o = self.calltinker("vibrate %s.xyz_2 a" % (self.name))
else:
warn_once("Asking for normal modes without geometry optimization?")
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
o = self.calltinker("vibrate %s.xyz a" % (self.name))
# Read the TINKER output. The vibrational frequencies are ordered.
# The six modes with frequencies closest to zero are ignored
readev = False
calc_eigvals = []
calc_eigvecs = []
for line in o:
s = line.split()
if "Vibrational Normal Mode" in line:
freq = float(s[-2])
readev = False
calc_eigvals.append(freq)
calc_eigvecs.append([])
elif "Atom" in line and "Delta X" in line:
readev = True
elif readev and len(s) == 4 and all(
[isint(s[0]),
isfloat(s[1]),
isfloat(s[2]),
isfloat(s[3])]):
calc_eigvecs[-1].append([float(i) for i in s[1:]])
calc_eigvals = np.array(calc_eigvals)
calc_eigvecs = np.array(calc_eigvecs)
# Sort by frequency absolute value and discard the six that are closest to zero
calc_eigvecs = calc_eigvecs[np.argsort(np.abs(calc_eigvals))][6:]
calc_eigvals = calc_eigvals[np.argsort(np.abs(calc_eigvals))][6:]
# Sort again by frequency
calc_eigvecs = calc_eigvecs[np.argsort(calc_eigvals)]
calc_eigvals = calc_eigvals[np.argsort(calc_eigvals)]
os.system("rm -rf *.xyz_* *.[0-9][0-9][0-9]")
return calc_eigvals, calc_eigvecs
def __init__(self, options, tgt_opts, forcefield):
if not evaluator_import_success:
warn_once(
"Note: Failed to import the OpenFF Evaluator - FB Evaluator target will not work. "
)
if not toolkit_import_success:
warn_once(
"Note: Failed to import the OpenFF Toolkit - FB Evaluator target will not work. "
)
super(Evaluator_SMIRNOFF, self).__init__(options, tgt_opts, forcefield)
self._options = None # The options for this target loaded from JSON.
self._default_units = (
{}) # The default units to convert each type of property to.
self._client = None # The client object which will communicate with an already spun up server.
self._reference_data_set = None # The data set of properties to estimate.
self._normalised_weights = (
None # The normalised weights of the different properties.
)
# Store a `Future` like object which can be queried for the results of
# a property estimation.
self._pending_estimate_request = None
# Store a mapping between gradient keys and the force balance string representation.
self._gradient_key_mappings = {}
self._parameter_units = {}
# Store a copy of the objective function details from the previous optimisation cycle.
self._last_obj_details = {}
# Get the filename for the evaluator input file.
self.set_option(tgt_opts, "evaluator_input", forceprint=True)
# Initialize the target.
self._initialize()
def normal_modes(self, shot=0, optimize=True):
logger.error('Normal modes are not yet implemented in AMBER interface')
raise NotImplementedError
# Copied from tinkerio.py
if optimize:
self.optimize(shot, crit=1e-6)
o = self.calltinker("vibrate %s.xyz_2 a" % (self.name))
else:
warn_once("Asking for normal modes without geometry optimization?")
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
o = self.calltinker("vibrate %s.xyz a" % (self.name))
# Read the TINKER output. The vibrational frequencies are ordered.
# The six modes with frequencies closest to zero are ignored
readev = False
calc_eigvals = []
calc_eigvecs = []
for line in o:
s = line.split()
if "Vibrational Normal Mode" in line:
freq = float(s[-2])
readev = False
calc_eigvals.append(freq)
calc_eigvecs.append([])
elif "Atom" in line and "Delta X" in line:
readev = True
elif readev and len(s) == 4 and all([isint(s[0]), isfloat(s[1]), isfloat(s[2]), isfloat(s[3])]):
calc_eigvecs[-1].append([float(i) for i in s[1:]])
calc_eigvals = np.array(calc_eigvals)
calc_eigvecs = np.array(calc_eigvecs)
# Sort by frequency absolute value and discard the six that are closest to zero
calc_eigvecs = calc_eigvecs[np.argsort(np.abs(calc_eigvals))][6:]
calc_eigvals = calc_eigvals[np.argsort(np.abs(calc_eigvals))][6:]
# Sort again by frequency
calc_eigvecs = calc_eigvecs[np.argsort(calc_eigvals)]
calc_eigvals = calc_eigvals[np.argsort(calc_eigvals)]
os.system("rm -rf *.xyz_* *.[0-9][0-9][0-9]")
return calc_eigvals, calc_eigvecs
import os
import numpy as np
from forcebalance.nifty import printcool_dictionary, warn_once
from forcebalance.output import getLogger
from forcebalance.target import Target
try:
from openff.recharge.charges.charges import ChargeSettings
from openff.recharge.esp.storage import MoleculeESPStore
from openff.recharge.optimize import ESPOptimization
from openff.recharge.smirnoff import from_smirnoff
except ImportError:
warn_once("Note: Failed to import the optional openff.recharge package.")
try:
from openforcefield.typing.engines import smirnoff
except ImportError:
warn_once("Note: Failed to import the optional openforcefield package. ")
logger = getLogger(__name__)
class Recharge_SMIRNOFF(Target):
"""A custom optimisation target which employs the `openff-recharge`
package to train bond charge correction parameters against QM derived
electrostatic potential data."""
def __init__(self, options, tgt_opts, forcefield):
def molecular_dynamics(self, nsteps, timestep, temperature=None, pressure=None, nequil=0, nsave=1000, minimize=True, anisotropic=False, threads=1, verbose=False, **kwargs):
"""
Method for running a molecular dynamics simulation.
Required arguments:
nsteps = (int) Number of total time steps
timestep = (float) Time step in FEMTOSECONDS
temperature = (float) Temperature control (Kelvin)
pressure = (float) Pressure control (atmospheres)
nequil = (int) Number of additional time steps at the beginning for equilibration
nsave = (int) Step interval for saving and printing data
minimize = (bool) Perform an energy minimization prior to dynamics
threads = (int) Specify how many OpenMP threads to use
Returns simulation data:
Rhos = (array) Density in kilogram m^-3
Potentials = (array) Potential energies
Kinetics = (array) Kinetic energies
Volumes = (array) Box volumes
Dips = (3xN array) Dipole moments
EComps = (dict) Energy components
"""
logger.error('Molecular dynamics not yet implemented in AMBER interface')
raise NotImplementedError
md_defs = OrderedDict()
md_opts = OrderedDict()
# Print out averages only at the end.
md_opts["printout"] = nsave
md_opts["openmp-threads"] = threads
# Langevin dynamics for temperature control.
if temperature != None:
md_defs["integrator"] = "stochastic"
else:
md_defs["integrator"] = "beeman"
md_opts["thermostat"] = None
# Periodic boundary conditions.
if self.pbc:
md_opts["vdw-correction"] = ''
if temperature != None and pressure != None:
md_defs["integrator"] = "beeman"
md_defs["thermostat"] = "bussi"
md_defs["barostat"] = "montecarlo"
if anisotropic:
md_opts["aniso-pressure"] = ''
elif pressure != None:
warn_once("Pressure is ignored because temperature is turned off.")
else:
if pressure != None:
warn_once("Pressure is ignored because pbc is set to False.")
# Use stochastic dynamics for the gas phase molecule.
# If we use the regular integrators it may miss
# six degrees of freedom in calculating the kinetic energy.
md_opts["barostat"] = None
eq_opts = deepcopy(md_opts)
if self.pbc and temperature != None and pressure != None:
eq_opts["integrator"] = "beeman"
eq_opts["thermostat"] = "bussi"
eq_opts["barostat"] = "berendsen"
if minimize:
if verbose: logger.info("Minimizing the energy...")
self.optimize(method="bfgs", crit=1)
os.system("mv %s.xyz_2 %s.xyz" % (self.name, self.name))
if verbose: logger.info("Done\n")
# Run equilibration.
if nequil > 0:
write_key("%s-eq.key" % self.name, eq_opts, "%s.key" % self.name, md_defs)
if verbose: printcool("Running equilibration dynamics", color=0)
if self.pbc and pressure != None:
self.calltinker("dynamic %s -k %s-eq %i %f %f 4 %f %f" % (self.name, self.name, nequil, timestep, float(nsave*timestep)/1000,
temperature, pressure), print_to_screen=verbose)
else:
self.calltinker("dynamic %s -k %s-eq %i %f %f 2 %f" % (self.name, self.name, nequil, timestep, float(nsave*timestep)/1000,
temperature), print_to_screen=verbose)
os.system("rm -f %s.arc" % (self.name))
# Run production.
if verbose: printcool("Running production dynamics", color=0)
write_key("%s-md.key" % self.name, md_opts, "%s.key" % self.name, md_defs)
if self.pbc and pressure != None:
odyn = self.calltinker("dynamic %s -k %s-md %i %f %f 4 %f %f" % (self.name, self.name, nsteps, timestep, float(nsave*timestep/1000),
temperature, pressure), print_to_screen=verbose)
else:
odyn = self.calltinker("dynamic %s -k %s-md %i %f %f 2 %f" % (self.name, self.name, nsteps, timestep, float(nsave*timestep/1000),
temperature), print_to_screen=verbose)
# Gather information.
os.system("mv %s.arc %s-md.arc" % (self.name, self.name))
self.md_trajectory = "%s-md.arc" % self.name
edyn = []
kdyn = []
temps = []
for line in odyn:
s = line.split()
if 'Current Potential' in line:
edyn.append(float(s[2]))
if 'Current Kinetic' in line:
kdyn.append(float(s[2]))
if len(s) > 0 and s[0] == 'Temperature' and s[2] == 'Kelvin':
temps.append(float(s[1]))
# Potential and kinetic energies converted to kJ/mol.
edyn = np.array(edyn) * 4.184
kdyn = np.array(kdyn) * 4.184
temps = np.array(temps)
if verbose: logger.info("Post-processing to get the dipole moments\n")
oanl = self.calltinker("analyze %s-md.arc" % self.name, stdin="G,E,M", print_to_screen=False)
# Read potential energy and dipole from file.
eanl = []
dip = []
mass = 0.0
ecomp = OrderedDict()
havekeys = set()
first_shot = True
for ln, line in enumerate(oanl):
strip = line.strip()
s = line.split()
if 'Total System Mass' in line:
mass = float(s[-1])
if 'Total Potential Energy : ' in line:
eanl.append(float(s[4]))
if 'Dipole X,Y,Z-Components :' in line:
dip.append([float(s[i]) for i in range(-3,0)])
if first_shot:
for key in eckeys:
if strip.startswith(key):
if key in ecomp:
ecomp[key].append(float(s[-2])*4.184)
else:
ecomp[key] = [float(s[-2])*4.184]
if key in havekeys:
first_shot = False
havekeys.add(key)
else:
for key in havekeys:
if strip.startswith(key):
if key in ecomp:
ecomp[key].append(float(s[-2])*4.184)
else:
ecomp[key] = [float(s[-2])*4.184]
for key in ecomp:
ecomp[key] = np.array(ecomp[key])
ecomp["Potential Energy"] = edyn
ecomp["Kinetic Energy"] = kdyn
ecomp["Temperature"] = temps
ecomp["Total Energy"] = edyn+kdyn
# Energies in kilojoules per mole
eanl = np.array(eanl) * 4.184
# Dipole moments in debye
dip = np.array(dip)
# Volume of simulation boxes in cubic nanometers
# Conversion factor derived from the following:
# In [22]: 1.0 * gram / mole / (1.0 * nanometer)**3 / AVOGADRO_CONSTANT_NA / (kilogram/meter**3)
# Out[22]: 1.6605387831627252
conv = 1.6605387831627252
if self.pbc:
vol = np.array([BuildLatticeFromLengthsAngles(*[float(j) for j in line.split()]).V \
for line in open("%s-md.arc" % self.name).readlines() \
if (len(line.split()) == 6 and isfloat(line.split()[1]) \
and all([isfloat(i) for i in line.split()[:6]]))]) / 1000
rho = conv * mass / vol
else:
vol = None
rho = None
prop_return = OrderedDict()
prop_return.update({'Rhos': rho, 'Potentials': edyn, 'Kinetics': kdyn, 'Volumes': vol, 'Dips': dip, 'Ecomps': ecomp})
return prop_return
import numpy as np
from forcebalance.nifty import warn_once, printcool, printcool_dictionary
from forcebalance.output import getLogger
from forcebalance.target import Target
try:
from openff.evaluator import unit
from openff.evaluator.attributes import UNDEFINED
from openff.evaluator.client import EvaluatorClient, ConnectionOptions, RequestOptions
from openff.evaluator.datasets import PhysicalPropertyDataSet
from openff.evaluator.utils.exceptions import EvaluatorException
from openff.evaluator.utils.openmm import openmm_quantity_to_pint
from openff.evaluator.utils.serialization import TypedJSONDecoder, TypedJSONEncoder
from openff.evaluator.forcefield import ParameterGradientKey
except ImportError:
warn_once("Note: Failed to import the optional openff.evaluator package. ")
try:
from openforcefield.typing.engines import smirnoff
except ImportError:
warn_once("Note: Failed to import the optional openforcefield package. ")
logger = getLogger(__name__)
class Evaluator_SMIRNOFF(Target):
"""A custom optimisation target which employs the `openff-evaluator`
package to rapidly estimate a collection of condensed phase physical
properties at each optimisation epoch."""
class OptionsFile:
"""Represents the set of options that a `Evaluator_SMIRNOFF`
from forcebalance.target import Target
logger = getLogger(__name__)
try:
import propertyestimator
from propertyestimator import unit
from propertyestimator.client import PropertyEstimatorClient, ConnectionOptions, PropertyEstimatorOptions
from propertyestimator.datasets import ThermoMLDataSet, PhysicalPropertyDataSet
from propertyestimator.utils.exceptions import PropertyEstimatorException
from propertyestimator.utils.openmm import openmm_quantity_to_pint
from propertyestimator.utils.serialization import TypedJSONDecoder, TypedJSONEncoder
from propertyestimator.workflow import WorkflowOptions
from propertyestimator.properties import ParameterGradientKey
except ImportError:
warn_once("Failed to import the propertyestimator package.")
try:
from openforcefield.typing.engines import smirnoff
except ImportError:
warn_once("Failed to import the openforcefield package.")
class PropertyEstimate_SMIRNOFF(Target):
"""A custom optimisation target which employs the propertyestimator
package to rapidly estimate a collection of condensed phase physical
properties at each optimisation epoch."""
class OptionsFile:
"""Represents the set of options that a `PropertyEstimate_SMIRNOFF`
target will be run with.
def molecular_dynamics(self,
nsteps,
timestep,
temperature=None,
pressure=None,
nequil=0,
nsave=1000,
minimize=True,
anisotropic=False,
threads=1,
verbose=False,
**kwargs):
"""
Method for running a molecular dynamics simulation.
Required arguments:
nsteps = (int) Number of total time steps
timestep = (float) Time step in FEMTOSECONDS
temperature = (float) Temperature control (Kelvin)
pressure = (float) Pressure control (atmospheres)
nequil = (int) Number of additional time steps at the beginning for equilibration
nsave = (int) Step interval for saving and printing data
minimize = (bool) Perform an energy minimization prior to dynamics
threads = (int) Specify how many OpenMP threads to use
Returns simulation data:
Rhos = (array) Density in kilogram m^-3
Potentials = (array) Potential energies
Kinetics = (array) Kinetic energies
Volumes = (array) Box volumes
Dips = (3xN array) Dipole moments
EComps = (dict) Energy components
"""
logger.error(
'Molecular dynamics not yet implemented in AMBER interface')
raise NotImplementedError
md_defs = OrderedDict()
md_opts = OrderedDict()
# Print out averages only at the end.
md_opts["printout"] = nsave
md_opts["openmp-threads"] = threads
# Langevin dynamics for temperature control.
if temperature != None:
md_defs["integrator"] = "stochastic"
else:
md_defs["integrator"] = "beeman"
md_opts["thermostat"] = None
# Periodic boundary conditions.
if self.pbc:
md_opts["vdw-correction"] = ''
if temperature != None and pressure != None:
md_defs["integrator"] = "beeman"
md_defs["thermostat"] = "bussi"
md_defs["barostat"] = "montecarlo"
if anisotropic:
md_opts["aniso-pressure"] = ''
elif pressure != None:
warn_once(
"Pressure is ignored because temperature is turned off.")
else:
if pressure != None:
warn_once("Pressure is ignored because pbc is set to False.")
# Use stochastic dynamics for the gas phase molecule.
# If we use the regular integrators it may miss
# six degrees of freedom in calculating the kinetic energy.
md_opts["barostat"] = None
eq_opts = deepcopy(md_opts)
if self.pbc and temperature != None and pressure != None:
eq_opts["integrator"] = "beeman"
eq_opts["thermostat"] = "bussi"
eq_opts["barostat"] = "berendsen"
if minimize:
if verbose: logger.info("Minimizing the energy...")
self.optimize(method="bfgs", crit=1)
os.system("mv %s.xyz_2 %s.xyz" % (self.name, self.name))
if verbose: logger.info("Done\n")
# Run equilibration.
if nequil > 0:
write_key("%s-eq.key" % self.name, eq_opts, "%s.key" % self.name,
md_defs)
if verbose: printcool("Running equilibration dynamics", color=0)
if self.pbc and pressure != None:
self.calltinker(
"dynamic %s -k %s-eq %i %f %f 4 %f %f" %
(self.name, self.name, nequil, timestep,
float(nsave * timestep) / 1000, temperature, pressure),
print_to_screen=verbose)
else:
self.calltinker("dynamic %s -k %s-eq %i %f %f 2 %f" %
(self.name, self.name, nequil, timestep,
float(nsave * timestep) / 1000, temperature),
print_to_screen=verbose)
os.system("rm -f %s.arc" % (self.name))
# Run production.
if verbose: printcool("Running production dynamics", color=0)
write_key("%s-md.key" % self.name, md_opts, "%s.key" % self.name,
md_defs)
if self.pbc and pressure != None:
odyn = self.calltinker(
"dynamic %s -k %s-md %i %f %f 4 %f %f" %
(self.name, self.name, nsteps, timestep,
float(nsave * timestep / 1000), temperature, pressure),
print_to_screen=verbose)
else:
odyn = self.calltinker(
"dynamic %s -k %s-md %i %f %f 2 %f" %
(self.name, self.name, nsteps, timestep,
float(nsave * timestep / 1000), temperature),
print_to_screen=verbose)
# Gather information.
os.system("mv %s.arc %s-md.arc" % (self.name, self.name))
self.md_trajectory = "%s-md.arc" % self.name
edyn = []
kdyn = []
temps = []
for line in odyn:
s = line.split()
if 'Current Potential' in line:
edyn.append(float(s[2]))
if 'Current Kinetic' in line:
kdyn.append(float(s[2]))
if len(s) > 0 and s[0] == 'Temperature' and s[2] == 'Kelvin':
temps.append(float(s[1]))
# Potential and kinetic energies converted to kJ/mol.
edyn = np.array(edyn) * 4.184
kdyn = np.array(kdyn) * 4.184
temps = np.array(temps)
if verbose: logger.info("Post-processing to get the dipole moments\n")
oanl = self.calltinker("analyze %s-md.arc" % self.name,
stdin="G,E,M",
print_to_screen=False)
# Read potential energy and dipole from file.
eanl = []
dip = []
mass = 0.0
ecomp = OrderedDict()
havekeys = set()
first_shot = True
for ln, line in enumerate(oanl):
strip = line.strip()
s = line.split()
if 'Total System Mass' in line:
mass = float(s[-1])
if 'Total Potential Energy : ' in line:
eanl.append(float(s[4]))
if 'Dipole X,Y,Z-Components :' in line:
dip.append([float(s[i]) for i in range(-3, 0)])
if first_shot:
for key in eckeys:
if strip.startswith(key):
if key in ecomp:
ecomp[key].append(float(s[-2]) * 4.184)
else:
ecomp[key] = [float(s[-2]) * 4.184]
if key in havekeys:
first_shot = False
havekeys.add(key)
else:
for key in havekeys:
if strip.startswith(key):
if key in ecomp:
ecomp[key].append(float(s[-2]) * 4.184)
else:
ecomp[key] = [float(s[-2]) * 4.184]
for key in ecomp:
ecomp[key] = np.array(ecomp[key])
ecomp["Potential Energy"] = edyn
ecomp["Kinetic Energy"] = kdyn
ecomp["Temperature"] = temps
ecomp["Total Energy"] = edyn + kdyn
# Energies in kilojoules per mole
eanl = np.array(eanl) * 4.184
# Dipole moments in debye
dip = np.array(dip)
# Volume of simulation boxes in cubic nanometers
# Conversion factor derived from the following:
# In [22]: 1.0 * gram / mole / (1.0 * nanometer)**3 / AVOGADRO_CONSTANT_NA / (kilogram/meter**3)
# Out[22]: 1.6605387831627252
conv = 1.6605387831627252
if self.pbc:
vol = np.array([BuildLatticeFromLengthsAngles(*[float(j) for j in line.split()]).V \
for line in open("%s-md.arc" % self.name).readlines() \
if (len(line.split()) == 6 and isfloat(line.split()[1]) \
and all([isfloat(i) for i in line.split()[:6]]))]) / 1000
rho = conv * mass / vol
else:
vol = None
rho = None
prop_return = OrderedDict()
prop_return.update({
'Rhos': rho,
'Potentials': edyn,
'Kinetics': kdyn,
'Volumes': vol,
'Dips': dip,
'Ecomps': ecomp
})
return prop_return