def describeNextReport(self, simulation):
"""
Get information about the next report this object will generate.
Parameters
----------
simulation : :class:`app.Simulation`
The Simulation to generate a report for
Returns
-------
nsteps, pos, vel, frc, ene : int, bool, bool, bool, bool
nsteps is the number of steps until the next report
pos, vel, frc, and ene are flags indicating whether positions,
velocities, forces, and/or energies are needed from the Context
"""
if self._startTime is None:
# First time this is called, initialize the timers
self._startTime = timeofday()
self._lastReportTime = timeofday()
self._timeStep = simulation.integrator.getStepSize()
self._timeStep = self._timeStep.value_in_unit(u.nanosecond)
self._firstStep = simulation.currentStep
stepsleft = simulation.currentStep % self._reportInterval
steps = self._reportInterval - stepsleft
return (steps, False, False, False, self._needEnergy)
def describeNextReport(self, simulation):
"""
Get information about the next report this object will generate.
Parameters
----------
simulation : :class:`app.Simulation`
The Simulation to generate a report for
Returns
-------
nsteps, pos, vel, frc, ene : int, bool, bool, bool, bool
nsteps is the number of steps until the next report
pos, vel, frc, and ene are flags indicating whether positions,
velocities, forces, and/or energies are needed from the Context
"""
if self._startTime is None:
# First time this is called, initialize the timers
self._startTime = timeofday()
self._lastReportTime = timeofday()
self._timeStep = simulation.integrator.getStepSize()
self._timeStep = self._timeStep.value_in_unit(u.nanosecond)
self._firstStep = simulation.currentStep
stepsleft = simulation.currentStep % self._reportInterval
steps = self._reportInterval - stepsleft
return (steps, False, False, False, self._needEnergy)
def describeNextReport(self, simulation):
"""
Get information about the next report this object will generate.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
Returns: A five element tuple. The first element is the number of steps
until the next report. The remaining elements specify whether that
report will require positions, velocities, forces, and energies
respectively.
"""
if self._startTime is None:
# First time this is called, initialize the timers
self._startTime = timeofday()
self._lastReportTime = timeofday()
self._timeStep = simulation.integrator.getStepSize()
self._timeStep = self._timeStep.value_in_unit(u.nanosecond)
self._firstStep = simulation.currentStep
stepsleft = simulation.currentStep % self._reportInterval
steps = self._reportInterval - stepsleft
return (steps, False, False, False, self._needEnergy)
def report(self, simulation, state):
"""
Generate a report and predict the time to completion (and
current/overall MD performance)
"""
if not self._hasInitialized:
self._initializeConstants(simulation)
self._hasInitialized = True
# Check for errors.
self._checkForErrors(simulation, state)
# Query for the values
values = self._constructReportValues(simulation, state)
now = timeofday()
total_time = now - self._startTime
partial_time = now - self._lastReportTime
self._lastReportTime = now
total_nsperday = ((values['step'] - self._firstStep) * self._timeStep /
total_time)
partial_nsperday = (self._reportInterval *
self._timeStep) / partial_time
# Get total and partial ns/day (currently ns/second)
total_nsperday *= 3600 * 24
partial_nsperday *= 3600 * 24
# Estimated time to completion (based on performance of last N steps
remaining_steps = self._totalSteps - values['step'] + self._firstStep
etc = partial_time / self._reportInterval * remaining_steps
if etc > 3600:
etc /= 3600
unitstr = 'hr.'
elif etc > 60:
etc /= 60
unitstr = 'min.'
else:
unitstr = 'sec.'
# Write the values.
with open(self.fname, 'w') as f:
f.write('-+' * 39 + '\n')
f.write('\n')
f.write(' On step %d of %d\n' %
(values['step'] - self._firstStep, self._totalSteps))
f.write('\n')
if self._totalEnergy:
f.write(' Total Energy = %12.4f\n' %
values['totalEnergy'])
if self._potentialEnergy:
f.write(' Potential Energy = %12.4f\n' %
values['potentialEnergy'])
if self._kineticEnergy:
f.write(' Kinetic Energy = %12.4f\n' %
values['kineticEnergy'])
if self._volume:
f.write(' Volume = %12.4f\n' % values['volume'])
if self._density:
f.write(' Density = %12.4f\n' % values['density'])
if self._temperature:
f.write(' Temperature = %12.4f\n' %
values['temperature'])
f.write('\n')
f.write(' Time for last %8d steps: %10.4f s. (%.3f ns/day)\n' %
(self._reportInterval, partial_time, partial_nsperday))
f.write(
' Time for all %9d steps: %10.4f s. (%.3f ns/day)\n' %
(values['step'] - self._firstStep, total_time, total_nsperday))
f.write('\n')
f.write(' Estimated time to completion: %.3f %s\n' %
(etc, unitstr))
f.write('\n')
f.write('-+' * 39 + '\n')
if remaining_steps == 0: self._startTime = None
def report(self, simulation, state):
"""
Generate a report and predict the time to completion (and
current/overall MD performance)
"""
if not self._hasInitialized:
self._initializeConstants(simulation)
self._hasInitialized = True
# Check for errors.
self._checkForErrors(simulation, state)
# Query for the values
values = self._constructReportValues(simulation, state)
now = timeofday()
total_time = now - self._startTime
partial_time = now - self._lastReportTime
self._lastReportTime = now
total_nsperday = (values["step"] - self._firstStep) * self._timeStep / total_time
partial_nsperday = (self._reportInterval * self._timeStep) / partial_time
# Get total and partial ns/day (currently ns/second)
total_nsperday *= 3600 * 24
partial_nsperday *= 3600 * 24
# Estimated time to completion (based on performance of last N steps
remaining_steps = self._totalSteps - values["step"] + self._firstStep
etc = partial_time / self._reportInterval * remaining_steps
if etc > 3600:
etc /= 3600
unitstr = "hr."
elif etc > 60:
etc /= 60
unitstr = "min."
else:
unitstr = "sec."
# Write the values.
with open(self.fname, "w") as f:
f.write("-+" * 39 + "\n")
f.write("\n")
f.write(" On step %d of %d\n" % (values["step"] - self._firstStep, self._totalSteps))
f.write("\n")
if self._totalEnergy:
f.write(" Total Energy = %12.4f\n" % values["totalEnergy"])
if self._potentialEnergy:
f.write(" Potential Energy = %12.4f\n" % values["potentialEnergy"])
if self._kineticEnergy:
f.write(" Kinetic Energy = %12.4f\n" % values["kineticEnergy"])
if self._volume:
f.write(" Volume = %12.4f\n" % values["volume"])
if self._density:
f.write(" Density = %12.4f\n" % values["density"])
if self._temperature:
f.write(" Temperature = %12.4f\n" % values["temperature"])
f.write("\n")
f.write(
" Time for last %8d steps: %10.4f s. (%.3f ns/day)\n"
% (self._reportInterval, partial_time, partial_nsperday)
)
f.write(
" Time for all %9d steps: %10.4f s. (%.3f ns/day)\n"
% (values["step"] - self._firstStep, total_time, total_nsperday)
)
f.write("\n")
f.write(" Estimated time to completion: %.3f %s\n" % (etc, unitstr))
f.write("\n")
f.write("-+" * 39 + "\n")
if remaining_steps == 0:
self._startTime = None
def report(self, simulation, state):
"""
Generate a report and predict the time to completion (and
current/overall MD performance)
"""
if not self._hasInitialized:
self._initializeConstants(simulation)
self._hasInitialized = True
# Check for errors.
self._checkForErrors(simulation, state)
# Query for the values
values = self._constructReportValues(simulation, state)
now = timeofday()
total_time = now - self._startTime
partial_time = now - self._lastReportTime
self._lastReportTime = now
total_nsperday = ((values['step'] - self._firstStep) * self._timeStep /
total_time)
partial_nsperday = (self._reportInterval*self._timeStep) / partial_time
# Get total and partial ns/day (currently ns/second)
total_nsperday *= 3600 * 24
partial_nsperday *= 3600 * 24
# Estimated time to completion (based on performance of last N steps
remaining_steps = self._totalSteps - values['step'] + self._firstStep
etc = partial_time / self._reportInterval * remaining_steps
if etc > 3600:
etc /= 3600
unitstr = 'hr.'
elif etc > 60:
etc /= 60
unitstr = 'min.'
else:
unitstr = 'sec.'
# Write the values.
with open(self.fname, 'w') as f:
f.write('-+' * 39 + '\n')
f.write('\n')
f.write(' On step %d of %d\n' % (values['step'] - self._firstStep,
self._totalSteps))
f.write('\n')
if self._totalEnergy:
f.write(' Total Energy = %12.4f\n' % values['totalEnergy'])
if self._potentialEnergy:
f.write(' Potential Energy = %12.4f\n' %
values['potentialEnergy'])
if self._kineticEnergy:
f.write(' Kinetic Energy = %12.4f\n' %
values['kineticEnergy'])
if self._volume:
f.write(' Volume = %12.4f\n' % values['volume'])
if self._density:
f.write(' Density = %12.4f\n' % values['density'])
if self._temperature:
f.write(' Temperature = %12.4f\n' % values['temperature'])
f.write('\n')
f.write(' Time for last %8d steps: %10.4f s. (%.3f ns/day)\n' %
(self._reportInterval, partial_time, partial_nsperday))
f.write(' Time for all %9d steps: %10.4f s. (%.3f ns/day)\n' %
(values['step']-self._firstStep, total_time, total_nsperday)
)
f.write('\n')
f.write(' Estimated time to completion: %.3f %s\n' % (etc, unitstr))
f.write('\n')
f.write('-+' * 39 + '\n')
if remaining_steps == 0: self._startTime = None
