parmed.openmm.StateDataReporter¶
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class
parmed.openmm.StateDataReporter(**kwargs)[source]¶ This class acts as a state data reporter for OpenMM simulations, but it is a little more generalized. Notable differences are:
It allows the units of the output to be specified, with defaults being those used in Amber (e.g., kcal/mol, angstroms^3, etc.)
It will write to any object containing a ‘write’ method; not just files. This allows, for instance, writing to a GUI window that implements the desired ‘write’ attribute.
Most of this code is copied from the OpenMM StateDataReporter class, with the above-mentioned changes made.
- Parameters
- fstr or file-like
Destination to write the state data (file name or file object)
- reportIntervalint
Number of steps between state data reports
- stepbool, optional
Print out the step number (Default True)
- timebool, optional
Print out the simulation time (Defaults True)
- potentialEnergybool, optional
Print out the potential energy of the structure (Default True)
- kineticEnergybool, optional
Print out the kinetic energy of the structure (Default True)
- totalEnergybool, optional
Print out the total energy of the system (Default True)
- temperaturebool, optional
Print out the temperature of the system (Default True)
- volumebool, optional
Print out the volume of the unit cell. If the system is not periodic, the value is meaningless (Default False)
- densitybool, optional
Print out the density of the unit cell. If the system is not periodic, the value is meaningless (Default False)
- separatorstr, optional
The string to separate data fields (Default ‘,’)
- systemMassfloat, optional
If not None, the density will be computed from this mass, since setting a mass to 0 is used to constrain the position of that particle. (Default None)
- energyUnitunit, optional
The units to print energies in (default unit.kilocalories_per_mole)
- timeUnitunit, optional
The units to print time in (default unit.picoseconds)
- volumeUnitunit, optional
The units print volume in (default unit.angstroms**3)
- densityUnitunit, optional
The units to print density in (default unit.grams/unit.item/unit.milliliter)
Methods
describeNextReport(simulation)Get information about the next report this object will generate.
finalize()Closes any open file
report(simulation, state)Generate a report.
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__init__(f, reportInterval, step=True, time=True, potentialEnergy=True, kineticEnergy=True, totalEnergy=True, temperature=True, volume=False, density=False, separator=',', systemMass=None, energyUnit=Unit({BaseUnit(base_dim=BaseDimension('amount'), name='mole', symbol='mol'): - 1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), timeUnit=Unit({BaseUnit(base_dim=BaseDimension('time'), name='picosecond', symbol='ps'): 1.0}), volumeUnit=Unit({BaseUnit(base_dim=BaseDimension('length'), name='angstrom', symbol='A'): 3.0}), densityUnit=Unit({BaseUnit(base_dim=BaseDimension('mass'), name='gram', symbol='g'): 1.0, BaseUnit(base_dim=BaseDimension('amount'), name='item', symbol=''): - 1.0, ScaledUnit(factor=0.001, master=decimeter ** 3, name='milliliter', symbol='mL'): - 1.0}))[source]¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__(f, reportInterval[, step, time, …])Initialize self.
describeNextReport(simulation)Get information about the next report this object will generate.
finalize()Closes any open file
report(simulation, state)Generate a report.