""" statedatareporter.py: Outputs data about a simulation This is part of the OpenMM molecular simulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org. Portions copyright (c) 2012 Stanford University and the Authors. Authors: Peter Eastman Contributors: Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ __author__ = "Peter Eastman" __version__ = "1.0" import simtk.openmm as mm import simtk.unit as unit from simtk.openmm.app import PDBFile import math class StateDataReporter(object): """StateDataReporter outputs information about a simulation, such as energy and temperature, to a file. To use it, create a StateDataReporter, then add it to the Simulation's list of reporters. The set of data to write is configurable using boolean flags passed to the constructor. By default the data is written in comma-separated-value (CSV) format, but you can specify a different separator to use. """ def __init__(self, file, reportInterval, step=False, time=False, potentialEnergy=False, kineticEnergy=False, totalEnergy=False, temperature=False, volume=False, density=False, separator=','): """Create a StateDataReporter. Parameters: - file (string or file) The file to write to, specified as a file name or file object - reportInterval (int) The interval (in time steps) at which to write frames - step (boolean=False) Whether to write the current step index to the file - time (boolean=False) Whether to write the current time to the file - potentialEnergy (boolean=False) Whether to write the potential energy to the file - kineticEnergy (boolean=False) Whether to write the kinetic energy to the file - totalEnergy (boolean=False) Whether to write the total energy to the file - temperature (boolean=False) Whether to write the instantaneous temperature to the file - volume (boolean=False) Whether to write the periodic box volume to the file - density (boolean=False) Whether to write the system density to the file - separator (string=',') The separator to use between columns in the file """ self._reportInterval = reportInterval self._openedFile = isinstance(file, str) if self._openedFile: self._out = open(file, 'w') else: self._out = file self._step = step self._time = time self._potentialEnergy = potentialEnergy self._kineticEnergy = kineticEnergy self._totalEnergy = totalEnergy self._temperature = temperature self._volume = volume self._density = density self._separator = separator self._needEnergy = potentialEnergy or kineticEnergy or totalEnergy or temperature self._hasInitialized = False 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. """ steps = self._reportInterval - simulation.currentStep%self._reportInterval return (steps, False, False, False, self._needEnergy) def report(self, simulation, state): """Generate a report. Parameters: - simulation (Simulation) The Simulation to generate a report for - state (State) The current state of the simulation """ if not self._hasInitialized: system = simulation.system if self._temperature: # Compute the number of degrees of freedom. dof = 0 for i in range(system.getNumParticles()): if system.getParticleMass(i) > 0*unit.dalton: dof += 3 dof -= system.getNumConstraints() if any(type(system.getForce(i)) == mm.CMMotionRemover for i in range(system.getNumForces())): dof -= 3 self._dof = dof if self._density: # Compute the total system mass. self._totalMass = 0*unit.dalton for i in range(system.getNumParticles()): self._totalMass += system.getParticleMass(i) # Write the headers. headers = [] if self._step: headers.append('Step') if self._time: headers.append('Time (ps)') if self._potentialEnergy: headers.append('Potential Energy (kJ/mole)') if self._kineticEnergy: headers.append('Kinetic Energy (kJ/mole)') if self._totalEnergy: headers.append('Total Energy (kJ/mole)') if self._temperature: headers.append('Temperature (K)') if self._volume: headers.append('Box Volume (nm^3)') if self._density: headers.append('Density (g/mL)') print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers) self._hasInitialized = True # Check for errors. if self._needEnergy: energy = (state.getKineticEnergy()+state.getPotentialEnergy()).value_in_unit(unit.kilojoules_per_mole) if math.isnan(energy): raise ValueError('Energy is NaN') if math.isinf(energy): raise ValueError('Energy is infinite') # Write the values. values = [] box = state.getPeriodicBoxVectors() volume = box[0][0]*box[1][1]*box[2][2] if self._step: values.append(simulation.currentStep) if self._time: values.append(state.getTime().value_in_unit(unit.picosecond)) if self._potentialEnergy: values.append(state.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)) if self._kineticEnergy: values.append(state.getKineticEnergy().value_in_unit(unit.kilojoules_per_mole)) if self._totalEnergy: values.append((state.getKineticEnergy()+state.getPotentialEnergy()).value_in_unit(unit.kilojoules_per_mole)) if self._temperature: values.append((2*state.getKineticEnergy()/(self._dof*0.00831451)).value_in_unit(unit.kilojoules_per_mole)) if self._volume: values.append(volume.value_in_unit(unit.nanometer**3)) if self._density: values.append((self._totalMass/volume).value_in_unit(unit.gram/unit.item/unit.milliliter)) print >>self._out, self._separator.join(str(v) for v in values) def __del__(self): if self._openedFile: self._out.close()