started work

wrappers/python/simtk/openmm/app/__init__.py

@@ -25,6 +25,7 @@ from modeller import Modeller
 from statedatareporter import StateDataReporter
 from element import Element
 from desmonddmsfile import DesmondDMSFile
+from checkpointreporter import CheckpointReporter
 
 # Enumerated values
 

wrappers/python/simtk/openmm/app/checkpointreporter.py

+"""
+checkpointreporter.py: Saves checkpoint files for 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) 2014 Stanford University and the Authors.
+Authors: Robert McGibbon
+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__ = "Robert McGibbon"
+__version__ = "1.0"
+
+import simtk.openmm as mm
+__all__ = ['CheckpointReporter']
+
+
+class CheckpointReporter(object):
+    """CheckpointReporter saves periodic checkpoints of a simulation.
+    The checkpoints will overwrite one and other -- only the last checkpoint
+    will be saved in the file.
+
+    To use it, create a CheckpointReporter, then add it to the Simulation's
+    list of reporters.
+    """
+    def __init__(self, file, reportInterval):
+        """Create a CheckpointReporter.
+
+        Parameters:
+         - file (string or open file object) The file to write to
+         - reportInterval (int) The interval (in time steps) at which to write checkpoints
+        """
+
+        self._reportInterval = reportInterval
+        if isinstance(file, basestring):
+            self._out = open(file, 'wb')
+        else:
+            self._out = file
+
+    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, False)
+
+    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
+        """
+        self._out.seek(0)
+        self._out.write(simulation.context.createCheckpoint())