path: root/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py

# Copyright 2006-2007 Nanorex, Inc.  See LICENSE file for details.
"""
Encapsulates all the particulars of a simulation.
The L{SimSpecification} class is essentially a hierarchical parameter set that
describes a cross-package compatible simulation specification.
All reusable configuration is captured here including motion paths
and jigs.

The object model makes use of
L{Parameter} objects to store most of the data. Parameter objects encapsulate
information necessary for viewing and editing single parameters via some GUI.
Parameter objects are instantiated via a ParameterFactory based on a given key
which maps to a unique parameter in the SimSpecification keyname-space. See
L{Parameter.ParameterFactory} for a description of the reserved keynames.

The following is the object model of the SimSpecification module:
IMAGE_1

The following is an example SimSpecification as it would appear in XML::
    <simSpecification name="Dual-H abstraction">
      <description>
        Abstraction of two hydrogens from the DC10 deposition tooltip.
      </description>

      <parameter key="timestep"               value="0.1e-15" />
      <parameter key="startStep"              value="0" />
      <parameter key="maxSteps"               value="10000" />
      <parameter key="stepsPerFrame"          value="10" />
      <parameter key="environmentTemperature" value="300.0" />
      <parameter key="environmentPressure"    value="100000.0" />

      <input name="abstractor">
        <parameter key="file" value="abstractor.mmp" />
      </input>
      <input name="seed">
        <parameter key="file" value="diamond-fragment.mmp" />
      </input>

      <motionPath name="MotionPath1">
        <interval>
          <parameter key="start" value="0.0" />
          <parameter key="end"   value="180.0e-15" />
          <velocity>
            <parameter key="fixed" value="true" />
          </velocity>
        </interval>
        <interval>
          <parameter key="start" value="180e-15" />
          <parameter key="end"   value="2345e-15" />
          <linearforce>
            <parameter key="speed"         value="200.0" />
            <parameter key="componentsXYZ" value="0.0 -5.0e-9 0.0" />
          </linearforce>
        </interval>
      </motionPath>

      <motionPath name="Anchor1">
        <interval>
          <parameter name="start" value="0.0" />
          <parameter name="end"   value="3300.0e-15" />
          <velocity>
            <parameter key="fixed" value="true" />
          </velocity>
        </interval>
      </motionPath>

      <operation name="Force Field/Quantum Chemistry">
        <parameter key="action" value="dynamics" />

        <method name="ND-1">
          <parameter key="engine"                 value="NanoDynamics-1" />
          <parameter key="atomSet"                value="BulkAtomSet1" />
        </method>

        <method name="GAMESS">
          <parameter key="engine"                 value="GAMESS" />
          <parameter key="atomSet"                value="Tooltip1" />
          <parameter key="method"                 value="Hartree-Fock" />
          <parameter key="basisSet"               value="3-21G" />
          <parameter key="functional"             value="" />
          <parameter key="multiplicity"           value="auto" />
          <parameter key="integrator"             value="coarse" />
          <parameter key="energyAccuracty"        value="1.0e-5" />
          <parameter key="maxConvergenceAttempts" value="10" />
          <parameter key="unscripted"             value="no" />
          <parameter key="applyFrom"              value="0.0" />
          <parameter key="applyTo"                value="20.0e-12" />
        </method>

        <constraint>
          <parameter key="motion"  value="MotionPath1" />
          <parameter key="atomSet" value="DC10" />
        </constraint>
        <constraint>
          <parameter key="motion"  value="Anchor1" />
          <parameter key="atomSet" value="H-abstractor" />
        </constraint>

        <measurement>
          <parameter key="measure" value="Thermo1" />
          <parameter key="atomSet" value="H-abstractor" />
        </measurement>
      </operation>

      <preSimulationChecks>
        <parameter key="all" value="false" />
        <parameter key="detectUnMinimized" value="true" />
        <parameter key="checkJigSanity" value="true" />
        <parameter key="detectUnusedJigs" value="false" />
        <parameter key="detectReactionPoints" value="true" />
        <parameter key="checkSpinMultiplicity" value="true" />
      </preSimulationChecks>
    </simSpecification>

Packages may add their own custom parameters and they will be stored along
with the reserved-key parameters. Custom parameters can be specified with
the information necessary for viewing and editing them via some GUI. Here
is what a fully defined parameter would look like in XML::
    <parameter key="simFlowScript" value="/Users/bh/tooltip_action.tcl">
      <label>Workflow script</label>
      <widget>filechooser</widget>
        <extension>.tcl</extension>
      <tooltip>Simulation workflow script file</tooltip>
    </parameter>
"""

from Parameter import ParameterSet

class SimInput(ParameterSet):
    """Simulation input files. See L{SimSpecification} for context."""


    def __init__(self, name):
        """Constructs a SimInput with the given name."""
        groupName = "Input files"


    def getName(self):
        """Returns this SimInput's name."""
        pass
    def setName(self, name):
        """Sets this SimInput's name."""
        pass


class Action(ParameterSet):
    """
    An external effect applied to a set of atoms.
    See L{SimSpecification} for context.

    This is an abstract/interface class and should not be instantiated.
    """
    pass


class Velocity(Action):
    """
    A fixed velocity applied to a set of atoms.
    See L{SimSpecification} for context.
    """


    def __init__(self):
        """Constructs a Velocity object."""
        groupName = "Velocity"


class LinearForce(Action):
    """
    A force applied to a set of atoms.
    See L{SimSpecification} for context.
    """


    def __init__(self):
        """Constructs a LinearForce object."""
        groupName = "Linear force"


class Torque(Action):
    """
    A rotary force applied to a set of atoms.
    See L{SimSpecification} for context.
    """


    def __init__(self):
        """Constructs a Torque object."""
        groupName = "Torque"


class Interval(ParameterSet):
    """
    A span of time and associated Action.
    See L{SimSpecification} for context.
    """


    def __init__(self):
        """Constructs an Interval object."""
        groupName = "Interval"


    def getAction(self):
        """Returns the Action subclass for this interval."""
        pass
    def setAction(self, Action):
        """
        Sets the Action subclass for this interval. Clobbers any existing
        Action.
        """
        pass


class MotionPath(ParameterSet):
    """
    A description of motion during simulation.
    See L{SimSpecification} for context.
    """


    def __init__(self, name):
        """Constructs a MotionPath with the given name."""
        groupName = "Motion path"


    def getName(self):
        """Returns this MotionPath's name."""
        pass
    def setName(self, name):
        """Sets this MotionPath's name."""
        pass


    def getIntervalArray(self):
        """Returns this MotionPath's Interval as an array."""
        pass
    def addInterval(self, interval):
        """Adds the given Interval and returns an Interval index."""
        pass
    def deleteInterval(self, intervalIndex):
        """Deletes the Interval with the given index from this MotionPath."""
        pass


class Method(ParameterSet):
    """A simulation scheme. See L{SimSpecification} for context."""


    def __init__(self):
        """Constructs a Method object."""
        groupName = "Method"


class Constraint(ParameterSet):
    """Application of a Motion path on an atom set."""


    def __init__(self):
        """Constructs a Constraint object."""
        groupName = "Constraint"


class Measurement(ParameterSet):
    """Application of a Measure on an atom set."""


    def __init__(self):
        """Constructs a Measurement object."""
        groupName = "Measurement"


class Operation(ParameterSet):
    """Describes the components of the actual simulation process."""


    def __init__(self):
        """Constructs an Operation object."""
        groupName = "Operation"


class SimSpecification(ParameterSet):
    """
    Encapsulates all the particulars of a simulation such as input files,
    entity traversal, level of theory, calculation, motion, and results.
    """


    def __init__(self, name):
        """Constructs a SimSpecification with the given name."""
        groupName = "Simulation specification"


    def loadFromFile(self, filepath):
        """
        Loads this SimSpecification from the given filepath.
        @return: (0=successful or non-zero error code), (error description)
        """
        pass


    def writeToFile(self, filepath):
        """
        Writes this SimSpecification to the given filepath.
        @return: (0=successful or non-zero error code), (error description)
        """
        pass


    def getName(self):
        """Returns this SimSpecification's name."""
        pass
    def setName(self, name):
        """Sets this SimSpecification's name."""
        pass


    def getDescription(self):
        """Returns this SimSpecification's description."""
        pass
    def setDescription(self):
        """Sets this SimSpecification's description."""
        pass


    def getParameter(self, key):
        """
        Returns the Parameter with the given key. A blank Parameter is returned
        if no Parameter with the given key has been set.
        """
        pass
    def getParameterArray(self):
        """Returns this object's Parameters in an array."""
        pass
    def setParameter(self, Parameter):
        """
        Sets the given parameter. Any existing Parameter with the same key will
        be clobbered.
        """
        pass


    def getSimInputArray(self):
        """Returns this SimSpecification's SimInputs in an array."""
        pass
    def addSimInput(self, Input):
        """
        Adds the given SimInput. Any existing SimInput with the same
        name will be clobbered.
        """
        pass


    def getMotionPathArray(self):
        """Returns this SimSpecification's MotionPaths in an array."""
        pass
    def addMotionPath(self, MotionPath):
        """
        Adds the given MotionPath. Any existing MotionPath with the same
        name will be clobbered.
        """
        pass


    def getOperation(self):
        """Returns this SimSpecification's Operation."""
        pass
    def setOperation(self, Operation):
        """
        Sets the given Operation. Any existing Operation will be clobbered.
        """
        pass


    def getPreSimulationChecks(self):
        """
        Returns this SimSpecification's pre-simulation check Parameters in an
        array.
        """
        pass
    def addPreSimulationCheck(self, Parameter):
        """
        Adds the given pre-simulation check Parameter. Any existing pre-check
        with the same key will be clobbered.
        """
        pass