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CE 530 Molecular Simulation
Lecture 4
Object-Oriented Programming and Etomica
David A. Kofke
Department of Chemical Engineering
SUNY Buffalo
kofke@eng.buffalo.edu
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Object-Oriented Programming
 Programming accomplished through the actions and
interactions of objects
• everything is an object
 Forces abstract thinking about the structure and activities of a
program
 Promotes re-use of code and extension to new applications
 Good design is difficult to develop
• requires thorough understanding of application
• conversely, its use facilitates a better understanding of application
presents a good vehicle for teaching
 It’s fun!
What is an Object?
 A fancy variable
• stores data
• can perform operations using the data
 Every object has a type, or “class”
• analogous to real, integer, etc.
Fortran: real x, y, z
Java:
Atom a1, a2;
• you define types (classes) as needed to solve your problems
public class Atom {
double mass;
Vector r, p;
}
• types differ in the data they hold and the actions they can perform on it
• every object is an “instance of a class”
a1 = new Atom();
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Makeup of an Object
 Fields (data)
• primitive types (integer, float, double, boolean, etc.)
• handles to other objects
complex objects are composed from simpler objects (composition)
 Methods (actions)
• “subroutines and functions”
• may take arguments and return values
• have complete access to all fields of object
 A class has an interface
• what the object presents to enable its manipulation
• implementation (how it accomplishes its operations) can be hidden
• object is viewed in terms of its “actions” and not its “thoughts”
 Inheritance
•
•
•
•
can define subclasses which inherit features of parent class
same interface, but different implementations
subclasses can be used anywhere parent class is expected
mechanism to change behavior of simulation
Detailed Look: Atom
parentGroup
(via node)
Space
makes
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AtomFactory
makes
type
coord
seq
node
next
(via seq)
Atom
previous
(via seq)
makes
any classes
allatomAgents[]
ia
makes
Integrator
childList
(via node)
 Click here for the complete API specification
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Etomica
 Application Programming Interface (API)
• Library of components used to assemble a simulation
• Can be used independent of development environment
Invoked in code programmed using Emacs (for example)
 GUI-based development environment
• Simulation is constructed by piecing together elements
• No programming required
• Result can be exported to run stand-alone as applet or
application
 Written in Java
• Widely used and platform independent
• Features of a modern programming language
• Object-oriented
 Vehicle for presentation of molecular simulation methods
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Etomica API
Simulation
SimulationGraphic
Space
Display
Vector, Tensor
Device
Coordinate, Orientation
Controller
Species
Phase
Boundary
Configuration
Potential
Meter
Integrator
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Simulation Elements: Simulation
Simulation
SimulationGraphic
Space
 Simulation
collects all the other elements
of the simulation
and ensures that they are connected for proper interaction
Display
Vector, Tensor
 Device
There is only one instance of a Simulation in anyCoordinate, Orientation
Controller
applet/application
Species
• Applet: runs in a web page
Phase
• Application: runs as a program, from command
line
 SimulationGraphic
Boundary
Configuration
• Subclass of Simulation used when preparing a simulation
with a
Potential
graphical user interface (GUI)
Meter
Integrator
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Simulation Elements: Space
 Space defines properties of the physical space in which the
simulation is performed Simulation
• Dimensionality
(1D, 2D, 3D, etc.); continuum
SimulationGraphic
Spacevs. lattice
•Display
Construction of vectors, tensors
Vector, Tensor
•Device
Makes Coordinate for placement in each Atom
Coordinate, Orientation
position and momentum vector
Controller
• CoordinatePair defines how distances are computed
Species
• Constructs various types of Boundary for placement
in each Phase
Phase
 Concrete classes
• Space1D
• Space2D
• Space3D
Boundary
Configuration
Potential
Meter
Integrator
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Simulation Elements: Controller
 Governs general plan of action for simulation
• For example:
run forever, as controlled by an interactive Stop/Resume button
Simulation
run a fixed number of relaxation/production
cycles, then quit
SimulationGraphic
run over
a series of state conditions for a fixed Space
duration at each
 Display
Oversees activities of Integrator
Vector, Tensor
• Makes
Device
connections between Integrator and other elements
Coordinate, to
Orientation
ensure proper functioning
Controller
• Turns Integrator on and off according to plan
Speciesof action
Phase
Entire Simulation
Entire Simulation
Initialization
Initialization
Initialization
Boundary
Reset block sums
Reset block sums
Reset block sums
Configuration
New configuration
New configuration
1 move per
cycle
1 move per
cycle
cycles per
block
cycles per
block
Add to block sum
Compute block average
blocks per
simulation
Compute final results
Add to block sum
Compute block average
blocks per
simulation
Compute final results
Potential
Meter
Entire Simulation
New configuration
1 move per
cycle
Add to block sum
cycles per
block
Integrator Compute block average
blocks per
simulation
Compute final results
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Simulation Elements: Integrator
 Adds the physics needed Simulation
to generate configurations properly
• variousSimulationGraphic
integration schemes introduced bySpace
developing a new
integrator
Display
Vector, Tensor
• Molecular dynamics integrators
Device
hard-potential dynamics
various kinds of soft-potential integrator
• Monte Carlo integrators
more later
Coordinate, Orientation
Controller
Species
Phase
 Places an Agent in each atom to assist integration
• for example, hard potential places Agent recording
collision time
collision partner
Boundary
Configuration
Potential
Meter
 Fires IntegrationIntervalEvent to notifyIntegrator
listeners that
simulation has proceeded one step
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Simulation Elements: Integrator
Simulation
 run method for top-level Integrator
class
SimulationGraphic
Space
public void
run() {
Display
Vector, Tensor
stepCount = 0;
int iieCount = interval+1;
Device
Coordinate, Orientation
while(stepCount < maxSteps) {
while(pauseRequested) doWait();
Controller
if(resetRequested) {doReset(); resetRequested = false;}
if(haltRequested) break;
Species
doStep(); //abstract method in Integrator. subclasses implement algorithms (MD/MC)
if(--iieCount == 0) { //count down to determine when a cycle is completed
Phase
fireIntervalEvent(intervalEvent); //notify listeners
of completion of cycle
iieCount = interval;
Boundary
}
if(doSleep) { //slow down simulation so display can keep up
Configuration
try { Thread.sleep(sleepPeriod); }
catch (InterruptedException e) { }
Potential
}
stepCount++;
} //end of while loop
Meter
fireIntervalEvent(new IntervalEvent(this, IntervalEvent.DONE));
} //end of run method
Integrator
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Simulation Elements: Phase
 Collects molecules that interact
Simulation
• holds root
of hierarchy of atoms/moleculesSpace
SimulationGraphic
• handles addition/removal of molecules
Display
• multiple phases possible in one simulation
Device
• sets up base lists of all atoms, molecules,Controller
species
Vector, Tensor
Coordinate, Orientation
defines which atoms are up or down from a given
atom
Species
 Holds a Boundary object (from Space) that
Phase defines the
boundary conditions used in the phase
Boundary
 Houses Configuration object that creates or saves aConfiguration
configuration of molecules
Potential
Meter
Integrator
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Simulation Elements: Meter
Simulation
 Measurement of simulation
property
SimulationGraphic
• Configurational
property in a phase
Space
Display potential
Device
energy
kinetic energy
density
structure
Vector, Tensor
Coordinate, Orientation
Controller
Species
• Each phase has by default kinetic and potential
Phase energy meters
others added as desired
• Can also keep track of other quantities of interest
simulation time
Potential
Boundary
Configuration
 Accumulator handles all block averagingMeter
and error analysis
• listener for IntegrationIntervalEvent
Integrator
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Simulation Elements: Species
Simulation
 Holds AtomFactory
type of
SimulationGraphicthat defines how a particular
Space
molecule is constructed
Display
Vector, Tensor
• how many atoms of which type
• nominal arrangement of atoms in molecule
Controller
Device
Coordinate, Orientation
 Places SpeciesAgent in each phase to manage
molecules
Species
there
Phase
• root of atom hierarchy for species in phase
• looping over molecules
• addition and removal of atoms
Potential
Boundary
Configuration
 Basis for defining interaction potential between molecules
Meter
• but does not by itself describe the pair potential
Integrator
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Simulation Elements: Potential
 Defines interaction between
atoms (and thereby molecules)
Simulation
• Hard potential
SimulationGraphic
Display
Device
Space
collision time
collision dynamics
• Soft potential
force, virial
• All potentials
energy
Vector, Tensor
Coordinate, Orientation
Controller
Species
Phase
Boundary
 Intermolecular potentials collect interatomic potential
• Potential1: intramolecular
• Potential2: intermolecular
 Hierarchical arrangement
• More later
Configuration
Potential
Meter
Integrator
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Simulation Elements: Display
Simulation
SimulationGraphic from the simulation
Space
 Presents information
Display
• display
Vector, Tensor
of configuration for animation
Device
• display of data
table
graph
 Connects to Meter to get information
 Listener of IntegrationIntervalEvent
Coordinate, Orientation
Controller
Species
Phase
Boundary
Configuration
Potential
Meter
Integrator
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Simulation Elements: Device
Simulation
 InteractiveSimulationGraphic
manipulation of simulation
Space
Display
• sliders,
buttons, comboBoxes etc. for setting propertiesVector,
andTensor
affecting course of simulation
Device
Coordinate, Orientation
Controller
Species
Phase
Boundary
Configuration
Potential
Meter
Integrator
Putting It Together
import etomica.*;
public class MySimulation extends SimulationGraphic {
//Constructor
public void init() {
//Instantiate classes
super(Space2D());
controller = new Controller (this);
integrator = new IntegratorHard(this);
potential = new P2HardSphere(this);
species
= new SpeciesSpheresMono(this);
phase
= new Phase(this);
display = new DisplayPhase(this);
//Tie elements together
this.elementCoordinator.go();
} //End of constructor
public static void main(String[] args) {
MySimulation simulation = new MySimulation();
simulation.makeAndDisplayFrame();
} //End of main
} //End of MySimulation class
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Running It
 Compile source
• javac filename
filename.java is the source file
filename should be the same as the class defined in the file
creates filename.class
 Run as an applet
for class named Applet1
<HTML>
<HEAD> <TITLE>Applet HTML</TITLE> </HEAD>
<BODY bgcolor="#ffffff">
<APPLET CODE="Applet1.class" archive=“etomica.jar" WIDTH=640 HEIGHT=350></APPLET>
</BODY>
</HTML>
need to reference etomica.jar, which contains simulation classes
Load html in browser
Enjoy your applet!
 Run as an application
• java filename