NeuronSharedCOnstants and NeuronConstants are consolidated into one c…

…lass (NeuronConstants)

js/neuron/NeuronConstants.js

@@ -13,6 +13,10 @@ define( function( require ) {
   var PhetFont = require( 'SCENERY_PHET/PhetFont' );
   var Color = require( 'SCENERY/util/Color' );
 
+  var clockFrameRate = 15;
+  var minActionPotentialClockDT = (1 / clockFrameRate) / 3000;
+  var maxActionPotentialClockDT = (1 / clockFrameRate) / 1000;
+
   return Object.freeze( {
     // Fonts
     CONTROL_PANEL_TITLE_FONT: new PhetFont( {weight: 'bold', size: 14} ),
@@ -25,7 +29,14 @@ define( function( require ) {
     PROJECT_NAME: "neuron",
     MEMBRANE_THICKNESS: 4, // In nanometers, obtained from web research.
     DEFAULT_DIAMETER: 150, // In nanometers.
-    SCREEN_BACKGROUND: '#ccfefa'
+    SCREEN_BACKGROUND: '#ccfefa',
+    CLOCK_FRAME_RATE: clockFrameRate, // fps, frames per second (wall time)
+    // Set up the clock ranges for the various modules.  Note that for this
+    // sim the clock rates are often several orders of magnitude slower than
+    // real time.
+    MIN_ACTION_POTENTIAL_CLOCK_DT: minActionPotentialClockDT,
+    MAX_ACTION_POTENTIAL_CLOCK_DT: maxActionPotentialClockDT,
+    DEFAULT_ACTION_POTENTIAL_CLOCK_DT: (minActionPotentialClockDT + maxActionPotentialClockDT) * 0.55,
+    TIME_SPAN: 25 // In seconds.
   } );
-
 } );

js/neuron/NeuronScreen.js

@@ -13,7 +13,7 @@ define( function( require ) {
   var NeuronModel = require( 'NEURON/neuron/model/NeuronModel' );
   var NeuronScreenView = require( 'NEURON/neuron/view/NeuronScreenView' );
   var NeuronClockModelAdapter = require( 'NEURON/neuron/model/NeuronClockModelAdapter' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
   var Screen = require( 'JOIST/Screen' );
 
   // strings
@@ -27,8 +27,8 @@ define( function( require ) {
     var neuronModel = new NeuronModel();
     // NeuronModelAdapter intercepts the default Step function and provides
     // "constant" clock and record Playback features to NeuronModel, see NeuronClockModelAdapter
-    var neuronClockModelAdapter = new NeuronClockModelAdapter( neuronModel, NeuronSharedConstants.CLOCK_FRAME_RATE,
-      NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT );
+    var neuronClockModelAdapter = new NeuronClockModelAdapter( neuronModel, NeuronConstants.CLOCK_FRAME_RATE,
+      NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT );
 
     Screen.call( this, neuronSimString, null /* no icon, single-screen sim */,
       function() { return neuronClockModelAdapter; },

js/neuron/chart/view/MembranePotentialChart.js

@@ -25,7 +25,7 @@ define( function( require ) {
   var inherit = require( 'PHET_CORE/inherit' );
   var Node = require( 'SCENERY/nodes/Node' );
   var Bounds2 = require( 'DOT/Bounds2' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
   var Line = require( 'SCENERY/nodes/Line' );
   var Panel = require( 'SUN/Panel' );
   var Path = require( 'SCENERY/nodes/Path' );
@@ -57,7 +57,7 @@ define( function( require ) {
 
   // This value sets the frequency of chart updates, which helps to reduce
   // the processor consumption.
-  var UPDATE_PERIOD = 1 * NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT; // In seconds
+  var UPDATE_PERIOD = 1 * NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT; // In seconds
 
   var bounds2 = new Bounds2( 0, 0, 0, 0 );
 

js/neuron/model/ModifiedHodgkinHuxleyModel.js

@@ -19,7 +19,7 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var DelayBuffer = require( 'NEURON/neuron/model/DelayBuffer' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
 
   /**
    Amount of time used for each iteration of the model.  This is fixed,
@@ -40,8 +40,8 @@ define( function( require ) {
     thisModel.perKChannels = 100;
     thisModel.elapsedTime = 0;
     thisModel.timeSinceActionPotential = Number.POSITIVE_INFINITY;
-    thisModel.m3hDelayBuffer = new DelayBuffer( MAX_DELAY, NeuronSharedConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
-    thisModel.n4DelayBuffer = new DelayBuffer( MAX_DELAY, NeuronSharedConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
+    thisModel.m3hDelayBuffer = new DelayBuffer( MAX_DELAY, NeuronConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
+    thisModel.n4DelayBuffer = new DelayBuffer( MAX_DELAY, NeuronConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
 
     thisModel.resting_v = 65;// final doesn't change
 

js/neuron/model/NeuronModel.js

@@ -30,7 +30,7 @@ define( function( require ) {
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var CaptureZoneScanResult = require( 'NEURON/neuron/model/CaptureZoneScanResult' );
   var TimedFadeInStrategy = require( 'NEURON/neuron/model/TimedFadeInStrategy' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
   var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
 
   // Default configuration values.
@@ -120,7 +120,7 @@ define( function( require ) {
    */
   function NeuronModel() {
     var thisModel = this;
-    var maxRecordPoints = Math.ceil( NeuronSharedConstants.TIME_SPAN * 1000 / NeuronSharedConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
+    var maxRecordPoints = Math.ceil( NeuronConstants.TIME_SPAN * 1000 / NeuronConstants.MIN_ACTION_POTENTIAL_CLOCK_DT );
     thisModel.axonMembrane = new AxonMembrane();
 
     // List of the particles that come and go when the simulation is working in real time.

js/neuron/model/PotassiumGatedChannel.js

@@ -16,7 +16,6 @@ define( function( require ) {
   var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
   var PieSliceShapedCaptureZone = require( 'NEURON/neuron/model/PieSliceShapedCaptureZone' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
   var MembraneChannelTypes = require( 'NEURON/neuron/model/MembraneChannelTypes' );
@@ -38,7 +37,7 @@ define( function( require ) {
 
   // Delay range - used to make the timing of the instances of this gate
   // vary a little bit in terms of when they open and close.
-  var MAX_STAGGER_DELAY = NeuronSharedConstants.MIN_ACTION_POTENTIAL_CLOCK_DT * 10; // In seconds of sim time.
+  var MAX_STAGGER_DELAY = NeuronConstants.MIN_ACTION_POTENTIAL_CLOCK_DT * 10; // In seconds of sim time.
 
   var RAND = {nextDouble: function() {
     return Math.random();

js/neuron/model/SodiumDualGatedChannel.js

@@ -19,7 +19,6 @@ define( function( require ) {
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var DualGateChannelTraversalMotionStrategy = require( 'NEURON/neuron/model/DualGateChannelTraversalMotionStrategy' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
   var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
   var MembraneChannelTypes = require( 'NEURON/neuron/model/MembraneChannelTypes' );
 
@@ -59,7 +58,7 @@ define( function( require ) {
 
   // Delay range - used to make the timing of the instances of this gate
   // vary a little bit in terms of when they open and close.
-  var MAX_STAGGER_DELAY = NeuronSharedConstants.MIN_ACTION_POTENTIAL_CLOCK_DT * 5; // In seconds of sim time.
+  var MAX_STAGGER_DELAY = NeuronConstants.MIN_ACTION_POTENTIAL_CLOCK_DT * 5; // In seconds of sim time.
 
 
   /**

js/neuron/model/WanderAwayThenFadeMotionStrategy.js

@@ -12,14 +12,14 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var MotionStrategy = require( 'NEURON/neuron/model/MotionStrategy' );
-  var NeuronSharedConstants = require( 'NEURON/neuron/common/NeuronSharedConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
   var TimedFadeAwayStrategy = require( 'NEURON/neuron/model/TimedFadeAwayStrategy' );
 
   // constants
   var CLOCK_TICKS_BEFORE_MOTION_UPDATE = 5;
   var CLOCK_TICKS_BEFORE_VELOCITY_UPDATE = CLOCK_TICKS_BEFORE_MOTION_UPDATE * 10;
-  var MOTION_UPDATE_PERIOD = NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT * CLOCK_TICKS_BEFORE_MOTION_UPDATE;
-  var VELOCITY_UPDATE_PERIOD = NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT * CLOCK_TICKS_BEFORE_VELOCITY_UPDATE;
+  var MOTION_UPDATE_PERIOD = NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT * CLOCK_TICKS_BEFORE_MOTION_UPDATE;
+  var VELOCITY_UPDATE_PERIOD = NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT * CLOCK_TICKS_BEFORE_VELOCITY_UPDATE;
   var MIN_VELOCITY = 500;  // In nanometers per second of sim time.
   var MAX_VELOCITY = 5000; // In nanometers per second of sim time.
 
@@ -46,8 +46,8 @@ define( function( require ) {
 
     // Set up random offsets so that all the particles using this motion
     // strategy don't all get updated at the same time.
-    this.motionUpdateCountdownTimer = RAND.nextInt( CLOCK_TICKS_BEFORE_MOTION_UPDATE ) * NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT;
-    this.velocityUpdateCountdownTimer = RAND.nextInt( CLOCK_TICKS_BEFORE_VELOCITY_UPDATE ) * NeuronSharedConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT;
+    this.motionUpdateCountdownTimer = RAND.nextInt( CLOCK_TICKS_BEFORE_MOTION_UPDATE ) * NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT;
+    this.velocityUpdateCountdownTimer = RAND.nextInt( CLOCK_TICKS_BEFORE_VELOCITY_UPDATE ) * NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT;
 
     this.velocityX = 0;
     this.velocityY = 0;