aakash58 / connchem Goto Github PK

Sim starts with Sodium Hydroxide

add button:
add 5 HCl

Description of Feature:
Zoom in on canvas to reveal a closer view of molecule interaction.  Should 
follow the active molecule.  Perhaps should be done in a sidebar panel, with 
pop out.

add button:
add 5 Sodium Hydroxide

add timer panel

What steps will reproduce the problem?
(This is on a macintosh)
1. Hover over "Select a Simulation" menu; menu opens
2. move away without clicking anything
3. attempt to select something from the main system File menu, for example.  
The "Select" menu does not go away, and gets in the way of using the system 
menus.

What is the expected output? What do you see instead?
• Menu should collapse/disappear when not hovering.

What steps will reproduce the problem?
1. run any simulation with multiple molecules on screen

What is the expected output? What do you see instead?
The physics engine (fisica) has a bug (may be in the underlying JBox2D library) 
which prevents some molecules from separating from each other or from the edge 
of the screen.

Java Applet has a tendency to slow down / speed up inexplicably in browsers.

Check to see if this occurs in standalone applications.

Description of Feature:
Every set needs, via the yaml file, to have a maximum number of molecules 
allowed in that sim.

Do you know how this issue might be addressed?
Tuan's code needs to be figured out, and a new subroutine needs to be setup 
limiting the number of molecules.

Description of Feature:
Menu panel needs a button which will advance to next simulation (if there is 
one).

Description of Feature:
Simulation needs to get initial molecule quantities from server database.

Do you know how this issue might be addressed?
refactor the getInitialSpecies() function.

Description of Feature:
Molecules should have a boolean value which can be turned on or off, which 
controls a "molecule trace."
This molecule trace is a colored line which indicates their location over time, 
and remains until cleared.

Do you know how this issue might be addressed?
I imagine an array of points, polled every "time unit", can be included in the 
Molecule class.  Then, each frame they will all be drawn, perhaps as tiny 
ellipses, or lines between the points (this latter is how the pH and molecule 
count monitors work).
Alternatively, a central array of points for the entire simulation might be 
drawn on top of the canvas background.  This will have to be a multidimensional 
array of points, as each molecule would need the ability to have a trace.

Description of Feature:
• Molecule quantity limit?  Perhaps 200?

Do you know how this issue might be addressed?
• When limit reached, all + buttons deactivated.

Description of Feature:
Eventually, we would like to allow the sidebars to overlap the canvas, to allow 
the potential for a larger canvas.  This would likely require scrollbars, or 
some other navigational aid to view occluded canvas sections.


Do you know how this issue might be addressed?
The main problem I see, is that the molecule canvas does not increase in size 
at runtime, because of some issue with the physics engine... sets boundaries at 
init.  May be tricky.


Please use labels and text to provide additional information.

[deleted issue]

Description of Feature:
Outputs for Gas Laws units, as well as perhaps other units, will need the 
ability to alter heat: add heat to system, remove heat from system

Do you know how this issue might be addressed?
the four edges of the canvas area need to turn red, blue, based upon heat added 
to/removed from system.

Need a knob, with settings 1-10: 5 keeps temperature the same, 4, removes temp, 
6 adds temp.

The system will need arbitrary limits, for cold and hot, which will keep system 
temperature from getting too low or too high.  These limits need to be set for 
the walls, not the entire system; the walls will store velocity (although they 
will not act on it).

Description of Feature:
• the Physics of the simulations need to allow for changes in states of 
matter.  Currently, the bouncing around looks fine for a gas, and when Gravity 
is added, for a liquid.  However, these two states cannot currently exist 
simultaneously, and Solids are not yet possible.


Do you know how this issue might be addressed?
There may be another way to do this, but it seems
1) requires the MySQL database to be running, with masses for each Species 
available.
2) inter-molecular gravity will need to be established.
3) if the molecule's velocity is greater than a threshold, then the molecules 
will not stick together; if it is less, then they will settle into a grid

• this feature will need to be modular enough to be turned on or off for 
individual simulations.

sim starts with Hydrogen Bromide

add button:
add 5 Cyanide Ion

Description of Feature:
• brainstorm for stoichiometry/multiple inputs for reactions.  This may be 
difficult.
• currently the reaction function allows for multiple inputs and outputs; the 
problem arises in that reactions currently only happen upon contact between two 
molecules.  The chances of three molecules interacting is extremely low.

Do you know how this issue might be addressed?
• Perhaps a reaction happens based upon molecules in a local vicinity.

What steps will reproduce the problem?
1. start any simulation

All simulations should begin with molecules not moving (paused sim).  However, 
instead they start moving right away, without the user clicking on the 
Play/Pause button.

This may be non-trivial, because molecules do not have time to build momentum, 
hence to store it when paused.  May need to start all molecules with default 
momentum, in whatever direction they are travelling.

Description of Feature:
• replace "track buttons" (for choosing sets) with a menu of all possible 
sets. 

Do you know how this issue might be addressed?
• Each set should have a short description (made available by database).  
Upon Simulation selection, the first Set should be selected and initialized.

Description of Feature:
• Liquids currently can't "slip past" one another, as they should.

Do you know how this issue might be addressed?
• Increase Gravity along the Y axis? As a molecule reaches the top of the 
simulation canvas, perhaps it experiences greater gravity, pulling it down to 
the bottom; at the bottom, however, the molecule experiences less gravity, 
which increases the amount of movement, especially for liquids.
• Decrease inter-molecular forces?
• Reduce friction?

main window is too large on large monitors: should have a maximum size.

What is the expected output? What do you see instead?
The p5 canvas does not expand to fill the real-estate of the monitor it is on.  
This is not a problem for small monitors, like the 13" MacBook, usual with our 
students.  However, on a larger monitor, it is very unattractive.

What steps will reproduce the problem?
1. load any simulation

What is the expected output? What do you see instead?
Supposed to see a pause icon when paused; see only play icon


Please use labels and text to provide additional information.

Description of Feature:
• When program starts, should be able to add arbitrary compounds (sandbox)
• Currently, many compounds selected from molecule chooser do nothing.

Do you know how this issue might be addressed?
• remove molecule chooser altogether?
• Make matrix of all used compounds, 2 x 2, for necessary reactions?  We 
already have some of these.
• mark compounds in molecule chooser which can react with current (already 
selected) compounds?  That is, current compounds form filter for reactions 
possible with compounds in molecule chooser.

Description of Feature:
• Gravity: too strong.  Molecules bounce too much.

Do you know how this issue might be addressed?
• Perhaps increase gravity for entire world?  2x?

What steps will reproduce the problem?
• Java slows down, when many items are on the screen; once Java slows down, 
the program flickers, and the problem can only be addressed by restarting the 
program.

Do you know how this issue might be addressed?
• too many "new" objects (via "new" keyword)?
• memory leak? (unlikely, due to garbage collection...)
• Move all I/O to program initialization; in other words, copy database 
tables into ArrayLists and HashMaps?
• or, do not check DB for compound interactions at each cycle, but instead 
only after an interval (one second?).  Thus, if two compounds are in direct 
contact with one another, they will not attempt DB I/O 60 times/second?
• reduce p5 framerate?
• change Java heap size?
• Reset button: also resets p5 (to dig out if already slow)?

What is the expected output? What do you see instead?
Currently, compounds attract each other (and form solids) based upon 
inter-molecular gravity (mass).  This should be achieved by polarity instead.

Description of Feature:
All Unit 8 sims need a configurable dashboard panel, which can provide readouts:
• concentration
• current pH
• time elapsed
• solution % dissolved
• solution % not yet dissolved

sim starts with Chlorine Ion

add button:
add 5 Boron Tetrachloride

Description of Feature:
• In molecule chooser, type first letter of molecule to go there, in order to 
save scrolling?

From staff meeting, first week of June, 2011: Speed control does not work, 
likely because of gravity.

Description of Feature:
On initial load, the simulation should have a popup box which indicates:
• Connected Chemistry logo and related text
• version number
• initial instructions for use.

this box can be turned off

Description of Feature:
• Water transparency slider.
• The Simulation needs a slider to make water transparent, or at least less 
noticeable.
• Perhaps this should be built into sidebar compound controls, and 
generalized beyond just water.

Description of Feature:
The canvas edges should convey energy (velocity) to molecules upon contact, or 
remove energy.
When canvas edges are "hot", they should be colored red.  When they are "cool" 
they should be colored blue.  This might be a sliding scale: a spectrum, that 
is, depending on how hot or cool the edges are, they should get more red or 
more blue respectively.  If they are inert, they should not have color (or be 
black).

Do you know how this issue might be addressed?
This may require removal of the floor and ceiling velocities of molecules, or 
setting floor and ceiling values on an individual molecule basis.

What steps will reproduce the problem?
1. run any simulation

• Make time panel smaller
• space out icons
• remove timer (should go in Dashboard)
• add button to advance to next simulation

What steps will reproduce the problem?
1. start any simulation

What is the expected output? What do you see instead?
the pH levels are both too low and too high.

Do you know how this issue might be addressed?
The algorithm needs adjustment.  We have discussed this in meetings before, and 
a solution was worked out (I think).  Essentially, it regards mapping estimated 
values to high/low points in the graph.

Talk with Mike and Allan for more information.

Description of Feature:
panel which allows variables for:
Pressure
Volume
Temperature
... to be frozen

Do you know how this issue might be addressed?
sliders?

this will take some thought.  Essentially you're exposing variables to the 
interface.

Description of Feature:
• Database in Jar file for Java Webstart; otherwise, Java WebStart includes 
database.

Do you know how this issue might be addressed?
• Not sure... WebStart might allow multiple files in the XML configuration

Should this project be refactored to be a standard Java application, with 
Processing imported as a library?  Discuss.

sim starts with Ammonia

add button:
add 5 HCl

The codebase needs significant commenting... due to the rapid redevelopment, 
many of the functions and classes are not well documented.

Should this be done via JavaDocs?

Description of Feature:
Panel for timing simulations.  Needs to have these features:
  •  stopwatch: start, pause, reset buttons.
  •  clocks: total time elapsed, time since last lap
  •  buttons should have the option to deactivate until after a specified time: that is, click button, button goes gray, 20 seconds elapse, button active again.
  •  when button activates again, should have the option to stop simulation
  •  this panel should be distinct from the main play/pause panel

Description of Feature to add:
This is a Test Feature

Other notes:
This feature goes in all simulations

Reaction data in the database should be pulled from the MySQL database rather 
than a flat file.

Currently this flat file is reactions.tsv

This will require alteration of the setupData() / setupReactionTable() 
functions.

• Molecules too large on screen.  Perhaps reduce scale x 75%?

• If substance is a solid at current temperature (especially at set 
initialization), it needs to appear into the simulation canvas as a solid.

Description of Feature:
In order to simulate changes in pressure, the canvas should have the ability 
(perhaps via a dial or scrollbar) to grow or shrink during the simulation.

Do you know how this issue might be addressed?
This may involve modifying the physics engine... currently, the boundaries for 
the canvas (the canvas edge bodies) have static location set at the beginning 
of the sim.  It may simply involve moving these bodies further in, or further 
out.
We will have to consider whether we should have a visual cue, like a "plunger" 
to indicate that the canvas is growing and shrinking.

• The pH tab is only for the Acid/Base unit; remove for others.
• Activate via YAML file.

What is the expected output? What do you see instead?
In all simulations, molecules move across the bottom of the screen when in 
aggregate (solid) form.  They should not.

Do you know how this issue might be addressed?
Perhaps add a bit of friction to bottom boundary?  Need to be careful that this 
does not affect system velocity.

add button:
add 5 HCl