# 0.00.09 (55303) Aug 16, 2011 8/16/11 dev version for discussion at Chem meeting 8/16/11 temporarily disable molecular dipole because it's currently incorrect 8/15/11 checked in a version of "real molecules" control that uses PComboBox instead of ComboBoxNode, #2982 8/15/11 tweak molecular dipole interface and fields 8/15/11 make molecule location a simple field, doesn't need to be a Property 8/15/11 intermediate implementation of molecular dipole model and view, not functional yet 8/15/11 generalize 2D isosurface placeholder, add to triatomic molecule 8/15/11 generalize "rotatable molecule" interface, add rotation handler to triatomic molecule 8/15/11 update atom locations when molecule angle or bond angles change 8/15/11 change request: use gray background for periodic table, to provide more contrast between selected and unselected cells 8/15/11 first pass at fleshing out "Three Atoms" tab, only partially functional 8/15/11 change request: make "bond dipoles" on by default in "Two Atoms" tab # 0.00.08 (55174) Aug 13, 2011 8/12/11 make sure that all PText instances have a call to setFont(PhetFont) 8/12/11 rename various TwoAtoms* classes to Diatomic* 8/12/11 javadoc throughout 8/12/11 fix Reset All so that it resets the molecule in Real Molecules 8/12/11 add currentMolecule property to Real Molecules model, observe in Jmol viewer and periodic table 8/12/11 reuse piccolo-phet's PeriodicTableNode 8/12/11 display element numbers in periodic table placeholder 8/12/11 Jmol: script to return element numbers, for use in periodic table 8/12/11 wire up "electron density" control in "Two Atoms" tab 8/12/11 Jmol: use different isosurfaces for homogeneous diatomic molecules 8/12/11 Jmol: wrote script to identify homogeneous diatomic molecules 8/12/11 change "bond dipoles" to "bond dipole" in Two Atoms tab 8/12/11 #3039, add Arrow.getHeadScale, use it to scale dipole cross 8/12/11 add cross to dipole by decorating arrow 8/11/11 cannibalize Vector2DNode for use in rewrite of DipoleNode 8/11/11 make TwoAtomsIsosurfaceNode observer atom locations, since those are the properties it relies on 8/11/11 rename "Test" control panel to "Electric Field" 8/11/11 first attempt at 2D isosurface 8/11/11 generalize molecule drag handler in MoleculeRotationHandler 8/11/11 add 3D perspective to E-field plates 8/10/11 restore "more" in bond type indicator 8/10/11 remove arrows and "more" from bond type indicator 8/10/11 Jmol: return status from developer scripts 8/10/11 adjust 2D dipoles to look more like Jmol dipoles 8/10/11 Jmol: swp atom labels so that they are numbered clockwise from upper left 8/10/11 Jmol: change atoms labels so that if there's only one atom of a type, it has no index (eg "C", not "C1") 8/9/11 Jmol: manually edit mol2 file for O3, swap y and z axes 8/9/11 Jmol: manually edit mol2 file for H2O, swap y and z axes, invert y axis 8/9/11 Jmol: manually edit mol2 file for CH2O, swap y and z axes, invert y axis, adjust labels 8/9/11 Jmol: manually edit mol2 orientation of atoms that involve swapping x and z axes, adjust labels 8/9/11 Jmol: manually edit atom names in mol2 files 8/9/11 Jmol: delete sdf and smol files, #3018 # 0.00.07 (54913) Aug 6, 2011 8/6/11 Jmol: execute scripts synchronously with JmolViewer.scriptWait, #3009 8/6/11 change Model control panel to Isosurface, with choices "none", "Electrostatic Potential", "Electron Density" 8/6/11 Jmol: add a proposed isosurface command for "electron density" view, for discussion 8/3/11 change request: add line separator between atom name and partial charge 8/3/11 change request: atom labels on by default # 0.00.06 (54831) Aug 3, 2011 8/3/11 add molecule angle to Reset All 8/3/11 align two-atom molecule with E-field 8/2/11 change Bond.dipoleMagnitude to Bond.deltaElectronegativity, since this is really what it is 8/2/11 revert work done on making dipole a vector, introduced many problems and seems redundant 8/2/11 hide View controls that are not relevant to a tab 8/2/11 tweak sizes and locations of some things, so that there are no collisions when rotating molecule 8/2/11 for 2-atom molecule, molecular dipole is identical to bond dipole 8/2/11 make Bond dipole field a vector instead of a scalar 8/2/11 add infrastructure for aligning molecular dipole with E-field over time 8/2/11 Jmol: limit display of partial charge to 2 decimal places 8/2/11 Implemented TwoAtomMoleculeNode.RotationHandler 8/2/11 Set position of partial charges relative to their associated atoms 8/2/11 Centered the play area in the panel 8/1/11 simple implementation of bond type (covalent/ionic) display # 0.00.05 (54624) Jul 29, 2011 7/29/11 reduce font size of MoleculeComboBoxNode (temporarily?), so that popup fits in the play area, workaround for #3025 7/29/11 Jmol: switch to mol2 files provided by KL, add additional molecules 7/28/11 Jmol: separate chem data files into separate directories, by file type # 0.00.04 (54576) Jul 27, 2011 7/27/11 Jmol: order molecules in combo box by increasing size/complexity 7/27/11 Jmol: make bond and atoms translucent when dipoles are visible 7/27/11 Jmol: use custom (colorblind) red for oxygen atoms 7/27/11 Jmol: remove duplicate code in readers for files and jar resources 7/27/11 Jmol: disable hovers 7/27/11 Jmol: disable zooming 7/27/11 Jmol: customize color and thickness of bonds, doc ball-and-stick script commands 7/27/11 Jmol: display partial charge as part of atom label 7/27/11 Jmol: increase font size of Jmol labels, set label color to black for all atoms # 0.00.03 (54557) Jul 27, 2011 7/27/11 Jmol: use KL's list of molecules and SDF files 7/27/11 Jmol: check in SDF files obtained from PubChem (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi) 7/27/11 Jmol: use KL's method of creating mep isosurface 7/26/11 intermediate implementation of partial charge view (not positioned correctly) 7/26/11 bond dipole view based on Vector2DNode 7/25/11 intermediate implementation of bond dipole view (offset and magnitude not functional) 7/25/11 add Bond to model 7/25/11 intermediate implementation of two-atom molecule rotation 7/25/11 intermediate check-in of two-atom molecule model and view # 0.00.02 (54482) Jul 25, 2011 7/25/11 Jmol: add "Import from file" option to Molecule combo box, so that non-developers can experiment Jmol file formats, see #3018 7/25/11 Jmol: tested more file formats, see #3018 7/21/11 Jmol: tested various file formats, see #3018 7/20/11 Jmol: add developer control for entering and executing scripts # 0.00.01 (54332) Jul 20, 2011 7/19/11 dev version to demonstrate Jmol features and integration in "Real Molecules" tab 7/19/11 Jmol: add classes that are dynamically loaded to proguard-template.pro 7/19/11 Jmol: add dipole offsets, so that dipoles don't intersect atoms and bonds 7/19/11 add placeholder for periodic table 7/19/11 add "Molecule" label to combo box control 7/19/11 render molecule combo box items at HTMLNodes 7/19/11 delete acetone, because we should only include real molecules with one central atom 7/19/11 add hand cursor to Jmol viewer node 7/19/11 add View control for atom labels 7/19/11 setForeground(red) for controls that are not implemented 7/19/11 remove Jmol atom labels 7/19/11 increase width of dipoles, default is a little difficult to see 7/19/11 add combo box for selecting real molecule 7/19/11 wire up Jmol viewer to controls 7/19/11 integrate Jmol into "Real Molecules" tab 7/19/11 remove dependencies on jmol-phet 7/18/11 feasibility test of many Jmol features 7/18/11 add dependencies on Jmol, create test harness for integration of Jmol with Piccolo 7/13/11 hide clock controls in all modules, this sim has no clock controls 7/12/11 add rudimentary E-field plates 7/12/11 converted to floating control panels 7/11/11 created electronegativity control 7/11/11 created control panels 7/11/11 set up localized strings 7/11/11 created project and set up skeleton