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Atomsmith Program Revision History

Version 1.5.0 changes
  1. Added "Print Model Image" to the File Menu.
  2. Completely redesigned the Gas Lab Interface. Now can simulate ideal or real gases. Calculates pressure via the Ideal Gas Law or via the van der Waals equation of state. Can plot P vs. V, P vs. T, PV/nRT vs. P or V vs. 1/P. Wall impacts are drawn.
  3. Completely redesigned the Script Console interface. It is now menued. The Insert Command(s) menu contains many sequences of commands that can be inserted automatically.
Version 1.4.2 changes
  1. Improved bond generation algorithm. This is based on covalent radii. Used to generate >16 bonds for certain models, which caused bond generation to fail. It's smarter now.
  2. Introduced "Professional Animation" features. Access to these features requires a different license than the Standard version.

    Professional Animation Version Features Include:
    • Animation capture modes that capture an animation frame any time the model or the camera view changes. This mode can be used to produce either bitmapped or POVRay raytraced animations.
    • Automated capture to sequences of bitmapped graphics files. These sequences are generated whenever the model or the camera view changes -- unlike the Standard version, which is limited to animation of specific types of simulations, as described above.
    • Bitmapped graphics files are stored in the PNG format rather than the BMP format. This compressed format results in files that are about 5-10% of the size of BMP files, with no loss of quality. When you are generating animation sequences of thousands of frames, this can result in large savings of disk storage -- typically gigabytes or hundreds megabytes per animation.
    • Automated capture to sequences of POVRay sequences raytracing scene files. Quoting from the POVRay web site, "The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics." Atomsmith POVRay animations feature higher quality graphics than from the standard bitmap option, including better lighting, shadowing, and antialiasing (to remove "jagged" edges).
    • Automated launching of the POVRay raytracing engine to render Atomsmith POVRay animations.
    • Loading of 3D models in the 3DS file format. Using this feature, you can load models of arbitrary 3D objects that are stored in the 3DS format. For example, you might display a model of a biological organ that contains the molecule represented by the Atomsmith molecular model that you are studying. Or you might display a 3D model of your company logo alongside the Atomsmith model. The 3DS model format is a common meta-format used by most 3D modeling programs such as Autodesk's 3D Studio, from which the name is derived.
Version 1.4.1 changes
  1. Added ability to display dispersion and dipole-dipole interactions. These are available in the Gas Lab Options dialog as well as in the View>>Display menu.
  2. Added a temperature control slider to the Molecular Dynamics Control Dialog. Also re-arranged the other controls.
  3. Added the Gas Lab Options dialog. Contains checkboxes for the display of dispersion, dipole-dipole and hydrogen bonding interactions. Also contains checkboxes for tracing picked atoms during simulations and allowing the box to be shrunk to sizes that allow high densities. Also contains a drop-down menu that selects the Model Type in the Model Window.
  4. When molecular surfaces are drawn or hidden, the camera no longer resets.
  5. Single (nonbonded) atoms are now represented as dots in Wireframe Mode and as a small sphere in Stick Mode.
  6. Added cholormethane and hexane to the menu of Gas Lab molecules.
  7. "Show Dispersion Interactions" and "Show Dipole-Dipole Interactions" are now available in the Model Window's main and popup menus. These have the same effect as those in the Gas Lab Options Dialog.
  8. Lone Pairs are now drawn on the outside of the spheres in the Spacefill Model Type.
  9. Now recognizes mol2 atom type S.O as being potentially chiral -- it's tetrahedral because of the lone pair. This is the chiral center of the drug molecule omeprazole (Nexium and Prilosec).
  10. Fixed orientation of double bonds and lone pairs on atoms with 3 bonds.
  11. Sometimes when the Clip Surface Only checkbox was checked, the molecule was still clipped. Fixed.
  12. Fixed drawing of polyhedra about atoms of type S.O.
  13. Atomic charges are now automatically calculated when a model is hydrated.
  14. Added checkboxes to view dispersion and dipole-dipole forces in the Quick Control Panel.
  15. Molecular formula in the Model Information Dialog is now reported with spaces between elements (e.g., "C2 H5" instead of "C2H5").
  16. When hydration shell is built or hydrogens are added, energy function parameters are now automatically updated.
  17. Fixed the drawing of molecular dipoles of molecules generated by hydration.
Version 1.4.0 changes
  1. Added the Atomsmith Gas Lab, a simulator that contains molecules in a box. Allows users to build a "box" of small molecules and watch them interact while controlling the temperature and changing the size of the box.
  2. Added "Copy Graphic To Windows Clipboard" command to the Model Window's Edit menu. These can be pasted into (e.g.) a Microsoft Word document or a drawing program.
  3. Added "Insert ACD/ChemSketch Model from Clipboard" to Model Window's Edit menu. Inserts a 2D or 3D model from ACD/ChemSketch. Also opens a window that contains a copy of the ChemSketch picture.
  4. Changed default opacity to 40% (from 50%)in Surface Settings Dialog. Also changed some of the cosmetics of the opacity slider.
  5. In the Common Chemicals model list, NaOH was listed at MaOH. Fixed.
  6. Added "Walls" Potential.
  7. Added D- and L- Lactic Acid condensation monomers to model library.
  8. Some van der Waals radii adjusted to conform to Bondi.
  9. Added energy function atom types for Kr, Xe, and Ne.
  10. File >> Open Model List... is now part of extended menus.
  11. Quick Control Panel's "Show Console Window..." button is now part of extended menus.
  12. Now draws dipoles for each molecule in the model. They are represented as red/blue cylinders capped by an arrowhead (a cone).
  13. Added the CircleAtom and AtomAtomArrow commands. These draw a circle around an atom and an arrowhead-capped arrow between two atoms, respectively.
  14. Added enabling/disabling of energy-related controls (e.g., "Run Dynamics" depending on whether energy function is available.
  15. Added Energy Status indicators to the toolbar of the Model Window. These are direct visual indicators of whether the current model has energy function parameters.
Version 1.3.1 changes
  1. When a shape search completes, it now updates the molecular surface.
  2. Added "Automatically Update Bonding" checkbox to Animation Dialog.
  3. Added progress indicator when reading large, multi-frame XYZ files.
  4. Fixed: Load an ion, merge an ion, merge an ion, resulting in an access violation.
  5. Added sodium energy function atom type.
  6. Fixed a bug where atoms with 16 bonds sometimes caused a crash.
  7. Added output frequency control to the .bmp animation output dialog.
  8. Added ability to hide/show all water molecules.
  9. Added ability to delete all water molecules.
  10. Added Resolution scripting command: "Resolution medium" or "Resolution high" Sets the sphere and cylinder drawing resolutions.
  11. Fixed bug: on each optimization step, the (optional) .bmp animation output occurred before the Model Window was repainted.
  12. Added the "ultrahigh" resolution option to the Surface scripting command.
  13. Increased from 21 to 25 the number of colors used to represent the electrostatic potential surface.