STM4 – change history

20110103

• Few fixes for 6.3 compilation
• Increased the number of measures for Measure Closer Atoms module
• Added better faces rendering to the Draw Simple Polyhedra module

20090430

• Added Energy vs. Distance (global) chart to Fingerprint Analysis module.
• Added an Energy Landscape visualization for the Fingerprint Scatterplot module.
• Fixed Enthalpy Transition module for structures with the same cell volume.
• Fixed crashes in Write Structure and Compute Solvent Excluded Surface.
• Fixed small alignement in CIF plugin.
• Added TracesSwDisplayApp to be used when there are problems with OpenGL volume rendering.
• Added option to Draw Simple Polygon to remove polygon central atom.
• Ported to 7.2.1 (linux only)

20090114

• Added the Read Fermi Bands module and FermiBandsApp full application.
• Finished the Read Fermi Surface module. Added surface interpolation.
• FpExtract writes a comment with the structure energy.
• If energies are present, FpExtract writes the structures ordered by increasing energy.
• Added new modules for the CrystalFp analysis: RadViz, Fingerprint SPE and Select Structures. They are under New Modules.
• Now Find Symmetries copies the global data to output.
• Added Write Summary module to output essential crystallographic data for each structure.
• Added Enthalpy Transitions module to find where, when increasing pressure, the minimum enthalpy structure changes.
• Fixed POSCAR reader to read a broader set of POSCAR constructs.
• Changed normalization constant in old Degree of order computation to (cell volume)^1/3.
• Added Energy vs. Volume for fingerprint analysis.
• Corrected Axis Glyph module to display unit cell data also if only unit cell data present in the structure.
• Axis Glyph module now can display axis labels for reciprocal unit cell (a*, b*, c*).
• Added quasi-entropy computation and display to Fingerprint Analysis module.

20081112

• Added Shel-X writer
• Added the choice of coordinates between cartesian and fractional for the CIF writer. This writer has still problems with symmetries represented as XYZ
• Corrected lattice reading for Shel-X reader and Apply Symmetries module.
• Corrected firing conditions for Delete Atoms module.
• Now compiles also on Windows Vista using Visual Studio 8.0 and AVS/Express 7.2

20080808

• Fixed Write Structure execution conditions
• Finished module documentations
• Fixed some compilation problem under 6.3 with Visual Studio 6
• Added module Find Symmetries that wraps the program KPLOT.
• Added a first implementation of Fermi surface computation from EIGENVAL VASP output file

20080715

• Fixed some compilation warnings under 6.3 with Visual Studio 6
• Fixed compilation problems under 7.2 on Linux x86_64 and Windows
• Fixed set of max > min in Threshold Data only when needed
• Added Gamess input reader
• Added "Color by Step" option to FpScatterplot
• Refactored the CrystalFp library at the core of the Crystal Fingerprints modules
• Removed STM3
• Added Gaussian fit for the Crystal Fingerprints analysis module
• Fixed some compilation warnings (using -Wall -pedantic -ansi)

20080410

• Fixed translation limits for Move Structure. Now if "Translate along basis vectors" is checked, the translation limits are -1..1
• Added loop_info output to ConvertNewToOld
• Fixed Write Structure that was not writing all frames from an animation
• Added unit cell and symmetry read from MOL2
• Added "Force Symmetry Group" capability to Apply Symmetries
• Fixed Gaussian Cube and PLT readers to transform the voxed data they read into node data
• Changed Gaussian reader and PLT reader to have smooth replication of the volume data in Replicate Lattice
• Added Draw Simple Polyhedra module. It is the porting of Find Polyhedra module under STM3

20071206

• Resolved the race condition in the Color Legend module that appears during reload of a saved application
• Fixed the Color Legend user interface in atom type mode. Removed the unused X max field and renamed some fields
• Fixed Apply Symmetries that was omitting some atoms, or adding duplicated atoms when asked to fill the unit cell
• Now Compute Bonds does not create bonds shorter than 0.5
• Some small user interface correction for Set Manual Bonds
• Now Set Manual Bonds selections could be saved and reloaded
• Added the module Merge Unit Cell that transfers the unit cell from one structure to another (useful for structures split between PLT for the volume and XYZ for the structure)
• Added module Interpolate Volume to up-sample a given scalar volume
• Changed firing conditions for Resample Tri module
• Fixed Replicate Lattice to correctly join volume data
• Fixed Accumulate Global Data for step increments not equal to 1. Added also a steps array output to be used in General Graph module
• Fixed Error Tube wrong endcap spheres subdivision value
• Fixed Select Fragments module user interface
• Now Set Manual Bonds permits the preservation of existing bonds
• X Ray Structure Factors module now include the General Graph module
• The Draw Unit Cell module (used inside Draw Unit Cell and Replicate Lattice) has been rewritten to use lines instead of a Structured Mesh
• Count Bonds now can count bonds going outside the unit cell to have the correct count for boundary atoms also
• Added color selection to the Draw Unit Cell module. It is active when "Black" toggle is set, but is not reachable from the user interface
• Fixed a font problem on Linux Suse 10.3 for Draw Structure panel
• Changed Merge Values to merge values to atom, bonds or global data
• Minor changes to Pick Unit Cell (the output port is now called structure_out)
• Added a Read Structure No Bonds module that read the structure without recreating the bonds

20071015

• Fixed DL_POLY HISTORY reader: now verifies that the timestep read is valid
• Fixed updating in Fingerprint Compare module
• Added gOpenMol PLT reader
• Fixed crash in Select Atoms (synch lost when cascaded)
• In MoleculeType.v changed xyz and bonds to float xyz[natoms][3] and int bonds[nbonds][2] to make them more usable also from V
• Corrected aesthetic problem in Draw Structure panel
• Added module Enclosing Ellipsoid
• Module Velocity Mean moved to Trajectory sub-library
• Changed fractional shift limits in Crop Structure to -1..+1
• Various changes to make STM4 compilable with AVS/Express 6.3. The corresponding Visual Studio files are under the msvc6 directory
• Draw Polyhedra: reduced faces specular reflection term to 0.1 to make them less shining
• Axis Glyph does not loose settings anymore
• Changed Blue-Red colormap to be consistent wit the other colormaps. Now it goes from blue to white (for negative values) and from white to red (for positive values)
• Color Legend now force the number of ticks if "Integer steps" is selected and makes the Tick field invisible
• In Solvent Excluded Surface added -hdensity parameter to the msms program invocation
• Added missing writer in PickUnitCellApp
• The atom selection part has been abstracted in a new module that in turn is used by the following modules: Compute Selected Bonds, General Backbone, Particle Density, Select Atoms, Accumulate Traces, Velocity Mean, Crop Structure, Draw Polyhedra, Set Rendering Mode, Measure Closer Atoms
• Fixed Select Atoms and Select Fragment to save the selection status if Freeze is set before saving the application
• Fixed the production of multiple coincident atoms from Symmetry module
• Added the module Interpolate Plane to create a plane passing through a given set of picked atoms in a least square way.
• Added the Crop From Plane module to remove atoms and volumetric data outside a given distance from a plane.
• Fixed an off-by-one problem in the PLT reader

20070831

• CIF reader: now takes atom types from atom names if the proper element type tag is not present
• Fixed warning in Draw Polyhedra
• CIF reader: fixed a problem if a field ends with an apostrophe
• Added module to delete atoms by clicking on them
• Changed default color schema for fragment coloring to conform to RasMol shapely color scheme
• Fixed minor GUI problems in Accumulate Traces module
• Color Legend: changed label "Intervals" to "Ticks"
• Bicolor Surface: fixed GUI (misplaced title)
• Fixed minor GUI problems in Time Legend

20070627

• Fixed a problem with Apply Symmetries
• Rewritten the Gulp reader. Now reads correctly almost all the test cases I have
• Added new bonds rendering mode in Draw Structure: All lines. It renders bonds and H-bonds all as lines (to reproduce the STM3 behavior)
• Added a "translate along basis vectors" mode to Move Structure
• Fixed a problem with Compute Bonds: it was ignoring some bonds involving H and N, O or F
• Made Velocity Mean module visible in the library
• Fixed layout for Draw Sw Structure panel
• Fixed coloring of residues read from a PDB file
• Added fragment color for water
• Solvent Excluded Surface now works on Mac also
• Added plane visibility toggle in Miller Plane
• Started introducing fake atoms with Z=0 to be the anchor for coordination bonds like the ones in ferrocene. Every usage should be checked to ensure proper treatment of those atoms.
• Fixed PDB reader to take element type from the right column
• Added reverse selection in Crop Structure (plus fixes for user interface)
• Fixed CIF reader to skip atoms with undefined coordinates
• Added by default a 10% increment to bonding distance (with the new set of values there were missing bonds)
• In PDB reader D atoms are converted to H
• In MOL2 reader if element is 'X' try to deduce the atom type from the atom name

20070605

• First official release of STM4