STM4 – change history
- 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
- 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)
- 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.
- 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
- 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
- Added a first implementation of Fermi surface computation from EIGENVAL VASP output file
- 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)
- 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
- 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
- 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)
int bonds[nbonds] 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
- 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
- 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
- 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
- First official release of STM4