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Changes From Ampac-8.16.6 to Ampac-8.16.7

• AMPAC
1. C.I. is now allowed with solvation (SM5.2, SM5.2R, SM5C, SM5CR, and COSMO). This involves a significant improvement in both the C.I. code and solvation code to remove this long standing limitation.
    
2. Keyword "Mulliken" is now fully supported in both the out and vis file. Previously, "Mullik" would produce Mulliken analysis but not Mulliken charges unless keyword "Sybyl" was also present. "Mulliken" now produces both the Mulliken analysis and charges as expected.
    
3. A small initialization bug with simulated annealing methods has been fixed.
    
4. A small initialization bug with IRC for certain specific cases has been resolved.
    
• AGUI
1. Quick launch can now be activated directly from the AMPAC and Gaussian dialogs. This is equivalent to the user hitting "Retain" to exit the dialog and then quick launching the "(Current)" scheme.
    
2. Add support for MINVIS keyword in AMPAC Dialog. This keyword eliminates the large matrices needed for surface generation to greatly reduce the size of the AMPAC vis file. AGUI will now correctly read in AMPAC jobs containing the MINVIS keyword.
    
3. Support for specifying a time with the t= keyword has simplified in the AMPAC dialog.
    
4. Option in AMPAC dialog to specify default verses non-default gnorm.
    
5. After a molecule has been symmetrized (a structure modification), disable viewing of its results.
    
6. The text editor for input a title in GaussDialog is free-format and so may allow blank lines to be entered in the title. Gaussian files produced with blank lines in the title will cause the job to fail because the portion of the title after the blank line is intepreted as the geometry. AGUI read in of these files may also report errors or crash. This problem has been fixed by automatically replacing blank lines in the title with "!" when writing a Gaussian input file.
    
7. In reading Gaussian jobs with methods that do not use a basis set (MM, semi-empirical, and compound), then switching to a different method (e.g. HF or DFT) the assumed basis set is custom/"no basis". This is now changed to default to 3-21g. For other methods (HF, DFT, etc.) that do use a basis set, if no basis is given in the keyword line, it will still properly come up as custom/"no basis".
    
8. Handle the window close button ("X") of Semichem Smart Slide dialogs correctly.
    
9. In the Redundant Coordinate editor, there was a bug that prevented entering values in the section of the dialog under the "Set Values" tab. This bug has been fixed.
    
10. In the Redundant Coordinate editor, if you set the value of the diagonal hessian, set the number of scan steps, or set the scan step size and then selected create new coordinate, then that change would be lost.

Changes From Ampac-8.16.5 to Ampac-8.16.6

• AMPAC
1. Symmetry identification routines have been revamped and improved. Difficulties in identifying symmetry for some cubic point groups (such as C60 with Ih symmetry) has been resolved. When an exact symmetry match is not found, AMPAC now reports the highest symmetry that the molecule satisfies. Individual atoms are now identified as "R3" symmetry and MO symmetry labels are identified as "A" symmetry.
    
2. The testsuite has been expanded to cover a broader range of symmetry types in subdirectory mpg_tests.
    
3. Fixed a problem for numeric count of symmetry labels of MOs, where the molecular poing group symmetry is unidentified. The numeric portion now gives the expected result.
    
4. The CHN/FULLCHN has been improved and upgraded to algorithm version 1.4. The reported problem "ERROR IN CHN21: SIZE IS ZERO!" has been resolved and will no longer appear.
    
5. The printing of the dipole moment in the output file has been fixed. Previously, the "TOTAL" component of the row "HYBRID" was being computed incorrectly. This has been fixed. All other components remain correct.
    
6. A rare memory allocation bug associated with C.I. that caused the program to crash has been fixed.
    
• AGUI
1. When an undefined internal coordinate (e.g., dihedral coordinate of 3rd atom) becomes defined after a reordering of atoms, always set the corresponding optimization flag to "Yes".
    
2. On Windows, use the full path name of a file when opening an editor instead of the DOS short-path name.
    
3. When viewing results, don't turn off "Inquire" if it is the current Builder mode.
    
4. Handle "Escape" key correctly (as equivalent to "Cancel" in most cases) in dialogs (e.g., Semichem Smartslide).
    
5. Fixed problem in recognizing D2d point group symmetry in some cases.
    
6. Fixed problem with Vibration and Atomic Charge dialogs showing old data after the dialogs are closed ("Close"), a new quick-launch is run for the molecule group and loaded and the dialogs are opened again.

Changes From Ampac-8.16.4 to Ampac-8.16.5

• AMPAC
1.  Disabled use of LAPACK (diagonalization) routines of Intel MKL libraries on Windows and Linux due to occasional (rare, but not rare enough) instabilities. More stable AMPAC diagonalization routines used instead.
    
• AGUI
1. Fixed crash-problem when parsing keyword lines containing unbalanced parentheses.
    
2. Fixed problem transferring charge and spin multiplicity of Gaussian result files without MO data to Ampac Calculation Setup.
    
3. Fixed obscure problem with Builder and other editing items staying disabled for active molecule after a corresponding vibration dialog is closed and no results are showing for the molecule and the Vibrations Preferences are set to "Show Dipole Derivative Unit Vector" but there are no such results for the molecule.
    
4. When opening a Gaussian LOG file, report when it corresponds to a job that did not complete normally, in addition to reporting specific errors and warnings about the file.

Changes From Ampac-8.16.3 to Ampac-8.16.4

• AMPAC
1.  Fixed (workaround) a problem with occasional Intel MKL diagonalization failures ("DSYEV" errors) on Windows and Linux.
    
2. Include MO numbers in MO symmetry labels, even when no symmetry is identified.
    
• AGUI
1. Added ability to stream output files from running AMPAC (Windows only) and Gaussian jobs (all platforms), submitted via AGUI, to read-only windows in order to monitor the progress of running jobs. For Gaussian jobs on Windows, this new feature also eliminates the only advantage of submitting Gaussian jobs via G03W.exe instead of directly to g03.exe. In AGUI on Windows, Gaussian jobs are submitted to g03.exe by default so that the (named) checkpoint files are written to the input file directory, as on Unix/Mac, instead of the Gaussian Scratch directory, and also to avoid the extra messages and windows of G03W.exe.
    
2. For "Recent Files", recognize both .gjf and .com extensions on both Windows and Unix/Mac-OSX.
    
3. Fixed problem with Builder mode reverting to "Place Fragment" mode after opening a file, viewing results and then closing/hiding results. After opening a file, Builder mode for corresponding molecule group is initially "Inquire" (to prevent accidentally editing molecule(s) from file) and now stays "Inquire" unless user explicitly changes it.
    
4. Fixed problem with occasional incorrect or inconsistent "enabled" states of the following main menu items and / or context menu items and, in some cases, corresponding tool buttons: "Recent Files", "Related Files", "Ampac Quick Launch", "Ampac Calculation Setup", "Gaussian Quick Launch", "Gaussian Calculation Setup".
    
5. Don't put full path of checkpoint file in %chk= line of Gaussian Calculation Setup after opening a Gaussian checkpoint file (formatted or unformatted).
    
6. After using "Save Temp Files" for Gaussian file(s), update the checkpoint file name in the %chk= lines of the corresponding Gaussian Calculation Setup settings.

Changes From Ampac-8.16.2 to Ampac-8.16.3

• AMPAC
1. Fixed a bug where the value in keyword HGAS=x.xxxx was being ignored in AMSOL calculations with keyword TRUES.
    
2. Fixed a bug in AMSOL solvation calculations for molecules with close O-O distances.
    
3. For CI calculations where the CI space is too small to contain the requested state, AMPAC will now print a helpful message and exit rather than crashing.
    
4. New keyword MINVIS in AMPAC. Using MINVIS prevents surface information (MOs and density matrices, overlap matrices) from being included in the .vis file. This dramatically reduces the size of the .vis file for most jobs, particularly for multistep jobs, like IRC, CHN, Reaction Path, etc. When MINVIS is specified the resulting VIS file will read in as usual in AGUI, except that surfaces and MO data will not be available.
    
5. AMPAC is now smarter about when to symmetrize and print MOs. It will not symmetrize and print MOs for SCFLOCAL, since this would be meaningless.
    
6. Minor "AMPAC 8 User Manual" fixes.
    
7. Minor testsuite changes.
    
• AGUI
1. Vast improvement in calculation speed and display quality of surfaces (from "Surfaces and Cubes" dialog and "MOs" dialog).
    
2. If ampac.key does not have AMSOL license and an AMPAC file containing AMSOL-related keywords is loaded into AGUI, disable the AMSOL-related keywords within AGUI (original file is unchanged unless saved over), after warning user.
    
3. Make the initial fractional coordinate and Cartesian coordinate values of the "Pending Atom" in the Atom List Editor (0.0,0.0,0.0) instead of the arcane (1/40,2/40/3/40) or (0.1,0.2,0.3). Prevent adding of the "Pending Atom" to the atom list if its (editable) coordinates are identical to an already existing atom.
    
4. In the "Cubes and Surfaces" dialog, display the cube increment values of the "Available Cubes" in Angstroms instead of atomic units, and indicate that Angstroms are being displayed with an "(A)".
    
5. In the "Gaussian Calculation Setup" dialog, change the "CGST" NMR method to "CSGT", both for display and for properly reading "nmr=csgt" Gaussian files.
    
6. In the "Gaussian Calculation Setup" dialog, fix problem with being forced to save a Gaussian input files when "Submit" is selected when the molecule was already loaded from a Gaussian input file and no changes have been made to it or the dialog settings.
    
7. Don't use the "Use PBC" setting as a "Gaussian Calculation Setup" dialog preference. Previously, if the "Gaussian Calculation Setup" preferences were not default, then "Use PBC" defaulted to "No" even when the system had TVs.
    
8. When PBC TVs are present, disable (and silently turn "off") the "Use PBC" control in the "Gaussian Calculation Setup" dialog when current settings (e.g., MP2) of the dialog are incompatible with PBC. Save the "Use PBC" state prior to it being disabled so that it is preserved if the current dialog settings become compatible with PBC.
    
9. When saving a file for a molecule for which results are showing (e.g., Atomic Charges), force the creation of a new molecule group and corresponding view window for the saved file so the displayed results don't disappear.
    
10. Fix problem with AGUI splash screen on some X11 systems sometimes being "hidden" behind initial view window or main AGUI window on startup.
     
11. Fix problem with the grid lines disappearing in the "Calculation Summary" dialogs after they are first shown.
     
12. Add a "Full" / "Constrained" indicator to the "Gradient Norm" or "RMS Gradient Norm" field of the "AMPAC Calculation Summary" dialog to clarify whether the value corresponds to all of the coordinates or just the unconstrained ones. Also, add a "Constrained Coords" field to the dialog to indicate the number of constrained coordinates which were used in the corresponding AMPAC calculation.
     
13. Fix problem with saving of postscript files when the view window caption is used as the Title and the caption contains parentheses.
     
14. Fix problem with reading and writing Gaussian PBC input files when atomic units is specified (units=au or units=bohr).
     
15. For MP2 NMR Gaussian log files, read in and display both the SCF and MP2 NMR results, instead of just the SCF NMR results.
     
16. When reading in NMR data from a Gaussian log file, don't write out an "nmrdata.txt" debug file.
     
17. When loading PDB files, don't put atoms in the "Low" layer unless the file contains both ATOM and HETATM records (in which case ATOMs go in the "Low" layer and HETATMs go in the "High" layer) or there are more than 500 total atoms.
     
18. When loading a file or files into AGUI with "Append All Files to Active Molecule", don't blow away the active molecule if the loaded files are invalid, i.e., contain no usable molecules.
     
19. Improve error and warning messages for missing, invalid, expired or about-to-expire ampac.key files.
     
20. If an AMPAC or Gaussian "Quick Launch" job fails, prompt the user to view the corresponding .out or .log file, just like is done after a job fails via a "normal" job submission.
     
21. When loading PDB Files, only offer to "Add Hydrogens" if necessary, i.e., only if there are any hydrogen-deficient atoms in the molecule. Also, offer to "Add Hydrogens" when loading MDL MOL and Sybyl MOL2 files, if necessary.
     
22. Fix problem with Point Group (and probably Space Group) symmetry consistency between symmetrizing, saving file, loading file and checking symmetry for some large systems. Sometimes, a previously "exact" point group would only be identified as "approximate".
     
23. Fixed problem reading floating point data of the form "data=x.xxx" when "data= x.xxx" was expected for some AMPAC and Gaussian result files with very large numbers.
     
24. When saving image files on MAC-OSX and X11 systems, set the saved-to directory as the current directory after saving.
     
25. On Linux and other non-Windows systems, the initial filename in the "Job Completed" dialog is no longer initially empty but contains the .out or .log file corresponding to the completed job, as was always the case on Windows.
     
26. When exporting an SVG image file, warn about overwriting a existing file when necessary, as is done elsewhere in AGUI when saving files.

Changes From Ampac-8.16.1 to Ampac-8.16.2

• AMPAC
1.  Fixed printing of IRC LENGTH and ENERGY to work with large numbers.
    
• AGUI
1. "Edit->Reorder->All Atoms by Bonding" now works in the Atom List Editor and "ZMat Tools->Reorder" now works in the Connection Editor.
    
2. When non-Ampac files are opened, the initial Ampac Calculation Setup settings for the corresponding molecules are determined by the Ampac Calculation Setup preferences.
    
3. When non-Gaussian files are opened, the initial Gaussian Calculation Setup settings for the corresponding molecules are determined by the Gaussian Calculation Setup preferences.
    
4. Added "Show Node" options ("None", "Active" and "All") to the context menu of Reaction Grid plots.
    
5. Added ability to save an SVG picture of the MO diagram in the MO dialog. Also added the ability to save the MO diagram data to a text file.
    
6. Added "Overwrite file?" message box, when appropriate, when saving (SVG) pictures or saving data text files for Vibrational Spectra plots, Reaction Path plots, MO diagrams, etc.
    
7. Fixed obscure ONIOM bug where adding "Add valence" or "Add hydrogens (and adding missing carboxyl oxygen to carboxyl-terminal amino acid residue) to a medium or low layer target atom copies all of the ONIOM data (e.g., link atom #, model atom data, etc.) from the target atom to the new atom, instead of just setting the layer of the new atom to the target atom.

Changes From Ampac-8.15.9 to Ampac-8.16.1

• AMPAC
1. Modified config_ampac.csh to handle library configuration for Mac-OSX platform, instead of using a separate configuration script.
    
2. Updated "AMPAC 8 User Manual".
    
3. Improved check_env.csh (Unix systems only).
    
4. Fixed AMPAC memory-allocation bug when PROTO or FILL keywords were being used.
    
5. Only symmetrize MOs in AMPAC if MO printing is requested (VECTOR or ALLVEC keyword) and if localized SCF MOs are not requested (SCFLOCAL).
    
6. Added testsuite/mpg_tests/mpg_t.dat file, i.e., added a test for "T" point group.
    
7. Fixed unix / DOS newline issue for testsuite/properties/prop_esp_sam1.dat and testsuite/properties/prop_esp_sam1d.dat files on Windows.
    
• AGUI
1. Fixed occasional crash-on-exit on AIX platform and possibly some other X11 platforms when AGUI was not run with the -standalone argument.
    
2.  Fixed problem with running g03.exe on Windows, for Gaussian 03 Revision >= C.02, which requires that GAUSS_EXEDIR be defined. Fixed by AGUI correctly defining GAUSS_EXEDIR after each launch (for child processes only) if it is not already defined.
    
3. Added ability to use mouse wheel to zoom molecule in and out of view windows.
    
4. Allow negative step sizes for Scan Coordinates in Redundant Coordinate Editor.
    
5. On X11 systems, make the initial filename for the Open Files dialog after job completion be the output file corresponding to the input file submitted.
    
6. Prevent initial directory in Save File dialog from being the AGUI temp directory, as could happen after running a quick-launch job or opening a checkpoint file.
    
7. Fix problem with initial directory in Save File dialog of AGUI sometimes not being the current working directory (was sometimes parent of current working directory).
    
8. Fixed problem with File->Related Files menu item of AGUI sometmes not working correctly.
    
9. Allow saving of temporary Gaussian Formatted Checkpoint file (via File->Save Temp Files) when a checkpoint file is opened.
    
10. Fixed problem with Gaussian / Ampac Calculation Setup dialogs not being efficiently reused.
     
11. Added missing "Display Format" dialog pages to AGUI Manual.
     
12. Don't disable "Chain" Job type in Ampac Calculation Setup dialog of AGUI if molecule group does not satisfy the criteria for Chain input. Instead, display a prominent warning in the dialog.
     
13. Fix Gaussian file parsing bug in AGUI for compound keyword strings which also define the method type (e.g., amber=hardfirst).
     
14. Gaussian file parsing fix in AGUI: correctly handle Custom methods.
     
15. Fix problem with saving of JPEG files on some IRIX systems due to JPEG library incompatibilities.
     
16. Fixed potential problems when searching for AGUI temp dir on Windows. Next-to-last test is for P_TmpDir (POSIX temporary directory, which is the root directory of current drive). Last test is for current directory. Make sure AGUI temp directory is readable / writable before using it and make sure that the root directory of a drive is not confused with the (undefined) "root" UNC directory.
     
17. Added preference for whether or not to create a new / empty view window on startup of AGUI.
     
18. Fixed problem with surface mapping and surface existence data being incorrectly read from registry.
     
19. When Temp Files are saved, make sure captions of all current view windows of saved files get updated.
     
20. Indicate that a temporary Gaussian formatted checkpoing file (one created by opening a Gaussian checkpoint file) is temporary by prepending "TEMP FILE: " to its caption. Such a file can now be saved using "File->Save Temp Files".
     
21. Added preference for molecule-based dialogs / windows (e.g., Smart Slider dialogs, Layer Selection dialogs, etc.) to stay on top of other dialogs / windows. This is especially useful, for example, when acting on maximized view windows with the molecule-based dialogs or when many view windows are open. There was already a preference for view-based dialogs (e.g., Display Format dialogs, Ampac Calculation Setup dialogs, etc).