# Revision History

## Winmostar V11

### Version 11.1.2 May/9/2022

[New Feature]
• Enabled to export of multi-frame wmm files from the animation manipulation area.
• Enabled to test the operation of GAMESS, LAMMPS, and Quantum ESPRESSO.
[Specification Change]
• The Reload function of the animation does not change the camera angle.
• In project mode, the order of actions in the working folders of LAMMPS and Quantum ESPRESSO has been changed.
• When the Crystal System is changed in the Crystal Builder, the Space Group is not updated if it is not necessary.
• The order of the following items in Quantum ESPRESSO's Result Analysis menu has been changed.
• Changed default values for Quantum ESPRESSO Keyword Setup.
• The Precision setting (tr2_ph) in the Quantum ESPRESSO Workflow Setup has been changed.
• Quantum ESPRESSO Workflow Setup now set K Points=Monkhorst-Pack when Preset=Optimize(Atom).
• Job Manager status is now displayed in the same color as the main window.
[Bug Fix]
• Fixed a bug that prevented some warning dialogs from appearing on first startup.
• Fixed a bug in window size adjustment at startup.
• Fixed a bug that caused range check errors when opening files in some situations.
• Fixed a problem that prevented export of multi-frame sdf and mol2 files from the animation operation area.
• Fixed a problem in which editing a molecular structure during animation display in project mode did not execute the process properly.
• Fixed a problem in which the project display area did not appear when clicking [File]-[Project]-[Open Temporary File].
• Fixed a problem in which the file format check did not work for some editing operations.
• A bug that prevented the job manager from correctly determining the end of the job in GAMESS for Intel compilers has been terminated.
• In file mode, Quantum ESPRESSO's band structure display function did not automatically set the input file for label acquisition.
• Range check errors are no longer generated when opening Quantum ESPRESSO output files that have errors during symmetry detection.
• "postprocess" can now be selected on the "Job Settings" window of Quantum ESPRESSO's Remote Job.
• Fixed a problem in which profile information disappears when changing the Profile Name in the Remote Server Profiles window.

### Version 11.1.1 April/28/2022

[New Feature]
• When opening cube files, external applications such as VESTA can now be specified ([Tools]-[Preferences])
[Specification Change]
• The camera angle is not changed at the start of a job in project mode.
• -[Add Atom]-[Add Dummy Atom to Center of Geometry of Selected Group] has been changed to work even when only one atom is selected for a group.
• Changed one of the display units in the Energy Level Diagram window from a.u. to hartree.
• The file used to determine the residue names of monatomic ions when assigning force fields in MD calculations has been changed.
• In the DPD Cell Builder, Block Polymer Builder, Random Polymer Builder, and Polymer Cell Builder, the fields for entering the number of monomers, repeat units, and polymers have been eliminated and are now entered in a dialog box.
• Changed the names of ESM-RISM-related buttons that appear in Actions in Quantum ESPRESSO's project mode.
• In the project mode of Quantum ESPRESSO, 1D RMS and 3D RMS for RISM calculations have been added to the actions.
• Changed the number of lines displayed when running a tail in a Quantum ESPRESSO remote job.
• Quantum ESPRESSO's NEB menu structure has been reconfigured.
• Revamped template scripts for FOCUS.
[Bug Fix]
• Fixed a bug that caused selected fragments to be blank when operating under the  menu.
• Fixed a problem in which a fragment could not be changed in -[Select Fragment].
• Fixed a problem in which the output file of the parent job remained when manually creating a continuation job in project mode.
• Fixed a problem in which calculations stopped in the middle when Optimize and NMR were selected in Easy Setup of Gaussian.
• Fixed a bug that prevented force field assignment when monatomic ions of Cu, F, Br, and I are included.
• Fixed a problem in which the camera position did not change properly after using the polymer cell builder.
• Fixed a problem in LAMMPS project mode where "Coordinate (Final)" was displayed in the action before the calculation was successfully completed.
• Fixed a bug that caused the vertical axis to be state/spin/eV even when nspin=1 in the DOS and PDOS display windows of Quantum ESPRESSO
• Fixed a problem with Quantum ESPRESSO's NEB calculations not running.

### Version 11.1.0 April/15/2022

[New Feature]
• A mode (project mode) for batch management of calculation progress and files is now supported. In project mode, you can run multiple jobs in succession, save input files in batches and run them at any timing, run remote jobs in a manner similar to local jobs, detect calculation errors, and switch work folders and display results with a single click. In addition, the existing operation method is now file mode, and the user can select between the two.
• Project mode is now supported in GAMESS, LAMMPS, and Quantum ESPRESSO.
• Added [File]-[Import File], [Export File], -[Move Atom]-[Translate with Hydrogens] buttons to the toolbar.
• Editing operations using the context menu are now supported in the molecular display area.
• Allows multi-frame mol2 files to be output in the animation display area.
• Buttons to move one frame forward or backward have been added to the animation display area.
• Self-diffusion coefficient, mean-square displacement, and displacement of selected atoms can now be calculated from [Options] in the animation display area.
• Scroll bars and Export functionality have been added to some text editing windows.
• Files in the Samples folder can now be imported with a single click. ([File]-[Import]-[Samples File])
• Enabled to export the structure to a file without making any changes to the current structure. ([File]-[Export File])
• Enabled to save and load lossless proprietary format (wmm) on molecular structures.
• In [File]-[Get Info], additional information (force field settings, etc.) on molecular structures can now be checked.
• The order of the fragment list can now be edited. (UserPref ragment_list.txt file)
• Job scheduler operation tests can now be performed in the [Test Connection] function of various remote job-related functions.
• Export and Import of settings are now supported in QM's Keyword Setup window.
• Animation inversion, skipping, and translational movement are now supported when displaying QM animations.
• Log contraction display for GAMESS, LAMMPS, and Quantum ESPRESSO is now supported.
• The GAMESS and Quantum ESPRESSO Keyword Setup window now allows the user to confirm the keywords to be output. (Preview tab).
• GAMESS, Gaussian solvent effects with SMD added.
• Added MP2 setting item to the GAMESS Keyword Setup window.
• Added IEF for solvent effects to the GAMESS Keyword Setup window.
• In the [MD]-[Solvate/Build Cell] function, SMILES input and specification of files other than mol2 are now supported.
• Density can be specified in mol/L in [MD]-[Solvate/Build Cell].
• In the polymer cell builder, it is now possible to set whether or not the polymer is twisted in the initial placement.
• In the LAMMPS Keyword Setup, an option was added to automatically disable the SHAKE method when CH4-like molecules are included.
• In the LAMMPS Keyword Setup, an option was added to automatically disable the PPPM method when the charge is not included.
• In the Quantum ESPRESSO Keyword Setup window, the pseudopotential and functional types can now be selected to narrow down the candidates for pseudopotential files.
• In the Quantum ESPRESSO Keyword Setup window, K_POINTS can now be automatically set by the density parameter of the reciprocal space.
• In the Quantum ESPRESSO Keyword Setup window, nbnd can now be set automatically.
• In the Quantum ESPRESSO Keyword Setup window, the ratio of ecutrho to ecutwfc can now be set.
• In the Quantum ESPRESSO Keyword Setup window, recommended values for ecutwfc are now displayed.
• AkaiKKR GUI is released.
• The command for submit executed at the time of remote job submission can now be confirmed. (submit_command.txt)
• In [Tools]-[Comformation Search(Balloon)], the clustering algorithm for candidate structures has been improved (using dihedral angles).
• Added the function to visualize log files of various processes in real time. ([Tools]-[Log Viewer])
• The Job Manager has been significantly modified to do automatic sending and retrieval of files to remote servers in project mode.
• Added the function to reset Job Manager settings (click [Help]-[Reset Job Manager] after enabling [Help]-[Debug Mode]).
• The OPLS-AA charge can now be calculated in the force field editing tool.
[Specification Change]
• Some processes now show a warning if the file path to be operated on contains multibyte characters.
• Changed file names of color and radius setting files (wm_system\wmx\wmx\atoms_*.wmx). atoms_new.wmx -> atoms_v10.wmx, atoms_old.wmx -> atoms_v4.wmx
• The values of physical constants have been unified with CODATA 2018.
• The name of the working directory has been changed to the working folder.
• The length of the file path displayed in the main window title has been increased.
• Default window size has been changed.
• The caption of each window has been changed.
• The display time and font size of hints (tooltips) are now variable. (Tools]-[Preferences])
• The [CH3], [C2H3], and [C6H5] buttons on the toolbar are now hidden by default.
• Fragment replacement operation in the molecule display area can now also be performed by Ctrl+Shift+right-clicking.
• The number of numerical digits displayed in the molecule display area has been increased.
• Changed so that the wheel zooms in/out only when the cursor is in the molecular display area.
• The animation window is now integrated within the main window.
• The values (e.g., energy) for the selected frame are now displayed in the graph in the animation display area.
• Dynamics Bond settings in the Animation Display area have been moved under the Options menu.
• Changed so that the change flag is not set during animation playback.
• It is now possible to set whether or not the coordinate display area is updated during animation playback. ([Tools]-[Preferences])
• The second keyword area was merged into the first keyword area.
• Alias characters (%WM_COORD%, %WM_XYZ%, %WM_ZMAT%) are used to indicate the location of coordinates in the keyword area.The design of the coordinate display area has been changed.
• The width of the coordinate display area is now saved even when the application is closed.
• The number of digits for editing coordinates in the coordinate display area has been increased.
• [Save csv] in various graph display functions has been changed to [Export csv].
• The various graph display functions can now be toggled to show or hide option settings.
• Changed default file format to wmm format.
• Files with the extension md are now recognized as xyz format.
• Default value for coordinate output and display format is now XYZ.
• File format is now switched to wmm format when editing files in formats that cannot be saved (e.g., log files).
• Keywords are now blank when creating a new file.
• [File]-[Append] changed to [File]-[Import File].
• The default setting of the program used to import SMILES was changed from OpenBabel to Balloon.
• [File]-[Coordinate Format] has been integrated into the Keyword Setup window for each solver, and the display is now toggled by [View]-[Coordinate Format].
• The Title information displayed in the upper left corner of the molecule display area has been changed to be displayed and edited by [File]-[Get Info].
• The order of the list of fragments has been changed.
• [Set distance] has been changed to [Set margin] in the cell creation function in various editing functions.
• [Box Vectors] in -[Create/Edit Cells]-[Edit Cells Manually] changed to [Lattice Vectors].
• In -[Create/Edit Cell]-[Edit Cell Manually], the number of digits displayed has been changed from 4 to 6 decimal places.
• In -[Create/Edit Cell]-[Transform Cell], [Move with keeping fractional coordinate] is now set to True by default.
• -[Change Density] has been merged into -[Create/Edit Cell]-[Transform Cell].
• Changed [View]-[Rotate]-[Rotate View] to [Around Line of Sight].
• Corrected the captions in the Keyword Setup window for various solvers.
• The [Save] and [Load] buttons in the various solver Keyword Setup windows have been changed to [Export] and [Import].
• [Extending Simulation] in the Keyword Setup window for various solvers has been changed to [Continue simulation].
• The names of internal files automatically generated when a remote job is executed have been changed. (winmos.o -> remotejob_stdout.txt, winmos.e -> remotejob_stderr.txt, winmos.x -> submit_stdout.txt)
• In the header of the template script for remote jobs, the option to specify the number of parallels for each job scheduler has been removed.
• Error details are now displayed in the [Test Connection] function of various remote job-related functions.
• The titles of various QM result display windows have been changed.
• The menus for the various result display functions of QM have been separated by item.
• [Save Image] in the IR spectrum display window has been changed to [Export Image].
• The MO Plot window has been renamed the Surface Setup window.
• In the Surface Setup window, the default settings for Draw Style and Transparency have been changed.
• [Save VRML] in the Surface Setup window has been changed to [Export VRML].
• The IRC animation merging function has been moved to [Tools]-[Append Trajectory] in the animation display area.
• When reading QM log files, dipole moment values are now displayed in the numerator display area.
• Default program paths for GAMESS and FDMNES have been changed.
• When opening GAMESS, Gaussian, or NWChem log files, MO, Charge, and Dipole are no longer displayed if SCF or Opt calculations have not converged.
• When opening the Easy Setup windows of GAMESS, Gaussian, and NWChem, the contents of the Keywords Setup window are now reflected.
• Changed MOPAC default keywords to be set in mopac_default.wmx instead of init.dat in the UserPref folder.
• [QM]-[GAMESS]-[Import from punch file]-[Import $VEC] and [Import$HESS] have been moved to [Import $VEC] and [Import$HESS] in the GAMESS Keyword Setup window, respectively.
• In the GAMESS Keyword Setup window, NPUNCH=0, DAMP was removed from the default settings.
• In the GAMESS Keyword Setup window, NZVAR of $CONTRL and DLC and AUTO of$ZMAT were changed to be set for monomolecules and 6 or more atoms.
• In the GAMESS Keyword Setup window, the OTHERS and FORCE columns for $BASIS and the ICAV and TABS columns for$PCM were added.
• SCF and NMR fields have been added in the Gaussian Keyword Setup window.
• In the Gaussian Keyword Setup window, the arrangement of various keyword items has been changed.
• In the GAMESS Keyword Setup window, the default value for IRC scores has been changed from 40 to 20.
• GAMESS now generates and transfers a configuration file (conf.sh) when executing a remote job.
• In the NWChem Easy Setup setup window, cis has been removed from the setup keyword when TDDFT is selected.
• The priority order of charges referenced when performing MD calculations on structures with multiple types of charges has been changed to User > NBO > Mulliken > Lowdin > ESP.
• In the result analysis function that uses Gromacs tools, the switch between single precision and double precision is now performed in [Tools]-[Preferences], instead of in the Gromacs Keyword Setup window.
• In the [MD]-[Solvate/Build Cell] function, [Add mol2 file] has been merged into [Add file].
• In [MD]-[Assign Charge Manually], [Use acpype] and [Use GAMESS] were changed to [AM1-BCC Charge] and [RESP Charge], respectively. Also, [Gasteiger charge] was added.
• The term "monomer" in polymer-related functions has been changed to "repeat unit".
• Layout of various polymer builders has been changed.
• Changed to display the structure in a separate window instead of the main window when the [Display] button of various polymer builders is clicked.
• The layout of the Polymer Cell Builder and the [MD]-[Solvate/Build Cell] function have been unified.
• The mol2 file is no longer saved when the polymer cell builder is executed, allowing the process to be redone.
• In the Random Polymer Builder and Polymer Cell Builder, the random number seed is now fixed by default.
• In [MD]-[Polymers]-[Register Repeating Unit], the name of the repeating unit is now entered after the OK button is pressed.
• The standard output file extension for Gromacs, MODYLAS, Amber, and OpenMX has been changed to stdout.
• Expanded the presets in the Keyword Setup window for Gromacs and LAMMPS and changed the presets selected by default.
• The type of force field is now described in the LAMMPS data file with a comment.
• The method of creating the data file for the final structure of LAMMPS has been changed (copying the Atoms section and before from the data file of the starting structure).
• If the LAMMPS binary used for a local job is not found, lmp_mpi is now searched for and used in addition to lmp_serial.
• DPD cell builder [Save], [Load] changed to [Export], [Import].
• The design of [Solid] - [Crystal Builder] was changed.
• Added esm_w, alpha_mix, and cell_dynamics=damp-w to the Quantum ESPRESSO Keyword Setup window.
• In the Phonon tab of the Quantum ESPRESSO Keyword Setup window, the item captions are now actual keywords.
• Folder settings for MOL and pseudo-potential files in Quantum ESPRESSO can now also be set in [Tools]-[Preferences].
• The layout and file structure of Quantum ESPRESSO's NEB execution function has been changed. (V10 licenses will be issued to those who wish to use the old format)
• The license check when loading files for Quantum ESPRESSO's NEB function has been aligned with other Quantum ESPRESSO related functions.
• The final structure retrieved from Quantum ESPRESSO's ion_dynamics=damp log should now be the structure after the End final coordinates.
• The layout of [Tools]-[Preferences] has been changed.
• Changed the default for [Tools]-[Preferences]-[Calculations]-[Modify charges from AmberTools to adjust total charge] to True.
• [Tools]-[Draw Molecule] can now also be executed via [File]-[Import]-[Structural Formula].
• In [Tools]-[Conformation Search(Balloon)], the structure after the search is selected in a separate window.
• When [Tool]-[Conformation Search(Balloon)] is executed, information other than coordinates is not changed.
• In [Tools]-[Molecular Surface Area & Volume], [Aspect Ratio], and [Radius of Inertia], analysis results are now displayed in a dialog box.
• [Save SDF] in [Tools]-[Superimpose Molecules] was changed to [Export SDF].
• The layout of the Edit Profile window in the Remote Job Submission window has been changed.
• When displaying a list of jobs on a remote server in the Remote Job Submission window, the list now displays lines other than those containing user names.
• The grep function in the remote job submission window has been changed to process only the log files of the target job.
• The [Job]-[Get Remote File and...] function in the remote job submission window now checks for files on the remote server and deletes files with the same name on the local machine before transferring files.
• Do not output winmos_ftp.txt when executing remote jobs in file mode.
• Changed so that when executed from the command line, if a dialog with choices appears, it will automatically select the first choice and proceed.
• The coordinate output format (XYZ or Z-Matrix) has been changed to follow the display format when executing from the command line and saving in gjf format.
• When molecular volume/surface area, aspect ratio, and radius of inertia are calculated by executing from the command line, the calculation results are now displayed on the console.
• The layout of Winmostar Job Manager has been changed.
• Changed the default background color of Winmostar Viewer to white.
• When Winmostar Viewer is launched, it now inherits the perspective settings of the calling Winmostar.
• The Representations window in Winmostar Viewer has been redesigned.
• Added kbar to the units of pressure in Winmostar Units.
• Re-created the data in Samples\water_liquid.data.
[Bug Fix]
• Fixed a problem that could cause a range check error when reading a Quantum ESPRESSO BOMD output file that was in the process of being output.
[Deprecated Feature]
• Support for p2n format has been discontinued.
• The function to edit text using the in-house editor in [File]-[Open in Text Editor] has been eliminated.
• The [Make a backup of working directory] setting in the Keyword Setup window for various solvers has been eliminated and is now always set to True.
• The automatic placement of rm1.rm1 files in MOPAC has been discontinued.
• In the GAMESS Keyword Setup window, the NODES (Firefly) field has been eliminated.
• FMO-related functions of GAMESS have been discontinued. (Will be re-addressed in the future)
• MOSF-related functions have been eliminated.
• The UFF force field, GAFF2 force field, and polymer builder are no longer supported in the Professional Edition Economy.
• [MD]-[Assign Charge Manually]-[Manual Input] has been eliminated. (Merged into -[Change Atom Property]-[Change Charge/Spin] and -[Edit Charge])
• The interface builder of the old specification has been discontinued.
• [Save as default] in the LAMMPS Keyword Setup window has been eliminated.
• [Calculate as rigid body] in the LAMMPS Keyword Setup window has been removed. (This will be re-addressed in the future.)
• Amber support has been removed. (Will be re-supported in the future. Can be used in debug mode)
• FDMNES support has been discontinued for Economy or Student Edition licenses.
• The supercell creation function of the old specification has been eliminated.
• [Solids]-[Cleave Plane] has been eliminated. (Integrated into [Solids]-[Slab Builder], available in debug mode)
• [Solids]-[Insert Vacuum] has been eliminated. (Integrated into -[Create/Edit Cell]-[Transform Cell] and [Solids]-[Slab Builder], available in debug mode)
• CONFLEX-related functions have been eliminated.
• Remote job connection function using putty has been removed.
• Support for t2sub, llsubmit, Sharetask, NSUB, and Rescale in the remote job submission function has been removed. (These functions will be re-supported in the future.)
• [Tools]-[Bat Queue] has been eliminated.

### Version 11.0.3 February/2/2022

[New Feature]
• Enabled to configure MP2 in GAMESS keywords setup window.
• Enabled to configure whether or not to twist polymer in Polymer Cell Builder.
• Enabled to use project mode for Quantum ESPRESSO.
[Specification Change]
• Moved $SYSTEM to Basic tab in GAMESS keywords setup window. • Changed to use fixed random seeds by default in Random Polymer Builder and Polymer Cell Builder. • Added presets in Gromacs and LAMMPS keywords setup windows. • Changed default presets of Gromacs and LAMMPS keywords setup windows. [Bug Fix] • Fixed a bug that prevented loading output file from terminated job for Quantum ESPRESSO. [Deprecated Feature] • Removed [MD]-[Assign Charges Manually]-[By Manual Entry]. ### Version 11.0.2 January/19/2022 [Bug Fix] • Fixed a bug in [QM]-[GAMESS]-[Show Extracted Log] and [MD]-[LAMMPS]-[Show Extracted Log]. • Fixed a bug that prevented LAMMPS jobs from being executed in project mode. • Fixed a bug that prevented Gromacs jobs from begin executed with job manager. ### Version 11.0.1 January/17/2022 [New Feature] • Added support for a mode (project mode) for managing the progress of calculations and files at once. Project mode allows for continuous execution of multiple jobs, detection of calculation errors, and display of results with a single click.In addition, the conventional operation method is now the file mode, and the user can choose between the two. • Enabled to use project mode for GAMESS and LAMMPS. • A screen to guide you through the operation procedure is now displayed when Winmostar is started. • Added [File]-[Import File], [Export File], -[Move Atom]-[Translate with Hydrogens] buttons to the toolbar. • Context menu editing is now supported in the molecule view area. • Added support for outputting multi-frame mol2 files in the animation display area. • Added buttons to move to the previous and next frame in the animation display area. • Added [File]-[Import Recent File]. • Added a function to output the structure to a file without making any changes to the current structure. ([File]-[Export File]) • Added the ability to save and load molecular structures in a lossless proprietary format (wmm). • The order of the fragment list can now be edited. (UserPref\fragment_list.txt file) • Export and Import settings are now supported in the QM keyword settings window. • Added support for reversing, skipping, and translating animations when displaying QM animations. • Log contraction display for GAMESS, LAMMPS and Quantum ESPRESSO is now supported. • The keywords to be output can now be confirmed in the GAMESS and Quantum ESPRESSO keyword setting windows. ([Preview] tab) • In the [MD]-[Place Solvent/Build Cell] function, the SMILES input and files other than mol2 are now supported. • In the LAMMPS keyword setting, added an option to automatically disable the SHAKE method when CH4-like molecules are included. • In the LAMMPS keyword setting, an option has been added to automatically disable the PPPM method when no charge is included. • In the Quantum ESPRESSO keyword settings window, you can now select the type of pseudopotential and functional to narrow down the candidates for the pseudopotential file. • In the Quantum ESPRESSO keyword setting window, K_POINTS can now be set automatically with the density parameter of the inverse space. • In the Quantum ESPRESSO keyword setup window, nbnd can now be set automatically. • The ratio of ectrho to ectwfc can now be set in the Quantum ESPRESSO keyword setup window. • In the Quantum ESPRESSO keyword setting window, the recommended value of ectwfc is now displayed. • Improved the clustering algorithm of candidate structures (using dihedral angles) in [Tools]-[Coordination Search (Balloon)]. • The Job Manager has been significantly modified so that it can automatically send and retrieve files to a remote server in project mode. • Added the ability to reset the Job Manager settings (enable [Help]-[Debug Mode], then click [Help]-[Reset Job Manager]). [Specification Change] • The file names of the color and radius setting files (wm_system\wmx\atoms_*.wmx) have been changed: atoms_new.wmx -> atoms_v10.wmx, atoms_old.wmx -> atoms_v4.wmx • Updated covalent radius, van der Waals radius, and atomic weight. • The values of physical constants have been unified to CODATA 2018. • Changed the name of working directory to working folder. • Increased the length of the file path displayed in the main window title. • Changed the default window size. • Variable display time and font size of hints (tooltips). ([Tools]-[Preferences]) • Hide the [CH3], [C2H3], and [C6H5] buttons in the toolbar by default. • Fragment substitution in the molecule view area can now be done by Ctrl+Shift+right-click. • Increased the number of digits displayed in the molecule display area. • Animation window has been integrated into the main window. • The Reload button in the animation window has been integrated into the [File]-[Reload] menu in the main window. • The value of the selected frame (energy, etc.) is now displayed in the graph in the animation display area. • The Dynamics Bond setting in the animation display area has been moved to the bottom of the Options menu. • Changed so that the change flag is not set when the animation is playing. • It is now possible to set whether or not the coordinate display area is updated during animation playback. ([Tools]-[Preferences]) • The second keyword area has been integrated into the first keyword area. • In the keyword area, alias characters (%WM_COORD%, %WM_XYZ%, %WM_ZMAT%) are now used to represent the location where coordinates are described. • The design of the coordinate display area has been changed. • The width of the coordinate display area is now saved even when the application is closed. • Increased the number of digits when editing coordinates in the coordinate display area. • Changed [Save csv] to [Export csv] in various graph display functions. • Option settings can now be toggled between visible and invisible in the various graph display functions. • Changed the default file format to wmm format. • Files with md extension are now recognized as xyz format. • The default value of coordinate output and display format is now XYZ. • When editing a file in a format that cannot be saved (such as a log file), the file format is now switched to wmm format. • Changed so that keywords are set to blank when creating a new file. • Changed [File]-[Append] to [File]-[Import File]. • Changed the default setting of the program used for importing SMILES from OpenBabel to Balloon. • [File]-[Coordinate Format] has been integrated into the keyword setting window of each solver, and the display switching is now done in [View]-[Coordinate Format]. • Title information that was displayed in the upper left corner of the molecule display area is now displayed and edited in [File]-[Get Info]. • Changed the order of the fragment list. • The notation of [Set distance] has been changed to [Set margin] in the cell creation function of various editing functions. • -[Add Dummy Atom] has been merged with [Add Atom]. • [Box Vectors] in -[Create/Edit Cells]-[Edit Cells Manually] has been changed to [Lattice Vectors]. • In -[Create/Edit Cells]-[Transform Cells], [Move with keeping fractional coordinate] is now set to True by default. • Merge -[Change Density] into -[Create/Edit Cells]-[Transform Cells]. • Changed [View]-[Rotate]-[View] to [Rotate Around Line of Sight]. • Corrected the caption of the keyword setting window for each solver. • Changed [Save] and [Load] buttons to [Export] and [Import] in the keyword setting window of each solver. • Changed [Extending Simulation] to [Continue simulation] in the keyword setting window of each solver. • The [Dump All Files] button in the solver keyword setting window is no longer available in project mode. (Because it is now possible to save the working folder without executing the calculation.) • The [Restore working directory] button in the keyword setting window of the various solvers has been disabled in project mode. (Because it is now possible to freely select the working folder from which to continue.) • [Semi-Empirical] menu and [QM] menu have been merged. • Changed the title of the QM results display window. • The menu of the QM results display function has been separated into different items. • [Save Image] in the IR Spectrum window has been changed to [Export Image]. • [Save VRML] in the MO Plot window has been changed to [Export VRML]. • The IRC animation merge function has been moved to [Tools]-[Append Trajectory] in the animation display area. • The value of dipole moment is now displayed in the molecule display area when a QM log file is loaded. • The default keyword of MOPAC is now set in mopac_default.wmx instead of init.dat in UserPref folder. • [QM]-[GAMESS]-[Read from punch file]-[Read$VEC] and [Read $HESS] were moved to [Import$VEC] and [Import $HESS] in the GAMESS keyword setting window, respectively. • NPUNCH=0 and DAMP were removed from the default settings in the GAMESS Keyword Settings window. • In the GAMESS keyword setting window, NZVAR in$CONTRL, DLC and AUTO in $ZMAT were changed to be set for single molecules and more than 6 atoms. • In the GAMESS keyword setting window, the "others" and "FORCE" columns of$BASIS and the "ICAV" and "TABS" columns of $PCM were added. • SCF and NMR fields have been added in the Gaussian keywords window. • In the Gaussian keyword setting window, the arrangement of the various keyword items has been changed. • Changed the name of MO Plot window to Surface Setup window. • In the Surface Setup window, the default settings for Draw Style and Transparency have been changed. • The priority order of the referenced charges has been changed to User>NBO>Mulliken>Lowdin>ESP when MD calculations are performed on structures with multiple types of charges. • UFF and GAFF2 force fields are no longer supported in the Professional Edition Economy. • In the results analysis function using Gromacs tools, the switch between single precision and double precision is now done in [Tools]-[Preferences] instead of in the Gromacs keyword settings window. • In the [MD]-[Solvate/Build Cell] function, [Add mol2 file] was merged into [Add file]. • In [MD]-[Assign Charge Manually], [Use acpype] and [Use GAMESS] were changed to [AM1-BCC Charge] and [RESP Charge], respectively. Also, [Gasteiger Charge] has been added. • The notation "Monomer" in polymer-related functions has been changed to "Repeat unit". • Layout of Polymer Builder has been changed. • When the [Display] button of the various polymer builders is clicked, the structure is now displayed in a separate window instead of the main window. • The layout of the Polymer Cell Builder and [MD]-[Solvate/Build Cell] functions have been unified. • When running the Polymer Cell Builder, the mol2 file is not saved, so that the process can be redone. • In [MD]-[Polymer]-[Repeating Unit Registration], the name of the repeating unit is now entered after the OK button is clicked. • Changed the extension of the standard output file of Gromacs, MODYLAS, Amber, and OpenMX to stdout. • The type of the force field is now described in the LAMMPS data file as a comment. • Changed the method of creating the data file of the final structure of LAMMPS (copying the Atoms section and before from the data file of the starting structure). • When the LAMMPS binary to be used in a local job cannot be found, lmp_mpi is now searched for and used in addition to lmp_serial. • Changed [Save], [Load] of DPD cell builder to [Export], [Import]. • Changed the design of [Solid] - [Crystal Builder]. • Folder settings for MOL and pseudopotential files in Quantum ESPRESSO can now also be set in [Tools]-[Preferences]. • The layout and file structure of the NEB executable in Quantum ESPRESSO has been changed. (A V10 license will be issued to those who wish to use the old format.) • The final structure retrieved from the log of ion_dynamics=damp in Quantum ESPRESSO is now the structure after the End final coordinates. • Changed the layout of [Tools]-[Preferences]-[Calculation]. • Changed the default of [Tools]-[Preferences]-[Calculation]-[modify charges from AmberTools to adjust total charge] to True. • [Tools]-[Draw Molecule] can now also be executed in [File]-[Import]-[Structural Formula]. • In [Tools]-[Comformation Search (Balloon)], the structure after the search can now be selected in a separate window. • When executing [Tools]-[Comformation Search (Balloon)], the information other than the coordinates are not changed. • The analysis results of [Tools]-[Molecular Surface Area & Volume], [Aspect Ratio], and [Radius of Gyration] are now displayed in a dialog box. • Changed [Save SDF] to [Export SDF] in [Tools]-[Superimpose Molecules]. • Changed so that when a dialog with choices appears when executing from the command line, it will automatically choose the first choice and proceed. • When executing from the command line and saving in gjf format, the coordinate output format (XYZ or Z-Matrix) now follows the display format. • When molecular volume/surface area, aspect ratio, and radius of gyration are calculated by executing from the command line, the calculation results are now displayed on the console. • The default background color of Winmostar Viewer was changed to white. • When Winmostar Viewer is launched, the perspective setting of the calling Winmostar is inherited. • Added kbar to the pressure unit of Winmostar Units. [Deprecated Feature] • Support for p2n format has been removed. • The text editing function using the in-house editor in [File]-[Open in Text Editor] has been removed. • The [Make a backup of working directory] setting in the keyword setting window of the various solvers has been abolished and is now always set to True. • The automatic placement function of MOPAC's rm1.rm1 file has been removed. • NODES (Firefly) column was removed from the GAMESS keyword setting window. • FMO-related functions of GAMESS were removed. (To be re-supported in the future) • MOSF-related functions have been removed. • The interface builder of the old specification has been abolished. • Abolished [Save as default] in the LAMMPS keyword setting window. • The [Calculate as rigid body] option in the LAMMPS keyword setting window has been removed. (To be re-supported in the future) • Support for Amber has been removed. (To be re-supported in the future) • Supercell creation function of the old specification has been removed. • Removed [Solid] - [Creave Plane]. (merged with [Solids]-[Slab Builder], available in debug mode) • Removed [Solid] - [Insert Vacuum]. (Integrated into -[Create/Edit Cell]-[Transform Cell] and [Solid]-[Slab Builder], available in debug mode) • CONFLEX-related functions have been removed. • The remote job connection function using putty has been abolished. • In the remote job submission function, the support of t2sub, llsubmit, Sharetask, NSUB, and Rescale was abolished. (It will be re-supported in the future.) • [Tools]-[Batch Queue] has been removed. ## Winmostar V10 ### Version 10.8.2 April/8/2022 [Bug Fix] • Fixed a problem in which some file formats could not be read when using the -lammps option from the command prompt. • Fixed a problem in which the configuration file (lmpset file) could not be read when using the -lammps option from the command prompt. • Fixed a problem with Preset=Minimize(fast) when using the -lammps option from the command prompt, where calculations would flow with Preset=Minimize(fast) if a non-existent configuration file was specified. • Fixed a problem in which the process did not terminate normally when starting from the command prompt and assigning a force field when monoatomic ions were included. • Fixed a bug in Quantum ESPRESSO where cells and joins were not drawn properly when displaying vector IR Raman vibration spectra. [Specification Change] • In [File]-[Export]-[SMILES], you can now choose to do or not do hydrogen completion. • The information dialog is no longer displayed when starting from the command prompt. • NWChem's NEB's Get Output File after Remote Job Execution now also retrieves xyz and epath files. ### Version 10.8.1 February/21/2022 [Bug Fix] • Fixed a bug that caused the error "... is not a valid component name. is not a valid component name." when displaying some windows has been fixed. • Fixed a bug that the remote job execution of LAMMPS using JM(Windows) could not be executed. [Specification Change] • Added a warning message when a path containing multibyte characters is processed using Cygwin. • When a calculation bat file is executed by double-clicking on it, the program now checks if it is actually executed. ### Version 10.8.0 January/04/2022 [Bug Fix] • Changed not to change periodically bonded molecules in -[Rearrange Atoms Based on Periodic Boundary Conditions]-[Undo Rearranged Structure on an Atomic Basis]. • Fixed a bug in which the occupancy was not taken into account only for the first asymmetric element that appeared when reading a CIF file in which the occupancy and the target operation are described simultaneously. • Fixed a bug where the various dialogs for selecting folders would not scroll to the folder selected by default. [Specification Change] • Changed to use pymatgen for CIF file reading. • Changed so that the target operation is inferred from the space group information when reading a CIF file that does not contain the target operation. • Changed to use common window to all solvers for the setting whether or not to update the coordinate display area when using the animation window. ### Version 10.7.5 April/8/2022 [Bug Fix] • Fixed a problem in which some file formats could not be read when using the -lammps option from the command prompt. • Fixed a problem in which the configuration file (lmpset file) could not be read when using the -lammps option from the command prompt. • Fixed a problem with Preset=Minimize(fast) when using the -lammps option from the command prompt, where calculations would flow with Preset=Minimize(fast) if a non-existent configuration file was specified. [Specification Change] • In [File]-[Export]-[SMILES], you can now choose to do or not do hydrogen completion. • The information dialog is no longer displayed when starting from the command prompt. ### Version 10.7.4 February/21/2022 [Bug Fix] • Fixed a bug that caused items to be displayed twice in the list in some windows. • Fixed a bug that caused unnecessary data to appear when [Options]-[Calc Average] in the graph display function was executed multiple times. • Fixed a bug in the graph display function that caused all points to be sorted in the x direction before being drawn. • Fixed a bug that prevented the X axis setting from switching properly in the Custom Plot function of the animation. • Fixed a bug that Reset positions of restrained atoms after run in LAMMPS keyword setting did not work effectively. (If you are using a template script for a remote job, you will need to recreate the template script.) • Fixed a bug that LAMMPS could not be executed in parallel in some environments. (If you are using a template script for a remote job, you will need to recreate the template script.) • Fixed a bug that the remote job execution of LAMMPS using JM(Windows) could not be executed. • Fixed a bug in Quantum ESPRESSO's State Density function that caused Range to be inappropriate when Shift origin to Efermi was checked. [Specification Change] • Changed so that the input file is given to LAMMPS itself at LAMMPS runtime with the -in option instead of the standard input. ### Version 10.7.3 January/04/2022 [Bug Fix] • Fixed a bug in the molecular orbital display where the display near the orbital boundary was distorted (V10.6.4 or later). • Fixed a bug that caused incorrect formatting when saving in gro format with residue names of six or more characters. • Fixed a bug in the force field editing tool that caused an address violation when the [Export top file] button was clicked for the second or later molecular species. • Fixed a bug in which the interface builder sometimes did not save the charges. • Fixed a bug that sometimes failed to load the output file of Constraint MD in Quantum ESPRESSO. [Specification Change] • Changed to correct residue names automatically when saving a gro file when the residue name contains more than 6 characters. ### Version 10.7.2 December/01/2021 [Bug Fix] • Fixed a bug in the Properties tab of the Quantum ESPRESSO Configure window where changes made to Values, other than the last one entered, were not reflected. • Fixed a bug that prevented reanalysis after changing the analysis conditions in the various results analysis windows of Quantum ESPRESSO. • Fixed a bug in the DOS display window of Quantum ESPRESSO where the display range could not be adjusted. [Specification Change] • Enabled to set Thread-MPI and OpenMP separately for local parallel computing in Gromacs. • Changed to read settings from precomputed files in Phonon Band and Phonon DOS windows in Quantum ESPRESSO. ### Version 10.7.1 November/10/2021 [New Feature] • Added an option to the preferences to output the residue number in the fifth column when saving in xyz format. • Enabled to assign different residue numbers to each molecule. (-[Automatically Adjust Atoms/Bonds]-[Assign Unique Residue Number to Each Molecule]) [Bug Fix] • Fixed a bug that caused heavy drawing in the main window when selecting a group. • Fixed a bug where Cube files could not be created if ECP was specified in the NWChem Configure window. • Fixed a bug in which ESP(Population Charge)/Surface cube files could not be created in some cases (V10.6.1 or later). • Fixed a bug that caused slow animation playback (V10.6.0 or later). • Fixed a bug where the coordinate display area was not updated after the animation was finished. [Specification Change] • Changed to recognize the value in the fifth column as the residue number when reading XYZ format. • Changed to show element names in simplified form in the coordinate display area during DPD calculations. ### Version 10.7.0 October/1/2021 [New Feature] • Enabled to open the top file in the Gromacs keyword configuration window. ([Options]-[Open top file]) • Added a setting to increase the number of digits displayed in the log in the LAMMPS Configure window. ([Output]-[Print log in high precision]) • Enabled to display the functional, pseudopotential type, and relativity of the selected pseudopotential file in the Quantum ESPRESSO keyword display window. • Added new items to Winmostar Unit Converter. [Bug Fix] • Fixed a bug that a job with the same file name could not be run at the same time when using GAMESS. • Fixed a problem in which the Basis Exception setting was not reflected in the NWChem Configure window. • Fixed a bug that Cube files could not be created when Exception or Spherical was specified for Basis in the NWChem Configure window. • Fixed a bug in the [Solvate/Build Cell] function that prevented the placement of 4 and 5 site water models. • Fixed a problem in which molecules without dihedral but with improper did not output improper when Dreiding was assigned. • Fixed a bug in Gromacs where the 1-4 interaction was not calculated when Dreiding or UFF was selected. [Specification Change] • Changed the format of the wmy file that is saved when registering fragments. • Changed to set the OpenSCAD program path in the Preferences window. • Changed the specification so that Quantum ESPRESSO pseudopotential files with extensions other than UPF will not be read. • Changed to create multiple polymers with different monomer sequences in advance in Random Polymer Builder, and Polymer Cell Builder randomly selects a polymer from among them. • Increased the number of digits displayed in the energy change function of Gromacs. • Changed to automatically adjusts the order of jkl particles so that the calculation of UFF improper does not depend on the initial coordinates for Gromacs. • Changed the way to get LAMMPS binary when executing a local job of LAMMPS. • Changed the default setting of [Tools]-[Preferences]-[Calculation]-[Modify charges from AmberTools to adjust total charge] to ON. • Changed to display the calculation result on the console when using the aspect ratio calculation function by starting from the command line. [Performance Improvement] • Accelerated Fchk file loading for Gaussian. • Accelerated force field assignment process. ### Version 10.6.4 November/10/2021 [Bug Fix] • Fixed a bug that caused the entire application to lose focus after some dialogs were closed. • Fixed a bug in [Select]-[Export groups to index file(ndx)] that the process was completed even when there were no registered groups. • Fixed a bug where Cube files could not be created if ECP was specified in the NWChem Configure window. • Fixed a bug in which ESP(Population Charge)/Surface cube files could not be created in some cases (V10.6.1 or later). • Fixed a bug that prevented some windows from being properly selected in the main window's Window menu. ### Version 10.6.3 October/1/2021 [Bug Fix] • Fixed a problem in which the Basis Exception setting was not reflected in the NWChem Configure window. • Fixed a bug that Cube files could not be created when Exception or Spherical was specified for Basis in the NWChem Configure window. • Fixed a bug in the [Solvate/Build Cell] function that prevented the placement of 4 and 5 site water models. ### Version 10.6.2 September/1/2021 [Bug Fix] • Fixed a bug in which replaceing an atom with a fragment containing an X atom (dummy atom) would result in a Z atom. • Fixed to not automatically regenerate the bond information in -[Rearrange Atoms Based on Periodic Boundary Conditions]. • Fixed a problem where the [Head to Tail]/[Head to Head] checkboxes were not reflected in the Polymer Builder (V10.6.0 or later). ### Version 10.6.1 August/3/2021 [New Feature] • Enabled to read XYZ animation files. [Bug Fix] • Fixed a problem in which the charge and dipole moments were not displayed when reading a log file in which the GAMESS structural optimization calculation was completed in one cycle. • Fixed a bug in which deuterium was not sufficiently confirmed in the force field assignment function of Gromacs and LAMMPS. • Fixed a bug that caused the second calculation to stop with an erro when B3LYP-D3 is selected for Hamiltonian and Optimize and (IR/Raman, TDDFT, NMR) are selected for Calculation Method in Gaussian's Easy Setup window. • Fixed a bug in [MD]-[Gromacs]-[Import Last Coordinates] where water molecules and other bonds were lost. • Fixed a problem with [Solid]-[Insert Vacuum] when there are atoms near the boundary. [Specification Change] • Changed to converted "* (asterisk)" to hydrogen when reading SMILES that contain the asterisks. [Performance Improvement] • Speeded up the the MO Plot approximately 2.5 times faster. ### Version 10.6.0 July/1/2021 [New Feature] • Enabled to display the coordinates of the pointer position in various graphs. • Added support for group selection by specifying the coordinate range in [Selection] - [Enter Selection Language]. • Enabled to change the fractional coordinates of an atom. (-[Move Atoms]-[Change Fraction Coordinate]) • Enabled to move the marked atoms in translation by hydrogen atoms. (-[Move Atom]-[Translatewith Hydrogen], Alt+drag) • Enabled to average the charge of the selected group. (-[Modify Selected Group]-[Average Charges of Group]) • Enabled to generate bonds between neighboring atoms in a group. (-[Modify Selected Group]-[Connect between Adjacent Atoms]) • Enabled to do batch operation for each selected atom in a group in -[Replace with Fragment]. • Enabled to view and adjust all charges in the -[Edit Charge] menu. • Enabled to specify the direction of view with the mirror index. ([View]-[Align View]-[Arbitrary Plane]) • Enabled to invert the direction of view. ([View]-[Align View]-[Invert]) • Enabled to change the direction of view in the a, b, and c axis directions. ([View]-[Align View]-[a/b/c-Axis]) • Enabled to rotate the view around the direction of view by specifying a numerical value. ([View]-[Rotate]-[View(Numerical)]) • Enabled to use positional constraints using spring potential in LAMMPS Setup. (Professional Edition Premium only) • Added Surface Tension to [Tools]-[Unit Converter]. • Enabled to use AM1-BCC charge assignment when invoked from the command line. (-am1bcc) (Professional Edition Premium only) • Enabled to read SMILES when invoked from the command line. (-smiles, -smilesbabel, -smilesballoon) (Professional Edition Premium only) • Enabled to create Gromacs and LAMMPS input files when invoked from the command line. (-gromacsfile, -lammpsfile) (Professional Edition Premium only) [Bug Fix] • Fixed a problem in which the input file used in the calculation was not assigned a charge correctly unless it was opened in the main window if you choose "No" when asked "Do you assign the same charge to atoms that are structurally equivalent?" in [QM]-[GAMES]-[Analyses]-[RESP Charges], • Fixed a problem in which the last digit of the charge before assignment was changed when assigning a force field in GAFF, GAFF2, and OPLS-AA/L+GAFF. • Fixed a problem in which the contents of the Manual Entry were reset after editing the Manual Entry in the LAMMPS Keyword Settings window and clicking the OK or Run button, and then relaunching the window. [Specification Change] • Changed the background of text in the molecule display area white when displaying charges or other information. • Changed the way element names (13th-16th characters) are identified when opening a non-standard PDB file. • Enabled to turn on/off the automatic execution of bond length adjustment and hydrogen atom completion after loading MOL files. ([Tools]-[Preferences]-[Basic]-[Automatically adjust bond length and add hydrogen atoms]) • Changed to list the version of Winmostar in some of the output files. • Changed to move the entire group in translation when using -[Move Atom]-[Translate] when selecting a group, • Changed the residue names of monatomic ions when assigning force fields to monatomic ions. • Added an option to automatically disable the SHAKE method when methane-like molecules are included in the LAMMPS Setup window. • Added an option to disable the PPPM method in the LAMMPS Setup window when the system does not contain any charges. • Changed to output the information on the bond potential with a coefficient of 0 when there is a bond in the group specified in Exception in the Assign Force Field function. • Changed the name of the temporary folder when assigning force fields. • Changed to crate polymers by the Polymer Builder with a 180-degree dihedral angle. Also, the dihedral angle between monomers is now randomly changed when inserting polymers in the Polymer Cell Builder. • Changed to cluster structures using Dihedral instead of RMSD in [Tools]-[Comformation Search]. • Added the date command to the beginning of the template script for remote jobs. • Changed to give the charge value as an argument when assigning a RESP charge when invoking from the command line. ### Version 10.5.5 September/1/2021 [Bug Fix] • Fixed a bug in which replaceing an atom with a fragment containing an X atom (dummy atom) would result in a Z atom. • Fixed to not automatically regenerate the bond information in -[Rearrange Atoms Based on Periodic Boundary Conditions]. • Fixed a problem where the [Head to Tail]/[Head to Head] checkboxes were not reflected in the Polymer Builder (V10.6.0 or later). ### Version 10.5.4 August/3/2021 [Bug Fix] • Fixed a bug that when [Use Balloon] is checked in [File]-[Import]-[SMILES], the message "Successful" is displayed even if the process fails and the molecular structure is not updated. • Fixed a problem in which the charge and dipole moments were not displayed when reading a log file in which the GAMESS structural optimization calculation was completed in one cycle. • Fixed a bug that caused the second calculation to stop with an erro when B3LYP-D3 is selected for Hamiltonian and Optimize and (IR/Raman, TDDFT, NMR) are selected for Calculation Method in Gaussian's Easy Setup window. • Fixed a bug in [MD]-[Gromacs]-[Import Last Coordinates] where water molecules and other bonds were lost. • Fixed a problem with [Solid]-[Insert Vacuum] when there are atoms near the boundary. ### Version 10.5.3 July/1/2021 [New Feature] • Added the display of HOMO and LUMO energy in the Energy Level Diagram window. • Added the display of the excitation configuration of the selected peak in the UV-Vis spectrum window. [Bug Fix] • Fixed a bug that prevented Z-Matrix from being updated in the following functions: [Transform Cell], [Wrap Around cell Boundary], [Change Density], [Modify Selected Group]-[Move(Numerical)], [Modify Selected Group]-[Rotate(Numerical)], [Interface Builder], [Slab Builder], [Generate Supercell], and [Convert Lattice]. • Fixed a bug that the keywords in the Setup window did not reflect the specification of cc-pV*Z basis functions in the Easy Setup window of GAMESS. • Fixed a problem in which the ECP setting remained in the Setup window when ECP was selected for the basis function and then selected something other than ECP from the choices again in the Setup and Easy Setup windows of GAMESS. • Fixed a bug that caused LAMMPS to fail to run in the OPLS-AA/L+GAFF force field. (V10.5.0 or later) • Fixed a bug that GAFF, GAFF2, and OPLS-AA/L+GAFF could not be assigned for some mol2 files. • Fixed a bug in which GAFF, GAFF2, and OPLS-AA/L+GAFF could not be assigned after using the polymer builder. (V10.5.0 or later) [Others] • Updated templates of LAMMPS and GAMESS for FOCUS supercomputer. ### Version 10.5.2 June/1/2021 [Bug Fix] • Fixed a bug that the program might freeze when the mouse was operated while loading a file with more than 10000 atoms. • Fixed a bug that caused an error message when changing the SOLVNT of$PCM in the GAMESS Preference window.
• Fixed a bug in the Gaussian Preference window where clicking [Save As Default]-[Clear Default Setting] would overwrite the default settings of GAMESS.
• Fixed a bug in the Gaussian animation display function that prevented IRC and ADMP calculation results from being displayed in V10.1.4 or later.
• Fixed a bug that when a job is started with an animation window of MOPAC, GAMESS, NWChem or Gaussian open, the job will be executed again when the open animation file is output.
[Specification Change]
• Changed to close the animation window automatically before the save dialog is opened when a job is started with the animation window of MOPAC, GAMESS, NWChem and Gaussian open.
[Others]
• Updated the template of Quantum ESPRESSO for FOCUS supercomputer.

### Version 10.5.1 May/10/2021

[Bug Fix]
• Fixed a bug that caused the display range of some graphs to be inappropriate.
• Fixed a bug that prevented the [MD]-[Insert Molecules] function from starting.
• Fixed a bug that prevented redoing [MD]-[Assign Charges Automatically] and [Assign Charges Manually]-[Manual Manual Entry].
• Fixed a bug in the Distance/Angle/Dihedral distribution function of Gromacs results analysis that interrupted the process when multiple groups with the same name appeared in the ndx file.
• Fixed a bug in which the aspect ratio was not calculated correctly for monoatomic models.
[Specification Change]
• Changed the specification of -[Adjust Axes]-[Invert X/Y/Z Axis] to -[Invert Coordinates/Chirality]-[Invert along X/Y/Z Axis] and -[Invert Coordinates/Chirality]-[Invert along A/B/C Axis].
• Supported parallel eye movement with Shift+dragging in the molecule display area of the sub-window.
• Modified the camera direction in the initial state in -[Create/Edit Cells]-[Transform Cells].
• Changed the default group name as the composition name in [Select]-[Register Selected Group].
• Changed the layout of the Quantum ESPRESSO Configure window.
• Corrected the default display range of the graph in the XANES spectrum display function of FDMNES.
• Changed to generate molecular structures in SMILES format instead of MOL format from JSME in the [Tools]-[Draw Molecule] function.
• Enabled to choose between OpenBabel and Balloon for generating molecular structures in the [Tools]-[Draw Molecule] function.

### Version 10.5.0 April/1/2021

[New Feature]
• Enabled to read and save mol2 files of molecules containing deuterium.
• Enabled to save csv files to various graph display functions. ([Options]-[Save csv])
• Enabled to change the occupancy of the site where the selected atom is placed. (-[Change Atom Property]-[Occupancy])
• Enabled to equally multiply the charge/spin density of selected atoms. (-[Change Atom Property]-[Charge/Spin]-[Scale])
• Enabled to concatenate and transpose multiple registered groups. ([Select]-[Concatenate and Transpose Groups])
• Enabled to use % operator (mod) in [Select]-[Enter Selection Language].
• Enabled to switch The display method of atoms on cell boundaries from [View]-[Items]-[Replicated Atoms at Cell Edge].
• Enabled to assign Dreiding force field for molecules containing deuteriums.
• Enabled to recalculate only the energy for each structure in the Gromacs trajectory file (xtc). ([MD]-[Gromacs]-[Configure]-[Options]-[Rerun from xtc...])
• Enabled to calculate the angle and dihedral angle distribution for any angle type in [MD]-[Gromacs]-[Analyses]-[Bond/Angle/Dihedral Distribution].
• Enabled to calculate Chandler correlation function for dihedral angles in [MD]-[Gromacs]-[Analyses]-[Bond/Angle/Dihedral Distribution].
[Bug Fix]
• Fixed a problem where charges using Acpype could not be assigned to the generated structure when OpenBabel was checked in [File]-[Import]-[SMILES].
• Fixed a bug that prevented the [Assign force Field parameters] window from being displayed under some conditions.
• Fixed a bug where bond distances, angles, or dihedrals were not calculated properly when atoms in the same molecule are not bonded together in [MD]-[Gromacs]-[Analyses]-[Bond/Angle/Dihedral Distribution].
• Fixed a problem in which the RMSD and radius of inertia calculation functions of the result analysis function did not work when [Enable double precision] was checked in the Gromacs keyword setting window.
• Fixed a bug that prevented the selection of groups for each molecular species under some conditions in the results analysis function of Gromacs.
• Fixed a bug in which Winmostar JM (Job Manager) would lock the folder containing the first bat file executed after startup.
[Specification Change]
• Changed no to show commas every three digits above the decimal point in various graph display functions.
• Enabled to resize the -[Edit Charge] window.
• Changed so that the index of atoms is sorted inside the program when [Select]-[Register Selected Group] is executed.
• Changed to sort the indexes of the marked atoms in descending order when a scan is selected in the MOPAC EasySetup window.
• Changed to assign the names of monomers and polymers as the atom names and substructures in the mol2 file created by the Polymer Builder.
• Changed [Polymerization Degree] in the Polymer Builder to [Degree of Polymerization].
• Changed not to create backup files in the working directory by default when Gromacs jobs are executed.
• Enabled to set whether to create backup files in the working directory when executing a Gromacs job.([MD]-[Gromacs]-[Congfigure]-[Options]-[Overwrites any output file without making a backup in working directory])
• Tightened the syntax check when reading Gromacs topology files.
• Changed not to overwrite the index (ndx) file for Gromacs continues job.
• Changed to show the values of specific heat and isothermal compressibility (Cvm, Cvp, Betat) in [Calc Ave] of the energy change function of LAMMPS as the integrated average value itself, instead of the average of the integrated average values.
• Changed the notation [User target group] to [Calculate for target group] in [MD]-[Gromacs]-[Analyses]-[Bond/Angle/Dihedral Distribution].
• Changed to use trjconv used to relocation atoms with periodic boundaries before calculating the bond distance, angle, or dihedral in [MD]-[Gromacs]-[Analyses]-[Bond/Angle/Dihedral Distributions].
• Moved [Show atoms at cell boundary on both sides] in [Tools]-[Preferences]-[View] to [View]-[Items]-[Replicated Atoms on Cell Edge] menu.

### Version 10.4.5 June/1/2021

[Bug Fix]
• Fixed a bug that the program would freeze when the mouse was operated while loading a file with more than 10000 atoms.
• Fixed a bug that caused an error message when changing the SOLVNT of $PCM in the GAMESS Preference window. • Fixed a bug in the Gaussian Preference window where clicking [Save As Default]-[Clear Default Setting] would overwrite the default settings of GAMESS. • Fixed a bug in the Gaussian animation display function that prevented IRC and ADMP calculation results from being displayed in V10.1.4 or later. • Fixed a bug that when a job is started with an animation window of MOPAC, GAMESS, NWChem or Gaussian open, the job will be executed again when the open animation file is output. [Specification Change] • Changed to close the animation window automatically before the save dialog is opened when a job is started with the animation window of MOPAC, GAMESS, NWChem and Gaussian open. [Others] • Updated the template of Quantum ESPRESSO for FOCUS supercomputer. ### Version 10.4.4 May/10/2021 [Bug Fix] • Fixed a bug that caused the display range of some graphs to be inappropriate. • Fixed a bug that prevented the [MD]-[Insert Molecules] function from starting. • Fixed a bug in the Distance/Angle/Dihedral distribution function of Gromacs results analysis that interrupted the process when multiple groups with the same name appeared in the ndx file. • Fixed a bug in which the aspect ratio was not calculated correctly for monoatomic models. [Specification Change] • Changed the layout of the Quantum ESPRESSO Configure window. • Corrected the default display range of the graph in the XANES spectrum display function of FDMNES. • Changed to generate molecular structures in SMILES format instead of MOL format from JSME in the [Tools]-[Draw Molecule] function. • Enabled to choose between OpenBabel and Balloon for generating molecular structures in the [Tools]-[Draw Molecule] function. ### Version 10.4.3 April/1/2021 [Bug Fix] • Fixed a bug in Gaussian's IR/Raman spectra that caused the coordinate system to shift when there was symmetry in the molecule in the display of vibrational modes and dipole/transition dipole moments in V10.2.0 or later. • Fixed an issue where the number of repeats was not cleared in [Solid]-[Generate Supercell]. • Fixed a problem in which the coordinates of the following K points were inappropriate in the band structure calculation function of OpenMX. BCC H point BCT2 Y point ORC Z point MCL M2 point MCLC3, MCLC4 F1 point • Fixed a bug in which the molecules displayed in the main window were sometimes not changed when selecting a point in the energy plot in the animation window. • Fixed a bug that the connection with the remote host may fail in remote job submission in some environments. [Specification Change] • Removed [QM]-[Gaussian]-[Analyses]-[Archive]. • Removed the add-on "ESM-RISM Calculation Module" and incorporated its equivalent functions into the Professional Edition Premium. ### Version 10.4.2 March/1/2021 [Bug Fix] • Fixed a bug that sometimes caused an error when reading Gaussian fchk files. [Specification Change] • Enabled to show oxygen-oxygen double bonds and nitrogen-nitrogen triple bonds automatically when showing a molecule. • Changed not to regenerates bonds in the interface builder. • Enabled to read XYZ files that contain tab characters. ### Version 10.4.1 February/2/2021 [Bug Fix] • Fixed a bug that prevented the ESP charge of Gaussian from being displayed. • Fixed a bug where the interface builder could generate unwanted bonds. [Specification Change] • Changed to show the self-diffusion coefficient as an exponent when its absolute value is small in the self-diffusion coefficient calculation function of Gromacs and LAMMPS. • Changed the names of working directories in some functions. • Changed some of the error messages displayed when outputting to the LAMMPS data file. ### Version 10.4.0 Janualy/4/2021 [New Feature] • Enabled to group select atoms or molecules adjacent to the selected group using Voronoi splitting. ([Selection]-[Expand Selection to Neighbor Atoms/Molecules]) • Enabled to draw atoms directly above the periodic boundary cell on both ends of the cell. ([Tools]-[Preferences]-[View]-[Show atoms at cell boundary on both sides]) • Enabled to specify the density with two fixed lattice constants in [MD]-[Solvate/Build Cell]. • Added a setting to make the charge of the entire molecule an exact integer value when calculating AM1/BCC, Gasteiger, and RESP charges using acpype and AmberTools, . ([Tools]-[Preferences]-[Calculations]-[Modify charges from AmberTools to adjust total charge]) • Enabled to export and import of polymer definition files in the LAMMPS cell builder. • Enabled to assign GAFF2 using acpype in the force field assignment function of LAMMPS and Gromacs. • Added dipole correction to the Quantum ESPRESSO Configure window. (Dipole Corr tab) [Specification Change] • Changed the name of the working directory for some processes. • Changed to show the RMS of charges at the bottom of the molecule display area. • Added "opt=tight" to Calc Type in the Gaussian Configure window. • Added the read_restart command as comment to the LAMMPS input script. • Added the restart command to the LAMMPS input script. • Added upto to the argument of the run command in the LAMMPS input script. • Modified slightly the bat file for LAMMPS local jobs. • Changed the upper limit of the number of DPD particle species from 6 to 20 in the DPD calculation function of LAMMPS. • Changed the FDMNES result display window to use Winmostar's common graph display function. ### Version 10.3.5 March/1/2021 [Bug Fix] • Fixed a bug that force field assignment failed in acpype for GAFF, GAFF2, and OPLS-AA/L+GAFF when importing molecules by selecting OpenBabel in [File]-[Import]-[SMILES]. • Fixed a bug that sometimes caused an error when reading Gaussian fchk files. [Specification Change] • Enabled to show oxygen-oxygen double bonds and nitrogen-nitrogen triple bonds automatically when showing a molecule. ### Version 10.3.4 February/2/2021 [Bug Fix] • Fixed a bug that prevented the ESP charge of Gaussian from being displayed. • Fixed the problem of missing atoms at line feed in the ndx file output when running LAMMPS and in the ndx output by the [Select]-[Export Groups to Index File (ndx)]. [Others] • Changed some of the error messages displayed when outputting to the LAMMPS data file. ### Version 10.3.3 Janualy/4/2021 [Bug Fix] • Fixed a bug in which Gromacs remote jobs failed on servers without the bc command such as FOCUS. • Fixed a bug in which reading the LAMMPS data file with a tilt box could cause the coordinates to shift. • Fixed a problem in which the items set by the checkboxes in the Save and Load functions of the Quantum ESPRESSO Conofigure window were not being changed properly. • Fixed a bug that prevented DCDFTBMD from using the default template script to run jobs. [Others] • Updated the template script for remote jobs for the FOCUS supercomputer. ### Version 10.3.2 December/1/2020 [New Feature] • Added ECP to the choice of basis function in the Easy Setup window of GAMESS Configure. • Added NBO charges to the charge choices in the Setup of Gaussian Configure. • Enabled to set external electric field (sin wave or fixed value) in LAMMPS Configure. ([Non-equilibrium (1)]-[Electric Field]) • Enabled to execute [Solvate/Build Cell] and run LAMMPS with the option when launching from command prompt. [Bug Fix] • Fixed a problem in which the SDF file was not output correctly when selecting [File]-[Export SDF File] in the Animation window if the file currently open was not a SDF file. • Fixed a problem in which the process was terminated abnormally when launched from the command prompt, depending on the path of the output file. [Specification Change] • Changed to show on the console when launched from the command prompt. ### Version 10.3.1 November/4/2020 [New Feature] • Enabled to change alpha, beta, and gamma of the lattice constants directly in -[Create/Edit Cell]-[Transform Cell]. [Bug Fix] • Corrected the behavior when an incorrect SDF file is read. • Fixed a problem where the deformation of a specific axis was on the laboratory coordinates (x, y, z) and the cell could not be deformed correctly when it was not a rectangular cell in -[Create/Edit Cell]-[Transform Cell]. • Changed to set the open-shell system keyword in the GAMESS Setup window when the doublet spin state or more is selected in Easy Setup of the GAMESS Configure. • Fixed a problem that prevented chloroform solvent calculations with Gaussian 09 and 16. • Fixed a problem in which an error occurred when using the UFF force field with water molecules and the process did not proceed. • Fixed a problem in which Gromacs continuous execution could be interrupted if the output file size exceeds 2GB. • Fixed a bug in the energy change function of LAMMPS that prevented the display of units for variables defined in the variable command (e.g., specific heat) when using LAMMPS after 2017. • Fixed a bug that the unit of interfacial tension (GamNsurf) is not displayed in the energy change function of LAMMPS. • Fixed a bug in which LAMMPS results processing with mdp and top files was interrupted in some cases. • Fixed a problem in which [Tools]-[Compose SDF File] could not be loaded depending on the path of the target file. • Enabled to transfer large files of 2GB or more on Remote Job Submission . • Fixed a bug in [Help]-[Check CygwinWM] that caused Gromacs tests to fail in environments with 32 cores or more. [Specification Change] • Disabled to undo an operation after clicking [File]-[New]. • Added a menu to register and delete fragments under the -[Select Fragment] menu. • Reverted the output contents of the next line of$DATA in the output GAMESS input file back to what they were before V9.
• Reduced the cutoff radius of the mdp file generated for result processing during LAMMPS execution by 0.1 nm when the cell size was small.
• Enabled to set the minimum number of atoms to skip the symmetry detection process by Spglib at the startup of the Quantum ESPRESSO Configure ([Tools]-[Preferences]).
• Supported SDF file input on [Tools]-[Compose SDF File].
• Changed the information in the first three lines of each structure output on [Tools]-[Compose SDF File].
[Others]
• Integrated surface cutout and vacuum layer insertion tutorials into the slab creation tutorial.

### Version 10.3.0 October/5/2020

[New Feature]
• Added the function to apply arbitrary tensile, compressive, and shear strains to a cell. (-[Create/Edit Cell]-[Transform Cell])
• Enabled to visualize the structure in real time in Create/Edit Cell. (-[Create/Edit Cell]-[Create Cell], -[Create/Edit Cell]-[Transform Cell])
• Added the function to revert a structure that is wrapped inside a cell for each atom to a structure that is wrapped inside a cell for each molecule. (-[Wrap Around Cell Boundary]-[Unwrap all molecules])
• Added an option to Gromacs to start a continuation job from a high-precision trajectory file instead of a low-precision coordinate file. ([MD]-[Gromacs]-[Configure]-[Advanced]-[Extend simulation from full-precision trajectory])
• Enabled to read reference vibration analysis results of Gromacs. ([MD]-[Gromacs]-[Analyses]-[Normal Mode Analysis])
• Added setting for Normal Mode Analysis to the Gromacs Configure Preset. (Minimize (NMA), NMA)
[Bug Fix]
• Fixed a bug that prevented running multiple jobs at the same time when for Remote Job Submission of GAMESS. If you are using a template, you will need to recreate the template.
• Fixed a bug where the current state was not saved when saving settings in the LAMMPS Configure window.
• Fixed a bug where information was being read only up to the middle of the log file in Energy Plot of LAMMPS if an OS or MPI message is inserted in the middle of a log file.
• Fixed a bug that caused an access violation when Spglib failed to detect a space group.
• Fixed a bug that nspin and press_conv_thr were not saved when saving settings in Quantum ESPRESSO Configure window.
• Fixed a bug that np1 values were being saved in nq2 and nq3 when saving settings in Quantum ESPRESSO Configure window.
• Fixed a problem in which the pseudopotential/MOL (solvent) file folder settings were sometimes not saved in Quantum ESPRESSO Configure window.
• Fixed a problem in which the state of press_conv_thr, tstress, and tprnfor in the main window could not be read when launching Quantum ESPRESSO Configure window.
• Fixed a problem where the Generate Supercell would force the outer atoms of a cell to collapse inside the cell.
• Fixed a bug that caused Winmostar Job Manager to lock the folder where the first bat file started at startup is located.
• Fixed a bug that caused a segmentation fault when multiple Winmostar starts up and the number of temporary folders (wm_system\wm_ systemwm_tmp*) reached the limit.
[Specification Change]
• Changed to show files with all supported extensions in Open File Dialog.
• Changed the export SMILES feature to not display the edit command window.
• Moved -[Create/Edit Cell] to -[Create/Edit Cell]-[Edit Cell Manually].
• Enabled to change the minimum index that automatically switches to wire view when zooming and rotating the field of view in Preferece window.
• Enabled to change the minimum index that automatically switches to wire view usually in the preferences.
• Enabled to change the scale of the X-axis the same scale of the measured spectra in the infrared Raman spectral window.
• Enabled to adjusted the name and size of the components and the scale of the X-axis in the NMR spectrum window.
• Changed the isosurface display of S-orbitals gray only for Density or Surface.
• Changed the cell position so that the solute molecule (origin) is in the center in the menu [MD]-[Solvate/Build Cell],
• Changed the design of [MD]-[Gromacs]-[Import ER].
• Enabled to set the dihedral angle of polymerization in all polymer builders.
• Changed to check the chirality of the model generated by Polymer Cell Builder and output to the log.
• Enabled to set the allowable distance between unbonded atoms for Polymer Cell Builder.
• Changed to show density in Interface Builder and Slab Builder.
• Changed the design of the Generating Supercell.
• Changed to show the super cell information as text instead of the original cell information in the Generating Supercell.
[Performance Improvement]
• Speeded up drawing by switching to wire display when zooming in or out with the mouse wheel.
• Speeded up Energy Plot of MD.
• Changed not to do extra space group analysis using Spglib when running Quantum ESPRESSO.

### Version 10.2.6 December/1/2020

[Bug Fix]
• Fixed a bug that prevented selection of the log extension in File]-[Open].
• Fixed a bug in the band structure of Quantum ESPRESSO that caused the x-axis (energy) to be 0.5 times greater when the csv output in the phonon band output function.

### Version 10.2.5 November/4/2020

[Bug Fix]
• Fixed a bug in Gaussian's log file animation where the structure was sometimes not reflected in the middle of the log file.
• Fixed a problem in which an error occurred when using the UFF force field with water molecules and the process did not proceed.
• Fixed a bug in the energy change function of LAMMPS that prevented the display of units for variables defined in the variable command (e.g., specific heat) when using LAMMPS after 2017.
• Fixed a bug that the unit of interfacial tension (GamNsurf) is not displayed in the energy change function of LAMMPS.
• Fixed a bug in which LAMMPS results processing with mdp and top files was interrupted in some cases.
• Fixed a bug in [Help]-[Check CygwinWM] that caused Gromacs tests to fail in environments with 32 cores or more.
[Specification Change]
• Disabled to undo an operation after clicking [File]-[New].
• Reduced the cutoff radius of the mdp file generated for result processing during LAMMPS execution by 0.1 nm when the cell size was small.

### Version 10.2.4 October/5/2020

[Bug Fix]
• Fixed a bug where -[Add Dummy Atom]-[Along 2 Marked Atoms] menu would sometimes fail to add atoms in the correct locations.
• Fixed a bug that could cause an error when checking to see if bonds passes through the ring structures in Polymer Cell Builder.

### Version 10.2.3 August/22/2020

[Bug Fix]
• Fixed a problem where the number of MPI processes could not be changed in the Gromacs Configure window.

### Version 10.2.2 August/11/2020

[Bug Fix]
• Fixed a problem in which the depth cueing of atoms in the foreground would sometimes appear to be deeper than the one in the background when perspective view was not used.
• Fixed a error in reading UV-Vis spectra of Gaussian and GAMESS with more than 5,000 peaks.
• Fixed a problem in which an incorrect abc axis appeared in the molecular display area when the cell did not exist.
[Specification Change]
• Changed perspective and depth cueing.
• Changed to use perspective view in the display preset Winmostar Cover Art.
• Changed the layout of the BoltzTraP results display window.
• Added support for window size in [Tools]-[Draw Molecule].

### Version 10.2.1 July/23/2020

[New Feature]
• Enabled to output a set of files needed for a calculation in the Gromacs Configure window. ([Options] tab - [Dump All Files for Remote])
[Bug Fix]
• Fixed a problem in which the distance between atoms is not the sum of the covalent bond radii when changing the element of the terminal atom.
• Fixed a bug that the analysis of space groups using spglib did not work. (V10.2.0 or later)
• Fixed a problem in which [Tools]-[Balloon] did not work. (V10.2.0 or later)
• Fixed a problem in which the model in the main window was destroyed when using [Help]-[Check CygwinWM].
[Specification Change]
• Changed the input field to be blank by default in [File]-[Import]-[SMILES].
• Changed to set the reference value of the vacuum to the potential energy at the specified coordinates instead of the maximum value of the potential energy in the potential energy distribution function of Quantum ESPRESSO.
• Changed -[Add Dummy Atom]-[To Center of Mass of Selected Group] to -[Add Dummy Atom]-[To Center of Geometry of Selected Group].
• Changed the behavior of [Solid]-[Slab Builder] partially.
• Changed the default extension to mol in the save dialog of [Tools]-[Comformation Search (Balloon)].

### Version 10.2.0 July/14/2020

[New Feature]
• Enabled to read MOL files in V3000 format.
• Enabled to output of cell sizes in Lattice records when saving in xyz format.
• Enabled to read Extended XYZ format (Tom)
• Changed to read/write periodic boundary cells in PDB format.
• Added a function to change all the atoms that could not be determined automatically (deuterium etc. in the CIF file) to hydrogen when reading file. (-[Automatically adjust Atoms/Bonds]-[Change Unknown Elements to Hydrogen])
• Added support for cells other than rectangular cells in -[Adjust Axes]-[Invert X/Y/Z axis].
• Enabled to input the absolute coordinates of the center of gravity of an editing group. (-[Modify Selected Group]-[Move (Numerical)])
• Enabled to move a selected group along an arbitrary vector.(-[Modify Selected Group]-[Move (Numerical)])
• Enabled to show cross-sectional area of a cell. Edit]-[Create/Edit Cell]-[Lattice Constants].
• Enabled to add atomic luster in the molecule view area.
• Enabled to adjust position and font size of Labels/Charges in molecule view area.
• Enabled to show only number or element name on label in molecule view area.
• Enabled to show abc coordinate axes in the molecule view area when the cell is not a rectangular shape.
• Enabled to change and save view settings at once. ([View]-[View Preset])
• Enabled to retrieve and show NBO charges from Gaussian log files.
• Enabled to use Universal Force Field (UFF) in MD calculations, so that greatly increasing the number of element/molecule types that can be calculated.
• Enabled to select RESP charge in the [MD]-[Assign Charges Automatically],
• Enabled to calculate RESP charges without directly controlling GAMESS calculations. ([MD]-[Assign Charges Manually])
• Enabled to specify the endpoints of the trajectory reading range in the various result analysis functions of Gromacs and LAMMPS.
• Enabled to vary target pressure lenearly in LAMMPS.
• Enabled to show the structure in real time when changing parameters in [MD]-[Interface Builder],
• Enabled to finely control cell size in the horizontal direction of the interface in [MD]-[Interface Builder].
• Enabled to finely control cell size in the distance between cells in [MD]-[Interface Builder].
• Enabled to read the structure in the main window in [MD]-[Interface Builder].
• Enabled to automatically reposition atoms outside of cells in [MD]-[Interface Builder].
• Added a function to create supercells based on the occupancy of the CIF file.
• Enabled to create a slab model with Cleave Plane, Insert Vacuum, and Generate Supercell at once with pymatgen. ([Solid]-[Slab Builder])
• Enabled to model molecules by drawing the structural formula directly. (Tools]-[Draw Molecule])
• Reduced the number of conformers by clustering simple structures in [Tools]-[Conformation Search (Ballon)].
• Enabled to calculate the vector perpendicular to the plane along a ring structure when the ring structure is selected as a group. ([Tools]-[Unit Normal Vector of Ring Structure])
• Enabled to use the [Automation] menu function in the Animation window even when the SDF file is not opened.
• Enabled to output multiple frame SDF files from Animation window . ([File]-[Export SDF File])
• Enabled to output each frame in the Animation window as files separately. The supported formats are XYZ, CIF, PDF, MOL, MOL2, MOPAC, CNDO/S, Gaussian, GAMESS and NWChem.
• Added a function to create supercells based on the occupancy of the CIF file.
• Enabled to create a slab model with Cleave Plane, Insert Vacuum, and Generate Supercell at once with pymatgen. ([Solid]-[Slab Builder])
• Enabled to model molecules by drawing the structural formula directly. (Tools]-[Draw Molecule])
• Reduced the number of conformers by clustering simple structures in [Tools]-[Conformation Search (Ballon)].
• Enabled to calculate the vector perpendicular to the plane along a ring structure when the ring structure is selected as a group. ([Tools]-[Unit Normal Vector of Ring Structure])
• Enabled to use the [Automation] menu function in the Animation window even when the SDF file is not opened.
• Enabled to output multiple frame SDF files from Animation window . ([File]-[Export SDF File])
• Enabled to output each frame in the Animation window as files separately. The supported formats are XYZ, CIF, PDF, MOL, MOL2, MOPAC, CNDO/S, Gaussian, GAMESS and NWChem.
[Bug Fix]
• Fixed a bug that fails to open SDF files that contained only one frame that outputed from Winmostar.
• Fixed a bug where Quick Optimization fails for the structure from mol and sdf files.
• Fixed a problem in which cleave plane of slab models failed on some crystals. (Use [Solid]-[Slab Builder].)
• Fixed a problem in which insert vaccum in slab models failed on some crystals. (Use [Solid]-[Slab Builder].)
• Fixed a problem in which the conversion to primitive cells failed for some crystals.
• Fixed the bug of bound check error occurring when converting to a primitive cell with the group selected.
• Fixed a problem in which template scripts could not be used when executing NEB of Quantum ESPRESSO on remote.
[Specification Change]
• Added Bq to [Select element for editing ops].
• Enabled to skip Force field assignments in the [Assign Force Field] window of MD.
• Changed to show detected space groups after converting to primitive cell.
• Enables to specify the tolerance of space group detection in the preferences.
• Changed to use Spglib convert to primitive cells. (e.g., [Solid]-[Convert Lattice])
• Changed to show a confirmation dialog after the conversion to a primitive cell.
• Modified the interpretation of priority list of pseudopotentials of Quantum ESPRESSO.
• Added pbe-rrkjus to the priority List of pseudopotentials of Quantum ESPRESSO.
• Changed to not allow OpenMX to run without a simulation cell.
• Chaned the name of Cygwin for Winmostar from cygwin_wm to CygwinWM.
• Enabled to count down and cancel the automatic shutdown of Job Manager before shutting down.
• Increased items to be checked in [Help]-[Check CygwinWM].
• Abolished [File]-[Save Ligand inp File...], [Automation]-[Saving Gaussian gfj File], [Change Only Current Frame], [Execute for Current Frame], [Export SDF File] and [Saving SDF File] in the Animation window.
• Changed Animation window so that [Running MOPAC] would not be affected by [Animation]-[Check All] and [Uncheck All].
[Performance Improvement]
• Accelerated -[Adjust Axes]-[Set to Principal Axes].
• Accelerated Force field Asignment using Acpype (GAFF, OPLS-AA+GAFF) was accelerated. (CygwinWM 2020/07/02 version)

### Version 10.1.6 August/22/2020

[Bug Fix]
• Fixed a problem where the number of MPI processes could not be changed in the Gromacs Configure window.

### Version 10.1.5 July/14/2020

[Bug Fix]
• Fixed a bug that caused the installer to be garbled on some operating systems.
• Fixed a bug in which saving mol2 files sometimes resulted in incorrect atomic types.
• Fixed a problem in which depth cueing was sometimes not immediately reflected.
• Fixed a problem in which inappropriate structures were generated when using OpenBabel in the [Import SMILES] function.
• Fixed the bug that pun, trj, and efp files were not generated when Default was selected for Shell Script on GAMESS Remote Job Submission.
• Fixed a bug where changes were sometimes not reflected after loading and editing a Gaussian input file and saving it.
• Fixed a problem in which the calculated values in the [Calc Ave] of the energy change window of various MD solvers were slightly shift.
• Fixed a problem in Acpype charge assignment that resulted in incorrect bond information after sorting by molecular species.
• Fixed a problem in which C1 was sometimes determined to be Cs in Point Group Analysis.
[Specification Change]
• Added template scripts for LAMMPS and Quantum ESPRESSO for the latest FOCUS supercomputer. Select lammps.focus200706.txt and quantumespresso.focus200706.txt in the Shell Script to update,
• Changed to use --gen2D option instead of --gen3D option when using OpenBabel for the [Import SMILES] function.
• Changed to use the same graph drawing function as the other functions in the BoltzTraP results window.

### Version 10.1.4 May/6/2020

[Bug Fix]
• Fixed a problem in which the display with the periodic boundary was broken when using -[Delete Cell]. (Even in previous version, there were no problems other than the appearance).
• Fixed a bug that sometimes prevented remote fchk creation in Gaussian remote job execution.
• Fixed a problem in which charge assignment was abnormally terminated for [MD]-[Assign Charges Automatically] when each molecule was not sorted by number.
• Fixed a bug that could cause interruption of the Gromacs process if a molecule has a long bond distance.
• Fixed a bug that a job's log file is not readable during spin-polarization calculations in Quantum ESPRESSO.
• Fixed a bug that OpenMP and MPI settings were not saved in OpenMX Prefercence.
• Fixed a bug that the behavior of the [Tools]-[Balloon] function depends on the file format.
[Specification Change]
• Added the latest DCDFTBMD binary to the Executable of the DCDFTBMD Preference.

### Version 10.1.3 May/6/2020

[Bug Fix]
• Fixed a bug that the parallel number of GAMESS saved is not reflected at the next startup.
[Specification Change]
• Restored the change in the specification of hydrogenation to group selected atoms in V10.1.1.
• Enabled to apply -[Add Hydrogens]-[To All Atoms], [To Marked Atom (1 Hydrogen)], [To Marked Atom (2 Hydrogens)], and [To Marked Atom (3 Hydrogens)] to group-selected atoms.

### Version 10.1.2 May/3/2020

[Bug Fix]
• Fixed a problem in which an error message was displayed when a large number of jobs were in the Job Manager.

### Version 10.1.1 May/1/2020

[New Feature]
• Added the function to place the atoms directly above the simulation cell on both sides of the interface in the Interface Builder.
[Bug Fix]
• Changed to show a message to prompt the creation of a Z-Matrix when no Z-Matrix is generated at the time of adding hydrogens, such as in a large scale system.
• Fixed a bug in which the position of the number at the end of the dipole moment arrow did not move.
• Fixed a bug where the content displayed was not updated when the Reset button was pressed in the MOPAC Preference window .
• Fixed a bug in which the [MD]-[Assign Charges Manually] function could not be used to assign a charge after reading a file in some formats, such as PDB or Quantum ESPRESSO's MOL format.
• Fixed a bug that prevented the use of template scripts when running Quantum ESPRESSO's NEB calculations on a remote job.
• Fixed a bug that could cause an error in the Job Manager on English version of Windows.
• Fixed a bug that prevented the Job Manager from editing the contents of the oldest job.
[Specification Change]
• Changed the specifications for adding hydrogen.
• Enabled to add hydrgens to silicon atoms.
• Changed to display the transition moment as a double arrow.
• Changed the default path for GAMESS.
[Performance Improvement]
• Acclerated the addition of hydrogen with group selection.
[Other]
• Reorganized Phonopy and BoltzTraP tutorials as part of the Quantum ESPRESSO tutorial.

### Version 10.1.0 April/6/2020

[New Feature]
• Supported histograms of dipole moments and autocorrelation functions in Gromacs and LAMMPS dielectric constants calculation.
• Added a function to calculate the distribution of distance, angle, and dihedral angle between selected atoms to the result analysis function of Gromacs and LAMMPS ([MD]-[Gromacs]/[LAMMPS]-[Analyses]-[Bond/Angle/Dihedral Distribution]).
• Added the function to transfer only xtc files from the remote server to the local machine executing remote jobs in Gromacs. ([Job]-[Get Remote File and...]-[Save XTC] in the [Remote Job Submission] window)
• Enabled to select whether or not to assign the same charge to an atom that is structurally equivalent in molecular in the RESP charge calculation function of GAMESS. Larger molecules are more likely to be successfully processed.
• Added support for BoltzTraP in OpenMX3.9.
• Enabled to st the number of jobs that can be processed at the same time in Job Manager. ([Tools]-[Preferences]-[Calculation]-[Max # of jobs])
• Enabled to display the average value of the specified range in the common graph display function.
[Bug Fix]
• Fixed a bug in which an Access violation could occur in some editing operations.
• Fixed a bug that could cause an error in the Job Manager on English Windows.
• Fixed a bug that the error "Timed out waiting on socket" could occur on Remte Job Submission.
• Fixed the bug that a job could not be deleted when Queue is JM(Windows) on Remte Job Submission.
[Specification Change]
• Changed to asks the user if the molecule should be changed to CH4 when the Configure window is opened with the molecule's initial structure (CH).
• Changed to create a working directory and a temporary file when executing [File]-[Import]-[SMILES] or [Tools]-[Conformation Search(Balloon)] function.
• Cahnged to untitle the file name after executing [File]-[Import]-[SMILES] or [Tools]-[Conformation Search(Balloon)] function
• Changed to call [MD]-[Assign Charges Automatically] if need when [MD]-[Gromacs]/[LAMMPS]-[Assign Force Field].
[Miscellaneous]
• Added the Graphite cif file to the Samples folder.

### Version 10.0.8 June/8/2020

[Bug Fix]
• Fixed a bug that sometimes prevented remote fchk creation in Gaussian remote job execution.
• Fixed a bug that a job's log file is not readable during spin-polarization calculations in Quantum ESPRESSO.
• Fixed a bug that OpenMP and MPI settings were not saved in OpenMX Prefercence.

### Version 10.0.7 May/6/2020

[Bug Fix]
• Fixed a bug that the parallel number of GAMESS saved is not reflected at the next startup.
[Specification Change]
• Restored the change in the specification of hydrogenation to group selected atoms in V10.0.6.
• Enabled to apply -[Add Hydrogens]-[To All Atoms], [To Marked Atom (1 Hydrogen)], [To Marked Atom (2 Hydrogens)], and [To Marked Atom (3 Hydrogens)] to group-selected atoms.

### Version 10.0.6 May/1/2020

[Bug Fix]
• Changed to show a message to prompt the creation of a Z-Matrix when no Z-Matrix is generated at the time of adding hydrogens, such as in a large scale system.
• Fixed a bug in which the position of the number at the end of the dipole moment arrow did not move.
• Fixed a bug where the content displayed was not updated when the Reset button was pressed in the MOPAC Preference window .
• Fixed a bug in which the [MD]-[Assign Charges Manually] function could not be used to assign a charge after reading a file in some formats, such as PDB or Quantum ESPRESSO's MOL format.
[Specification Change]
• Changed the specifications for adding hydrogen.
• Enabled to add hydrgens to silicon atoms.
• Changed the default path for GAMESS.
[Performance Improvement]
• Acclerated the addition of hydrogen with group selection.
[Other]
• Reorganized Phonopy and BoltzTraP tutorials as part of the Quantum ESPRESSO tutorial.

### Version 10.0.5 April/6/2020

[Bug Fix]
• Fixed a bug that the appropriate UI was not displayed when clicking [Select]-[Select by Molecular Species], [Select by Molecules], [Select by Elements], or [Enter Selection Language].
• Fixed a bug in which the default file type was selected as MOPAC when the keyword of various solvers was set and the file was saved as another file name when initial status.
• Fixed a bug that the appropriate keywords were not selected by default when the MOPAC Configure window was opened after some operations or after loading files of some formats.
• Fixed a bug in Configure window of Quantum ESPRESSO that the valence electron number of some pseudopotential files could not be obtained automatically.
• Fixed a bug that could cause an error in the Job Manager on English Windows.
• Fixed a bug that the error "Timed out waiting on socket" could occur on Remote Job Submission.
• Fixed the bug that a job could not be deleted when Queue is JM(Windows) on Remote Job Submission.
[Specification Change]
• Changed the name of the [Advance] tab in the various Configure window to [Advanced].
• Changed the name of [MOPAC]-[Analyses]-[Vibration] was changed to [IR].
• Changed the order of [Energy Terms] in [MD]-[Gromacs]-[Energy Plot].
[Miscellaneous]
• Added the MOPAC dihedral angle scan tutorial.

### Version 10.0.4 March/19/2020

[Bug Fix]
• Fixed the problem that some contents set by Enter Scanning Condition in Easy Setup of Gaussian were not reflected in the Gaussian Setup window.
• Fixed the bug that the file path might be moved under the Winmostar installation folder when importing SMILES.

### Version 10.0.3 March/2/2020

[Bug Fix]
• Fixed an issue where an error occurs when installation was completed after overwriting installation was canceled once.
• Fixed a bug where files could not be specified in some [Open] dialogs.
• Fixed an error that occurred when [Output Directory] in the Quantum EPSRESSO Configure window was set to Continue while the log file (pwout file) of Quantum ESPRESSO was open.
[Specification Change]
• Changed the default extension of saved file from lmp_set to lmpset when pressing [Save] and [Load] buttons in LAMMPS Configure window. It is possible to load a file saved with the previous version.

### Version 10.0.2 February/10/2020

[Bug Fix]
• Fixed a bug where the error message for an invalid license could not be easily seen over other messages.
• Fixed a bug that occasionally zoom out and blurs while zoom in with mouse operation.
• Fixed a bug that caused an error if the terminal monomer was not specified in the Block Polymer Builder.
• Fixed a bug that sometimes caused an access violation when the force field assignment failed.
• Fixed a bug that the default file proposed by [MD]-[Gromacs]-[Import Last Coordinate(gro)] is not the final structure but the start structure.
• Fixed an error that appeared when executing a new job again without changing the file name after executing a job in Gromacs and LAMMPS.
• Fixed a bug that the Configure window could not be opened normally after using the Save as Default function in LAMMPS Configure.
• Fixed a bug that could cause an error when creating a LAMMPS data file for a large-scale polymer.
• Fixed a bug that charges were not kept in Generate Supercell.
• Fixed the bug that NWChem is executed by the default script of GAMESS remote job submission.
• Fixed the bug that CONFLEX could not be started on the local PC.
• Fixed an error that occurred when saving with the default file name when executing [Tools]-[Conformation Search (Balloon )].
• Fixed a bug where the solver selection combo box has a blank in the Remote Job Submission window.
• Fixed a bug that jobs were not executed with Queue = Run when using the template script in the Remote Job Submission.
• Fixed a bug that caused an error when clicking on three atoms in the ball-and-stick display on the Superimposse Molecules window.
• Modified URL of [Help]-[Web Manual].
[Specification Change]
• Changed Various windows not hidden behind the main window.
• Renamed "ESP(Mulliken)" in MO Plot window to "ESP(Population Charge)".
• Changed not to output dihedrals in triangular bond by assignment of Dreiding force field.
• Enabled to switch double and single precision without modifying the template script for Gromacs remote jobs.
• Changed not to accept Gromacs remote job template scripts generated before V10.0.1.
[Performance Improvement]
• Accelerated creation and reading of LAMMPS data files for large-scale polymers.
• Accelerated Dreiding force field assignment.

### Version 10.0.1 January/20/2020

[Bug Fix]
• Modified the title bar notation.

### Version 10.0.0 January/15/2020

[New Feature]
• Enabled the depth expression of the main window. ([View]-[Enable Depth Cueing])
• Enabled to display for patent application in 3D view.
• Enabled to display gradationin 3D view.
• Added registration and selection of group selection. ([Select]-[Register Selected Group], [Select Registered Group])
• Added a function to translate atoms in all frames in the Animation window. ([Animation] window-[Tools]-[Translate All Atoms])
• Added some DFT functionals and dispersion correction to Setup and EasySetup of QM solvers.
• Added the function to calculate RESP charge using Gaussian.
• Added a function to automatically assign charges to multiple molecules before executing MD calculation. ([MD]-[Assign Charges Automatically])
• Added a setting to sort each line of dump file output of LAMMPS by id. ([MD]-[LAMMPS]-[Configure]-[Output]-[Sort dump file by id])
• Changed to output the registered group to ndx file so that it can be selected later for LAMMPS.
• Added the function to set the cutoff radius so that it does not exceed half the system size in Gromacs and LAMMPS Configure window. ([Modify cutoff radii not to exceed L / 2] on the [Interaction] tab)
[Bug Fix]
• Fixed a bug that could cause an error in the [Solid]-[Build Cluster Model] menu.
[Specification Change]
• Changed the default file name untitled.
• Changed the specifications for command line execution.
• Changed some shortcut keys using Alt key.
• Changed the format when saving xyz file in [File]-[Save] and [Save As].
1st line: Number of atoms
2nd line: line: Comment
3rd and subsequent lines: Coordinates of atoms
• Changed the name of the [Convert] button to [Import] in the SMILES import window.
• Changed the name of [Select element used in editing operations] on the toolbar to [Select element for editing ops].
• Added [Open Project], [Open Recent Project], and [Project Browser] buttons to the toolbar. (Experimental, only for Quantum ESPRESSO NEB calculation)
• Enabled to zoom in and out by dragging left and right simultaneously in the main window, .
• Changed not to deplicate the number of four marker atoms.
• Put the result analysis functions of various solvers together in the sub menu of the main menu.
• Changed the [Energy Change] and [Animation] buttons on the toolbar to be pulled down for solvers with some energy changes and animation functions.
• Added [Select fragment] and [Select element for editing Ops] in the  menu.
• Changed default attribute of cell boundary from None to Periodic.
• Changed "samples" and "manual" folders in the Winmostar installation folder to "Samples" and "Manual".
• Changed the default choice of overwrite confirmation dialog that appears when saving various files to No.
• Changed [Series] notation to [Y Axis] in [Custom Plot] window called from Animation window.
• Removed [Excel] button and added [File]-[Export CSV] menu in Animation window.
• Changed the name of [ESP2] in the MO Plot window to [ESP2 (Mulliken)].
• Changed settings are not reflected in Easy Setup function of Semi-Empirical QM and QM until the OK button is pressed.
• Removed the check of [Reset before applying changes] by default in Easy Setup functions of Semi-Empirical QM and QM.
• Set a different name for Semi-Empirical QM and QM working directory for each solver.
• Changed the default QM calculation method from HF/STO-3G to B3LYP/6-31G*.
• Changed GAMESS Basic COORD default value from ZMTMPC to UNIQUE.
• Changed to use mpirun instead of mpiexec by default in NWChem remote job scripts.
• Changed the name of [Import] button of [MD]-[Solvate/Build Cell] function to [Same as main window].
• Changed to untitile the file name after executing [MD]-[Solvate/Build Cell] and [Solid]-[Crystal Builder].
• Removed the Force Field tab from the Gromacs and LAMMPS Configure, and separated the equivalent function into the [MD]-[Gromacs/LAMMPS]-[Assign Force Field] menu.
• Changed to open the Force Field setting window automatically on Gromacs and LAMMPS Configure.
• Moved [constraints] setting to [Advance] tab in Gromacs Configure.
• Changed default parameters in Gromacs Configure as follows.
shake-to of Preset with "(fast)": 1e-4 -> 1e-5
constraints of Preset with "(fast)": hbonds -> all-bonds
• Changed to read charge and force field information is automatically in the Gromacs animation function if there is a top file.
• Moved [Random Seed], [Tdamp], [Pdamp] setting to [Basic] tab in LAMMPS Configure.
• Moved [Constrain hydrogen atoms] setting to [Advance] tab in LAMMPS Configure.
• Enabled to select general force field type in [Force Field/Potential File] of LAMMPS Configure.
• Changed to set [Pulled atoms] and [Restrained atoms] of LAMMPS Configure from the registered group.
• Changed the layout of LAMMPS Configure, and moved the display/edit field of in file to Manual entry tab.
• Changed the default parameters in LAMMPS Configure as follows.
Shake tolerance of Preset with "(fast)": 1e-4 -> 1e-5
• Changed to leave the name of the potential file used in comments in the data file generated during DPD calculation.< Added Grimme-d3 to the choice of vdw-corr of Quantum ESPRESSO Configure.
• Changed the default parameters in Quantum ESPRESSO Configure as follows.
degauss: 0.05 -> 0.01
• Changed the default parameters in Quantum ESPRESSO Nudged Elastic Band Configure as follows.
• Changed not to output E = Efermi line when displaying band structure of Quantum ESPRESSO.
• Moved [Solid]-[Phonopy], [BoltzTraP] menu under [Solid]-[Quantum ESPRESSO].
• Changed Job Manager UI significantly.
• Change the folder structure created on the remote server from "~/(Windows user name)/(solver name)/(job name)" to "~/wm_(Windows user name)/(solver name)/(job name)".
• Change to write the version of Winmostar as a comment in the template script of the remote job.
• Changed not to use Putty by default for Remote Job Submit.
• Enabled to execute UNIX commands by entering them in the log display text box on the Remote Job Submit window.
• Changed shortcut key of [View]-[Copy Image] of Winmostar Viewer.
[Deprecated Feature]
• Discontinued the function before V8 that does not use Packmol in [MD]-[Solvate/Build Cell] function.
• Discontinued support for project files created in V9 or earlier.
• Disabled Remote Job Submit in V8.
• Disabled 2D display.

## Winmostar V9

### Version 9.4.12 March/15/2021

[Bug Fix]
• Fixed a bug where an error occurs while assigning MD force field.

### Version 9.4.11 May/18/2021

[Bug Fix]
• Fixed a bug in the installer.

### Version 9.4.10 Janualy/4/2021

[Bug Fix]
• Fixed a bug where the number of MPI processes could not be changed in the Gromacs Configure window.

### Version 9.4.9 July/14/2020

[Bug Fix]
• Fixed a bug where changes were sometimes not reflected after loading and editing a Gaussian input file and saving it.
• Fixed a problem in which C1 was sometimes determined to be Cs in Point Group Analysis.

### Version 9.4.8 May/6/2020

[Bug Fix]
• Fixed a bug that the parallel number of GAMESS saved is not reflected at the next startup.
[Specification Change]
• Restored the change in the specification of hydrogenation to group selected atoms in V9.4.6.
• Enabled to apply -[Add Hydrogens]-[To All Atoms], [To Marked Atom (1 Hydrogen)], [To Marked Atom (2 Hydrogens)], and [To Marked Atom (3 Hydrogens)] to group-selected atoms.

### Version 9.4.7 May/3/2020

[Bug Fix]
• Fixed a problem in which an error message was displayed when a large number of jobs were in the Job Manager.

### Version 9.4.6 May/1/2020

[Bug Fix]
• Changed to show a message to prompt the creation of a Z-Matrix when no Z-Matrix is generated at the time of adding hydrogens, such as in a large scale system.
[Specification Change]
• Changed the specifications for adding hydrogen.
• Enabled to add hydrgens to silicon atoms.
[Performance Improvement]
• Acclerated the addition of hydrogen with group selection.

### Version 9.4.5 April/6/2020

[New Feature]
• Enabled to set the number of jobs that can be processed at the same time in Job Manager. ([Tools]-[Preferences]-[Calculation]-[Max # of jobs])
• Improved Job Manager to be almost the same as V10.
[Bug Fix]
• Fixed a bug in which the values of the solute_epsilon and solute_sigma keywords were not updated when opening the Configure window after opening the Quantum ESPRESSO input file (pwin file).

### Version 9.4.4 March/2/2020

[Bug Fix]
• Fixed a bug that sometimes caused an access violation when the force field assignment failed.

### Version 9.4.3 January/20/2020

[Bug Fix]
• Fixed a bug that could cause an error in command line execution.
• Fixed a bug that covalent bonds were not displayed in some molecular structures when calculating GAMESS RESP charges.
• Fixed a bug that could cause an error in the [Solid]-[Build Cluster Model] menu.

### Version 9.4.2 Decwember/4/2019

[New Feature]
• Added automatic rotation function in Winmostar Viewer.
• Enabled to set seed of random number when using Packmol in [Solvate/Build Cell] menu.
• Added Quantum ESPRESSO 3D-RISM and Laue-RISM RMS visualization functions ([Solid]-[Quantum ESPRESSO]-[3D/Laue-RISM RMS RMS Change for Last Step])
• Enabled to show RMS changes of Quantum ESPRESSO RISM calculation directly from the remote job window. ([Get & Plot ...] function)
[Bug Fix]
• Fixed a bug that caused an error in [File]-[Export]-[Image] menu.
• Fixed a bug that the captured image of Winmostar Viewer is shifted.
• Fixed a bug that bonds are not displayed in a system with a cell that is largely off the origin.
• Fixed a bug that the [Cube] button disappears when the Selected MO is changed in Gaussian fchk reading Cubegen window. (V9.1.2 or later)
• Fixed a bug that Gaussian Franck-Condon calculation may not be able to read if there are many peaks.
• Fixed a bug that Quantum ESPRESSO could not read the electronic status of files with file names including Japanese.
• Fixed a bug that may cause an error in continuous calculation using Quantum ESPRESSO version 6.
• Fixed a bug that large files could fail to be transferred in remote jobs when Putty is not used.
• Fixed a bug that the progress bar may get stuck while transferring a remote job file.
[Specification Change]
• Changed NSTATE from 5 to 10 when TDDFT was selected in GAMESS Easy Setup window. (Specification before V9.2.3)

### Version 9.4.1 November/5/2019

[New Feature]
• Added the function to swap coordinate axes. (-[Recoordinate Axes]-[Swap Axes])
• Added the function to invert the coordinate axes. (-[Recoordinate Axes]-[Invert X/Y/Z Axis])
• Added the function to rotate the group by entering the Euler angle. (-[Modify Selected Group]-[Orbit Group (Numerical)])
• Added a function to output only the currently displayed frame to a file during animation display. (Animation window-[File]-[Export Current Frame])
[Bug Fix]
• Fixed a bug that LAMMPS OPLS force field generation does not give an appropriate error message when there is an atom type that does not support OPLS.
• Fixed a bug that the Animation window is hidden when [File]-[Save As] is executed while the Animation window is displayed.
[Specification Change]
• Added hints for OpenMX keyword setting window.
• Added basic tutorial of GAMESS, Gaussian and NWChem.

### Version 9.4.0 October/7/2019

[New Feature]
• Enabled to calculate the inertia radius along the principal axis of inertia in the Gromacs inertia radius calculation function.
• Enabled to change the size of histogram in Gromacs and LAMMPS density distribution calculation function.
• Enabled to create groups in Gromacs and LAMMPS density distribution calculation window. (Create Group button)
• Added a button to display the result processing program log in the result analysis window of Gromacs and LAMMPS.
• Added the graphing function of RMS change of 1D-RISM calculation in ESM-RISM calculation of Quantum ESPRESSO.
• Enabled to set THIRDDIAG and DAMPXHZETA in DCDFTBMD keyword setting window.
• Added a function to copy text data of a specific column in various graph display functions. ([Options]-[Copy Columns])
[Performance Improvement]
• Speeded up the progress display.
• Reduced memory consumption so that approximately twice as much data can be read in when loading OpenMX and DCDFTBMD animations.
[Bug Fix]
• Fixed a bug that the sub window that appeared in the front was hidden behind in some processes.
• Fixed a bug that the copy range of the image shifts in the UV-Vis display window of CNDO/S.
• Fixed a bug that the Gromacs keyword setting window does not close under some conditions when closing it.
• Fixed a bug that caused processing to fail when reading an animated gro file in Gromacs trajectory editing function .
[Specification Change]
• Enabled to set multiple license keys at the same time.
• Enabled to enter vdw_corr freely in Quantum ESPRESSO keyword setting window.
• Added support for Quantum ESPRESSO version 6. (The recommended version remains 5.2.1.)
• Changed not to show the emboss of the outer frame in the graph copy function.
• Changed to show the progress bar when transferring with remote jobs.
• Changed to output unit of solubility parameter to csv in Hansen SP calculation function.
• Changed [Tools]-[Unit Converter] function to stand-alone application.

### Version 9.3.5 Decwember/4/2019

[Bug Fix]
• Fixed a bug that caused an error in [File]-[Export]-[Image] menu.
• Fixed a bug that the captured image of Winmostar Viewer is shifted.
• Fixed a bug that bonds are not displayed in a system with a cell that is largely off the origin.
• Fixed a bug that the [Cube] button disappears when the Selected MO is changed in Gaussian fchk reading Cubegen window. (V9.1.2 or later)
• Fixed a bug that Gaussian Franck-Condon calculation may not be able to read if there are many peaks.
• Fixed a bug that Quantum ESPRESSO could not read the electronic status of files with file names including Japanese.
[Specification Change]
• Changed NSTATE from 5 to 10 when TDDFT was selected in GAMESS Easy Setup window. (Specification before V9.2.3)

### Version 9.3.4 November/5/2019

[Bug Fix]
• Fixed a bug that LAMMPS OPLS force field generation does not give an appropriate error message when there is an atom type that does not support OPLS.

### Version 9.3.3 October/7/2019

[Bug Fix]
• Fixed a bug that reads the input file with GAMESS basis function specified for each atom and reads it as Lp if there is a diffuse function.
• Fixed a bug that force field bond parameters may not be correct in MODYLAS.
• Fixed a bug that some atoms are not displayed by Cleave Plane.
• Fixed a bug that caused Winmostar to stop responding when a fragment was saved with a file name from the beginning.

### Version 9.3.2 September/3/2019

[New Feature]
• Changed to display transition orbit numbers in the UV-Vis window.
[Bug Fix]
• Fixed a bug that the extension was not set properly when a file name includes a period in some save dialogs.
• Fixed a bug that User Charge could not be deleted in [Edit Charge] menu.
• Fixed a bug that some pull-down menus in various keyword setting windows are not displayed.
• Fixed a bug where one atom may be missed when the third line of MOPAC data is blank.
• Fixed a bug that recombination does not occur when displaying in Winmostar Viewer after executing [Tools]-[Invert Trajectory] in Animation display of Gaussian and MOPAC IRC calculation.
• Fixed a bug that the layout of LAMMPS keyword setting window is broken.
• Fixed a bug that causes an address violation when the Dump All Files button on the LAMMPS or Quantum ESPRESSO keyword setting window was pressed when the remote job submission window was not opened once after starting Winmostar. (V9.3.0 or later)
[Specification Change]
• Enabled to set charge for each atom in [Edit Charge] menu.
• Enabled to autoscale the vertical axis of UV-Vis window.
• Changed to show the vibration mode number in the IR Spectrum window.
• Changed the extension selected in [File Type] to have priority over the extension directly entered in [File Name] in the [MD]-[Interface Builder] save dialog.

### Version 9.3.1 August/5/2019

[New Feature]
• Added free volume calculation function to result analysis of Gromacs and LAMMPS.
• Enabled to calculate the inertia radius on the inertia main axis in Gromacs's inertia radius calculation function.
• Enabled to continuously calculate the supercell generated by Phonopy using Quantum EPSRESSO using the remote job submission function.
[Performance Improvement]
• Accelerated bond generation.
[Bug Fix]
• Fixed the bug that the format may not be correct when saving xyz/txy file.
• Fixed the bug that could prevent atom selection in some environments.
• Fixed the problem that the topology file can not be created if GAFF or OPLS-AA/L + GAFF is selected as the force field when placing a single atom by using [Solvate/Build Cell].
• Fixed the bug that the value of ecdmin was not set properly when entering a decimal value in the Gromacs ER method setting.
• Fixed the bug in acpype execution with the cygwin_wm versioin 04/02/2019.
• Fixed the bug that ERmod sometimes became extremely slow with cygwin_wm version 03/20/2019 or later.
• Fixed the bug that the working folder is moved to wm_system\wm_tmp_1 In the MOL file creation function of Quantum ESPRESSO.
• Fixed the bug that unselected MOL files are also copied to the working directory when running Quantum ESPRESSO. (Even previous versions do not affect the calculation results)
• Fixed the bug that invalid SDF file is saved in Animation window.
• Fixed the bug that drawing is not updated by fragment registration.
[Specification Change]
• Changed to generate Z-Matrix only for small molecules after reading xyz file.
• Changed not to disappear tool buttons when changing the window size.
• Changed to show progress bar with bond regeneration and drawing.
• Enabled to calculate the RESP charge also in Optimize/PCM calculation of GAMESS.
• Changed to set UNK automatically when the residue name is blank in [Solvate/Build Cell].
• Changed not to display the emboss around the graph image in the graph display function of MD and solid menus.
• Changed not to ask about application of the atom relocation function when atoms are placed directly above the periodic boundary in the Interface Builder.
• Enabled to set eccore in Gromacs ER method settings.
• Changed the default display range of X-axis in the Solvent Pair Distribution Function of Quantum ESPRESSO.
• Changed to load the generated MOL file to the main window automatically in the MOL file creation function of Quantum ESPRESSO.
• Enabled to execute when the server shell is csh and Queue is Run for Remote Job Submission.
• Changed to save settings for [Send Local Fchk] etc. in Remote Job Submission.
• Enabled to connect using only the private key without setting the public key when connections does not use putty in Remote Job Submission.
• Enabled to use multi-stage SSH connections with port forwarding when connections does not use putty in Remote Job Submission.
[Miscellaneous]
• Added a tutorial for OpenMX molecular dynamics calculation.

### Version 9.3.0 July/7/2019

[New Feature]
• Added 10 tool buttons to the toolbar.
• Added the function to visualize the coordinate axes and the origin position.
• Enabled to calculate radial distribution functions in the Animation window when using Amber, MODYLAS, Quantum ESPRESSO, OpenMX, and DCDFTBMD. ([Tools]-[Radial Distribution Function])
• Enabled to calculate the mean square displacement and self diffusion constant in the Animation window when using OpenMX and DCDFTBMD. ([Tools]-[Mean Square Displacement / Diffusion Constant])
• Implemented frame thinning function in Animation window. ([Tools]-[Skip Frames ...])
• Added a mode to execute 1D-RISM calculation only when using Quantum ESPRESSO for ESM-RISM. ([Solid]-[Quantum ESPRESSO]-[Keywords Setting]-[RISM(2)]-[Run only 1D-RISM])
• Added the function to automatically generate solvent(MOL) file for ESM-RISM compatible Quantum ESPRESSO. ([Solid]-[Quantum ESPRESSO]-[Generate MOL File])
• Added the function to create a table of chemical potential between solvents when using ESM-RISM compatible Quantum ESPRESSO ([Solid]-[Quantum ESPRESSO]-[Solvent Pair Distribution Func]-[Obtain Chemical Potentials ...] )
• Added the function to cap the dangling bond with hydrogen in the [Insert Vacuum].
• Renewed the DCDFTBMD related functions.
• Enabled to calculate Hansen solubility parameter by command line option.
• Enabled to output of surface tension and thermal conductivity with the solubility parameter calculation module.
• Enabled SSH connection to the remote server without using Putty by checking [Connection]-[Do Not Use Putty for Connection] in remote job submission. (experimental)
• Created function to force creation of the working directory of a job whose processing has been interrupted and to use the [Get All Files] button when using a remote job. ([Tool]-[Submit Remote Job]-[Job]-[Force Job Finalization])
• Added a unit conversion tool specialized for atomic and molecular systems. ([Tool]-[Unit Converter])
[Performance Improvement]
• Reduced the startup time.
• Accelerated the animation display function of Quantum ESPRESSO up to about 30 times.
[Specification Change]
• Added the atom, and when the coordinate was specified by Ctrl+click, the editing state was not released.
• Changed to keep editing state when you specify coordinates by Ctrl+click in [Add Atom].
• Enabled to delete atom or delete group by Delete key.
• Enabled to add hydrogen to multi selected atoms.
• Disabled to move the toolbar.
• Changed to display the current frame and the total number of frames in the title of the Animation window.
• Added progress bar to show progress of reading of Groamcs, LAMMPS trajectories.
• Changed the boundary condition of the created cell to be Periodic instead of None in [MD]-[Solvate/Build Cell] and [Insert Molecules].
• Enabled to relocate atoms taking into account periodic boundaries when selecting a file that has atoms outside the cell in [MD]-[Interface Builder].
• Changed to display a warning if there is a possibility that the sum of system charges is not 0 when keywords are set in Gromacs, LAMMPS, MODYLAS.
• Removed *_after.zip on the remote server at the time of sending the file when using remote job.
• Removed *_after.zip on the local machine at the time of Get file when using remote job.
[Miscellaneous]
• Added Gaussian IRC + MEP calculation tutorial.

### Version 9.2.5 August/5/2019

[Bug Fix]
• Fixed the bug that the format may not be correct when saving xyz/txy file.
• Fixed the bug that could prevent atom selection in some environments.
• Fixed the bug in acpype execution with the cygwin_wm versioin 04/02/2019.
• Fixed the bug that ERmod sometimes became extremely slow with cygwin_wm version 03/20/2019 or later.
• Fixed the bug that invalid SDF file is saved in Animation window.
• Fixed the bug that drawing is not updated by fragment registration.
[Specification Change]
• Changed to generate Z-Matrix only for small molecules after reading xyz file.

### Version 9.2.4 July/7/2019

[Bug Fix]
• Fixed the bug that caused an error in loading mol2 with multiple models.
• Fixed the bug that the save dialog is not displayed when you execute MOPAC etc after changing the element in the atom list.
• Fixed the bug that pressing Custom Plot in the Animation window after importing mol2 with multiple models causes an error.
• Fixed the bug that the text color change of the molecule display area is not reflected in the 3D view.
• Fixed the bug that the charge of the whole molecule is misrecognized as positive when negative in the RESP charge calculation function of GAMESS.
• Fixed the bug that the processing is not completed properly when some elements are included in the RESP charge calculation of GAMESS, when using cygwin_wm of 04/02/2019 or later.
• Fixed the bug that parallel number specified in the keyword setting window of GAMESS is not reflected in the remote job profile pbs_gamess.
• Fixed the bug that spectra of multiple steps are displayed overlapping when reading Gaussian TDDFT calculation output.
• Fixed the bug that the process was terminated in a 32-bit environment in [MD]-[Solvate/Build Cell] and [Insert Molecules], when using packmol. (V9.2.0 or later)
• Fixed the bug that the arrangement of atoms outside the cell was not properly considered in [MD]-[Solvate/Build Cell] and [Insert molecules].
• Fixed the bug that [Density] is not updated when [Import] button is pressed in [MD]-[Solvate/Build Cell].
• Fixed the bug that fails to generate gro and ndx files in the calculation of systems including solid wall of LAMMPS.
• Fixed the bug that model change information is not updated by functions such as [Generate Supercell] and [Inserting Vacuum].
• Fixed the bug that Quantum ESPRESSO keywords setting window did not start up with some lattice types.
• Fixed the bug that the number of keywords set to TempControl was not correct when [MD]-[Type]-[NVT-NH] or [NVT_VS] was selected in the OpenMX keyword setting window.
[Specification Change]
• Added "1" to NSTATE combobox in the DFT tab of GAMESS keywords settings window.

### Version 9.2.3 June/7/2019

[New Feature]
• Added the function to delete charge or set to user charge.
• Added APF and APFD to Hamiltonian in the keyword setting of Gaussian.
[Bug Fix]
• Fixed the bug that incorrect atom type is saved when saving mol2 file containing carbonyl group.
• Fixed a bug that could not calculate GAMESS PIO.
• Fixed the bug that the optimization flag was not loaded in the main window when loading Quantum ESPRESSO files (pwin and pwout files). (Occurs on V9.1.0 or later)
• Fixed the bug that the atomic species list may not be set properly if the model in the molecule display area is updated when Pseudo Potential with an asterisk is selected in the Quantum ESPRESSO keyword setting window.
• Fixed a bug that pprism is not executed when using the ESM-RISM calculation template for FOCUS(focus_qe_eis).
• Fixed the bug that can not run the calculation using various templates for FOCUS from April 9, 2019.
• Fixed the bug that the value of fcp_mu continues to increase each time the keyword setting window is reopened when the constant-mu calculation of Quantum ESPRESSO is executed.
• Fixed an issue where the items displayed in the list were not reset in the Custom Plot function of the Animation window.
[Specification Change]
• Changed the lattice constant of samples/al_slab.cif.
• Changed to show file name in title bar of UV/Vis, IR/Raman, and NMR spectrum window.
• Enabled to execute it even if the server side user is not the administrator when JM(Windows) is selected for remote job execution.

### Version 9.2.2 May/13/2019

[Bug Fix]
• Fixed the problem that the pictures of [View]-[Wrap Around Cell Boundary] is not accurate.
• Fixed a bug that the pictures of -[Wrap Around Cell Boundary] is not correct.
• Fixed a bug that the display may not be reflected immediately after [Create/Edit Cell].
• Fixed a bug that would cause an error if there is an "&" in the keyword line when reading the output of MOPAC2016 Version 19 or later.
• Fixed a bug that caused an error when reading vibration analysis output of MOPAC2016 Version 19 or later.
• Fixed a bug that changed information is not reflected in the title bar when changing keywords in QM and semi-experience QM.
• Fixed a bug that would cause an error if you execute MD after saving a system containing ions in mol2.
• Fixed a bug in which two lines of ffnonbonded include statements were output when using the Dreiding force field.
• Changed unable to set other than amber03 for ions and water in the case of the Dreiding force field.
• Fixed the problem that atomic layer near z = Lz disappears by the slight adjustment of the slider when trying to put the slab at the position of the maximum value of base by inserting the vacuum layer.
• Fixed the problem that when a model with charge is displayed in the main window and creating a model using [Insertion Vacuum] or [Cleave Plane], it is misrecognized as having a charge.
• Fixed the problem that when creating a supercell, the axis and atomic coordinates deviate when a cell whose A and B axes are not parallel is created in the XY plane using the lattice conversion function.
• Fixed an issue where the optimization flag was not read when reading the input file of Quantum ESPRESSO. (V9.1.0 or later)
[Specification Change]
• Added a warning if the file name to be saved contains anything other than single-byte alphanumerics, underscores, and periods.
• Changed not to cut off residue names in atomic list in XYZ format.
• Changed to include residue information etc. by reading and writing of mol2.
• Changed to show only atoms belonging to a group when [Current Group] is selected in [Create Group] of radial distribution function.
• Fixed an issue where LAMMPS 2019 Feb did not generate final data file.
• Changed to be ubnabled to selsect dodecahedron and octahedron when using PackMol in the [Solvate/Build Cell] menu, .
• Changed to show the content of the submission command with options when submit a job by Remote Job Sumission.
• Enabled to use Windows server with OpenSSH server and Job Manager for Remote Job Submission.
• Changed to select the last profile selected for remote job execution at restart.

### Version 9.2.1 April/23/2019

[Specification Change]
• Supported conventional cell and primitive cell interconversion of base-centered monoclinic lattice.

### Version 9.2.0 April/9/2019

[New Feature]
• Enabled to select elements from the periodic table.
• Added the function to shift the total value of the charges of the group selected structure to the input value. (-[Modify Selected Group]-[Shift Charges of Group] menu)
• Enabled selection of atoms using charge value in [Select]-[Enter Selection Language]. (Example: charge 1.00)
• Added Easy Setup function of MOPAC.
• Added the input support function of MOPAC scan calculation. ([Semi-Experical]-[MOPAC]-[Configure]-[Easy Setup])
• Added Gaussian input support function for scan and IRC calculation. ([QM]-[Gaussian]-[Configure]-[Easy Setup])
• Improved the probability of successful placement of molecules with higher density or larger number of molecules than before by using Packmol in the [MD]-[Solvate/Build Cell] and [Insert Molecule]. ([Tool]-[Preferences]--[Use Packmol instead o gmx in [MD]-[Solvate/BuilCell])
• Added the function to display only log file or energy when executing remote jobs of Gromacs and LAMMPS ([Get & Open Log] and [Get & Plot Energy] buttons)
• Added a preset for ReaxFF in the LAMMPS Setup window.
• Added density distribution and dielectric constant to LAMMPS result analysis function.
• Added viscosity calculation function by Green-Kubo equation using LAMMPS.
• Enabed to calculate specific heat and isothermal compressibility using LAMMPS. ([MD]-[LAMMPS]-[Configure]-[Output]-[Calc Fluctuation Properties])
• Added the function to graph the heat transfer autocorrelation function when calculating the thermal conductivity using LAMMPS. ([MD]-[LAMMPS]-[Autocorrelation Function] menu)
• Enabled to display the temperature of unconstrained atoms only when Position Restaraint is specified in LAMMPS. (Select TempFree in Energy Terms)
• Enabled to plot energy with interatomic distance, angle, lattice constant, etc. on the horizontal axis in the Animation window. ([Cutsom Plot] button)
• Enabled to invert MOPAC and Gaussian trajectories in the Animation window. ([Tools]-[Invert Trajectory])
• Increased the number of physical property values (melting point, boiling point, viscosity, standard enthalpy and standard Gibbs free energy) that can be predicted by the solubility calculation module.
• Enabled to save remote job settings at any time in the Remote Job Submission window. ([File]-[Save Setting File] menu)
• Enabled to get only standard output (winmos.o) and standard error (winmos.e) on the remote server when executing remote job submission. ([Job]-[Get Remote File and ...]-[Open stdout], [Open stderr] menu)
[Bug Fix]
• Fixed the bug that can not add atoms when the number of atoms is large.
• Fixed the bug that fails to execute the continuous job in the new Gromacs. (at least confirmed with Gromacs 2018.3)
• Fixed the bug that always displays "Do you want to load updated keywords?" when you open the Quantum ESPRESSO Setup windows whie Car-Parrinello calculation keyword is appearing in the main window.
• Fixed the bug that the setting of [Tool]-[Preferences]-[Calculation]-[Foribily slee after GAMESS run] was not saved .
[Specification Change]
• Changed to generate bonds correctly when reading the free version of cif file.
• Enabled to copy information such as charge by copying a group and pasting a group.
• Chaged to select from the form in [View]-[Wrap Around Cell Boundary].
• Enabled to arrange randomly in Polymer Builder.
• Enabled to specify the maximum number of atoms to automatically generate bonds when opening gro file ([Tool]-[Preferences]--[Max # of atoms to generate bonds])
• Speed up reading of LAMMPS data file.
• Changed the file name of the heat transfer autocorrelation function from hextflux.d to autocurr_heatflux.d which is output when calculating the thermal conductivity of LAMMPS.
• Supported to output mdp and top file when LAMMPS calculation.
• Speed up the creation of large supercells.
• Enabled to acquire the K point path automatically when displaying the band structure and phonon band of Quantum ESPRESSO.
• Enable dto change nr1b, nr2b and nr3b directly in Quantum ESPRESSO Setup Window.
• Created a menu to save SDF files in the Animation window. ([Automation]-[Saveing SDF File])
• Changed to interrupt the processing when the auomatically executed connection test to the server failed when executing various processing of the remote job.
• Changed not to duplicate the template file when a file under the UserPref folder is selected in [File]-[Import Setting File] of the remote job window.
• Exchanged the CSV rows and columns output by the solubility calculation module.
• Changed the version of AmberTools for the cygwin package for Winmostar (cygwin_wm) from 14 to 18.
• Enabled to check the version of cygwin_wm in [Help]-[Check cygwin_wm].
• Enabled to select multiple models in [Superposition Molecules].
• Added a button to check/uncheck all in [Superposition Molecules].
• Changed to align only the checked molecules in [Superposition Molecules].
• Changed the tool menu toolbar not to have two lines when changing the window size.

### Version 9.1.5 June/7/2019

[Bug Fix]
• Fixed the bug that the optimization flag was not loaded in the main window when loading Quantum ESPRESSO files (pwin and pwout files). (Occurs on V9.1.0 or later)
• Fixed the bug that the atomic species list may not be set properly if the model in the molecule display area is updated when Pseudo Potential with an asterisk is selected in the Quantum ESPRESSO keyword setting window.
• Fixed a bug that pprism is not executed when using the ESM-RISM calculation template for FOCUS(focus_qe_eis).
• Fixed the bug that can not run the calculation using various templates for FOCUS from April 9, 2019.
• Fixed the bug that the value of fcp_mu continues to increase each time the keyword setting window is reopened when the constant-mu calculation of Quantum ESPRESSO is executed.
• Fixed an issue where the items displayed in the list were not reset in the Custom Plot function of the Animation window.
[Specification Change]
• Changed the lattice constant of samples/al_slab.cif.
• Changed to show file name in title bar of UV/Vis, IR/Raman, and NMR spectrum window.

### Version 9.1.4 May/13/2019

[Bug Fix]
• Fixed a bug that the pictures of -[Wrap Around Cell Boundary] is not correct.
• Fixed a bug that the display may not be reflected immediately after [Create/Edit Cell].
• Fixed a bug that would cause an error if there is an "&" in the keyword line when reading the output of MOPAC2016 Version 19 or later.
• Fixed a bug that caused an error when reading vibration analysis output of MOPAC2016 Version 19 or later.
• Fixed a bug that changed information is not reflected in the title bar when changing keywords in QM and semi-experience QM.
• Fixed a bug in which two lines of ffnonbonded include statements were output when using the Dreiding force field.
• Changed unabe to set other than amber03 for ions and water in the case of the Dreiding force field.
• Fixed the problem that atomic layer near z = Lz disappears by the slight adjustment of the slider when trying to put the slab at the position of the maximum value of base by inserting the vacuum layer.
• Fixed the problem that when a model with charge is displayed in the main window and creating a model using [Insertion Vacuum] or [Cleave Plane], it is misrecognized as having a charge.
• Fixed the problem that when creating a supercell, the axis and atomic coordinates deviate when a cell whose A and B axes are not parallel is created in the XY plane using the lattice conversion function.
• Fixed an issue where the optimization flag was not read when reading the input file of Quantum ESPRESSO. (V9.1.0 or later)

### Version 9.1.3 April/23/2019

[Specification Change]
• Supported conventional cell and primitive cell interconversion of base-centered monoclinic lattice.

### Version 9.1.2 April/9/2019

[Bug Fix]
• Fixed the problem that the molecular structure is wrong when there is an error in the calculation result of CNDO/S.
• Fixed the bug that $PCMCAV keywords were confused with$PCM by adding PCMCAV to GAMESS Setup. • Fixed the bug that would cause an error if there were fixed atoms in reading of Gaussian vibration analysis output. • Fixed the bug that was not set if you open the window again after setting the set keyword in OtherSetting in the keyword setting window of NWChem. • Fixed the bug that the [Draw (2D)] button that can not be used in the MO Plot window may appear. • Fixed the bug that incorrect Z-Matrix is generated when reading LAMMPS data file. • Fixed the bug that xlo, ylo and zlo were not reflected in the origin of cell when reading LAMMPS data. • Fixed the bug that can not execute ermod. • Fixed the problem that the display was broken when opening the MOL file of ESM-RISM version Quantum ESPRESSO in 32bit environment. • Fixed the bug that [Cleave Plane], [Insert Vacuum], and [Build Cluster Model] menus do not show bonding. • Fixed the bug that sometimes the atoms unselected when converting to Bravais lattice. • Fixed the bug that [Preference]-[View]-[Color]-[Background(3D)] did not work. [Specification Change] • Changed to read also atomic names and charges when opening a MOL file of ESM-RISM version Quantum ESPRESSO. • Changed to interrupt processing if MOL file did not conform to XML format when opening the MOL file of ESM-RISM version Quantum ESPRESSO. ### Version 9.1.1 March/12/2019 [Bug Fix] • Fixed a bug that NWChem can not be used in student edition. • Fixed a bug that changes made in the Remote Job submission window are not saved when Winmostar is exited with the Remote Job submission window open. [Specification Change] • Expanded the atom type of mol2 file that can be read. • Changed not not to close the window when canceled after pressing Run button in various keyword setting windows. • Changed to adjust the zoom automatically after creation of the system in the DPD cell builder. • Changed the message at the time of license setting. ### Version 9.1.0 February/12/2019 [New Feature] • Added Hansen solubility parameter (Hansen SP value) tutorial. • Added a function to forcibly sleep immediately after execution of GAMESS. ([Tools]-[Preference]-[Calculation]) [Bug Fix] • Fixed a problem that COSMO calculation can not be done with MOPAC7(mop7w70). • Fixed a bug that b3lyp could not be set for tddft in Gaussian's EasySetup. • Fixed a problem that some functions such as [View]-[Wrap Around Cell Boundary] can not be used after using the DPD Cell Builder. [Specification Change] • Enabled to output PNG file in [File]-[Export]-[Image] menu. • Changed not to read the file again after overwriting the file. • Changed optimization flag to be separate for Z-Matrix and XYZ. • Changed not to set change flag after continuing job execution of Gromacs, LAMMPS, and MODYLAS • Changed not to generate lines of "Displayed Molecule" or "Water" in list in [MD]-[Solvate/Build Cell]. • Enabled to execute some menus that were grayed out and could not be executed when cells were not defined. ### Version 9.0.3 March/3/2019 [Bug Fix] • Fixed a bug that NWChem can not be used in student edition. • Fixed a bug that changes made in the Remote Job submission window are not saved when Winmostar is exited with the Remote Job submission window open. [Specification Change] • Changed to adjust the zoom automatically after creation of the system in the DPD cell builder. ### Version 9.0.2 February/12/2019 [Bug Fix] • Fixed a problem that Gromacs' Chi parameter and DPD parameter calculation function make those values 1/2 of their original value. • Corrected tab order in the OpenMX keyword setting window. • Fixed a bug where the spelling of scf.ElectronicTemperature was wrong when OpenMX keyword was set. • Fixed bug that scf.ProExpn.VNA can not be set when OpenMX keyword is set. • Fixed bug that %WM_NUM_PROC%, %WM_NUM_THREAD% and %WM_NUM_PARALLEL% are not reflected in remote jobs of Gromacs, ERmod, LAMMPS, QE, and OpenMX. ### Version 9.0.1 January/28/2019 [Bug Fix] • Fixed a problem that bond order may be wrong with some molecules including C-S bond. • Fixed a problem that more hydrogen was added in  - [Add hydrogens] - [To all atoms] menu for some molecules including benzene ring. • Fixed a bug that highlighting of molecule list does not change when group was selected by clicking atoms on the screen while holding Ctrl key. • Fixed a problem that can not draw graph when plotting incomplete text data such as log file under calculation. • Fixed a problem that saving GAMESS input file by command line argument may cause an error. • Fixed a problem that can not enter real numbers in the upscale keyword of Quantum ESPRESSO Keywords Setup. • Fixed a problem that may cause an error in the display of the Fermi surface of Quantum ESPRESSO. • Fixed a bug that remote job can not be submitted in trial version. • Fixed a bug that could result in error in calculation of aspect ratio by command line argument. ### Version 9.0.0 January/15/2019 [New Feature] • Enabled to show the number and composition of selected group in the molecular display area. • Enabled to change the speed of Zoom In/Out of molecular display area by mouse wheel, and Zoom In/Out smoothly by default. • Increased drawing speed due to the change of the graph drawing engine, and resizing is now supported. • Added 11 buttons of frequently used functions in the toolbar. • Added a function to match the viewing point of the camera to the atom with the marker. ([View]-[View Marked Atom] menu) • Enabled to transparently display group selected atoms. ([View]-[Transparency] menu) • Added a function to set the edge of the cell to the origin of coordinates. (-[Recoordinate Axes]-[Set Origin tTo Lower Bounnds of Cell] menu) • Enabled to create a cubic cell with cell size directly specified. (Changed to create a cube cell by default in the [Create] function of the [Create/Edit Cell] menu.) • Supported to non-rectangular cells in -[Wrap Around Cell Boundary]. • Added [Select] menu and supported to flexible selection of molecules and atoms. • Changed to add atoms selected in the main window to the index (ndx) file and enabled to designate as Group when analyzing MD calculation result(radial distribution function etc.). ([Select]-[Add Selected Group to Index File]) • Added [Run] buttons to various Keyword Setting windows. • Changed to show the explanation of all keywords when mouse pointer is overlapped on GAMESS Keywords Setup window. • Added a function to create a liquid phase by aligning the molecules displayed on the main window. ([Add Displayed Molecule] button of [MD]-[Solvate/Build Cell] menu) • Added serting fields on Quantum ESPRESSO Keywords Setup window for upscale, max_seconds, laue_buffer_left, laue_buffer_right, rism3d_maxstep, rism1d_maxstep, solute_epsilon, and solute_sigma. • Enabled to visualize only energy change, animation, and log file during Quantum ESPRESSO remote job execution. ([Get & Open ...] button on Remote Job Submission window) • Enabled to read MOL file for ESM-RISM. • Enabled to extract only the trajectory of the selected atoms and to create a new trajectory file on Animation window. ([Tools]-[Extrat Trajectory for Selected Atoms] menu) • Enabled to load additional settings from existing configuration files on Remote Job Submission window. • Added a function that only executes the script without using the scheduler in Remote Job Submission. • Added a profile to submit LAMMPS and Quantum ESPRESSO jobs to Focus system. (focus_lammps, focus_qe) • Added [Window] menu, now supports display of window list currently open and redisplay of result analysis window. • Redesigned the manuals and released both HTML version and PDF version. (Using Sphinx) [Bug Fix] • Fixed a problem that the processing was not interrupted normally even if processing was interrupted by the cancel button etc. when pressing the old sendsub button in Remote Job Submission. [Specification Change] • Attach middle version to version number. • Added wm_system folder and gathered files that users do not edit directly. • Changed to reloaded file in the main window after saving file in some formats. • Changed to set automaticaly the UserData folder under the Winmostar installation folder as the current directory when opening the files under the samples folder. • Added a status bar to the main window and Crystal Builder window to display messages. • Moved the zoom function on the status bar. • Added tool buttons to the toolbar and rearranged them according to the menu. • Changed the chg button to a tool button. • Changed to display icons of tool buttons on corresponding menus. • Changed the layout of various menus and windows and the name of UI parts. (Refer to the user manual for details) • Enabled to close various windows with Esc key. • Changed to add an asterisk to the file name of the title bar when changing the model. • Unified the background color of the student version and the free version into the same as the product version. • Changed to use tabs to switch the display of XYZ and Z-Matrix in the atom list. • Changed not set the magnification ratio 100% as the upper limit for [View]-[Zoom In/Out] menu. • Renamed Winmostar 3D to Winmostar Viewer. • Added a setting to move atoms to pasted atoms and it is valid by default for -[Modify Selected Group]-[Paste Group]. • Changed to create a cube cell by default for [Create] function on -[Create/Edit Cell] menu. • Changed to execute from a form for -[Wrap Around Cell Boundary] menu • Unified the flow of file saving and processing start confirmation when executing various solvers. • Consolidated GIF animation and CSV output functions of various result display windows (IR, Animation, etc.) into [Export] button. • Renamed [Load], [Save], and [Reset] buttons in Keyword Setup window of Semi-Empirical QM and QM to [Reset], [Save as Default], and [Clear Default Settings] respectively. • Added VECTORS to MOPAC default keywords. • Moved the [with Reset] checkbox in the QM keyword setting window to the EasySetup window and renamed it to [Reset before applying changes]. • Moved Parallel number setting for GAMESS and NWChem from the main menu and the preference window to the keyword setting window. • Changed composition of the GAMESS Keyword Setting window. • Enabled to use the file extension gms even when executing the local job of GAMESS. • Changed to create cells automatically if cells are not defined in the main window when setting keywords of MD and Solid. • Changed to display the fact that the keyword was set in the keyword display area after setting the MD keyword. and the solver is not executed unless it is in the state with that display. • Integrated the function of [Put the molecule on the main window] check box into the function of [Add Displayed Molecule] button in [MD]-[Solvate/Build Cell]. • Changed the definition of the thermal conductivity of each component (Kx, Ky, Kz) so as not to K = Kx + Ky + Kz but K = (Kx + Ky + Kz) / 3 in the thermal conductivity calculation function of LAMMPS, • Changed to generate gro file and ndx file only when new job is started for LAMMPS. • Placed [OK] and [Cancel] buttons in Crystal Builder and moved the data to the main window with the [OK] button. • Deleted the [File]-[Close] menu of Crystal Builder. • Changed -[Lattice] function of Crystal Builder to be shown always on the right side of the window. • Enabled to call -[Repeat] function of Crystal Builder from the main window as a super cell creation function. • Changed to display Crystal Builder as a modal window. • Enabled to cross-reference when clicking on the display screen of Crystal Builder and the asymmetric element list respectively. • Changed to select a asymmetric element row of Crystal Builder by clicking once, and to be editable when clicked again from selected state. • Enabled to call functions such as [Cleave Plane] and [insert Vacuum] directly from the main window. • Disabled the [Solid]-[Build Cluster Model] menu for student version. • Changed to ask whether to convert the structure of the main window to primitive cell automatically if possible for Solid Keyward Setup. • Changed ESPRESSO_PSEUDO to be the same as outdir in local job when Quantum ESPRESSO is executed. • Changed the configuration of the Quantum ESPRESSO Keywords Setup window. • Changed outdir keyword of pwin file saved with Output Directory = Continue from outdir of the file opened when saving the file to utdir of the file opened at Keyword Setup for Quantmu ESPRESSO. • Changed [Automatically convert to primitive cell] to [Set ibrav and celldm] and check it if the preset is [SCF+Band+DOS] or [SCF+Bands(Fermi surf)] and uncheck for the others for Quantum ESPRESSO Keywords Setup. • Changed to calculate PDOS when the perset is [SCF+Band+DOS] for Quantum ESPRESSO Keywords Setup. • Changed to set occupations=smearing when the perset is [SCF+Band(Fermi surf)] for Quantum ESPRESSO Keywords Setup. • Changed default values of keywords as atomic_position unit: angstrom ecutwfc: 25 ecutrcho: 225 mixing_beta: 0.3 • Changed to plot only Estimated Accuracy in [Quantum ESPRESSO's [SCF Energy Change] function. • Added [Open MOL Files] to the RISM tab of the Quantum ESPRESSO Keyword Setup. • Changed the log file name of FDMNES from fdmnes.log to the same of input file name with extension log. • Disabled the BoltzTraP GUI in the student version. • Changed the expression '%WINMOSTARDIR%\bin' to '%BINDIR%' for program paths.. • Moved Remote Job Submission to [Tools] menu. • Changed the setting file (ini file) name of the remote job submission to winmos_profile.ini and changed the format. • Changed the remote directory specification method of Remote Job Submission. • Unified the script file name of Remote Job Submission as "solver.***.txt". • Changed the aliases that can be used in Remote Job Submission script. • Added "export LANG=C" to the beginning of various remote job template scripts. • Deleted profiles for TSUBAME 2 and some others. • Added au.cif to the samples folder. ## Winmostar V8 ### Version 8.039 November/13/2019 [Bug Fix] • Fixed the bug that incorrect atom type is saved when saving mol2 file containing carbonyl group. ### Version 8.038 May/13/2019 [Bug Fix] • Fixed a bug that would cause an error if you execute MD after saving a system containing ions in mol2. • Fixed a bug in which two lines of ffnonbonded include statements were output when using the Dreiding force field. • Changed unable to set other than amber03 for ions and water in the case of the Dreiding force field. • Changed to include residue information etc. by reading and writing of mol2. ### Version 8.037 Febarry/12/2019 [Bug Fix] • Fixed a problem that Gromacs' Chi parameter and DPD parameter calculation function make those values 1/2 of their original value. • Corrected tab order in the OpenMX keyword setting window. • Fixed a bug where the spelling of scf.ElectronicTemperature was wrong when OpenMX keyword was set. • Fixed bug that scf.ProExpn.VNA can not be set when OpenMX keyword is set. ### Version 8.036 January/28/2019 [Bug Fix] • Fixed a problem that may cause an error in the display of the Fermi surface of Quantum ESPRESSO. ### Version 8.035 January/15/2019 [Bug Fix] • Fixed a problem that it becomes 2D display and it becomes impossible to zoom in / out when dragging and dropping the file to the icon of Winmostar. • Fixed a problem that inserting mol2 file as "Fixed" in [MD]-[Solvate/Build cell] may cause an error. • Fixed a bug that sometimes caused an error with [MD]-[Insert Molecules]. • Fixed a bug that [Partial Move] would cause an error after reading large LAMMPS data file. • Fixed a problem that different values are set for soln and refs and can not be calculated when ecdmin is changed in ERmod's Options. • Fixed a bug that could not read cif file with _atom_site_aniso_ key. • Fixed a problem that Quantum ESPRESSO 's pwout file can not be acquired while it is open in the main window in Remote Job Submission. [Specification Change] • Changed to check [View]-[Centering] when [File]-[New] is executed. ### Version 8.034 December/25/2018 [Bug Fix] • Fixed a bug that Exchange Indices/Sort By Molecule Speceis sometimes resulted in incorrect display of bonds. • Fixed a bug that cause an error for large system of [Sort By Molecule Species]. • Fixed a problem that information such asHESS disappears by GAMESS Keywords Setting.
• Fixed a bug that caused an error when trying to make a solute only system with MD Cell Builder.
• Fixed a bug that Gromacs tuns with mpi on local even if checking MPI (for Remote Job) on Groamcs Keywords Setting.
• Fixed a bug that fragment attachment might be misaligned with FragmentER.
• Fixed a problem that lines containing parentheses are not read correctly when reading the input file of Quantum ESPRESSO.(V8.033)
• Fixed a problem that can not calculate HSP from the structure read from a specific dat file format.
[Specification Change]
• Changed the number of digits of the angle between selected atoms in 3D View to the same as the number of digits in 2D View.
• Abolished the specification that forcedly reset the second line of the DATA input group when using Easy Setup of GAMESS. • Enabled to set the limit number of atoms to show atom list and that for Z-Matrix auto generation. ### Version 8.033 December/5/2018 [New Feature] • Supported local job execution of Windows native version ESM-RISM compatible Quantum ESPRESSO. • Enabled to plot the change of Fermi Energy on Quantum ESPRESSO animation. • Supported NQSII for remote job submission. [Bug Fix] • Fixed a bug that failed to save PDB file when the keyword setting field is empty. • Fixed a bug that -[Undo] can not be used in some functions such as [File]-[Append], -[Add Hydrogens]-[Use OpenBabel] or [MD]-[Interface Builder]. • Fixed a problem that range check error occurred when [File]-[Append] is executed with the group selected. • Fixed a problem that residue informations was lost when saving PDB after [Partially Delete]. • Fixed a problem displayed as Mulliken Charge in the molecule display area when User Charge is loaded. • Fixed a bug that CNDO/S runs and causes abnormal results even if there are elements with no parameters. • Fixed a bug that NWChem can not be used in trial version. • Fixed a problem that decompression failed after getting a large size over several hundred MB zip file at remote job execution. • Fixed a bug that PDB residue information might be missing in [MD]-[Solvate/Build Cell] menu. • Fixed a bug that atoms misaligned when arranging water molecules of 4 or 5 sites in [MD]-[Solvate/Build Cell] menu.(from V8.033) • Fixed a bug that could not read the Quantum ESPRESSO input file that contains a line with no comma at the end of the line and a 1 character value. • Fixed a bug that displayed "Do you want to load keywords changed on main window?" even if keywords are not changed on the main window after setting solute_lj to other than uff in Quantum ESPRESSO Keywords Setting. • Fixed a bug that coordinates were not loaded from the output file when relax calculation is executed with all atomic coordinates fixed for Quantum ESPRESSO. • Fixed a problem that charge change can not be plotted on animation window when using damp for Quantum ESPRESSO FCP calculation. • Fixed a bug that range check error occurred when specifying the pwout file whose structure optimization converged in one step in NEB calculation of Quantum ESREPSSO • Fixed a bug that could not load input file properly if a halfwidth space is between celldm and parentheses. [Specification Change] • Changed to Group Select the added structure after [File]-[Append]. • Changed to center the camera automatically after reaing a file. • Enabled to select on Preferentce window wheter centering the camera automatically after reaing a file or not. • Enabled to set Scale in Cubegen. • Changed to display a warning message when pressing Remove without atoms selected in the Crystal Builder. • Changed to set the outdir to ESPRESSO_PSEUDO when executing the local job of Quantum ESPRESSO. • Changed to use mpiexec.exe in the same folder of pw.exe if exists for local execution of Quantum ESPRESSO. • Changed the default parameter file path of FragmentER. • Changed to avoid errors that occur when there are adjacent atoms in fragments added in FragmentER. • Changed to make the CHECK folder empty before executing Check in FragmentER. ### Version 8.031 November/12/2018 [Specification Change] • Changed default values of mdiis1d_step and mdiis3d_step of Quantum ESPRESSO to same values in the implementation of Quantum ESPRESSO for ESM-RISM. ### Version 8.030 November/8/2018 [New Feature] • Enabled to display of transition dipole moment of GAMESS, Firefly and NWChem. • Added a RISM(2) tab to set seven types of RISM related keywords anew in the Quantum ESPRESSO keyword setting window. • Enabled to use DCDFTBMD interface with student version. [Bug Fix] • Fixed a problem that [File]-[Import]-[SMILES] processing is interrupted when the structure displayed in the main window was updated. • Fixed a problem that Partially Detlete misses the charge information. • Fixed a bug that the dipole moment vector becomes wrong for Wire display in 3D display. • Fixed a bug that EnergLevel window is displayed at Cube Plot. • Fixed a problem that MO can not be displayed at the first startup when reading output of Gaussian and GAMESS. • Fixed a problem that transition dipole moment can not be displayed for Gaussian 03. • Fixed a bug that Open Cubegen failes in MO display when Eigenvalues in Gaussian log file is "**********". • Fixed a bug that PIO calculation failes when Eigenvalues in Gaussian log file is "**********". • Fixed a bug that td setting was not reflected in Td combo box on Gaussian keyword setup window. • Fixed a bug that the [Save Cube] check box was not displayed in Gaussian's fchk reading. • Fixed a bug that the [gif] and [jpeg] check boxes in the Animation window did not work. • Fixed a bug that [Solvate/Build Cell] may cause incorrect bonding. • Fixed a problem that the position of the origin of the cell is unconditionally treated as (0, 0, 0) in the process of displaying a warning when particles are present in the vicinity of Lz/2 when using the ESM method of Quantum ESPRESSO. • Fixed a problem that ESM-RISM calculation of Quantum ESPRESSO does not run when particles were present at Lz/2 < z < Lz. • Fixed a bug that ATOMIC_SPECIES cards could not be calculated because duplicate ATOMIC_SPECIES cards were output when job start or pwin file was changed by changing only the atom position after job start of Quautum ESPRESSO or reading pwin file. (V8.029 or later) • Fixed a problem that a dialog informing that the keyword was changed opens even though the keyword was not changed on the main window when opening the keyword setting window after starting calculation using RISM in Quantum ESPRESSO. • Fixed a problem that displayed "Duplicates not allowed" when executing NEB calculation of Quantum ESPERSSO. • Fixed the unit of Seebek coefficent to V/K by loading result of BoltzTraP. • Fixed a bug that default file name was not registered when clicking on energy change of DCDFTBMD. • Fixed a bug that caused an error when opening the energy change of DCDFTBMD twice. [Specification Change] • Increased the number of digits of charge in mol2 file saved. • Improved accuracy when entering values in the text box in -[Partially Edit]-[Partially Move (Slider)]. • Enabled to use the Windows 10 game bar (capture tool) with Winmostar 3D. • Added the keyword MMOK with the [Reset] button of MOPAC Setup. • Enabled to read overflowed gro files. • Changed to output fcp_dynamics with the same value as ion_dynamics when executing FCP calculation using RISM compatible version Quantum ESPRESSO. • Enabled to replace0 and 1 in remote job submission script for Quantum ESPRESSO. • Animation, Point Group Analysis and Remote Job Submission window are not always displayed at the forefront. ### Version 8.029 October/2/2018 [New Feature] • Enabled to the use of wild card (*) in Quantum ESPRESSO's pseudopotential priority list (qe_pseudo_priority_list.d). [Bug Fix] • Fixed a problem that change is not saved when pressing the enter key in the numerical value input field in -[Create/Edit Cell] menu. • Fixed a problem that the graphical display of charges may be displayed in reverse order. • Fixed a bug in which the remote job terminated abnormally on a remote server on which dos2unix was not installed. • Fixed a bug that the MO could not be displayed at the first startup by reading UV-Vis spectrum (*.lst) of CNDOS. • Fixed a bug that sometimes MO can not be displayed when the basis is SPD when reading UV-Vis spectrum (*.lst) of CNDOS. • Fixed a bug that the [cube] button was not displayed when fchk file was read in 3D view. • Fixed a bug that the atom position may shift in animation of vibration spectrum. • Fixed a bug that all but water molecules were grouped into UNK group when GAFF, OPLS-AA/L was set as the force field of MD calculation. • Fixed a problem that the ion_dynamics keyword is not output and ions move if ion_dynamics=none is selected when cp.x is used in the calculation of Quantum ESPRESSO. • Fixed a bug that SOLVETS setting in the keyword setting window did not reset even when pressing the Reset button in Quantum ESPRESSO Keywords Setup window. • Fixed a bug that the display was incorrect when pressing Symmetrize button of Point Group Analysis in 3D view. • Fixed a problem that the rotary-inversion axis was hidden on the rotation axis when doing Point Group Analysis in 3D view. • Fixed a problem that the symmetric point color was not set when doing Point Group Analysis in 3D view. [Specification Change] • Changed to warn when Winmostar installation path contains space or multibyte characters. • Changed to warn when a file name contains space or multibyte characters when saving file. • Changed to remain the history in the pull-down menu in the Method column of the remote job submission window. • Changed to use Ctrl+click to select lines for more than one molecular types in -[Select Molecules]. • Changed to warn when selecting Hamiltonian which is not capable for the binary of MOPAC calculation. • Changed the specification of PDB Edit function of GAMESS. • Enabled to select the list of absorption peaks on the UVVis spectrum. • Changed the system size setting method in polymer cell builder to the same method as [Solvate/Build Cell] function. • Enabled to omit selecting the topology file when selecting the animated gro file as the trajectory file in the result analysis function of Gromacs. • Changed to output kspace_* command after read_data command in LAMMPS keyword generation. • Changed to import the contents of the keyword display area of the main window for the Quantum ESPRESSO keyword setting window. • Changed to display the ATOMIC_SPECIES card in the keyword display area when reading the input file (*.pwin) of Quantum ESPRESSO. • Enabled to specify tprnfor and tstress keyword in the Quantum ESPRESSO keyword setting window. • Changed not to distinguish between uppercase and lowercase letters in Quantum ESPRESSO's pseudopotential priority list (qe_pseudo_priority_list.d). • Added setting for pseudopotential of GBRV in Quantum ESPRESSO pseudopotential priority list. • Changed to read priority list of pseudopotential when pressing Reload pseudo files button of Quantum ESPRESSO Keywords Setup window. • Changed the order of keywords in Quantum ESPRESSO keyword save file (*.qeset). • Changed to give priority to the keyword entered in Other field in Quantum ESPRESSO Keywords Setup window over the keyword set on the tab other than the Other tab. • Changed to exclude combinations of left-handed translation vectors among automatically searched lattice candidates for [Cleave Plane]. • Replaced Putty0.60 to Putty0.70 for Remote Job Submission. • Change to display Animation and Remote Job on the front of the main window. • Added a button to open the UserPref folder in the preference window. • Changed the file format for xmgrace generated when displaying various graphs. • Enabled to read MOL2 and SDF files with multiple molecules in Superimpose. • Added hint messages to some UI controls. ### Version 8.027 August/21/2018 [Bug Fix] • Fixed a bug that POV-Ray got error when 3D display. • Fixed a problem that the result of [View]-[Zoom]-[Fit in Window] may differ between 3D and 2D. • Fixed a problem that saved picture by [File]-[Export]-[Image] becomes a picture a little before with 3D view. • Fixed a bug that file name and program name may be wrapped on the Animation window. • Fixed a bug that atom list was not updated after editing in PDB file with [QM]-[GAMESS]-[PDB]-[Edit PDB file]. • Fixed a bug that failed to create GROMACS top file with system containing nitrogen atom on aromatic ring. • Fixed a problem that the tilt factor does not become 0 in case of cuboid cell when creating the data file of LAMMPS. • Fixed a problem that charges may not be displayed immediately after calculating the charge of the monomer of the glass transition tutorial. • Fixed a bug that atoms closer to the periodic boundary were illegally deleted when saving a structure with large unit lattice in the Crystal Builder. • Fixed a problem that the ion_dynamics keyword was not output except for calculation=md when generating an input file of Quantum ESPRESSO. • Fixed a bug that could not display animation when ion_dynamics=damp for Quantum ESPRESSO. • Fixed a problem that a range check error occurred when opening the keyword setting window, after executing the calculation in which pseudo-potential files with different suffixes are mixed or after loading the pwin file for Quantum ESPRESSO. • Fixed a problem that charge was not loaded when showing animation of FCP (constant-mu) calculation by Quantum ESPRESSO supporting RISM. [Specification Change] • Added a unit to display the volume of the molecular display area of the main window. • Corrected the display of CNDO/S keyword setting window. • Added HF/STO-3G data to the reference spectrum list of the NMR spectrum display window. ### Version 8.026 August/1/2018 [Bug Fix] • Fixed a bug that "Add Hydrogen" might fail. • Fixed a bug that -[Z-Matrix] -[Add Atom] menu sometimes fails. • Fixed a bug that atoms highlighting did not return to normal even if -[Partially Edit]-[Partially Delete] menu is canceld. • Fixed a problem in which background color was not immediately reflected even if [Color Set] was changed on the Preference window. • Fixed a bug that tilt factors were not set when creating LAMMPS data file other than rectangular cells. • Fixed a problem that sometimes "backbone atoms are not set" error message appears in the Dissipative Particle Dynamics tutorial. • Fixed a bug that one atom was deleted when cif reading or creation of structure with crystal builder, when the fraction coordinates are close in large cell. ### Version 8.025 July/24/2018 [New Feature] • Enabled to show the charge/spin density of the whole system in the main window. • Enabled to set the charge and spin density of the selected atoms.(-[Atom]-[Change Charge/Spin Densities])) • Enabled to show the radius logarithmically when displaying electric charges in the main window. ([Tools]-[Preference]-[View]- [Charge Scale] - [Log scale]) • Added Quantum ESPRESSO's Nudged Elastic Band (NEB) method GUI and tutorial. ([Solid]-[Quantum ESPRESSO]-[Keywords Setup(NEB)]) • Enabled to plot the energy change during SCF calculation from the log file of Quantum ESPRESSO. ([Solid]-[Quantum ESPRESSO]-[SCF Energy Change]) • Enabled to select atoms to be plotted to show the partial density of states of Quantum ESPRESSO . • Changed to read magnetic moment when reading spin polarization calculation output of Quantum ESPRESSO (pwout) • Supported for input_dft setting and automatic generation of vdW_kernel_table in Quantum ESPRESSO keywords setting. • Added choice of diagonalization=rmm in Quantum ESPRESSO keyword setting when using EIS license. • Enabled to specify the vertical axis width when drawing the band structure of Quantum ESPRESSO. • Enabled to read Mulliken charge and Spin density when reading mxout by OpenMX interface. • Released the BoltzTraP interface officially. • Released a tutorial of the BoltzTraP interface. • Added MOPAC basics, MEP/IRC edition, CNDO/S basics, NWChem basics, Quantum ESPRESSO BOMD edition, and Remote Job tutorial. [Bug Fix] • Fixed a problem that an error might occur at startup when displaying the type of electric charge. • Fixed a problem that fails to show MO of vibration analysis result of Gausian16. • Fixed a problem that keywords are not aquired when reading output of calculation result using GPU in Gausian16 (%gpucpu). • Adjusted the pull down menu of %nprocshared of Gaussian Setup to the number of cores of TSUBAME 3.0 • Fixed a problem that the cell size may change in [MD]-[Insert molecule] menu. • Fixed a problem in which Monoclinic's b, c setting is reversed by saving Quantum ESPRESSO's pwin or lattice conversion. • Fixed a bug that does not recognize the pwout file of continued job when loading Quantum ESPRESSO's BOMD animation. • Fixed a problem that remote jobs were not executed when Quantum ESPRESSO continued job was executed. • Fixed a bug that can not be processed when a non-pwin file is open in the main window when Quantum ESPRESSO continued job is executed. • Fixed a problem that coordinates are not output correctly to pwin file outputted when Quantum ESPRESSO continued job is executed. (There is no effect on the calculation result) • Supported three letter labels such as gS1 when rendering the band structure of Quantum ESPRESSO. • Fixed a bug where label position shifted or blank area occurred when the path was interrupted in the middle when drawing the band structure of Quantum ESPRESSO. • Fixed a problem that the display collapses when drawing the band structure of Quantum ESPRESSO, when the value written in band.dat becomes 8 characters. • Changed to switch the label on the vertical axis when writing band diagrams of Quantum ESPRESSO (E-E(fermi)) when shifting to EFermi, and (E) when not shifting. • Fixed a problem that can not acquire Edge Energy when using the latest FDMNES. • Supported for passwords including double quotation marks in remote job submission. [Specification Change] • Enabled to read bond types from GLD and MLD files. • moved [Superimpose] menu from [File] menu to [Tools] menu, and changed specification drastically. • Speeded up [Partially Delete] in large scale system. • Fixed part of the messages of the  menu operation. • Changed 3D display to default. • Made various display functions available in 3D. • Changed to save the settings of perspective, space filling model, window size etc. • Changed the number of digits of volume and density showed in the main window. • Enabled to set Start/Restart in NWChem Keywords Setup. • Changed the NEB function of NWChem not availabled in the student version. • Changed NWChem's default memory usage from 200 MB to 400 MB. • Speeded up Gromacs' gro file reading. • Deleted the template script for the remote job of the old format LAMMPS (lammps.txt). • Made the Crystal Builder view 3D. • Changed kpath_default.txt to be specified with lattice instead of ibrav in Quantum ESPRESSO. • Added lattice = BCT, RHL, ORCF, MCLC, TRI (corresponding to ibrav = 5, 7, 10, 13, 14 respectively) to kpath_default.txt in Quantum ESPRESSO. • Supported ibrav = 9, Orthorhombic C Centered (ORCC) at Quantum ESPRESSO pwin saving or lattice conversion menu. • Changed to load Mass, PseudoFile, starting_magnetization, Hubbard_U, Hubbard_alpha into the keyword window when reading the input file of Quantum ESPRESSO. • Enabled to recognize even when numbers are included in atom names when reading input files of Quantum ESPRESSO. • Enabled to recognize even if units such as ATOMIC_POSITIONS are enclosed in parentheses when reading the input file of Quantum ESPRESSO. • Changed so that the top item of the Propeties tab is displayed when Propeties is set in Preset Setting in Quantum ESPRESSO keyword setting. • Change the Constant-mu (FCP) setting so that it matches the format of RISM-ESM if trism =. True. Or [Use RISM-enabled QE] is checked in the Quantum ESPRESSO keyword setting. • Changed to change label automatically when changing Molecule of SOLVENTS of RISM in Quantum ESPRESSO keyword setting, • Changed to output the if_pos flag of ATOMIC_POSITIONS also to pwin file when Quantum ESPRESSO continued job is executed. • Changed to show the keyword setting window when saving the OpenMX input file while the OpenMX keyword is not set in the main window. • Changed to clear the keyword column at the bottom right of the main window when setting OpenMX keywords. • Expanded the effective digit number of alpha and beta spins of mxin to 6 decimal places on the OpenMX interface. • Supprted cygwin_wm for BoltzTraP interface. • Limited Graph display on BoltzTraP to Gnuplot. ### Version 8.024 July/10/2018 [New Feature] • Added button to share SSH connection (Share SSH connections) on Remote Job Submission window. [Bug Fix] • Fixed a bug that bonding information may not be correct in PDB save. • Fixed a problem that the numerical value of electric charge is hidden when graph of electric charge is displayed. • Fixed a bug that saving model without Z-Matrix in MOPAC dat file in XYZ format causes error. • Fixed a problem that MOPAC charge reading may cause an error. • Fixed a bug that unnecessary %chk=temp might be included with Gaussian's EasySetup. • Fixed a bug in bond information by creating data for PIO Lummox. • Fixed a problem that fcp calculation does not run when using Quantum ESPRESSO with RISM calculation. • Fixed a bug that MixingStarPulay and criterion positions are reversed in OpenMX Keywords Setting. [Specification Change] • Speeded up loading mol2 files of large scale system. • Enabled to open CONFLEX Setting window even without CONFLEX Windows version binary. • Enabled to switch local job and remote job on the CONFLEX Setting window. • Changed to save in file when executing the calculation on the CONFLEX Setting window. ### Version 8.023 June/18/2018 [Bug Fix] • Fixed a problem that all symmetric elements were not reproduced when creating crystal structure with crystal builder or loading CIF file. ### Version 8.022 May/31/2018 [New Feature] • Added GAMESS and Gaussian basic tutorials. • Added density accumulation function and unit change function in Quantum ESPRESSO solvent density and energy distribution function. • Enabled to set input file name when FDMNES is executed. • Enabled to save CIF file other than P1 in Crystal Builder. [Bug Fix] • Fixed a problem that red and blue of the color bar are reversed in contour display of MO on Winsmostar 3D. • Fixed a bug that warning appeared for system containing water and protein when running Gromacs. • Fixed a bug that improper_style was not cvff but umbrella and could not be calculated when OPLS-AA/L + GAFF is selected for LAMMPS, • Fixed a bug that SOLVENT, rism1d_conv_thr, rism1d_conv_thr are not changeable on the [RISM] tab of Quantum ESPRESSO Keywords setting. • Fixed a problem that FDMNES can not be executed with "Use Unicode UTF-8 for worldwide language support" checked in Windows preferences. [Specification Change] • Changed so that errors of cell parameters are less likely to occur with [Solvate/Build Cell]. • Increased the tolerance of cell parameters in the Interface Builder. • Enabled to select a pseudopotential file starting from "(element name)_" for Quantum EPSRESSO. • Enabled to check lfcpopt when esm_bc=bc1 in the Quantum ESPRESSO Keywords Setting, . • Changed to create input file from the keyword field of the main window for FDMNES. • Changed to put axis vector to output of aspect ratio. ### Version 8.021 May/10/2018 [New Feature] • Added a function to translate partial structure with slider. ( - [Partially Edit] - [Partially Move (Slider)]) • Eanbled to assign the force field with GAFF when adding monoatomic ions with [Solvate/Build Cell] function. • Added molecular composition information to the ndx file generated before LAMMPS execution to be able to select the group by composition at the time of analysis of results. • Added lspinorb, noncolin keyword on Quantum ESPRESSO Keywords Setup window. • Added "Other" tab that allows you to enter keywords freely in the Quantum ESPRESSO Keywords Setup window. • Added OpenMX tutorial menu. • Supported reading OpenMX out file (and mxout file from this version). • Added Relax (variable cell) which sets MD.type = RFC 5 to OpenMX Keywords Setup. • Supported setting and reading of MD.Fixed.XYZ keyword of OpenMX. • Added ibrav = 1, 4, 6, 8, 9, 11, 12, 14 to kpath_default.txt. [Bug Fix] • Fixed a problem that some layout collapses when pressing the Other button of GAMESS Keywords Setup window. • Fixed a bug that improper dihedral of GAFF was not properly set when generating LAMMPS data file. • Fixed a bug that failed to copy a parameter file that does not exist when executing the latest FDMNES. • Fixed a problem that the lattice constant given by celldm, a is interpreted as angstrom instead of bohr, in case of the unit of CELL_PARAMETERS, ATOMIC_POSITIONS is alat when reading Quantum ESPRESSO input file. • Fixed a problem that a warning message appears when tot_magnetization is -1 in the Quantum ESPRESSO Keywords Setup. • Fixed a problem that candidates for lattice selection might not be listed when Filter=Ortho in Cleave Plane of Crystal Builder. • Fixed a problem that the correct value might not be output by the aspect ratio calculation function. [Specification Change] • Changed to add data_ keyword when saving CIF. • Changed to set atomic name as residual name instead of UNK when adding monoatomic ions with [Solvate/Build cell] function. • Enabled to choose whether to generate gro and ndx file every time or not in LAMMPS Keywords Setup. • Changed Gromacs installation on Remote host to unnecessary for LAMMPS remote job execution because ndx file is generated before job execution rather than at the job execution. • Changed to issue a warning when atoms exist near Lz/2 for Quantum ESPRESSO with ESM method. • Changed lfcpopt to lfcp, and changed the unit of fcp_mu from Ryd to eV when specifying the trism keyword of Quantum ESPRESSO. • Expressed Preset's Opt of OpenMX keyword setting as Relax. • Changed the timing to generate pdf of the OpenMX calculation result not when executing the job but when selecting various result analysis menu. • Changed the extension of standard output file of shell script at OpenMX execution from out to log. • Changed to generate mxout file saved after OpenMX execution by copying out file instead of std file. • Changed the choices of extension of OpenMX input/output file. • Changed the reference of kpath_default.txt to the reference of Quantum ESPRESSO. • Changed the default K-point path for ibrav=2. • Set Filter=Ortho as default when selecting lattice for Cleave Plane of Crystal Builder. ### Version 8.019 April/16/2018 [New Feature] • added a function to download pseudo potential file for Quantum ESPERSSO. [Bug Fix] • Fixed a bug that Dreiding force field might not be set correctly in some systems. • Fixed a bug that trying to save files in OpenMX format by default when running MOPAC. (V.8/017 or later) • Fixed a bug that can not automatically determine the type of solver from keywords in the main window. (V.8/017 or later) ### Version 8.018 April/12/2018 [Bug Fix] • Fixed a bug that some older node-locked licenses do not work. • Fixed a problem that error occurs while loading Quantum ESPRESSO pwout file which does not include Force. • Fixed a bug that sometimes caused errors due to loading Lowdin charge of Quantum ESPRESSO. ### Version 8.017 April/10/2018 [New Feature] • Added A file history drop down menu to the "Open file" tool button. • Added "Reload File" "Save File As" "Open Folder" "Full Window" tool button. • Enabled to specify exceptions for Regenerate Bonds in Preference window. • Enabled to selecte the setting of each solver in  - [Atom] - [Change optimization flag]. • Enabled to show the density of each component in  - [Select by molecular type unit] window. • Enabled to output MOPAC, Gaussian, GAMESS, NWChem animation in animated gro format Enabled to show the energy change of the LAMMPS job being executed on the local machine. • Enabled to use monoatomic ion in creating input file of LAMMPS. • Added Suggest function of repeat number in Interface Builder. • Enabled to set ATOMIC_POSITIONS unit (angstrom, crystal) on Quantum ESPRESSO Keywords Setup. • Enabled to output the PDOS of Quantum ESPRESSO's LSDA calculation. • Added Properties tab on Quantum ESPRESSO Keywords Setup window, and various result processing can be executed continuously after pw. • x execution. • Added tot_magnetization, Hubbard_U, diagonalization keyword in Quantum ESPRESSO keyword setting window. • Changed to show the number of valence electrons calculated from the currently selected pseudo file, and if nbnd is less than the number of valence electronics, an error is issued in the Quantum ESPRESSO keyword setting window. • Enabled to generate and show cube file of Potential distribution of Quantum ESPRESSO. • Enabled to set the default k point path for each ibrav in UserPref\kpath_default.txt for Quantum ESPRESSO. • Enabled to set the priority of the pseudo file selected by default in Quantum ESPRESSO with UserPref\qe_pseudo_priority_list.txt. • Enabled to copy the image of graph with right click on the graph in the Quantum ESPRESSO result display window. • Enabled to change the default extension of Quantum ESPRESSO's input/output file in Preference window. • Added Preset on OpenMX Keywords Setup. • Added Reset button on OpenMX Keywords Setup. • Enabled to set Hubbard.U.Values on OpenMX Keywords Setup. • Enabled to set AU, Ang, Frac unit on OpenMX Keywords Setup. • Enabled to set hybrid MPI and OpenMP parallel execution on OpenMX Keywords Setup. • Enabled to read Definition.of.Atomic.Species keyword on OpenMX Keywords Setup. • Enabled to set scf.ProExpn.VNA, MD.Opt.DIIS.History, MD.Opt.StartDIIS, MD.Opt.EveryDIIS keywords on OpenMX Keywords Setup. • Enabled to read Temp.Control, scf.lapack.dste, MD.NH.Mass.HeatBath on OpenMX Keywords Setup. • Enabled to read OrderN.HoppingRanges, OrderN.KrylovH.order, OrderN.KrylovS.order, OrderN.Exact.Inverse.S, OrderN.Recalc.Buffer, OrderN.Expand.Core on OpenMX Keywords Setup. • Enabled to read Hubbard keywords when reading OpenMX input file. • Enabled to read Atoms.SpeciesAndCoordinates.Unit (frac/Ang/AU) when reading OpenMX input file. • Enabled to read Atoms.UnitVectors.Unit (Ang|AU) when reading OpenMX input file. • Adjusted the shaping of input with space characters when setting OpenMX keywords. • Enabled to post calculation and visualize PDOS for OpenMX. • Changed to support for reading OpenMX input files with dat, in, mxin#, dat# extension. • Enabled to change the default extension of OpenMX's input/output file in Preference window. • Added BoltzTraP interface.(WSL only, experimental) • Enabled to set height, width and thickness on Transform Unit Cell form of Cleave Plane mode. • Enabled to select new lattice candidates on Transform Unit Cell form of Cleave Plane mode. • Enabled to use Gnuplot for graph rendering engine in various result display windows in Preference window. (Experimental, partially unsupported) [Bug Fix] • Fixed a problem that some errors occurred when reading an empty file in some processing. • Fixed the color bar of the contour map not to move even if the viewpoint is translated on Winmostar 3D. • Fixed a problem that the optimize flag is not properly displayed in the initial state in  - [Atom] - [Optimization Flag Change], • Fixed a bug that CODO/S UVVIS results form is not shown. • Fixed a bug that Gaussian and GAMESS remote jobs could not be submitted when there was no MD license. • Fixed a problem that the Dreiding force field may not be set correctly in systems containing SP3 oxygen atoms. • Fixed a bug that GIF output from the animation window was created in the installation folder. • Fixed a bug that WSL failed to draw energy graphs of LAMMPS, Gromacs. • Fixed a problem that WSL caused an error by adding Group with dynamic distribution function of LAMMPS. • Fixed a bug that LEaP can not be executed with WSL. • Fixed a bug that sander can not be executed with WSL. • Fixed a bug that related program on WSL after Windows 10 Fall Creators Update can not be executed. • Fixed a bug that celldm was not set correctly in the structure determined as Monoclinic, Orthorhombic, Rhombohedral, or Triclinic (ibrav = 14 in internal processing) when saving input file for Quantum ESPRESSO. • Fixed a bug that the crystal structure was deviated when Quantum ESPRESSO input file was open, set "Output Directory" as "Create", check "Automatically convert to primitive cell" and save again. • Fixed a bug that In Quantum ESPRESSO various result processing file selection dialog, default bug that the appropriate file was not selected was Fixed. • Fixed a bug that proper file was not selected by default in the file selection dialog of various result processing of Quantum ESPRESSO. • Fixed a problem that a range check error appeared when opening an out file running on the local machine when animating the Quantum EPSRESSO's constant-mu calculation, • Fixed a bug that a, b, c, cosAB, cosAC, and cosBC keywords were not loaded properly when opening the input file of Quantum ESPRESSO. • Fixed a bug that the keyword celldm, a, b, and c are not loaded if they are in uppercase letters when opening the input file of Quantum ESPRESSO. • Fixed a problem that the number of display digits was small and the graph shifted in the band structure drawing of Quantum ESPRESSO. • Fixed a problem that OpenMX input file cannot be read when the file has mixed newline characters. • Changed the default shell of the remote job template for PBS to bash and fixed a problem that the C shell system does not work in the some default environment. [Specification Change] • Enabled to resize  - [Selection Molecules] window. • Added the time of each step to the animated gro file output from the Animation window. • Set a menu bar in the Animation window. • Changed to open automatically the keyword setting window when LAMMPS execution is selected without setting the keyword of LAMMPS. • Removed Adjust check box and adjusted the cell size at all times in the Interface Builder. • Changed internal process to deal with rhombohedral lattice as rhombohedral instead of triclinic lattice when converting lattice and running Quantum ESPRESSO. • Dropped {} after ATOMIC_POSITIONS when setting Quantum ESPRESSO Keywords. • Deleted Bands and DOS from the Preset in the Quantum ESPRESSO Keywords Setup window. • Changed input checking mechanism in the Quantum ESPRESSO Keywords Setup window. • Removed parentheses of unit of ATOMIC_POSITIONS, CELL_PARAMETERS when exporting the input file of Quantum ESPRESSO. • Changed the script of remote job template for Quantum ESPRESSO. • Accelerated processing at the first launch of the Quantum ESPRESSO Keywords Setup window. • Moved the contents of the Bands/DOS tab of the Quantum ESPRESSO keyword setting to the Properties tab. • Changed to the extension of the file according to the type of the opened file when the [Set] button is pressed in the Quantum ESPRESSO Keywords Setup window. • Abolished the specification to automatically uncheck "Automatically convert to primitive cell" at the timing set to "calculation = md" or "Output Directory = Continue" in the Quantum ESPRESSO Keywords Setup window. • Changed some file names of the intermediate files in various result processing of Quantum ESPRESSO. • Changed to show error message when VPS file was not found when opening OpenMX Keywords Setup. • Deleted Advance setting checkbox in OpenMX Keywords Setup. • Changed the order of tabs on OpenMX Keywords Setup. • Changed to interprete the character strings %WM_NUM_THREAD%, %WM_NUM_PROC%, %WM_NUM_PARALLEL% as thread number, number of processes, and product of them respectively in Method and template script in Remote Job Submission. • Changed the script header of PBS remote job template. • Changed the message when creating a script of a template in the Remote Job Submission window. ### Version 8.013 March/9/2018 [Bug Fix] • Fixed a bug that SmoothSolid of MO display is displayed same as Solid. • Fixed a bug that import button did not work when Gaussian was set on combo box as solver program . • Fixed a problem that the range check error occurs when the peaks of ultraviolet-visible absorption spectrum are 2000 or more. • Fixed a bug that [Automatically convert to primitive cell] is unchecked on startup in Quantum ESPRESSO keyword setting window. (V.8.011 or later) • Fixed a problem that a range check error occurred when launching the Quantum ESPRESSO keyword setting window. • Fixed a problem that scf.criterion and scf.MixingStarPulay positions are reversed on OpenMX keyword setting window. • Fixed a bug that file reading and job execution of Gromacs, LAMMPS, Quantum ESPRESSO, OpenMX can not be performed under Student license. (V.8.011 or later) • Fixed a bug that the console window was not displayed when putty was invoked with the putty button. • Fixed a bug that only a part of MAC addresses can be acquired in the 64 bit version. [Specification Change] • Changed the default value of scf.criterion to 1.0e-6 in OpenMX. • Changed to recognize outdir even if data-file.xml in outdir is outputted with other name in Quantum ESPRESSO related function. ### Version 8.011 Febrary/9/2018 [New Feature] • Krylov was added to scf.EigenvalueSolver for OpenMX keyword setting. • Added parameters related to MD temperature control and heat bath to OpenMX keyword setting. [Bug Fix] • Fixed a bug that images can not be saved as JPG in Winmostar 3D. • Fixed a problem that part of the MOPAC's IRC output reading may be missed. • Fixed a problem that it is not possible to display molecular orbits by reading Firefly output. • Fixed a problem that atom list was not updated when reading Gaussian's Fchk file. • Fixed a bug that NWChem's restart calculation output file failed to load. • Fixed a bug that multiple line text such as K_POINTS was not set properly in Quantum ESPRESSO keyword setting [Save] and [Load]. • Fixed a bug that the index was shifted by 1 in FDMNES target atom selection. • Fixed a bug that the crystal builder did not zoom with mouse wheel operation. • Fixed a bug that the Winmostar icon disappears from the task bar while running the crystal builder. • Modified HoppingRanges to be set as number, instead of on/off. • Fixed a bug that parameter can not be set for 2 character element in OpenMX keyword setting. • Fixed a bug that the settings returned to the original depending on the order of operations in the OpenMX keyword setting. • Fixed a bug where all coordinates became the origin when ATOMIC_POSITIONS crystal in Quantum ESPRESSO input file. [Specification Change] • changed some Japanese error message, which appears even if the language setting is English, to English • Changed so that keywords already set on the main window can be read on OpenMX keyword setting. • Changed to display the Krylov related items of OrderN only when scf.EigenvalueSolver = Krylov in OpenMX keyword setting. • Changed to add columns such as Euler angles when scf.SpinPolarization = NC in OpenMX keyword setting. • Changed to switch the rightmost column of atom coordinates on when scf.SpinPolarization = NC, and off otherwise. • Changed default value of omxprm.txt to OpenMXViewer default value in OpenMX keyword setting. ### Version 8.007 January/10/2018 [New Feature] • added shortcut key (Ctrl + 4) for [View]-[Zoom]-[Fit to Window] menu. • enabled to show lattice constants and kind of charges on [Preference]-[View]-[Select]. • added -[Atom]-[Change Opt Flags] menu to change atom optimization flags at once. • added [Import] button on Calculation tooolbar. • added shortcut key (Ctrl + [, Ctrl +]) to move between tabs on each keyword setting window. • added CIS and CCSD on GAMESS Keywords Setup Window. • added [Dump .mdp File] button on Option tab of Gromacs Keywords Setup Window. • enabled to input text manually on Phonon tab of Quantum ESPRESSO Keywords Setup Window. • enabled to read/write optimization flags of degree of freedum for Quantum ESPRESSO. • enabled to read input/output file of Quantum ESPRESSO even if the extension is .in/.out. • enabled to load/save Quantum ESPRESSO Keywords Setup values from/to qeset file. • enabled to set pseudo potential file not installed on the local machine. • enabled to open selected pseudo potential file with text editor on Quantum ESPRESSO Keywords Setup. • enabled to set BOMD keywords, to show animation and graphs for energy and temperature on Animation window. • enabled to read Quantum ESPRESSO input file with CELL_PARAMETERS alat. • separated OpenMX Keywords Setup window into tabs for indivisual settings. • enabled to set PAO, VPS, alpha, beta spin for each atom kind for OpenMX. • added to shortcut key for [File]-[Save As] menu on Crystal Bulder. [Bug Fix] • fixed a problem that optimization flags are not cleared when reading cif, mol, or sdf file. • fixed a problem that atom list lines are not aligned for large PDB file. • fixed a problem that atoms can not be selected sometimes on 3D View. • fixed a problem that Quantum ESPRESSO output file without SCF calculation is not readable. • fixed a problem that gmx convert-tpr running between gmx grompp and gmx mdrun does not run in Gromacs continuation job. • fixed a problem that the format is broken when the number of atoms is 100,000 or more when saving gro file. • fixed a problem that you can not run Quantum ESPRESSO after saving the input file of Quantum ESPRESSO. • fixed a bug that a, b, c, cosAB, cosAC, cosBC are not properly considered when reading the input file of Quantum ESPRESSO. • fixed a problem that comment-out was not taken into consideration when reading the input file of Quantum ESPRESSO. • fixed a bug that root directory was selected by default when reading Quantum ESPRESSO files generated other than Winmostar. • fixed a bug that some Conflex settings do not work in remote job submission after V8. [Specification Change] • removed the Windows Subsystem for Linux (Bash on Windows) license and made it available for free edition. • expanded the displayable maximum number of divisions of the cube file from 200 to 600. • added a sample file of graphene - water - graphene system. (samples/graphene_water_graphene.mol2) • changed some criteria for judging the type of file from the contents of the keyword input section at the upper right of the main window. • changed the order of pull down of solver selection on the main window. • changed to show warnings when deviating from the prescribed format when saving the gro file with a large number of atoms. • changed to interrupte the series of processing when generation of MD force field (itp) file fails. • changed to show messages when there are coefficients that were not automatically assigned when assigning GAFF or OPLS force field using acpype. • changed the layout of the Quantum ESPRESSO keyword setting window. • changed part of setting criterion of restart_mode in Quantum ESPRESSO input file creation. • changed to show the keyword setting window when saving in the Quantum ESPRESSO format with the Quantum ESPRESSO keyword not set. • changed part of the remote job submission script for Quantum ESPRESSO. If you are using a customized script, we recommend that you generate it again with 8.007. • changed not to show ATOMIC_SPECIES and ATOMIC_POSITIONS records in the keyword display part at the lower right of the main window when loading the input file of Quantum ESPRESSO. • enabled to double-click the item name to check it on the Quantum ESPRESSO result analysis window. • changed some behavior when graph output failed on the Quantum ESPRESSO result analysis window. • changed to output the keyword setting file (qeset) automatically to the working directory of Quantum ESPRESSO. • changed Quantum ESPRESSO 's differential density / energy (.esm 1) display function to show not only the difference but also the density and energy of the selected esm1 file. • changed to output formatted floating point number data for the structure when OpenMX keyword setting. • changed the name of the sample file of remote job input script for LAMMPS for FOCUS from "lammps.txtfo" to "lammps.txtfoc". • changed the layout of the remote job submission window. • changed to execute sftp test automatically if sftp test is not executed at least once when executing remote job submission. • added the pwd command at the beginning of various remote job submission scripts. • changed the layout of the environment setting window and established the [Calculation] tab. • made installation of Node.js unnecessary for the calculation of Hansen SP value. ### Version 8.006 December/8/2017 [New Feature] • enabled to show HOMO-LUMO gap on Energy Level window. • added CIS to CITYP and CCTYP on GAMESS Keywords Setup window. • addedPCM on GAMESS EadySetup window.
• added SCRF=PCM on Gaussian EasySetup window.
• added SCRF=PCM on Gaussian Keywords Setup window.
• added ccd and ccsd for Hamiltonian on Gaussian Keywords Setup window.
• changed to show Hildebrand SP value when calculating Hansen SP.
[Bug Fix]
• fixed the bug that on file is not saved in the opening file path for saving image on Winmostar 3D.
• fixed the bug that Gaussian input file using atom names for Z-Matrix connectivity relations caused error.
• fixed the bug that "Pull Atoms" and "Restrained Atoms" are not shown on LAMMPS Keywords Setup for some environment.
• fixed the bug that when LAMMPS data file os not generated correctly when same kind molecules appears more than once.
• fixed the bug that fails to convert lattice after reading lattice converted Quantum ESPRESSO pwin file.
• fixed the bug that unable to symmmetrize Ih point group.
• fixed the bug that unable to calculate Hansen SP for large molecule.
[Specification Change]
• enabled to change element combobox manually.
• enabled to change/add element with element combobox or moelcule information pane.
• changed GAMESS default path.
• changed behavier when failing to read LAMMPS data file.
• enabled to read LAMMPS data file even when Coeff section is not ordered as ID numbers.
• enabled to read LAMMPS log file's multiple thermo output for Energy Graph, but thermo_style must be same.
• changed how to read Quantum ESPRESSO input file in order to CELL_PARAMETERS when ATOMIC_POSITION = CRYSTAL.
• changed to show Rescale [info-c] test output even when error occurs for Remote Job Submission.
• enabled to use program_name.*.txt for Remote Job Submission input text.
• changed intermidiate file format sfor Hansen SP.

### Version 8.005 November/13/2017

[Bug Fix]
• fixed the bug layout is off for enlarged display.
• fixed the bug Potential File is reset when showing Quantum ESPRESSO Keywords Setup window.
[Specification Change]
• enabled to calculate Hansen solubility parameter without Cygwin.

### Version 8.004 November/4/2017

[New Feature]
• enabled to choose 64bit or 32bit Winomstar to be installed on 64bit Windows.
• enabled to recognize Bravais lattice automaticcally and convert conventional cell and primitive cell each other
• changed to recognize translation vector of conventional cell automaticcally and set it as Band.KPath.UnitCell on OpenMX Keywords Setup.
[Bug Fix]
• modified shape of dipole moment.
• fixed the bug that unable to run Gromacs unless Gromacs Keywords Setup launched.
• fixed the bug that first appeared atom's charge is used for all atoms of same atom kind for LAMMPS data file.
• fixed the bug that ion_dynamics and ion_velocities are not printed in pwin file when calculation is md or cp and ion_dynamics is none for Quantum ESPRESSO Keywords Setup.(only after V.8.002)
• fixed the bug that recognizing body-centered lattice ibrav=3 for some crystal without centering body center when running Quantum ESPRESSO.
[Specification Change]
• modified toolbar icons.
• changed not to launch Winmostar if the license is invalid or nothing.
• enabled to read mol2 file with RESP charge attached by antechamber (AmberTools).
• enabled to make LAMMPS restart file without Gromacs installed for Remote Job Submission.
• revised shellscript generated when runnig HSP function.

### Version 8.001 October/2/2017

[New Feature]
• b>64bit application.
• changed to set 32bit/64bit and Japanese/English automatically for the installer.
• b>enabled to draw 3D (beta version) on main view.
• enabled to choose Cartesian/Spherical for basis functions on NWChem Keywords Setup window.
• enabled to specify exceptions for basis functions on NWChem Keywords Setup window.
• b>enabled to use Nudged Elastic Band (NEB) and Zero Temperature String on NWChem Keywords Setup window.
• enabled to set memory amount to be used on NWChem Keywords Setup window.
• enabled to set accuracy for initial guess on NWChem Keywords Setup window.
• enabled to set ECP on NWChem Keywords Setup window.
• enabled to set noautoz for geometry on NWChem Keywords Setup window.
• enabled to set x-axis align to molecule's principal axis of inertia for protein.
• enabled to extract part of molecule showed on main window from trajectory for MD Import Trajecotry menu.
• b>enabled to run Gromacs sequentially.
• enabled to make Ramachandran plot for Gromacs.
• enabled to calculate velocity autocorrelation and frequency spectrum for Gromacs.
• enabled to rotate and decimate trajectory for Gromacs.
• enabled to calculate space distribution function for Gromacs.
• enabled to customize remote job script for Gromacs.
• enabled to use any kind of molecules for Gromacs ER/BAR method.
• enabled to kill all jobs submitted to remote at once for Gromacs BAR method.
• enabled to select groups for density distribution for Gromacs.
• b>enabled to calculate thermal conductivity for LAMMPS.
• b>enabled to use Preset on LAMMPS Keywords Setup window.
• enabled to run elongation and annealing calculation for inorganics and DPD for LAMMPS.
• enabled to calculate surface tension for LAMMPS.
• enabled to calculate SAXS for LAMMPS.
• enabled to customize remote job script for LAMMPS.
• enabled to rescale average temperature and density on LAMMPS Keywords Setup window.
• added ouput of normal strain to log file for LAMMPS.
• enabled to save files for LAMMPS and Quantum ESPRESSO Remote Job Submission.
• b>enabled to run SCF, bands, DOS calculation sequentially.
• enabled to run remote job for Quantum ESPRESSO Phonon and permitivity.
• enabled to run OpenMX on local.
• enabled to customize OpenMX remote job script.
• enabled to make nano cluster on Crystal Builder.
• added items for MD on DC-DFTB Keywords Setup window.
• enabled to specify the directory for SK files on DC-DFTB Keywords Setup window.
• enabled to calculate Hansen Solubility Parameter.
[Specification Change]
• moved Zoom, Atom and Bond sliders to popup of the toolbar for view.
• moved annotation selection to the toolbar for view.
• changed location of part of main menus.
• added shotcut key for view point selection (Ctrl+1, 2, 3).
• changed to show "done." after zip file is extracted on Remote Job Submission window.
• changed part of script generated for PBS remote job.
• changed the time to show hints (baloon help) to 60 seconds.
• changed maximum number of backup working directory for MD and Solid solvers
• changed to save degree of parallelization setting for MD and Solid solvers
• changed to reset point of view after building on [MD]-[Solvate/Build Cell].
• changed not to show verbose message on [MD]-[Insert Molecules].
• changed to delete intermediate files before overwriting them for analysis of MD results.
• moved constrains to Basic tab and modved refcoord-scaling to Advance tab on Gromacs Keywords Setup window.
• enabled to select whether to use local data or remote data from which running extending simulation for Gromacs remote job.
• changed layouts of Gromacs ER method window.
• enabled to set number of threads for Gromacs BAR mehod on BAR method window.
• changed to rescale velocity and cell size after job instead from before job for Gromacs.
• changed to select local path to save data every time after getting data of remote job for Gromacs ER/BAR method.
• changed to use PPPM and shake for hydrogens as default on LAMMPS Keywords Setup.
• changed to stop post procedure when failing to run LAMMPS.
• moved SHAKE setting to Basic tab on LAMMPS Keywords Setup window.
• modified bat file for LAMMPS.
• changed not to check MPI is installed on local for LAMMPS and Quantum ESPRESSO remote job.
• changed to show keyword names as it is and to show the meanings on hints on Quantum ESPRESSO Keywords Setup window.
• modified bat file for Quantum ESPRESSO.
• removed pseudo_dir keyword from input file and changed to search pseudo potential files from ESPRESSO_PSEUDO environmet variable for Quantum ESPRESSO.
• changed not to use MPI for Quantum ESPRESSO epsilon.x run.
• changed layouts of Quantum ESPRESSO result window.
• enabled to input keywrord directly in pulldown menus on Quantum ESPRESSO Keywords Setup.
• enabled to select cp.x for SCF calculation on Quantumm ESPRESSO Keywords Setup.
• enabled to shift x-axis to Fermi energy on Quantum ESPRESSO partial DOS window.
• ncreased number of digits of partial DOS plot file (xvg) for Quantum ESPRESSO.
• changed to make working folder for DC-DFTB remote job submission.

## Winmostar V7

### Version 7.031 October/2/2017

[New Feature]
• added items for MD on DC-DFTB Keywords Setup window.
• enabled to specify the directory for SK files on DC-DFTB Keywords Setup window.
[Specification Change]
• changed to make working folder for DC-DFTB remote job submission.
[Bug Fix]
• fixed the bug that values of Coulomb Type and Cutoff Scheme are not saved on Gromacs Keywords Setup.
• fixed the bug that failes to read gro file without last empty line.

### Version 7.028 September/4/2017

[Bug Fix]
• fixed the bug that unable to make data file with OPLS+GAFF for LAMMPS.
• fixed the bug that error occurs for auto generation of covalent bonds when the cell has a edge less than 4 Angstrom.
• fixed the bug that Create group fails on LAMMPS result analysis window.
• fixed the bug that settings fo Phonon dispersion are not saved on Quantum ESPRESSO Keywords Setup (after V7.025).
[Specification Change]
• changed not to delete temp folder after quitting Winmostar.
• changed to remove trj file before GAMESS run.
• changed to generate gro file when running LAMMPS so that the whole system is a same molecule for units=metal.
• enabled to use np variable as parallelization degree for LAMMPS Remote Job Submission. ### Version 7.026 August/20/2017 [New Feature] • added Student license. [Bug Fix] • fixed the bug that changing the keywords on Output tab would not affect the input script in some cases in LAMMPS Keywords Setup. • fixed the bug that aspect ratio is inaccurate for some cases. [Specification Change] • added splitter between list and graph for IR and UVVis display. • deleted an unnecessary warning message which appears when "MD | Insert Molecules" was called. • moved DC-DFTB to add-ons menu bar • moved Fragment ER to add-ons menu bar • moved CONFLEX to add-ons menu bar ### Version 7.025 August/7/2017 [New Feature] • enabled to run OpenMPI build Gromacs on Remote Job Submission. • enabled to draw NAMD energy change graph of NAMD on Fragment ER window. • eanbled to see log file on remote server (tail g) for Quantum ESPRESO Remote Job Submission. • eanbled to edit remote job script for Quantum ESPRESO Remote Job Submission. • added a menu to launch cygwin console window. • added Gromacs tutorial (Protein) • added Gromacs tutorial (Interfacial Tension) • added Gromacs tutorial (Dielectric Viscosity) • added Gromacs tutorial (Vapor Pressure, Surface Tension) • added LAMMPS tutorial (Melting Point) • added Quantum ESPRESSO tutorial (ESM) • added Quantum ESPRESSO tutorial (Phonon) • added Quantum ESPRESSO tutorial (Dielectric Function) • added Quantum ESPRESSO tutorial (Fermi Surface) • added Quantum ESPRESSO tutorial (Spin Polarized) [Bug Fix] • fixed the bug that manually inputted keywords are cleared when SHAKE is disabled for methane-like molecular on LAMMPS Keywords Setup. • fixed the bug that Quantum ESPRESSO pseudo potential folder is not set correctly when one of the folders in layers of the folder begins with a numeric character . • fixed the bug that a part of setting remains when canceling Quantum ESPRESSO Keywords Setup. • fixed the bug that an error occurs if changing atom coordinates while OpenMX animation. • fixed the bug that an error occurs if running Quantum ESPRESSO from pre-existing pwin without launching Quantum ESPRESSO Keywords Setup window. [Specification Change] • added a tool to convert from Gromacs input to MODYLAS input in Winmostar package. • modified and changed free engyer calculation summary, graph, and CSV output on Fragment ER window. • changed not to set density for adding water on Fragmet ER window. • changed to update the atom list for Quantum ESPRESSO animaion less than 3000 atoms. • added MD.Type=RFC5 on OpenMX Keywords Setup. • changed to show error message for Rescale [info-c] test of Remote Job Submission. • changed time showing hints to 10 seconds. ### Version 7.022 July/7/2017 [New Feature] • added units in the graph and statistical report (Calc Ave) in LAMMPS Energy Plot. • added Reset button to Quantum ESPRESSO Keywords Setup. [Bug Fix] • fixed the bug that some intermediate files would be unnecessarily locked by Winmostar. • fixed the bug that fails to asign Dreiding forcefield for LAMMPS. • fixed the bug that the specified file would not be loaded when a pwin or data file was selected. • fixed the bug that the specified file would be locked in Quantum ESPRESSO Animation (pwout). ### Version 7.021 July/4/2017 [New Feature] • added [File]-[Append] menu. • added -[Sort By Molecule Species] menu. • added ballon help on MOPAC Keywords Setup. • added IRC keywords in GAMESS Keywords Setup. • added HSSEND keywords in GAMESS Keywords Setup. • changed to import charges in top file on Gromacs Keywords Setup. • enabled to estimate size of genetated trr file on Gromacs Keywords Setup. • enabled to output CSV and copy result for Hildebrand solubility parameter and Chi/DPD parameter of Gromacs. • enabled to generate bonds dynamically for LAMMPS animation (DynBond button). • ncreased supported job schedulers for MODYLAS. • added out [MD]-[MODYLAS]-[Edit .out File] menu. • added [MD]-[Fragment ER] menu. • enabled to show logarithmic graph on MD MSD window. • enabled to specify file with drag & drop on Gromacs Energy Plot. • enabled to use restriction of distance, angle, and dihedral in specified atoms. • enabled to specify data range for Calc Ave on Gromacs Energy Plot window. • enabled to calculate partial density of states for Quantum ESPRESSO. • added Gromacs tutorial(Solubility, DPD parameter). • added LAMMPS tutorial(Polymer modeling). • added LAMMPS tutorial(Elongation). • added LAMMPS tutorial(DPD). • added Amber tutorial(Basic). • added Quantum ESPRESSO tutorial(Relaxation). • added Quantum ESPRESSO tutorial(First Principle MD). • added Quantum ESPRESSO tutorial(Work function). • enabled to use go/back buttons of multifunctional mouse. [Bug Fix] • fixed the bug that atom coordinates are not updated after adding hydrogen using OpenBabel. • fixed the bug that -[Partially Edit]-[Partial Clean] sometimes makes molecule distorted. • fixed the bug that -[Exchange Indices] sometimes results wrong Z-Matrix. • fixed the error with ghost atoms in GAMES input file. • fixed the bug that specified atom is not seelcted for bond/angle calculator. • fixed the bug that gro button moves while resizing animation window. • fixed the bug that residue numbers and residue names are misaligned for reading Amber coordinate file. • fixed the bug that files are locked while some procedures. [Specification Change] • changed to add extension automatically to the saved file even if the file name has ".". • changed the message for confirmation of overwriting when saving file. • changed to keep all cell information for adding hydrogen using OpenBabel. • accelerated bond generation. • arranged MOPAC Keywords Setup window layouts. • changed warning message of Solvate/Build Cell. • changed to set atom name from atom species name when saving gro file. • changed shell script for Gromacs run. • splitted Gromacs Solubility/Chi/DPD Parameter into Hildebrand Solubility Parameter and Chi/DPD Parameter. • changed to check input items before closing LAMMPS Keywords Setup window. • added Restrain tab for LAMMPS Keywords Setup, and moved Distance Restraint and Position Restraint to the tab and Pull to Non-Equilibrium(1) tab. • changed to set molecule names as MOLXX, where XX is molecule species number, from UNK for gro file before LAMMPS run. • added molecular number suffix to atom types generated by LAMMPS Exception. • enabled to use Improper for assigning LAMMPS Dreiding forcefield. • changed to remove unnecessary parameter line from LAMMPS data file. • changes to use bond_types, angle_types, dihedral_types, and improper_types for assigning LAMMPS Dreiding forcefield. • changed to get work directory for Amber leap from saved crd file name instead of the file opend. • changed default value as zero for LJ parameter of Exception atoms in MD Keywords Setup ForceField setting. • changed to switch to logarithmic display for absolute value in Calc Ave for LAMMPS, Quantum ESPRESSO, MODYLAS Energy Plot. • ararnged OpenMX Keywords Setup layouts. ### Version 7.020 June/1/2017 [Bug Fix] • fixed the bug that Amber energy, pwin or Quantum ESPRESSO animation files would be locked. • fixed the bug that the graph of the energy term containing '#' would not appear on the Gromacs Energy Plot window. • fixed the bug related to the number of threads requested for LAMMPS. • fixed the bug that fails to save a OpenMX mxin file just after open the file. [Specification Change] • enbaled to save PDB file which has more than 100,000 atoms and/or 10,000 residues. • changed to make a backup of a log file for OpenMX. • changed not to show a confirmation dialog on the remote job submission when the main model has no change. • supported the job schedulers other than PBS for OpenMX. ### Version 7.019 May/9/2017 [New Feature] • enabled to use Rescale for Remote Job Submission. • added DC-DFTB interface. • enabled to constrain intramolecular coordinates for Gromacs. • added a molecular modeling tutorial of metal complexes. • added a tutorial of structual optimization using DC-DFTB. [Bug Fix] • fixed the bug that Remote Job Subimission window is fixed foreground after Test[sftp]. • revised the link to the PIO web site. [Specification Change] • enabled to change IR/Raman frequency vector's thickness along with bond thickness. • changed to check and select a molecule at the same time in the Exception window of the Force Field setting window. • changed to add suffixes specifying the molecular species to the atom types when Dreiding is selected for MD. ### Version 7.017 April/20/2017 [New Feature] • changed to set "pop=full,gfprint" after Link1 when Link1 exists for GAMESS EasySetup. • Added a button to save mddef file in MODYLAS keywords setup. [Bug Fix] • fixed the bug that the atom list is not updated sometimes after editing the molecule. • fixed the bug that fails to regenerate Z-Matrix sometimes when the first atom is deleted. • fixed the bug that fails to read Z-Matrix of GAMESS input file occasionally. • fixed the bug that the file extension becomes MOSF for "Save As" menu after reading GAMESS (*gms) input file. • fixed the bug that error occurs when energy is 0eV for reading Gaussian TDDFT output file. • fixed a bug about the layout of UI parts on the windows to issue cygwin commands. • fixed a but that Restore Working Directory does not work on MODYLAS keyword setup. • fixed a bug that the viewpoint is not reset when crystal builder is re-opened. [Specification Change] • changed not to delete the copied input file in GAMESS install folder when the original input file is in the folder. • changed the unit of GAMESS IR intensity to (Debye/amu-Angstrom)^2. • changed to pop the Remote Job Submission window to front after sftp. • changed not to show an unnecessary dialog when submitting a job using SLURM or llsubmit. • enabled to set the directory to store pseudo potential files for Quantum ESPRESSO. ### Version 7.016 April/6/2017 [New Feature] • enabled to apply -[Change Density] by atom. • enabled to use NEC HPC OnLine for Remote Job Submission. • enabled to make and read SMASH input file. • enabled to drag and drop a mol2 file in [MD]-[Solvate/Build Cell]. • enabled to drag and drop a file in [MD]-[Interface Builder]. • enabled to use an output file for Quantum ESPRESSO in [MD]-[Bond/Angle Calculator]. • added Presets in Gromacs Keyword Setup. • added dielectric constant, viscosity and density profile calculation for Gromacs. • enabled to show the total simulation time in Gromacs Keyword Setup. • added the functions to rescale density and/or temperature for Gromacs. • enabled to use SHAKE for water molecules for LAMMPS. • enabled to output the extended Hamiltonian for LAMMPS. • enabled to use the [tail g] button in Remote Job Submittion for LAMMPS. • added MODYLAS interface (beta version). • added OpenMX interface (beta version). • enabled to compute IR/raman spectra, phonon dispersion, and dielectric function for Quantum ESPRESSO. (official release) • enabled to show the accumulated DOS for Quantum ESPRESSO. • enabled to visualize the Fermi surface for Quantum ESPRESSO. • enabled to set keywords for spin polarized calculation for Quantum ESPRESSO. • enabled to show the labels for special high-symmetry points in [Solid]-[Quantum ESPRESSO]-[Band Structure]. • added the function to diagnose cygwin_wm. • added tutorials for dielectric constant, viscosity, fermi surface and spin polarized cauculations. [Bug Fix] • fixed the bug that the atom list on the main window would not be updated when called -[Change Density]. • fixed the bug that one cannot save in the PDB format after loading a PDB file and added atoms. • fixed the bug in some open dialogs that one can not show files (*.*). • fixed the bug that the .data file loader for LAMMPS would not complete its process in a limited case. • fixed the bug that a simulation cell would not appear in Winmostar 3D viewer for Quantum ESPRESSO. [Specification Change] • changed to reset the position of camera when selecting [File]-[New]. • changed to close the Animation window when selecting [File]-[New] or [File]-[Open]. • changed to detect H2 (hydrogen) molecules when automatically generating chemical bonds.s • changed to show log files on the fly in -[Add hydrogens]-[pdb2gmx] and [MD]-[Generate Ions]. • changed to take into account Chain records in PDB files in -[Add hydrogens]-[pdb2gmx] and [MD]-[Generate Ions]. • enabled to show MO for any basis set if the basis set is assigned for all atoms. • changed to specify the number of sites for water in [MD]-[Solvate/Build Cell]. • changed to show the number of molecules inserted in [MD]-[Generate Ions]. • rearranged the Interface Builder window. • changed to output the atomic number in the second column of top file. • rearranged the Gromacs Keywords Setup window. • changed to select [Set # of grids for fourer space] by default. • added the following keywords in Gromacs Keywords Setup window. comm-mode, nstcomm, gen-seed, fourier-spacing, pcoupletype, nh-chain-length, nsttcouple, nstpcouple, vdc-modifier, coulomb-modifier, rcoulomb-switch and gen-temp. • changed to terminate a shell script just after mdrun of Gromacs abnormally exits. • rearranged the Apply button in LAMMPS Keywords Setup window. • added the following keywords in LAMMPS Keywords Setup window. tchain, pchain, shake-tol and dump xyz. • changed the default value for the maximum number of iterations for SHAKE to 1000 for LAMMPS. • added some energy terms to be shown in LAMMPS. • changed not to use mpirun to convert a .restart file to a .data file using LAMMPS. • changed the shell script for remote LAMMPS jobs to improve robustness. • changed to ask regeneration of a data file when an unmodified data file is opened on the main window. • enabled to load a .data file with any types of intramolecular potential functions. • Rearranged the Quantum ESPRESSO Keywords Setup window. • added the "noinv" keyword in the Quantum ESPRESSO Keywords Setup window. • changed to disable the setting for "Automatically convert to primitive cell" when extending a simulation. • enabled to change the range of the DOS plot for Quantum ESPRESSO. • changed to write the cell parameter using the previous data when extending a simulation. • changed the location of intermediate files of ph.x to the working directory. • enabled to enter the labels for special high-symmetry points in [Solid]-[Quantum ESPRESSO]-[Phonon Band Structure]. • changed to connect phonon band structures when two continuous k-points give the same structures. • changed to fix the preset after changing the individual keywords in Quantum ESPRESSO Keywords Setup. ### Version 7.014 March/1/2017 [Bug Fix] • fixed the bug that output file is not generated in Firefly run. • fixed the bug that 3D view of ESP2/Surface is not colored for Gaussian. ### Version 7.013 March/1/2017 [New Feature] • enabled to set absolute position restraints on LAMMPS Keywords Setup even for energy minimization. • tuned performance of LAMMPS data generator. [Bug Fix] • fixed the bug that fails to read SDF file without  in the end. • fixed the bug that the graphene MOL2 file saved has wrong atom types and bond types. • fixed the bug that the molecule moves to wrong position on 3D animation and vector view for QM vibration calculation. • fixed the bug that some necessary files are not properly copied for Gromacs BAR calculation. • fixed the bug that the LAMMPS script file for pulling or position restraints contains unnecessary line breaks. • fixed the bug that input files are not generated when the system contains water molecules and Dreiding is selected for LAMMPS. • fixed the bug that the .data file for extending jobs contains unnecessary "Improper Coeffs" records when several versions of LAMMPS are called. • fixed the bug that dihedral parameters of GAFF or OPLS are not properly set for LAMMPS. [Specification Change] • enaled to read PDB file with atoms which have names like PA, PB, or PG and do not have element symbols. • changed to consider periodic boundary condition for bond regeneration. • changed to show progress while Firefly runs. • changed to update the atom lists after the Animation form closed. ### Version 7.011 February/6/2017 [New Feature] • added tutorials for interfacial tension, melting point, phonon and dielectric function calculations. [Bug Fix] • fixed the bug that symmetric operations in CIF file cannot be read when it is written in upper case. • fixed the bug that some NWChem output files are not readable. • fixed the bug that only one NMR peak appears for NWChem. • fixed the bug that the movecs file is not moved when a file prefix is specified in START directive for NWChem. • fixed the bug that the potential files selected for LAMMPS is not copied into the working directory. • fixed the bug that angle potentials for Dreiding are not correctly set only in Winmostar V.7.010 . • fixed the bug that the number of repeat is not updated in Crystal Builder. [Specification Change] • enabled to use GAMESS 2016 version. ### Version 7.010 February/1/2017 [New Feature] • enabled to change valus of "Zoom", "Atom" and "Bond" parameters with edit boxes on top-right of the main window • added [File]-[Reload] menu • enabled to pack system into the cell by moving atoms at -[Pack into PBC Cell] • enabled to calculate torsion angles at [MD]-[Bond/Angle Calculator] • added the settings for the Dreiding force field on Gromacs Keywords Setup • enabled to automatically assign charges for LAMMPS • added the settings for the GAFF and OPLS-AA/L force fields on LAMMPS Keywords Setup • enabled to set exceptions for force field assign on LAMMPS Keywords Setup • enabled to set absolute position restraints on LAMMPS Keywords Setup • enabled to select water models on LAMMPS Keywords Setup • tuned performance of LAMMPS data reader [Bug Fix] • fixed the bug that optimization flags are not shown in comboboxes when selecting an atom • fixed the bug that atom names written in PDB are recognized incorrectly in some cases • fixed the bug that optimization flags of added atoms are not set after [Partially Replicate] • fixed the bug that atom lists are no updated after [Build Ring] • fixed the bug that the atom list is not updated for -[Pack into PBC Cell] • fixed the bug that "Bonding Factor" is reset when restarting Winmostar • fixed the bug that some keywords on ".in File (4)" and ".in File (5)" tabs do not affect the text box in LAMMPS Keywords Setup • fixed the bug that the number of cores requested by LAMMPS on WInmostar Job Manager is always one even when MPI is used • fixed the bug that upper cases and lower cases of monomer(.wmo) filename are not distinguished on Polymer Builder • rearranged the post-processing window for Quantum ESPRESSO • fixed the bug that two letter elements like Zn become dummy atoms after Point Group sAnalysys [Specification Change] • changed to show "Angle" value down to 3 decimal places, and fixed the numbers of digits for other values • arranged OpenSCAD Setting • changed to use MinGW build NWChem from cygwin build one • changed to set bond orders from the bond length when reading LAMMPS data file • changed the default value of charge on LAMMPS Keywords Setup from "Use user-defined charges" to "Assign charges" • changed to allow five column data for Pair Styles record in LAMMPS data reader • changed to allow charmm angle style in LAMMPS data reader • changed to obtain atom IDs from the first column of Atoms record in LAMMPS data reader • changed the default value of force field on LAMMPS Keywords Setup from "Dreiding" to "GAFF" • changed not to issue the command for SHAKE when "units" is not set to "real" • changed to allow Kpoints=Automatic when calc=bands on Quantum ESPRESSO Keywords Setup • enabled to read the units of ATOMIC_POSITIONS and CELL_PARAMETERS with parentheses or without any brackets in Quantum ESPRESSO pwin reader • changed to show point charges after executing [MD]-[Assign Charges]-[By Acpype] • changed to show a warning message when any charges are not defined and [MD]-[Polymer]-[Register Monomer] is called • eanbled to stop calculation when checking "Pause" on Job Manager ### Version 7.009 January/10/2017 [New Feature] • enabled to show the structure generated by symmetry operation when reading a cif file in the main window. • enabled to export CHARMM coordinate file. ([File]-[Export]-[CHARMM crd File]) • enabled to select partially with atom list. • enabled to pack molecules out of the cell into the cell. (-[Pack into PBC Cell]) • enabled to change density of the system. (-[Change Density]) • enabled to assign point charge using acpype. ([MD]-[Assign Charges]-[by Acpype]) • added [View]-[Reset] menu. • enabled to change scale for OpenSCAD. • enabled to set charge and multiplicity on Gaussian EasySetup window. • enabled to set charge and multiplicity on GAMESS EasySetup window. • enabled to show the average of enrgy and thermodynamic quantities on Energy Plot window for LAMMPS, Amber and Quantum ESPRESSO. • enabled to generate cell automaticaly on LAMMPS Keywords Setup. • added Pulling (e.g. moving a selected atom at constatnt velocity) on LAMMPS Keywords Setup. • enabled to output animated gro file from LAMMPS trajectory, so that it enables to work with VMD. • enabled to compute length and angles of specified atoms and the histogram of that for MD trajectory. ([MD]-[Bond/Angle Calculator]) • enabled to set timeout for MD analysys tools. • enabled to compute IR/raman spectra, phonon dispersion, and dielectric function for Quantum ESPRESSO. (for testing) • added the link to molecular modeling tutorial for organic molecule and supermolecule. [Bug Fix] • enabled to downgrade Winmostar by overwriting. • fixed the bug of Z-Matrix reference atom when removing 2nd atom. • fixed the bug that the atom list is not updated for -[Add Hydrogens]-[Using pdb2gmx], [MD]-[Solvate/Build Cell], and [MD]-[Generate Ions]. • fixed the bug that the input keywords are not read for import menus of Semi-Empirical and QM. • fixed the bug that element name with more than one letter become one letter when using acpype on Gromacs Keywords Setup window. • fixed the bug that extra information is added to xvg file for LAMMPS Energy Plot. [Specification Change] • changed the default value of scale for VRML to the same value for OpenSCAD • adjusted the order of energy on Animation window for Gaussian IRC output. • changed to require installation of Cygwin for LAMMPS Keywords Setup. • removed ".data File" tab on LAMMPS Keywords Setup and integrated to -[Create/Edit Cell] and [MD]-[Assign Charges]-[By Manual Entry]. • changed to read the number of cell boundary crossed from LAMMPS data file. • changed not to clear charges for MD trajectory animation. • changed the layouts of output window for Quantum ESPRESSO. ### Version 7.007 December/7/2016 • enabled to undo/redo for -[Add Hydrogens]-[using pdb2gmx], [MD]-[Solvate/Build Cell], [MD]-[Generate ions]. • modified to show optimization flags of Z-Matrix with 2 digits • modified to be able to change Z-Matrix connectivity with edit boxes under the list. • modified to show Na,Nb,Nc and indices of atoms at the same time in -[Z-Matrix]-[Change Connectivity]. • fixed the bug that the visualization of charges can not be turned in periodic condition. • enabled to visualize multiple bond in OpenSCAD. • enabled to change the number of partitions in OpenSCAD • enabled to output Blender coordinate system in OpenSCAD • corresponded the coordinate system of OpenSCAD with that of VRML. • accelerated file transfer in remote job submission. • fixed the bug that an error occurred in [MD]-[Generate ions]. • changed to delete Bond section in data file when bonds does not exist in DPD. • fixed the bug that BSO file cannot be opened in CONFLEX window. ### Version 7.005 November/15/2016 • fixed the bug that saving a file fails when the extension of the file is explicitly specified in [File]-[Export]-[Image]. • fixed the bug that behavior of XYZ checkbox and [File]-[Save As XYZ] menu are different. • fixed the bug that coordinates are slightly wrong when saving a group. • fixed the bug that failing to draw draw the model with red bonds and a cell. • fixed the bug that Energy Level Diagram is not updated when importing MO file with the MO import window opend after importing another MO file. • fixed the bug that extra blank liines are inserted when importing Gaussian keywords after "--Link1--". • fixed the bug that failing to read and save ONIOM when importing Gaussian keywords. • fixed the bug that an error occurs when importing a fchk file. • changed how to determine the solute molecule in [MD]-[Gromacs]-[Start ER]. A molecular species whose number of molecules is one will be treated as the solute molecule. • added the setting of ecdmin in [MD]-[Gromacs]-[Start ER]. • fixed the bug the setting of Cubic Cell is not saved when the window is closed in [MD]-[Polymer]-[Polymer cell builder]. • changed to rewind the list in animation window automatically when [|>] button is clicked. • fixed the bug that after symmetrizing of the molecule with Point Group Analysys, and clicking s[File]-[New], the last molecule appears on the main window again when showing Point Group Analysys again. ### Version 7.003 November/1/2016 • enabled to keep information of a cell with REMARKs when saving and reading a PDB file. • changed [File]-[Launch File Explorer] menu to [Open Folder]. • added -[Create/Edit Cell] menu to create and edit a cell. • enabled to rotate the molecule on z-axis even when the point of view is on z-axis. • enabled to select whether to show a cell or not by [View]-[Select]-[Cell] menu. • fixed the bug that an error occurs when running CNDO/S and saving as a different file after setting CNDO/S keywords. • enabled to fix specified molecues and to make force fireld paraemters for them manually for Gromacs. • enabled to run computation of a solid-liquid interface system with Gromacs. • fixed the bug that contents on [ForceField] tab are not reset when pressing [Reset] button on Gromacs Keywords Setup. • fixed the bug that error occurs when restoring a working directory after reading tarjectory. • enabled to run stretching calculation with LAMMPS. • enabled to run annealing calculation with LAMMPS. • enabled to fix the distance of any atoms for LAMMPS. • added potential energy and kinetic energy to output log of LAMMPS. • changed to show details when failing to assign Dreiding force field for LAMMPS. • added "special_bonds dreiding" and "pair_modify mix arithmetic" to default LAMMPS input. • fixed the bug that time constants of temperature and presure control become 1/1000 when units=metal. • fixed the bug that fails to make a system with charge on Interace Builder. • fixed the bug the ibrav of Monoclinic (b setting) cannot be detected correctly when running Quantum ESPERSSO. • changed Quantum ESPRESSO Keywords Setup window to be modal. • fixed the bug that CIF files including _geom keywords cannot be read. • enabled to use CONFLEX menu with QM pack. • fixed the bug that the orientation of a GAMESS input including a point group S2n, O, Oh, T, Th, or Td does not corresponded with master frame. • fixed the bug that the point group Dnd cannot be symmetrized. • added tutorial menus for English. • enabled to show English captions of buttons on message dialogs. ### Version 7.002 October/18/2016 • changed names and layouts of windows. • enabled to show additional PDB data when XYZ checked. • fixed the bug that atom coordinates are incorrect when editing the edit boxes under the atom lists when XYZ checked. • modiied the behavior when changing selected atom by editing the edit box under the atom lists. • modified to set first and last atoms as a former selected atom and a selected atom. • fixed the bug that sometimes fails to read samples\nial.cif • changed to keep atom names of PDB file while reading/saving. • changed to make an error when saving a MOL file for a molecule which has too many atoms for MOL. • assigned Shift-Ctrl-S for [File]-[Save As] menu. • added [File]-[Launch File Explorer] menu. • fixed the bug that keywords becomes upper case when [File]-[Save As XYZ] checked. • fixed the bug that undo sometimes fail. • fixed the bug that Partial Center of Mass with only dummy atoms fails. • changed to make Z-Matrix after the position is fixed for Partialy Paste. • modified a selected atom after Make Ring. • fixed the bug that fails to Replace Group to an isolated atom. • Changed to set also orientation of a cell for [Orientation]-[Set] • fixed the bug that sometimes fails to Clean. • Changed to invert a cell for Mirror Image. • fixed the bug that direction is incorrect for Space-Filling Model in Three View. • fixed the bug that directions of bonds are incorrect for OpenSCAD. • fixed the bug that [MOPAC]-[Import]-[Force(out)] sometimes fail. • ncreased digit number after decimal point of a GAMESS input file from 6 to 10. • changed to output intermediate files to working folder for calculating GAMESS RESP charge. • changed [GAMESS]-[FMO] menu as [PDB] menu and changed the location. • enabled to change the number of molecules by double-clicking molecule list on [MD]-[Solvate/Build Cell]. • fixed the bug that fails to import non-cubic cell for [MD]-[Solvate/Build Cell]. • fixed the bug that extra covalent bonds are sometimes generated on [MD]-[Solvate/Build Cell]. • changed to show hints when hovering a cursol on keywords on Gromacs Keywords Setup. • fixed the bug that ER fails when a file and folders are not specified in order of solution, solvent, and solute. • enabled to control anisotropic pressure for LAMMPS. • ncreased the number of log output items for LAMMPS. • enabled to select whether to make a buckup of working folder or not for LAMMPS. • changed to use the value of "# of time steps" as the number of time steps for LAMMPS minimization. • enabled to restore working directory for LAMMPS. • added same items on Gromacs Keywords Setup to LAMMPS Keywords Setup. • moved MPI setting to Options tab on LAMMPS Keywords Setup. • changed the default value of Ensembles to minimize on LAMMPS Keywords Setup. • added Reset button on LAMMPS Keywords Setup. • modified to read potential files for metal for LAMMPS Remote Job Submission. • added batch avarage on Energy Graph of LAMMPS , Amber, and Quantum ESPRESSO. • enabled to select Head and Tail atoms after [MD]-[Polymer]-[Register Monomer] menu launch. • changed to select Cubic Cell as default on Polymer Cell Builder. • fixed the bug fails to make a polymer when monomers has a sulfur atom. • fixed the bug fails to make a polymer cell when the drive to save a file in is differ from the install directory. • fixed the bug that contents of file is mol2 even if saving as cif on Interface Builder. • added Exchange Axis to Crystal Builder. • fixed the bug that opened file continue to be locked for Crystal Builder. • enabled to read a cif file with _space_group_symop_operation_xyz for Crystal Builder. • fixed the bug that unable to select latice points for Cleave Plane. • fixed the bug that fails to keep the value of Firefly NODES from version 6. • enabled to set background color etc. concurrently even if Color Set is selected. • fixed the bug that orientation of a molecule which has Cnv by Point Group Analysys differs from that of GAMESS master frame. • fixed the bug that Winmostar terminates when animation window is closed while runnig animation. ### Version 7.000 October/1/2016 • changed the icons. • changed to show the file name on the title bar. • changed the layouts of the install folder. • changed the default file path to UserData folder. • added tool buttons for View menus and Preference menu. • enabled to Delete/Change element at once with Del/Chg button when atoms are multi selected. • enabled to select/unselect one molecule by clicking with Shift key pressed. • enabled to expand/shrink the view window and the textareas by mouse dragging. • moved Connect, All Atoms, and Mark on the control panel to View menu. • moved undo button to -[Undo Text] menu. • moved Debug button to [Help]-[Debug] menu. • enabled to show Cartesian coordinates instead of Z-Matrix. • merged [Edit1] and [Edit2] menus to  menu. • reconstructed [QM1] and [QM2] menus to [Semi-Empirical] and [QM] menus. • changed [Others] menu to [Tools] menu. • moved [Others]-[Import SMILES] menu to [File]-[Import]-[SMILES] menu. • enabled to output SIMLES and chemical structure as SVG format with [File]-[Export] menu. • assigned Ctrl-Z shortcut key to -[Undo] and Ctrl-Y to -[Redo] respectively. • enabled to Undo/Redo more precisely. • moved -[Rotation] menu to [View]-[Rotation] menu . • changed to highlight target atoms to be edit for menus like -[Atom]-[Move Atom]. • gathered the bond related menus to submenus of -[Bond]. • moved [View]-[Aromatic Ring]-[1-2save(mol)] to [Tools]-[Preference] window. • added -[Add Hydrogens]-[Using pdb2gmx] and [Using OpenBabel] menu. • gathered the menus related for parially edit to submenus of -[Partially Edit]. • added -[Partially Edit]-[Partially Orientate] menu. • added -[Partially Edit]-[Partially Cut], [Partially Copy] and [Partially Paste] menus. • gathered the group related menus to submenus of -[Group]. • removed [Edit2]-[Back to Origin] and [Set Origin to Center of Mass] menus and use [View]-[Centering] as a substitute. • changed to use Look From Z Axis tool button in place of [Edit2]-[Orientation]-[back to Default] menu. • removed [View]-[maximize] menu. • added [View]-[Three View] menu. • added [View]-[Move Viwepoint] menu. • changed the axes of [View]-[Rotation]-[X-Axis], [Y-Axis] and [Z-Axis] from the axes of view to the absolute coordinate axes. • added [View]-[Rotation]-[Eye Vector Axis] menu, which is same of previous [Edit2]-[Rotation]-[Z-Axis]. • moved [View]-[Color Set], [Color], [VDW radius] and [Select]-[KeyWD Font] to [Tools]-[Preference] window. • renamed [View]-[Method]-[BS1] and [BS2] to [Plain] and [Normal] respectively. • changed the expression of the perspect view. • gathered [View]-[Jmol] etc. to [View]-[External Viewer] submenus. • fixed the bug that the simulation cell penetrates the ground when showing a sparse system using Ray Tracing(POV-Ray). • renamed [View]-[Copy to Clipboard] menu to [View]-[Copy Image]. • gathered the menus for each solvers to the submenus of each solvers for [Semi-Empirical], [QM], and [Solid] menu. • enabled to use the result of Point Group Analysis on GAMESS keywords Setup. • enabled to run NWChem parallel with MPI. • added [MD]-[Solvate/Build Cell] menu to build a cell with specified density. • added [MD]-[Generate Ions] menu to place monoatomic ions to the system shown. • added ForceField tab on Gromacs Keywords Setup to make forcefield for the system shown. Addition to the conventional functions, calculating and auto generating/specfying the topology file for a mixing system of polymers and low molecules are available. • removed Preprocess tab on Gromacs Keywords Setup, and changed to use ForceField tab, -[Add Hydrogens]-[Using pdb2gmx], [Using OpenBabel], [MD]-[Solvate/Build Cel] and [Generate Ions] menus instead. • changed the default values of rvdw, rcoulomb, nstxout and nstenergy on Gromacs keywords Setup to 1.0, 1.0, 100 and 10 respectively. • changed to save the gro file and the top file when starting a new Gromacs calculation. • enabled to build the simulation cell automatically with the size set on ForceField tab of Gromacs Kewords Setup when starting Gromacs run without a simulation cell. • added [MD]-[Gromacs]-[Solubility/Chi/DPD Parameters] menu to compute Hildebrand solubility parameter, Chi parameter and DPD aij parsameter based on cohesive energy. • removed [MD]-[Gromacs]-[Save as Solvent] and integrated it to [MD]-[Solvate/Builds Cell] menu. So that solvents are saved as mol2 format and the forcefiled type is specified on ForceField tab of Gromacs Keywords Setup. • added "Extending Simulation" on LAMMPS Keywords Setup to run continuous job with the velocities of the previous run. • changed to save a data file insted of a mol2 or cif file when starting LAMMPS. • changed to save LAMMPS output files to the folder with postfix "_lmp_tmp" • changed to generate a gro file always when running LAMMPS. • changed to compress output files to a zip file for Gromacs and LAMMPS Remote Job Submission. • added [MD]-[Polymer]-[Map Monomers] menu to build the system for all atom MD from a DPD system . • removed the Crystal Builder wizard, and changed to use it as manually. • changed not to bring back to the main window after saving a file on Crystal Builder. • changed to abort the job before running cp.exe in Quantum ESPRESSO when the output folder(outdir) name includes a space, which cp.exe does not support. • enabled to make an animation gro file on Quantum ESPRESSO animation window. • added [Tools]-[Preference] menu. • changed to save the setting to UserPref\wm_set.ini instead of atoms1.wmx • fixed the bug that the calculation of Sterimol Parameters with specific camera angle. • enabled to symmetrize and extract asymetric units with Point Group Analysis. • moved [Others]-[Run with JM] and [Path] menus to [Tools]-[Preference] window. • moved [Help]-[Language], [no Advertisement] and [License Setting] menu to [Tools]-[Preference] window. ## Winmostar V6 ### Version 6.020 September/1/2016 • added Delete button to remove selected molecules on [Edit2]-[Select Molecules..] menu. • enabled to specify a file name for POV-Ray output. • enabled to change the Profile name easily on the Remote Job Submission window. • enabled to show the graph of Energy Distribution Function on [Gromacs]-[Import ER]. • enabled to edit continuation at all time, and edit gen-vel at all time except for energy minimization on Gromacs Keywords Setup. • changed to delete the Pair Coeff section from a data file after run when unit=metal, so that the data file is available for restart job. • changed to keep the file name on the main window as the first selected mol2 file when importing LAMMPS trajectory. • fixed the bug that fails to make the polymer including a 4 coordinated nitrogen on Polymer Builder. • fixed the bug that an error occurs on Inteface Builder with the number of repeat in the direction of C axis is more than 1. • enabled to output CSV file on Quantum ESPRESSO interface. • added [Generating Simulation Cell] item on [Option] tab for Quantum ESPRESSO Keywords Setup, so that the simulation cell is automatically set if the cell does not exist. • fixed the bug that spaces in keywords are deleted when reading a pwin file. • fixed the bug that extra cell parameters are saved when saving pwin after reading a pwin file except ibrav=0. • fixed the bug that the accuracy set for Point Group Analysys is not used properly. ### Version 6.019 August/1/2016 • added -PIC5H5 to Parts Select. • assigned a keyboard shortcut to the menu [View]-[Copy to Clipboard]. • extended the limit number of iso surface vertices from 30,000 to 100,000 on 3D view. • accelerated calculating normal vectors of iso surface vertices on 3D view. • enabled to zoom in/out with a mouse wheel on 3D view. • changed to toggle "gif" checkbox off when the animation with "once" and "gif" checked finishes on 3D view. • enabled to run GAMESS with node parallel computation. • fixed the bug that some MOPAC data are recognized as NWChem data. • changed to take over the value of Basis on the Setup window to that of GAMESS and Gaussian EasySetup window. • added TVZ to the bases of GAMESS EasySetup. • added tzv(TZ_(Dunnig)) to the bases of NWChem EasySetup. • changed the default value of constraints to hbonds on Gromacs Keywords Setup. • fixed the bug that nstenergy is not saved to gmxset file on Gromacs Keywords Setup. • fixed the bug that the file name changes to the trr file when changing frames of Groamcs trajectory animation. • changed to output the data file of the last step for LAMMPS. • enabled to calculate Radial Distribution Function and Mean Square Displacement even if LAMMPS ran with "Specify data file" checked • enabled to Create Group for LAMMPS Radial Distribution Function and Mean Square Displacement. • fixed the bug that the error occurs when clicking the 3D buton again before 3D window appears for MD animation. • added the button to reload pseudo directory on Quantum ESPRESSO Keywords Setup. • enabled to select Smearing and degauss only for Occupations=Smearing on Advance tab of Quantum ESPRESSO Keywords Setup. • ncreased the history of job manager from 50 to 200. ### Version 6.018 July/1/2016 • changed the button names "Rep" and "Chng" to "Repl" and "Chg" on the main window. • enabled to change radius of ball and stick for OpnSCAD. • modified to be consistent the positions, orientation, and scale of files for VRMML and OpenSCAD. • fixed the bug that [Load] button sometimes do not work properly in GAMESS Keyword Setup. • changed the recommended version of LAMMPS. • enabled to use "rigid" and "Constrain Hydrogen" in LAMMPS Keyword Setup. • relaxed the criterion to determin the kind of elements from mass when reading LAMMPS datafile. • enabled to read the LAMMPS data file with atom_style charge. • ncreased the number of digits of cordinates in the input file of Quantume ESPRESSO. • fixed the bug that Quantum ESPRESSO do not run when clicking the Set button of the Quantum ESPRESSO Keyword Setup window which appears when trying to run Quantum ESPRESSO without setting keywords. • changed to read the generated Quantum ESPRESSO input file after running Quantum ESPRESSO in main window. • changed "Automatically Detect ibrav" to "Automatically Convert to Primitive Cell" in Quantum ESPRESSO Keywords Setup. • enabled to show the diffrence of electron density and energy graph after ESM/constant-mu aclculation of Quantum ESPRESSO. • added the buttons to reset the camera direction in reciprocal vectors in Crystal Builder. • added the [View]-[Centering] menu in Crystal Builder. • modified the position of the periodic table in Crystal Builder. • fixed the bug that the symmetry operation of specific format cif file is not readable. • modified the behavior when closing some mesasge dialogs with "x" button. ### Version 6.016 June/1/2016 • fixed the bug that an error occurs when deleting atoms of a large system. • fixed the bug that an error occurs when the number of bonds increase while 3D animation. • enabled to select MOZYME by the check box on MOPAC Keywords Setup. • enabled to show the edges of a MO cube file on the 3D view. • enabled to calculate scatter function for Groamcs. • changed the names of ER and BAR Settings menues. • changed to alert when starting extending simulation while the previous job is running. • changed not to show the dialog noticing creation of the working directory for Amber and Quantum ESPRESSO. • changed to show the unit on LAMMPS Energy Plot Window. • added the option "time" to the default thermo_style on LAMMPS Keywords Setup. • enabled to run Quntum ESPRESSO with Remote Job Submission. • enabled to set the keywords for constant-mu and ESM method for Quantum ESPRESSO Keywords Setup. • enabled to show the tot_charge change of constant-mu animation. • enabled to show potential energy distribution and work function with Quantum ESPRESSO. • enabled to run projwfc.x of Quantum ESPRESSO. • added the option "fixed" to Occupation and the setting of Electron Max Step and vdW Correction to Quantum ESPRESSO Keywords Setup. • enabled to select whether to take the backup of working directory of Quantum ESPRESSO or not. • fixed the bug that an unnecessary dialog is shown when the cell size changes while Quantum ESPRESSO animation. • changed to run bands.x and dos.x when selecting Band Structure and Density of States. • changed to complement the grids of cube file when showing 3D MO of Quantum ESPRESSO. • fixed the bug of determining Bravais lattices for Quantum ESPRESSO. • fixed the bug that WM failed to read a pwin file with no commas. • changed LDOS checkbox off as default on FDMNES Keywords Setup. • enabled to insert vacuum with Crystal Builder. • fixed the bug that duplicated atoms on periodic boundaries are saved for Crystal Builder cif file saving. • fixed the bug that an edit box continue to show while scrolling the assymmetric unit window on Crystal Builder. • changed the max repeat number to 20x20x20 for Crystal Builder. • modified the camera directions of the three views on Crystal Builder. • changed Cleave Plane menu to the sub menu of Tool on Crystal Builder ### Version 6.015 May/10/2016 • fixed the bug that unable to read a big crystal system, which has much more bonds than atoms. • changed to delete the number from atom names when reading a CIF file. • fixed the bug that the positions of the molecule and the cell are misaligned when saving mol2 after Partially Move the molecule. • changed the location for temporary saved files from /tmp to the user area for Remote job Submisssion. • enabled to clear the setting on EasySetup of GAMESS and Gaussian. • enabled to select MPLEVL from pull-down on GAMESS Keywords Setup. • added the setting for RESP charge on EasySetup of GAMESS Keywords Setup. • enabled to import RESP charge of GAMESS. • enabled to show spin density of Gaussian output. • enabled to read high accuracy coordinate of Gaussian archive (Import->Archive). • extended the maximum number of characters of a MO file name from 40 to 80. • adjusted the width of the controls on the Energy Plot window. • adjusted the width of the controls on the UV-VIS Spectrum window. • adjusted the width of the controls on the IR/Raman Spectrum window. • enabled to show the MO of a cube file which has a triclinic cell. • enabled to calculate the average of statistics including molal volume, coefficient of thermal expansion, specific heat at constant volume/pressure, volume elasticity modulus, and enthalpy on Gromacs Energy Plot. • enabled to normalize energy by the number of molecules on Gromacs Energy Plot. • changed to alert when nstxout is more than nsteps on Gromacs Keywords Setup. • changed the order of integrator on Gromacs Keywords Setup. • added the interface for sander of AmberTools. • splitted Amber Keywords Setup window for LEaP and sander. • splitted Start Amber menu for LEaP and sander. • changed to set a coordinate file and a topology file explicitly on the Amber interface. • enabled to run semi-empirical QM/MM/MD with the Amber interface. • fixed the bug that the molecule spreading out the cell causes an error on Interface Builder. • enabled to show three views on Crystal Builder. • enabled to select BS1 or BS2 for the view on Crystal Builder. • added the log at the bottom of the wizard of Crystal Builder to show the number of atoms, lattice constans, etc. • changed the UI for editing asymmetric elements on Crystal Builder. e.g. changing coordinates by clicking the lists, fixing the input by enter, etc. • enabled to select atom elements with the periodic table on Crystal Builder. • set the maximum repeat up to 10x10x10 on Crystal Builder. • accelerated reading file and creating bonds on Crystal Builder. • enabled to read a file by drag & drop on Crystal Builder. • ntegrated the operation after resetting the lattice of Cleave Plane to Crystal Builder. • changed the layouts of Quantum ESPRESSO Keywords Setup. • enabled to use MPI parallel run on the Quantum ESPRESSO interface. • enabled to use triclinic cell on the Quantum ESPRESSO interface. • enabled to calculate and show band structure and DOS on the Quantum ESPRESSO interface. • enabled to set the continuation of a job explicitly on Quantum ESPRESSO Keywords Settting. • changed Charge Density Cutoff always editable on Quantum ESPRESSO Keywords Settting. • added the button to open the pseudo potential folder on Quantum ESPRESSO Keywords Settting. • fixed the bug that some textboxes cannot be blank on Quantum ESPRESSO Keywords Settting. • fixed the bug that some settings are saved even when canceling on Quantum ESPRESSO Keywords Settting. • fixed the bug that line feeds are inserted to the K Points textbox automatically on Quantum ESPRESSO Keywords Settting. • added the checkbox to set whether detecting ibrav automatically or not on Quantum ESPRESSO Keywords Settting. • enabled to read all ibrav for reading a Quantum ESPRESSO input/output file(pwin,pwout). • enabled to read the .save directory which has any prefix and is created by other environments on Quantum ESPRESSO Keywords Import. • fixed the bug that an error ocurs when reading Quantum ESPRESSO output file(pwout) that the unit of coordinate is not bohr. • enabled to use triclinic cell on the FDMNES interface. • fixed the bug that an error occurs when closing a message dialog window directly. ### Version 6.014 April/14/2016 • fixed the bug that a error occurs when you drag & drop a input data file to the desktop icon or double-click a file associated with Winmostar. • fixed the bug that Remote Job Submission fails when the login shell is csh or tcsh. ### Version 6.013 April/1/2016 • fixed the bug that register monomer fails. ### Version 6.012 April/1/2016 • enabled to select molecules by thier type. ([edit2]-[Select Molecules]) • changed to skip TER record when reading PDB. • changed to launch POV-Ray from the POV-Ray setting window. • enabled to expand and shrink by the gesture to the touch panel. • accelerated and thread parallelized openCubeGen (Displaying MO and Density). • accelerated to make iso-value surface using cuboids instead of cubes only. • fixed the bug that error occurs when changing directories in reading a Cube file. • enabled to setPCM in GAMESS Keywords Setup.
• enabled to select Dunning basis set from the pull-down menu in GAMESS Keywords Setup.
• fixed the bug that pull-down menu of basis set is not enough in Easy Setup of GAMESS Keywords Setup.
• enabled to select Dunning basis set from the pull-down menu in Gaussian Keywords Setup.
• fixed the bug that making a gro file from a trr file fails when the calculation time is less than 1 ps.
• enabled to assign force field to the system including a protein and a ligand.
• changed [Save as CSV] button to [Excel] button in MD Energy Plot.
• enabled to select a item by double-click in MD Energy Plot.
• enabled to submit remote jobs of the free energy calculation by BAR method..
• changed the layout of BAR setup.
• fixed the bug that Register Monomer fails from a MOPAC arc file.
• added the Quantum ESPRESSO interface.
• enabled to calculate XAFS spectra by FDMNES.

### Version 6.010 March/2/2016

• enabled to read LAMMPS data file with units=metal or units=lj.

### Version 6.009 March/1/2016

• enabled to output Excel data from UV-Vis absorption spectrum.
• changed the default value of GAMESS XYZ parameter from COORD=CART to COORD=UNIQUE.
• fixed the bug that some GAMESS XYZ data cannot be read.
• fixed the bug that the cube file with the record more than 80 characters cannot be read.
• fixed the bug that Winmostar freeze when displaying 3D mod MO with many surfaces.
• enabled to display backbone when reading a gro file.
• enabled to read LAMMPS data file.
• enabled to use dash shell at remote server for remote job submission.
• enabled to use customized script (lammps.txt) for LAMMPS remote job sbmission.
• fixed the bug that the alert appears when Windows is goint to shutdown without quiting Winmostar.

### Version 6.006 February/1/2016

• enabled to clear the history of used files.
• enabled to display molecules for patent application.
• enabled to display molecules without gradiation.
• changed the layouts of ER and BAR method and changed the default unit to kcal/mol.
• enabled to use unt=lj for LAMMPS Keywords Setup.
• added the DPD (DPD Cell Builder and DPD Potential Editor) menu

### Version 6.005 January/7/2016

• enabled to use color setting for OpenSCAD data.
• changed the default value of Box Size for Grromacs Keywords Setup.
• enabeld to set solvents up to four for Grromacs Keywords Setup.
• changed from extending Nsteps as sum of runs to extending additional Nsteps for Gromacs Extending Simulation.
• changed to end the calculation when the run fails to insert molecules for Gromacs insert-molecule.
• changed how to set Miller index for Cleave Plane.
• fixed a bug for Point Group Analysis (Sn and Th Group).

### Version 6.004 December/10/2015

• enabled to use double and triple bond for POVRay.
• fixed the bug that the solvent files are not readable in Groamcs Keywords.
• fixed the bug that the atom types are not saved correctly in Interface Builder.
• fixed the bug that the gif file is not saved for many frame animation.

### Version 6.003 December/4/2015

• changed display of Winmostar and Winmostar 3D.
• enabled to use ball-stick, global illumination, infinite plane, depth of field, background color change, and anti-aliasing for POV-Ray.
• enabled to output OpenSCAD data.
• fixed the bug that unnecessary Link1 data is not removed in Gaussian EasySetup.
• enabled to set Energy for Method of GAMESS Keywords Setup.
• fixed the bug that the unit is wrong for the cell import in Gromacs Keywords Setup.
• enabled to save XTC for LAMMPS dump file.
• enabled to calculate radial distribution function and mean-square displacement for LAMMPS output.
• enabled to adjust automatically the scale resolution for the graph of MD results.

### Version 6.002 November/6/2015

• enabled to save as cif file.
• set shortcut Ctrl+E to number exchange.
• ncresed max number of redo/undo from 20 to 50.
• fixed the bug that hits are not shown.
• fixed the bug that display is wrong when editing the model with Pack in PBC cell.
• modified the display of bonds with Pack in PBC cell.
• changed to show prompts after executing commands in the remote job submission window.
• fixed the bug that NZVAR is sometimes invalid in GAMESS Keywords Setup.
• added EasySetup in GAMESS Keywords Setup.
• fixed the bug that orientations sometimes wrong when saving Z-Matrix of Gaussian and NWChem.
• fixed the bug that Gromacs cannot be executed with MPI on remote servers.
• added pressure setting field in LAMMPS Keywords Setup.
• changed to set pair_coeff depending on pair_style in LAMMPS Keywords Setup.
• fixed the bug that the tilting cell size is wrong when reading LAMMPS trajectory.
• fixed the bug that MPI is not available for Polymer Cell Builder.
• enabled to calculate automatically the cell size of x and y direction in Polymer Cell Builder.
• changed to regenerate bonds when repeat number is more than one in Interface Builder.
• enabled to read/write cif files in Interface Builder

### Version 6.001 October/6/2015

• fixed the bug that the display of the GRO file from long time MD is wrong.
• fixed the bug that the display of the trajectory from extending simulation with gen-vel=no is wrong.
• updated the version of ERmod from 0.3.1 to 0.3.2.
• enabled to use OpenMP when running free energy calculation (ER method).
• fixed the bug that the position of the cell is wrong when importing LAMMPS trajectory.
• fixed the bug that Point Group Analysis does not launch.

### Version 6.000 October/1/2015

• added EasySetup for GAMESS and NWChem Keywords Setup.
• enabled to change the font size in the keyword input area.
• changed to transform the characters from lowercase to uppercase in MOPAC Keywords Setup.
• enabled to calculate solvation free energy by Energy Representation method (ERmod) or Bennett Acceptance Ratio (BAR) method with the MD option.
• enabled to switch single/double precision for GROMACS.
• enabled to submit job for ERmod.
• modified to grayout invalid keywords in GROMACS Keywords Setup.
• added verlet-buffer-tolerance in GROMACS Keywords Setup.
• enabled to use LAMMPS for the metal and crystal system.

## Winmostar V5

### Version 5.016 September/10/2015

• extended the limit number of UV-VIS spectrum peaks from 200 to 2,000.
• modified the criteria of C-S bond order determination.
• enabled to use N.pl3 atom type for Polymer Builder.
• added MTTK in pcoupl of Groamacs Keywords Setup.

### Version 5.015 August/6/2015

• modified a part of covariant radius of Period 4 element.
• enabled to display changing cell volume of MD trajectory in Winmostar 3D.
• enabled to switch whether to "Pack in PBC cell".
• changed to make residue data after reading cif file so that gro file can be saved.

### Version 5.014 July/16/2015

• changed the installer to be with code signing.
• fixed the bug that atom number is not shown when the charge display is "numerial".
• disabled to edit the replace part combobox and the replace element combobox.
• fixed the bug that the directions of "Copy Group" are the axes of the display.
• fixed the bug that the second text area is not cleard after reading Gaussian output.
• fixed the bug that the run fails when nose-hoover & extending simulation & gen_vel = no & concatenate .edr and .trr file = yes. for Gromacs Keywords Setup.
• added "density" to the default value of "thermo" in LAMMPS Keywords Setup.
• changed to consider numerical error when judging whether the cell is cuboid or not in LAMMPS Keywords Setup.
• fixed judging whether the cell is periodic or not when importing LAMMPS trajectory.
• changed not to be error when the polymer is self interfered in Polymer Builder.
• enabled to make the polymer that contains amide bonds with Polymer Builder.

### Version 5.012 June/16/2015

• added data of NMR reference materials.
• changed not to move coordinate by Center of Gravity.
• fixed the bug that Center of Gravity does not work when reading a Gromacs GRO file (V5.010).
• fixed the bug of reading MOPAC IRC (V5.009,C5.010).
• enabled to set molecule as object and calculate the cumulative number in Gromacs - Radial Distribution Function menu.

### Version 5.010 May/8/2015

• changed to make arc -> mol conversion bat when making SDF -> MOPAC exection bat.
• modified mol file reading with command line arguments.
• fixed a bug that Mulliken charge is not read of Gaussian09D.01 output.
• fixed a bug that the first atom is placed to origin after reading mol2 file.
• added a function to submit job to LAMMPS on a server.
• added [Reset] button on Gromacs keywords Setup.
• enlarged the text field of Temperature Coupling on Groamcs Keywords Setup.
• changed the default value of maxwarn on Groamcs Keywords Setup from 1 to 10.

### Version 5.009 Apr/10/2015

• 7 colors to 9 colors for Rainbow 3D display.
• enabled to launch CONFLEX.
• fixed a bug that atom position become inaccurate when replacing a part for the first atom.
• enabled to save mol2 file with the cell information of MD(LAMMPS,Gromacs) calculation result.
• enabled to display the cell when reading a mol2 file with cell information.
• enabled to import cell information for LAMMPS and Groamcs Keyward Setting.
• enabled to launch LAMMPS MPI parallel execution.
• changed to set dump and data file names when launching LAMMPS dynamically.
• fixed a bug that multi tc-grps is not set in Gromacs Keyward Setting..

### Version 5.007 Mar/11/2015

• enabled to draw the molecular surface based on the Van del Waals radii.
• enabled to draw electrostatic potential from point charges.
• enabled to draw electrostatic potential map and molecular orbital map.
• supported Groamcs 5.0.4.
• renewed Gromacs Keywards Setup.
• added thermo_style into input script of LAMMPS setup.
• enabled to select whether to use Job Manager or not.

### Version 5.006 Feb/12/2015

• enabled to choose language.
• enabled to display red or blue circle corresponding to positive or negative charge.
• enabled to obtain total energy in Gaussian ONIOM output.
• fixed a bug that fails to import reference material for NMR result window.
• fixed a bug that first atom coordinate is incorrect for reading XYZ data.
• fixed a bug that failes to import Mulliken charge in Gaussian09 output.
• added npt for Ensemble, specifying data file, input file generation/modification, and saving/loading calculation condition in LAMMPS Setup window.
• enabled to display estimated volume and density on pre-mdrun tab of Gromacs Setup window.
• enabled to display volume and density on the modeling window.

### Version 5.004 Jan/8/2015

• enabled to execute MOPAC continuously when reading SDF files.
• enabled to use NQS for Remote Job Submission.
• enabled to execute absolute path commands for Remote Job Submission.
• fixed a bug that eivenvalues which have a lot of digit number are not read when displaying MO from Gaussian 09.
• fixed a bug that the orbital energy of Gaussina 09 fchk file is not read .
• fixed a bug that error ocuurs for Gaussian data with comma.
• enabled to concatnate Gromacs output files with the file of previous run.
• enabled to calculate RMSD (g_rms) and radius of gyration (g_gyrate) to analyze proteins for Gromacs output.
• enabled to display timesteps when executing Gromacs.
• enabled to specify a trr file for Gromacs Import Trajectory.
• enabled to specify a edr file for Gromacs Energy Grph.

### Version 5.003 Dec/4/2014

• enabled to display superposition of gaussian functions.
• enabled to change VDW radii.
• added enlarge button for text input area.
• enabled to specify 4 atoms for changing atom and deleting atom
• enabled to delete all atoms except selected atoms.
• enabled to calculate radius of inertia.
• fixed a bug that shift value of superposition display is wrong somtimes.
• fixed a bug that error ocuuurs for many bonds for 3D display.
• enabled to calculate mean squre displacement and diffusion constatnt for Gromacs.
• enabled to calculate radial distribution function for Gromacs.
• enabled to specify maximum and minimum of energy graph for Gromacs.
• enabled to output csv of energy graph for Gromacs.
• enabled to revert to previous run when Extending Simulation ended abnormally for Gromacs.
• enabled to use user made potential file (.itp file) for Gromacs.

### Version 5.002 Oct/27/2014

• enabled to do conformational search.
• enabled to input the molecular structure with SMILES.
• enabled to read IRC output by Gaussian09.
• fixed the bug when displaying the bond order of aromatic ring by 1 and 2.

### Version 5.001 Oct/3/2014

• updated the manuals.
• changed the categorization of Gromacs MDP parameters.
• enabled to save default values for Gromacs Keywords Setup.

### Version 5.000 Oct/1/2014

• enabled to change ball-and-stick model view from pull-down menu.
• fixed a bug to fail MO display for MOPAC2012.
• enabled to change cell size in Gromacs trr file.
• enabled to read charges from out file for MOPAC2012.
• enabled to display UV-VIS spectrum of TDDFT for NWChem.
• enabled to display infrared Raman spectrum and animate oscillation for NWChem.
• fixed a bug RemoteDir is not copied for Profile copy in Remote Job Submission..
• changed not to make zmatrix for reading the Groamcs gro file which has more than 10,000 atoms.
• changed to use default browser for menus opening URL.
• changed Gromacs keyword setting significantly.

## Winmostar V4

### Version 4.105 Jul/9/2014

• enabled to display the bond order of aromatic ring as 1-2.
• modified the method of calculating the bond order of heterocyclic compound.
• fixed a bug to fail in reading the nwchem input file including "SYMMETRY C1".
• fixed a bug to fail in reading Chelp,Chelpg output after Gaussian09RevD.01.
• changed the default keyword of GAMESS as NPUNCH=0.

### Version 4.104 May/15/2014

• changed to hide not frequently used buttons for Remote Job Submit, and show them when Advanced check button is checked.
• fixed a bug of reading when changing directry for MOPAC import/MO(mgf).
• changed to display Excel table of coordinate comparison for [datSave] of Superimpose window.
• fixed a bug that MO of Beta orbital is not displayed for reading MOPAC6 mgf file .
• fixed a bug of "No file" error for Gaussian import MO.

• changed [GAMESS import]-[$VEC from punch] overwrite to additional write. • enabled to read$HESS from GAMESS punch file ( [GAMESS import]-[$HESS from punch] ). • enabled to use SLURM for Remote Job Submission. • enabled to use two-step ssh connection for Remote Job Submission. • enabled to use Gaussian09D.01 for PIO analysis. ### Version 4.102 Jan/8/2014 • enabled to choose 6-311 basis seet for Gaussian/GAMESS setup. • enabled to set$id in the script for the scratch setting of GAMESS execution.
• added automatic generation of PBS script for GAMESS job submission.
• set $ZMAT DLC=.T. AUTO=.T. automatically for optimization of GAMESS Setup. • read$HESS part in pun file when importing out file of GAMESS Hessian results.
• added the function to read $VEC in GAMESS punch file. (import/$VEC from punch)

### Version 4.101 Nov/27/2013

• enabled to display NMR spectrum for NWChem.
• added Shielding checkbox for NWChem.
• fixed an out of bound error when reading SDF of CONFLEX.
• enabled to change the size of the joblist window of Job Manager.

### Version 4.100 Sep/30/2013

• fixed a bug that clean failes when sample name has a multibyte charactor.
• enabled to read/write other settings in property directive for NWChem input file.

### Version 4.030 Sep/6/2013

• separated the text box for ls and cat command.
• set lower convergence condition for Antechamber in Gromacs calculation.
• enabled to read complex basis setting for NWChem.

### Version 4.029 Aug/23/2013

• enabled to use remote job submission of Gromacs for LSF batch system.

### Version 4.028 Aug/20/2013

• changed layouts of the manuals.
• fixed a bug that MOPAC Mulliken charged is not imported.
• fixed a bug for Job Manager in the case that a user name has white space.

### Version 4.027 Aug/13/2013

• enabled to encrypt the password in the remote job submission setting file.
• fixed a bug for reading ONIOM data for Gaussan.
• fixed a bug when solvent model is None for Gromacs.

### Version 4.026 Aug/6/2013

• changed the names and the positions of various menus.
• updated the manuals to be consistent with current Winmostar.
• changed Gromacs keyword setup form to be tab form.
• fixed garbled Japanese characters in Job Manager.
• enabled to delete jobs in Job Manager.

### Version 4.025 Jul/24/2013

• created the menus for NWChem, [Keyword Setup], [Start NWChem] and [Import].
• created the menu to save as solvent of Gromacs.
• added 'box' and 'angles' option for Gromacs's editconf and 'maxsol' option for genbox.
• changed layout of Gromacs Keyword Setup
• enabled to save Gromacs GRO file.
• changed to make working directory for Gromacs calculation.
• moved 'hydrogen bond display' to 'add bond' next to 'triple bond'
• enabled to save whether to show dipole moment.
• enabled to save the background color of 3D display.
• enabled to save whether to show 'All Atoms'. ( 'off' by default )
• modified to make optimized index to be 1 if that is other than 0,1,-1 or T while saving MOPAC dat file.
• changed Cygwin default path to 'C:\cygwin_wm'

### Version 4.024 Jun/17/2013

• mproved Gromacs extending simulation.

### Version 4.023 Jun/11/2013

• ocalized warning message for Japanese version.
• enabled to display transition dipole moment.
• enabled to do Gromacs extending simulation.

### Version 4.022 May/9/2013

• changed partly how to display ion bonding
• fixed bugs of pdb reading and enhanced for GROMACS calculation.
• enabled to select options of user charge for Acpype in GROMACS calculation.

### Version 4.021 May/1/2013

• enabled to read/write charge for mol2 file.
• modified atom types for mol2 file.
• rebuild dos2unix.exe for misrecognition of anti-virus softwares.

### Version 4.020 Apr/15/2013

• enabled to read GRO file of GROMACS.
• changed the reading method of TRR file of GROMACS.

### Version 4.019 Mar/28/2013

• enabled UNIX Server MPI and SMP parallelization of GROMACS.
• arranged job submission console.

### Version 4.016 Feb/13/2013

• changed development environment from Delphi XE2 to Delphi XE3.
• fixed a bug that the molecular orbital is not displayed from TDDFT output of Firefly(PC-GAMESS).
• fixed a bug that the the mesh of molecular orbital is not displayed with Intel(R) HD Graphics4000 GPU.
• changed the default display of molecular orbital from face to mesh.

### Version 4.015 Feb/04/2013

• enhanced to support WinGAMESS version 2012.05.
• added the select box of CITYP for Firefly on GAMESS setup.

### Version 4.014 Jan/30/2013

• changed to display the molecular imformation in front of the molecule.
• changed to draw molecular orbital as faces by defalut instead of meshes.
• fixed a bug when the file is not found for [import] of SubmitJob.

### Version 4.013 Jan/8/2013

• changed gjf and mol2 format for high accuracy.
• adjusted shrink display and atom selection for large moleculs.
• fixed a bug of PDB file drag and drop to the Winmoster icon.

### Version 4.012 Dec/25/2012

• enhanced RemoteDir function for Linux(Unix) job submission.
• reconstructed dos2unix.exe and unix2dos.exe.

### Version 4.011 Dec/13/2012

• use double precision for internal variables.
• enabled to write mol2 files.
• enhanced launch options.

### Version 4.010 Nov/24/2012

• display 3D automatically when reading ChemDraw mol file.
• made scale factor editable for IR spectrum display.

### Version 4.009 Nov/20/2012

• added charge setting of Acpype for Gromacs.
• accelated 3D view for moleculars which consists from over 1000 atoms.
• revised calculation manual.
• fixed a bug for French environment.

### Version 4.008 Nov/06/2012

• modified hydrogen addition in case there is aromatic ring bond.
• coordinates adjustment automatically when C-C bond length was wrong for hydrogen addition (all atoms).

### Version 4.007 Oct/29/2012

• enabled to zoom in/out with mouse wheel.
• fixed a bug to fail launching Winmostar for some language environment.

### Version 4.006 Oct/26/2012

• accelerated 3D graphic.
• enhanced to display molecular formula.

### Version 4.005 Oct/19/2012

• added Amber and Gromacs calculation function.

### Version 4.004 Oct/17/2012

• fixed the bug of fail to add H when deleting a part.

### Version 4.002 Oct/09/2012

• fixed the bug of unix server function for user account with multibyte character.

### Version 4.001 Oct/06/2012

• adopted to IRC of GAEMSS.
• adopted to nonharmonic oscilator calculation of GAEMSS.
• fixed the bug unable to launch in english environment.

### Version 4.000 Sep/23/2012

• changed rules of the license.

## Version 3.808d Aug/23/2012

adopted to the hydrogen bond display.
• adopted to the operation of CTRL + rectangle pick and CTRL + atom pick.
• enabled to set NProcShared of Gaussian and NCPUS of GAMESS with $np in job submit function to Linux(UNIX) machines. • enabled to set Gaussian checkpoint file as %chk=$1 in job submit function to Linux(UNIX) machines.
• enabled to change the default values of GAMESS keywords ([Load],[Save],[Reset] in the setup dialog).
• adopted to comment line begining of "*" in the data of MOPAC 2009 or later.

### Version 3.808 Jun/06/2012

• changed the development environment to Delphi XE2 from Delphi 7.
• released 64bit version.

### Version 3.807e May/10/2012

• adopted to the case of 0 atoms in Gaussian restart data.
• fixed the bug that element names are not read properly in PDB file.
• modified to display Energy change in graph display of Import/Animation.
• modified to transform full-width character of method to half-width character in job submit function to Linux(UNIX) machines.

### Version 3.807 Mar/07/2012

• adopted to GAMESS-FMO (making input file and visualization of output).
• adopted to graph display in Import/Animation.
• adopted to the new MGF file of MOPAC2009.
• modified to display WinGAMESS output to a DOS window.
• fixed the bug of reading error of structure in Gaussian Import/Animation of V3.806o,p,q,r.
• fixed the bug of reading error IRC structure in Gaussian Import/Animation.
• fixed the bug of reading fchk file of Gaussian by version up of OpenCubegen.
• fixed the bug of reading independent function in Gaussian fchk file.
• enabled to structure input in Gaussian fchk file.
• adopted to reading with drag & drop and reading recently used file of Gaussian fchk file.
• adopted to OpenCubegen in Gaussian fchk file.
• fixed the bug of inability to read Gaussian output of periodic boundary condition.
• adopted to the batch process function of PIO calculation.
• added job submit function to FOCUS (only in Tencube/WM)
• adopted to Windows user ID including space in job submit function to LINUX(UNIX) machine (only in Tencube/WM).
• adopted to Gaussian fchk file transfer in job submit function to LINUX(UNIX) machine (only in Tencube/WM).
• fixed the bug that parts are displayed more than once in parts list display.
• fixed the bug that initial structure is used in MO display of GAMESS structure optimization output file.
• fixed the bug of error in MO display of GAMESS output for some basis sets.
• fixed the bug that some comment line(!) is not recognized sometimes in GAMESS input data.
• fixed the bug of error in reading eigen value from CNDO/S output.

### Version 3.806 Jul/15/2011

• enabled to change the default values of Gaussian keywords ([Load],[Save],[Reset] in the setup dialog).
• added Zindo to Gaussian setup.
• adopted to the 32bit and 64bit WinGamess new binary format.
• added PDB form output (-opdb) to the execution parameter.
• added Automatic termination (-end) of file read to the execution parameter
• corrected the trouble of the parameter reading at execution.
• added new function to reflect newly registered parts among the multiple sessions of Winmostar
• added job submitting function for TSUBAME (Tokyo Institute of Technology )(Only in Tencube/WM )
• modified to consider bond information for hydrogen adittion.
• modified to keep bond information for all hydrogen deletion.
• adopted to user ID written in chinese character in the job submitting function to the Linux(UNUX) machine (Only Tencube/WM :).
• corrected the trouble of reading "," in the password in the job submitting function to the Linux(UNUX) machine (Only Tencube/WM :).
• corrected the inability of reading the Raman output of newest version of GAMESS.
• corrected the inability of clearing ONIOM in the new session.
• corrected a touble that the undo button of the key word text stay on at full screen display.
• corrected the bug of reading error of Multiplicity in Gaussian reading.
• corrected the bug of the error when "Density Matrix:" is missed in Gaussian output MO reading.
• corrected the bug of the reading error of ESP charge in Gaussian09 output.

### Version 3.805 Jan/14/2011

• added partial cleaning function to correct inability of cleaning the molecule with llarge number of atoms. This enables the cleaning of the molecule with more than 200 atoms by dividing into small segments
• added undo button, that replace the key word text to those before reading.
• added Preservation function (GIF,JPEG) of IR spectrum chart.
• made change on the condition of the ring construction and a part of the numbering.
• mproved the speed of the PIO analytical program .
• added the new function to put the dummy atom to the position where partial center of gravity had been requested (edit/others/partial center of gravity).
• The condition of the hydrogenation has been readjusted.
• corrected the inability of synclonozation of the optimization flag along with the exchange in permutation and the atom number.
• corrected the trouble in V3.804e that all optimization flag becomes 1 when MOPAC was saved .
• corrected the trouble in V3.804h that a part of optimization flag becomes "0" when parts were added.
• corrected the trouble in V3.804k that the optimization flag some times blanked in reading a calculation result file.
• corrected the trouble in Gaussian input that the specification of the isotope my cause an error.
• corrected the trouble of the Freq output of Gaussian09 that the vibration vector is not displayed.
• corrected the trouble of the Submit Job screen that a part of the text might dropped out.
• applied mask to hinder the password of the Submit Job screen.
• corrected the trouble of the Submit Job screen that the number of parameters in method exceeds nine causes an error.
• corrected the trouble of the PDB input that the element name might be missread.
• corrected the trouble of Import/Animation of Gaussian, MOPAC, and GAMESS that a molecular orientation have a chance to be in correct.
• corrected the trouble in displaying the space-filling model that an atomic pair having close coordinates causes an error.
• corrected the trouble in reading the GAMESS output that the program might freeze when no coordinates exist.
• modified the [Exel] button in Energy Diagram to provide Exel table.
• adopted PIO analysis with Gaussian09
• adopted PIO analysis with the results obtained from other computer (Gaussian,GAMESS).
• adopted DRC output from GAMESS.
• adopted MD output(*.trj) from GAMESS.
• ncluded d-orbital in MO display of CNDO/S.
• added new function to exclude one atom from the initial 2 atom-condition.
• collected the trouoble in drag and drop operation of Gaussian output file that the file some times refused as no Gaussian format.
• collected the trouoble in remote job manager of Linux(UNUX) machine that error might occur in getting large size output file.
• modified the ON-OFF of [Display Multiple Bonding] to be savable attribute.
• collected the trouoble in Windows7 that some part of the text of the Pull-Down menu corrupt.
• collected the trouoble in Gaussian Import/Opt that some times failes to read structure.
• collected the trouoble in Adding Hydroge Atom that the bond length on the first atom sometimes exceeds regular length.
• collected the trouoble in Vivration Analysys of MOPAC2009 that some times fails to read when Tv atom exists.
• modify the format of COMPND line in PDB saving in order to be able to read from Molecules;iPhone application.