ChangeLog

2 September 2022

XTB supported : Draw Geometry/Semi-Emperical (XTB, MD, MDConfo).

Gabedit can compute energy, optimize a geometry, make a MD and MD search conformation using XTB methods.

Under windows : You should define the directory (Main menu/Preferences/Others) and the command (xtb by default) to execute (Main/menu/commands) the program.

18 May 2022

Minor bugs fixed (load the result file, management of window sizes and positions by the system and users).

The result file is not loaded automaticaly. Load only if the user click on update button.

11 May 2022

Window key o(under Linux) or Alt key (under windows OS) f the keyboard to unselect atoms

8 February 2022

CIF : _space_group_symop_operation_xyz is now supported

Gaussian output file with different basis sets for one type of atom : Supported

27 July 2021

normalisation of RDF : bug fixed

27 May 2021

read Energy from the comment line of xyz file if multiple geometries

26 August 2020

Compute Cremer-Pople parameters for pyranose.

29 July 2020

Compute the type of conformer for a saccharide : pyranose (1C4, 4C1, ....) & furanose (3E, 2T2, ....)

Gabedit can Compute the type of conformer for one molecule or for several ones (Animation/MD or Animation/Geom. Conv of Display window)

12 May October 2020

remove gdk_gl_font_use_pango_font.

new style of labels on GL windows

31 October 2019

Rotate fragment without rotation of all structure

13 June 2019

Change Error in Warning if the electronic density is negative during NCI analysis

12 June 2019

remove call fit_windows_position

22 January 2019

minor bug fixed : set origin to center of molecule

17 January 2019

Gabedit can now read orbitals& geometry from WFX file.

It can also export orbitals in a WFX file.

5 December 2018

Mopac gradients output file format changed in 2018. Gabedit supports now this new format.

31 October 2018

Export structure in CIF file (with or without symmetry operators).

Reduction to primitive Cell.

Reduction to Niggli or Delaunay Cell.

Computing of space group & symmetry operators.

Standardize cell (to conventional or primitive).

Generate k-points along high symmetry lines, for band structure calculations.

Get a prototype crystal from a database implemented in Gabedit.

13 October 2018

read CIF file

Build slab : Crystallography/Build slab

1 October 2018

read Direct poscar file : if u_<0 or u_i>1 for an atom=> shift to set it on the cell

27 September 2018

Build superCell : Crystallography/Build superCell

Create clusters using Wulff construction : Crystallography/Build cluster using Wulff construction

21 June 2018

Global and local reactivity indices (By Finite difference or Frontier Molecular Orbitals) : Display window/Reactvity Indices

14 June 2018

New tool to compute the thermochemistry : Display window/Animation/Vibration

03 April 2017

Bug fixed for set center to origin

30 March 2017

The format of .hess and .out files of Orca4 are slightly different from them of Orca3.

Gabedit can now read .hess and .out file of Orca4 (and Orca3)

08 February 2017

Energy, geometry optimization, MD, MD Conformations search by an external (generic) program are

now supported. Gabedit creates an input file for the external program, this program compute energy, dipole, gradients or optimize the geometry.

This program must produce an output file supported by Gabedit.

The input file for the external program (or script) created by gabedit contains :

First line is an integer : 0 for energy, 1 for gradients and 2 for optimization

Second line contains the text "Geometry"

third line number of atoms, charge and multiplicity of the molecule.

From forth line, symbol, mmtype, pdftype, residuname, interger, charge, interger, integer, x y z and connectivities (xyz in Ang)

The external program must produce an output file with :

energy in atomic unit in the first line

dipole in atomic unit in the second line

gradients (atomic units) in next lines if gradients are required

Geometry in next lines if the geometry optimisation is required.

As examples, see :

The script runDFTBPGabedit (page web of gabedit) as an example

The script runGamessPM3 is another example (page web of gabedit).

01 February 2017

Energy, geometry optimization, MD, MD Conformations search by MMFF94, MMFF94s, UFF and Ghemical potentials are

now supported via openbabel.

obgradient, obopt programs and the 2.3.2 folder of parameters are needed and to be installed

in C:\OpenBabel under windows, $HOME/OpenBabel under unix (MacOS and Linux). The location of this folder

can be changed but the directory must be changed via Preferences/Other gabedit window.

OpenBabel directory can be download from Gabedit web page for each OS.

24 January 2017

Compute the type of conformer for a saccharide (1C4, 4C1, ....)

Compute the anharmonic spectrum by QM/MMFF94 method using iGVPT2 program.

Read the harmonic and anharmonic spectra from an iGVPT2 output file.

25 August 2016

DeMon2k is now supported by Gabedit. Gabedit can create input files, run demon and visualize the results using the molden file created by demon2k

27 April 2016

Gabedit can now read the geometry from POSCAR and from vasprun.xml

25 April 2016

Save geometry in POSCAR

Scale cell

1 April 2016

Tools for VASP :

Read dielectric function from a VASP xml file and compute optic properties Optic,

read data from vasprun.xml and plot DOS, pDOS and, Bands structures

8 September 2015

Gabedit can not read the hessian from .hess orca file.

After reading of the hessian, Gabedit compute frequencies, modes and effective masses

30 June 2015

Export in CChemI : update

Tv accepted (used by Gaussian and Mopac for periodic system)

Using Tv, Gabedit can generate other cells

1 June 2015

QFF tools are implemented : Display/Vibration + main menu Tools/QFF

11 March 2015

bug fixed : geometry in Display window if ECP used.

13 February 2015

read geometries (Optimization or M. Dynamic) from VASP OUTCAR file

15 May 2014

Bug fixed to read dummy atom from molpro output file

07 March 2014

Bug fixed to read the last geometry from mopac output file(no bug with the first geometry, no bugs if aux file)

25 October 2013

new tool to remove half cube grid

remove implicit declaration warning

24 October 2013

new tool to compute the integral of the function on the grid

30 September 2013

run orca from Draw geometry : bug fixe (new input format with orca, without params)

19 August 2013

Bug fixed for reading basis with d,f,.. orbitals from a fchk file. Only fchk file is concerned by this bug (There was no bug for reading from a .log file)

PM7 added to list of Mopac Hamiltonian list.

24 July 2013

Gabedit can now calculate the lambda diagnostic for CT (see Peach et al. J. Chem. Phys. 128, 044118 (2008))

18 July 2013

Gabedit can now symmetrize a molecule (see Largent et al. J. Comput Chem. 33 (2012) 1637-1642)

08 July 2013

new parsers to read :

UV-Visible spectrum from a Gamess unrestricted TDDFT calculation

Raman spectrum from a QChem output file

Anharmonic IR spectrum(VT2) from a Gaussian (D01) output file

Anharmonic IR spectrum(VSCF, VSCF-PT2) from a Gamess output file

02 May 2013

bug fixed : analytical gradient for PairWize potential with OMP

02 April 2013

bug fixed : set distance, angle, dihedral in DrawGeomCairo bug fixed

bug fixed : analytical gradient for PairWize potential

05 March 2013

bug fixed : read geometries convergence with non scf method from a molpro log files

New DFT functionals in Gaussian interface

16 September 2012

bug fixed : read personal fragment under windows

14 September 2012

set molecule in the standard orientation

Align selected and not selected fragments

05 September 2012

Bug fixed : reading of the number occuped beta orbitals from a fchk file.

25 July 2012

Bug fixed : read orbitals with ECP from a GAMESS-US output file

19 July 2012

NCI (Non covalent interactions index) analysis implemented

Dummy atom in an orca input file bug fixed

Read orbitals&Geometry from an orca ouput file with a dummy bug fixed

Insert a non-bonded atom in "Draw geometry window" bug fixed

07 July 2012 :

Psi4 partially supported : input file, geometries, frequencies, UV Spectrum

20 June 2012 :

Bug fixed : computing of double&triple bonds

10 June 2012 :

Warning with -Wformat have been fixed

29 March 2012 :

Filter (Gaussian, Blackman, Blackman-Harris,...) in GabexitXYPlot window (not fully tested)

08 Marsh 2012 :

read gamess geometries in Display window : bug fixed

02 Marsh 2012 :

GENNBO files : read any type of orbitals

27 February 2012 :

NBO basis (file .31) : read geometry

06 October 2011 :

Orca input file : constraint removed if no fixed atom.

03 October 2011 :

Bug fixed for saving geometry in mol forma

15 September 2011 :

Bug fixed for reading orbitals from a ORCA output file

Bug fixed for drawing colorcoded planes (under windows OS)

13 Jyly 2011 :

NWChem is now supported

Geometry and charges can be read from a aimall sum file

10 June 2011 :

Bug fixed for animated vibration/threshold

Bug fixed : orbitals read from a molpro output file (define NOrb)

1 June 2011 :

Group of the third atom can be rotated in Draw Geom window.

30 April 2011 :

pair radial distribution

RMSD for a trajectory

Reading dipole from a ADMP output file and computing of auto correlation dipole function (not fully tested)

7 April 2011 :

Fourier Transformation in GabexitXYPlot window (not fully tested)

5 April 2011 :

Orthonormalization of Mopac MO (only normalisation on old versions)

10 March 2011 :

Local rotation bug fixed

Screen capture (using png or tif) under window bug fixed

22 February 2011 :

Show cell in Display window

Bug : Update coordinates after a move fragment

20 Junuary 2011 :

Read beta orbitals from fchk file : Bug fixed

Rotation of a fragment by mouse : bug fixed

22 December 2010 :

new tools for select atoms : multiple selection

20 December 2010 :

Atoms can be fixed dunring MD

Screen capture of geometry drawing window in ppm or bmp : A bug were fixed

02 December 2010 :

Multigrid method : multipolaire developpement at the center of charge. Multipole order 3 is now used.

Comformational search with semi-emperical : A bug fixed.

08 November 2010 :

add Space Fill option to "Draw Geom"" window

02 November 2010 :

Migration to OpenGL for "Draw Geom" window.

Remove DRAWGEOMGL variable from CONFIG file to obtain a "Draw Geom" with old style(Cairo).

25 October 2010 :

Bug fixed : Gabedit can now read the partial charges from Gamess (FireFly) output file

18 October 2010 :

Bug fixed : conversion from Hartree/Bohr to kcal/Ang for FireFly gradient

9 October 2010 :

The center of the molecule is not changed after insertion of atoms.

16 September 2010 :

Bussi thermostat implemented( velocity scaling)

G. Bussi and M. Parrinello,

"Stochastic Thermostats: Comparison of Local and Global Schemes", Computer Physics Communications, 179, 26-29 (2008)

10 September 2010 :

Andersen thermostat changed.

11 July 2010 :

Parallelization using OpenMP.

Parallelized Code :

- Computing of Grid for Orbitals, Electronic density, Electrostatic potential (Multigrid Method)

- Computing of AIM charges

- Computing of Coulomb integral

- Computing of Spatial overlap

- Computing of MM potential and its gradients

- Computing of NMR spectra

1 July 2010 :

migration from gtkglarea to GtkGLExt

08 Jun 2010 :

Text with rotation in XYPlot and ContoursPlot windows.

One can add margins in XYPlot and ContoursPlot windows.

One can add images (from file or clipboard) in the ContoursPlot window.

06 Jun 2010 :

Read orbitals, geometry and normal modes from a fchk Gaussian file.

Read grid from a openDX file.

One can add images (from file or clipboard) in the XYPlot window.

Bug fixed : screen capture of opengl window in png and tif files format.

05 May 2010 :

Reading of orbitals from the new mopac aux file format (including the compressed format).

New themes for the XYPlot and ContoursPlot windows.

01 May 2010 :

One can add texts (and change it) in the XYPlot and ContoursPlot windows.

One can add lines (and change it) in the XYPlot and ContoursPlot windows.

Save all data in a Gabedit file format on the XYPlot and ContoursPlot windows

Read data from a Gabedit file format on the XYPlot and ContoursPlot windows

The legend options can be changed by a double click on the legends

28 April 2010 :

The opacity for surface in openGL windows can be changed

The label bug under XYPlot window (with gtk2.18) is fixed

5 April 2010 :

The bond lengths can be fixed during a MD simulation.

1 April 2010 :

Partial optimization is now possible with the MM potential.

29 March 2010 :

Computing of spatial overlap matrix <ii|delra(ri,rj)|jj>.

A contours plotting tool have been implemented.

22 March 2010 :

Bug fixed : reading correctly the geometries with a Pd or a Cd from aux file

Add a tool for Optimizing geometry using/Sparkle from the Draw Geom window

New fast method for compute NMR spectrum

24 February 2010 :

Bug fixed : if disk is not C: (under window) for run Gamess

10 February 2010 :

Add PM6-DH2 to list of openmopac methods

09 February 2010 :

Add tif format to list of image formats supported by gabedit

01 February 2010 :

Bug to Add hydrogen with a NH2-terminal from a pdb template has fixed

15 January 2010 :

In animation Geom. Conv. tools of OpenGL window :

If ONIOM is in keyword, the HW and OW are writeen at "Low" layer in Gaussian input file.

The MM type are now readed from a Gabedit file (in GEOMS format)

11 January 2010 :

Gabedit can read geometries from a IRC Gamess, PCGamess(Firefly) file.

22 December 2009 :

In Draw geometry window, numbers of atoms are not changed after editing of atoms.

By default, only one surface is showed in Display Window(this can changed by the users).

10 December 2009 :

Bug fixed with error message after MOLECULAR ORBITALS from Gamess

Bug fixed for CltrZ and u : The geometry in xyz is now apdate after this operation.

Bug fixed for change by Measure window : The geometry in xyz is now apdate after this operation.

If f key is pressed, the selection is free even if one click on an atom.

If g key is pressed, the group attached to cliked atom is selected

9 December 2009 :

Bug fixed for reading dipole with "field-independent" basis from a gaussian output file

11 November 2009 :

the n,p, f and l keys can be used for selecting a geometry on the "Geom.Conv" window.

9 November 2009 :

Computing of the electrophilic, nucleophilic and radical susceptibilities for a molecule.

23 October 2009 :

Implementation of a tool to predict the masses and abundances of the isotopes for a given molecule.

Atomic weights and isotopic compositions for All Elements are taken from

http://physics.nist.gov/PhysRefData/Compositions/

21 October 2009 :

Bug fixed for creation of an orca input file with constraints.

19 October 2009 :

Bug fixed for reading beta orbitals form orca output file.

13 September 2009 :

Computing of AIM charges [See W. Tang et al J. Phys. Cond.. Matt. 21, 084204(09)]

3 September 2009 :

Copy images to clipboard.

21 August 2009 :

Computing of the <ii|1/r12|jj> coulomb integral, analytically with GTF and numerically with GTF and STF.

19 August 2009 :

The scale for the vibration vectors can be negative.

The threshold for the vibration vectors can be changed.

Gabedit can now read the raman activity from a Gamess or PCGamess output file.

The vibration vectors are added to the povray file.

23 July 2009 :

Gabedit can create a pov file and run povray interactively.

The povray and the opengl cameras are identical.

Show the MO coefficients.

Draw the DOS (the density of states)

Square a grid. (phi^2)

Apply a restriction to grid.

20 July 2009 :

Show coefficents of orbitals.

Draw the density of states.

11 July 2009 :

Orca 2.7 is now supported.

26 May 2009 :

Implementation of reaction path calculation with openmopac

Translation and rotation are removed at beginning of a MD simulation.

18 May 2009 :

Gabedit can create a input file for the 7.4 version of molcas : xyz, zmat, Full symmetry, ....

Migration from m2msi to grid format for molcas

Bug fixed for computing of electronic density if orbitals (from molden file) not sorted by occupation number.

13 April 2009 :

New capping possibility for the polypeptide builder.

A undo is implemented for the polypeptide builder.

2 April 2009 :

Gabedit can read the esp charges from Gaussian. Gabedit read the esp

charges. If they are not available, Gabedit read the natural charges. If they

are not available, Gabedit read the Mullekan charges.

20 march 2009 :

Gabedit can read the normal modes from a molpro 2008 out file.

Gabedit can read the first and last geometries from a gaussian out file with a "nosymm" calculation.

The problem of connectivity after the change of number of center (in XYZ geometry editor) is corrected.

19 February 2009 :

Undo / Redo have been implemented for the draw window.

17 February 2009 :

The user can set the value of the distance, bond angle or dihedral angle in the Mesure notebook.

3 color map types are implemented for the opengl window.

07 February 2009 :

The user has complete control over the bonds displayed in a drawing.

The drawing of the molecule atom by atom have been simplified.

The drawing of the molecule fragment by fragment have been simplified.

Gabedit read connectivities from gabedit, hin, pdb, mol2 and mol files.

18 January 2009 :

A bug is fixed : the beta orbitals from a MOPAC UHF calculation are normalized correctely.

No problem with the old versions of Gabedit for the Alpha orbitals from MOPAC.

14 January 2009 :

The bug for generation of Geometry with SYMMETRY for input file of Gamess or PCGamess has been fixed.

The bug for read geometrie during a MD Conformation search with PCGamess has fixed.

10 December 2008 :

All deprecated Gdk, Gtk and pango functions has removed.

The stick&ball can be scaled in the Display window.

The user can change the order of atoms by changing the number of atom in the Geometry editor.

The bug during read of geometries from a molpro log file is fixed.

30 November 2008 :

The background color of the Draw and Display windows are saved at the end of session.

They are restored in the next session.

The .dat Gamess file is copied in the directory of the input file at the end of the run.

One can run guassian under windows (locally) without runWg03.bat file

(but not tested. I have not gaussian under windows).

11 November 2008 :

A Molecular dynamics conformational search is implemented using a PM6/MOPAC or AM1/PCGamess method.

One can optimize, calculate the ESP fit charges and energy by MOPAC or PCGamess by one click

from the "Draw Geometry" window.

2 November 2008 :

Increase speed of selection on the XYplot window.

The identical molecular structures are removed after a Molecular dynamics conformational search.

24 july 2008 :

Migration from GDK drawing functions to Cairo: Cross-device Rendering for Vector Graphics.

Cairo is now used for the XYplot gabedit widget(used by gabedit for draw spectrums).

Cairo is now used for the geometry drawing window.

Geometry can be exported in eps, ps, pdf or svg file.

The curves of XYplot window can be exported in eps, ps, pdf or svg file.

New tool for compute distance between 2 points on XYPlot window.

"Control+left button" can be used for do a zoom on XYPlot window.

10 july 2008 :

A Molecular dynamics conformational search is implemented using a MM potential (Amber 99).

During the production stage Gabedit selects a number geometries.

At the end of the molecular dynamic simulation, each selected geometry is optimized.

Finaly the geometries are sorted by energy and saved in a file.

The very similar geometries can be removed by Gabedit.

Gabedit can also optimize these geometries, interactively, using Mopac or PCGamess.

Gabedit can also creates input files for Mopac, PCGamess or Gaussian for a post processing.

25 june 2008 :

Gabedit load the eps charges from a Mopac output file(last geometry) if one is available

24 june 2008 :

Under unix, the user can run gamess without any changes to the scripts of gamess.

18 june 2008 :

The user can set a title for the openGL window (Set/Title)

Gabedit can create slides for several orbitals by one

click(Orbitals/Slideshow).

25 may 2008 :

The user can change the coordinates of atoms directly from the list of atoms.

The user can change bond, angles and dihedral in the Z-matrix editor of atoms directly from the list of atoms.

Gabedit recalculate the bond, angle and diedral angle value considering the new atomic connectivity index.

19 may 2008 :

The bug due to not ordering atoms in a molden (from molpro) file has been

corrected.

6 may 2008 :

Gabedit can export the opengl window in eps, ps, pdf, svg file.

28 April 2008 :

New windows for ECD spectrum.

New windows for read NMR spectrum from a text file.

11 february 2008 :

MEP can be calculated from the charges of atoms

21 junary 2008 :

Gabedit can read the natural orbitals from Gaussian output file

13 December 2007 :

The MEP (Molecular electrostatic potential) can be calculated by Gabedit

MEP can be calculated by Multipole approximaiton

MEP can be calculated by solving the poisson equation

using Multigrid (V-cycle) or Congugate gradient methods

The surface for any function can be color mapped by the MEP

20 November 2007 :

Gabedit can show the SAS

7 November 2007 :

Cartoon mode fro draw geometry

New algorithm for compute NMR spectrum

Export of XY plot in svg format

26 octobre 2007 :

Export of XY plot in svg format

2 September 2007 :

Gabedit can read Q-Chem grid file

Gabedit can create an input output file of Q-Chem

15 March 2007 :

Gabedit can create an input output file of Q-Chem

1 March 2007 :

Gabedit can read the output file of Q-Chem(Orbitals+Vibration+IR+UV)

20 February 2007 :

Gabedit can read the output file of PCGAMESS(Orbitals+Vibration+IR+UV)

9 February 2007 :

Gtkplot library has removed.

New windows for draw IR, Raman and UV/Visible spectrum.

10 November 2006 :

Implementation of an "Unit conversion utility".

10 September 2006 :

Read the MD trajectory from a Gaussian output file.

17 June 2006 :

ELF : Compute Electron Localized function using the MO

30 May 2006 :

Contours for nagative values in dotted lines

18 May 2006 :

Compute Amber types of atoms using the symbols and the bonds types

Show multiple bonds type in Geometry draw window

Save correct bonds type in .hin file

Read Localized orbitals from GAMESS output file (RHF ou UHF)

Show multiple bonds in OpenGL, including with stick mode.

Create Povray geometry with multiple bonds.

The ability to select and freeze atomic positions during energy

minimizations(including the generation of appropriate keywords in the

GAMESS and Gaussian input file).

The ability to select and set the ONIOM Layer.

21 April 2006 :

Show/Hide hydrogen atoms.

Show symbols/distances in OpenGL window.

Find and show the cycles of a molecule.

6 June 2006 :

Read and show the geometries for a Gaussian (03) Molcecular dynamique calculation.

1 January 2005

Migration from Gtk+1.2 to Gtk+2. All deprecated functions and widgets has removed.

Gabedit is now a GUI for MPQC software.

Gabedit is now a GUI for Molcas.

The M2MSI ascii file (File generated by Molcas)(Orbitals and density ) is now supported.

Gabedit can display the hydrogen bonds.

You can build a nanotube.

You can now visualize the geometry convergence using a Dalton output file.

You can now read (and animate) the normal modes from a Dalton output file.

ssh protocole is now supported.

You can generate the initial structures of PolyPeptide, NucleicAcid and PolySaccharide.

You can optmize the geometry using MM calculation.

The ADF tape 41 file(text format)(Orbitals and density ) is now supported.

The difference between 2 densities is now supported.

I added a window for facility the use of Open Babel.

I added a window for draw Infra Red and Raman spectrums.

Molpro2002 is now supported.

Gaussian03 is now supported.

Gabedit can now create an isosurface colorcoded with another grid.

You can also visualize the geometry convergence using a Molden or a Gabedit file.

you can now read frequencies and normal modes from an ADF(version 2004) output file

you can now create a MNG (or GIF) animated file (for vibration and rotation).

Gabedit can now create a povray file for geometry, surfaces (including

colorcoded surfaces), contours (colorcoded), colorcoded planes.

Gabedit can now visualize several surfaces.

Gabedit can now animate the contours and the colorcoded planes.

You can now read normal modes of imaginary frequencies from a Molpro output file

You can now visualize the geometry convergences, loaded from a Gabedit,

Gaussian, Molpro, MPQC, XYZ or Molden file. You can also create a MNG (or GIF)

animated file from this visualisation.