press F8 to apply inversion symmetry
Now we will continue to edit the H2O2
molecule. If we select the O-O bond and change interatomic distance -
only one atom will move. If we want to move a group (O-H), we have to
highlight this group first.
[PLACEHOLDER: screenshot — H₂O₂ molecule with the O–O bond selected (shown in blue); no atoms highlighted yet — the starting state before pressing F7]
There are different ways to highlight atoms into a group. One can do
this manually, clicking on an atom with pressed Shift button. Or, it
is possible to highlight connected (bonded) atoms, in respect to a
selected bond. Select an O-O bond and press F7 button. All atoms,
which are connected to the first selected atom will be 'highlighted', and
shown as cyan-colored. Finally, holding a Shift key, and dragging a
rectangular area by mouse - all atoms inside this rectangle will
become highlighted.
Now we can move all highlighted atoms simultaneously:
If you change the length of the O-O bond, all highlighted group will
move accordingly. Note that unselection (Space key, or mouse middle
click) will remove selection first, and the second use of unselect
button will remove highlighting of a group.
The modified value (of a bond length or an angle) is shown on the
information line of the screen. Sometime you would like to observe
another value during a modification of coordinates. To achieve such
behavior, select a bond, or an angle, and press F6 button. Now you
can make another selection and make modifications in the geometry.
But in this case originally selected value will be watched. Pressing
Shift-F6 key switches off the watching mode.
GV contains a short list of
molecular fragments, which can be added to a molecule. Press F3 key,
to get a list of available fragments. Clicking on a picture with a
fragment, you will add this fragment into your screen. If no atoms
are selected, the fragment will be added somewhere around the current
molecule. If one atom is selected, the fragment will be inserted near
the selected atom. Note, that once a fragment has been selected, an
Insert key will insert this fragment.
Example. Let's make mesitylene (1,3,5-trimethylbenzene).
[PLACEHOLDER: screenshot — benzene with 3 alternate hydrogen atoms highlighted cyan (Shift+click); the other 3 H atoms and all 6 C atoms are unchanged]
select another C atom, and press
Insert
select third C atom, and press Insert
To make modifications of coordinates via distances and angles, you
might need dummy (reference) atoms. These dummy atoms can be set by
End button. If there is no selected atoms, 'End' key will add dummy
atoms located on X- Y- and Z- axis. If a bond is selected, the dummy
atom will be placed in the middle of the bond. For example, if you
have a planar molecule, but it is not oriented according to Cartesian
axis, you can add dummy atoms on each axis, highlight all atoms in the
molecule, and select a dihedral angle between the plane of the
molecule and desired plane, created by dummy atoms.
Program GV can recognize the
symmetry elements of a molecule, or apply symmetry operations for
all, or highlighted atoms in the molecule. If no selection is made, F8 key
displays symmetry elements of the molecule.
Two symmetry engines are available: msym (default) and
findsym. Press Shift-F8 to toggle between them.
If some atoms are selected, F8 key will apply a symmetry
operation: in case of only one atoms being selected inversion, in
case of a bond, translation or C2 axis, and
in case of an angle - a mirror plane. This feature can be used to
construct symmetrical molecules.
Let us start from a benzene molecule. Delete two hydrogen
atoms (in ortho positions), and select two carbon atoms (with broken
bonds). Press 'v' to use C2 instead of
translation. Pressing F8 key will duplicate the structure, creating
naphthalene.
If,
during such transformation coordinates of a new atom are very close
to another atom - the average coordinates will be used. For example,
if you have an almost planar molecule, you can flatten it, by
applying a mirror plane symmetry. Let move one carbon atom in benzene
out of plane for a small angle.
Now
we can select 3 carbon atoms, and press F8 to mirror the molecule.
Moved carbon atom will return into the plane.
Also
note, that if a part of the molecule is highlighted, the symmetry
operation will be applied only for highlighted part.
In the example
below, we highlighted 2 atoms, and select 2 another. F8 will translate
highlighted group into vector defined by selected atoms.
GV can be customized. Press F9 key
to save current setting. It will create a directory .molcasgv
in user HOME directory, with default settings for used colors,
initial sizes etc. User can edit this files to reset the default
values.
GV can remember a ViewPoint (the
current orientation of the molecule) and save it to a file. Later
this file can be used to rotate another molecule accordingly. Use
keys (v/V) to save or restore Viewpoint.
In some occasions, user would like to change the order of atoms in
XYZ file. Although the simplest way to do this includes usage of
editor, GV provides some tools for
resorting. If two atoms are selected, and # button pressed, selected
atoms will exchange their order. Pressing # resorts atoms.
GV provides some possibilities to
modify appearance of the picture. To highlight some part of the
molecule,
user can highlight a part of the molecule, and use '-' key
to make these atoms looks pale. 'A' key changes the
look of
atoms.
[PLACEHOLDER: screenshot — molecule with some highlighted atoms rendered pale/faded using the ‘−’ key; the highlighted group appears washed out against the fully opaque rest of the molecule]
GV understands some extensions of
XYZ file. At the end of XYZ file it is possible to add lines #sphe
(followed by 2 coordinates), #axis (followed by 2 coordinates), #tria
(followed by 3 coordinates) to add correspondingly a sphere, an axis,
or a triangle.
Tutorial: Loading CIF and SEWARD/GATEWAY files
GV automatically recognises CIF
and MOLCAS SEWARD/GATEWAY input files and converts them to XYZ
internally — no external tools required.
CIF files (Crystallographic Information Files, extension
.cif):
Run gv structure.cif
GV reads the unit cell,
symmetry operators, and atomic coordinates, expands them into the
asymmetric unit, and displays the result.
[PLACEHOLDER: screenshot — GV window showing a crystal structure loaded from a .cif file,
with unit cell axes visible]
SEWARD/GATEWAY input files (MOLCAS input, typically
.inp or any file containing
&GATEWAY or &SEWARD):
[PLACEHOLDER: screenshot — GV window showing a molecule loaded from a MOLCAS .inp file;
compare with the original input to show correct geometry expansion]
Tutorial: Periodic structures and cluster generation
When a coordinate file contains unit cell vectors (e.g. an XYZ
file exported from a periodic calculation, or loaded from a CIF), GV
shows the cell axes on screen and enables cluster generation.
[PLACEHOLDER: screenshot — GV showing a periodic crystal structure with the three unit cell
axes (a, b, c) drawn in red/green/blue]
To generate a cluster of concentric shells around a chosen atom:
Click on the atom that should be
at the centre of the cluster (it will be highlighted in blue).
Press C.
GV builds a supercell, cuts
it into clusters of increasing radius (each adding one coordination
shell), writes them to
basename_clusters.molden, and
immediately opens that file. The largest cluster is shown first.
Cell axes are removed and the atom selection is cleared.
[PLACEHOLDER: screenshot — atom selected (blue) in a periodic structure before pressing C]
[PLACEHOLDER: screenshot — largest cluster loaded from _clusters.molden;
selected atom is at the origin, surrounded by coordination shells]
Use PageDown to step through smaller clusters
(or PageUp for larger ones). The cluster frames are stored in
Molden geo format, so all the Molden navigation keys apply.
[PLACEHOLDER: screenshot — a smaller cluster after pressing PageDown several times;
status bar shows current frame number and atom count]
Tutorial: MOPAC geometry optimization
GV can drive a MOPAC semi-empirical geometry optimization and
reload the result directly, without leaving the viewer. This
requires the $MOPAC environment variable to
point to the MOPAC binary.
Setup (once, e.g. in ~/.bashrc):
export MOPAC=/opt/mopac/mopac
export MOPAC_KEYWORDS="PM7 GNORM=0.01"
# optional; default is PM6
Open an XYZ file in GV.
Make sure no atoms are selected
(press Space or middle-click to deselect).
Press M.
GV writes a .dat input file, runs
MOPAC, parses the optimized Cartesian coordinates from the
.out file, overwrites the
.xyz file, and reloads it.
[PLACEHOLDER: screenshot — molecule before MOPAC optimization (e.g. manually distorted geometry)]
[PLACEHOLDER: screenshot — same molecule after optimization; status bar shows
"MOPAC done" or similar; bond lengths are now at equilibrium values]
Note: this feature is not available in the WebAssembly build.
Tutorial: Watch mode (auto-reload)
Watch mode lets you monitor an ongoing calculation in real time.
GV polls the current file and automatically reloads it whenever the
file changes on disk.
Open the output XYZ file that your
calculation is writing to (e.g. opt.xyz).
Press F6 to start watching.
Each time the calculation writes a
new geometry, GV reloads and displays it. Use m to animate
through the accumulated frames.
Press Shift-F6 to stop watching.
[PLACEHOLDER: screenshot — GV in watch mode; status bar indicates "Watch: opt.xyz";
molecule is mid-optimization with partial geometry change visible]
Watch mode works for XYZ, molden, and multi-frame files. It is
particularly useful combined with m (animation) to see the
trajectory build up as the calculation runs.
Record and Playback
GV can record a session to a text
file and play it back later. This is useful for creating reproducible
demonstrations, automated tests, or batch processing scripts.
To start recording, launch GV with:
gv --record session.gvr molecule.xyz
All keyboard, mouse, and menu events are written to
session.gvr with millisecond timestamps.
To play back:
gv --play session.gvr molecule.xyz
The playback file may also contain script directives (without
timestamps) to control the session:
|
Directive
|
Purpose
|
|
speed <factor>
|
Playback speed multiplier (e.g. 2.0 = twice as fast).
|
|
wait <ms>
|
Insert an extra pause (milliseconds) before the next event.
|
|
open <filename>
|
Load a different molecule or grid file during playback.
|
|
status <text>
|
Display a message in the GV status bar.
|
|
echo <text>
|
Print a message to standard output.
|
Lines beginning with # are treated as comments.
[PLACEHOLDER: screenshot — GV window during session playback; status bar shows “Playing back session.gvr”; molecule is mid-rotation or mid-edit as the recorded events replay]
Batch Export and Headless Rendering (OSMesa build)
For server-side or automated rendering without a display,
GV can be compiled against the OSMesa
off-screen rendering library:
make osmesa (requires
libosmesa6-dev)
The OSMesa build renders entirely in memory; no X11 display, GPU,
or xvfb is needed. Combined with the
-q flag, it exports PNG images and exits:
gv -q -o all -v molecule.lus
This exports every orbital to separate PNG files named
molecule_MO001.png,
molecule_MO002.png, etc. The -v
flag applies an automatic best viewpoint. The -o
flag accepts all, a single number, or a
comma-separated list of orbital numbers.
[PLACEHOLDER: screenshot — a directory listing or file manager showing the exported PNG files (molecule_MO001.png, molecule_MO002.png, …) produced by the OSMesa headless build]
WebAssembly / Browser Build (Emscripten)
GV can be compiled to WebAssembly
for in-browser visualization:
make -f Makefile.emscripten
(requires Emscripten SDK)
The browser build provides the same core visualization features as
the native build. Grid density differences (Diff menu in the
toolbar) are fully supported: load a second .lus
file, choose Minus or Plus and Same-space or
Align (Kabsch rigid-body alignment), then click Compute
Diff to display the result immediately.
The following features are not available in the WebAssembly
version:
MOPAC geometry optimization (key
M) — requires a local binary.
Sub-window multiview panels — the
browser uses canvas overlays instead.
Font mode cycling (key
F) — font is fixed.
Key remapping via
gv.keys file.
Record/playback (--record /
--play) — file access is sandboxed.
The JavaScript interface exposes functions such as
gv_load_file,
gv_compute_diff,
gv_key_page_up,
gv_save_png,
gv_make_clusters, and others, allowing
the browser UI to control GV programmatically. PNG images are
downloaded directly via the browser's download mechanism.
[PLACEHOLDER: screenshot — GV running in a web browser; toolbar buttons (Save, Diff, Actions, Options, Colors, Cell) are visible at the top; a molecule or orbital is displayed in the canvas below]
Visualization of orbitals with GV
To visualize orbitals and density by program GV
you have to compute a grid file (.grid)
first by using GRID_IT program from
MOLCAS package.
Note that the quality of the picture depends on
the keywords used in GRID_IT input.
Orbitals can be browsed by PageUp/PageDown key, or selected by a
menu, invoked by the right mouse button. If you know the symmetry and
number of an orbital, you would like to display, you can press F4 (or
=) key, and press # followed by symmetry and orbital number, e.g. (#
1 3).
In order to change isosurface value, you can use + or - key, or
press F4 key, and type a desired isosurface value.
Sometime you would like to filter orbitals, shown by GV.
Pressing Delete key you can hide an orbital. All hidden orbitals will
become visible if Insert key is pressed. Alternatively, you can apply
a filter to hide some orbitals by a criteria: symmetry number (s),
orbital energy (e), occupation number (o), or typeindex (i). Usage of
filters is clear from the following example: Press F4 key and type #:
followed by a filter command - #:s14 to display orbitals only
from symmetry 1 and 4, #:e-2:1 to display orbitals in an
energy range between -2 and 1.
When the grid file is loaded, GV
displays subspaces (frozen, inactive, RAS1, RAS2, RAS3, secondary,
deleted). User can modify the typeindex of the orbital, save (F2 key)
the INPORB file (it will have an extension GvOrb),
and use this file in the following RASSCF
calculation without having to reorder the orbitals. In order to
modify the index of the displayed molecule, user can use a menu, or
press one of the keys: fi123sd. Pressing Space key (or middle mouse
button) changes the typeindex in a loop.
It is possible to display all orbitals of the grid file
simultaneously. Press F3 key to get the screen with all orbitals.
By default, the background (rainbow colors) for each orbital
corresponds to the type index information. Clicking on an individual
orbital you can use the same keys to modify it's type, or delete it
from the screen. Pressing F3 button again, or Escape will close the
multiview mode. Using PageUp/PageDown in multiview mode will
increase/decrease the sizes of subscreens. These features of GV
can be quite helpful for selecting the different orbital spaces in
RASSCF calculations.
GV can also be used to compare
densities from different GRID_IT
calculations. A command
gv --minus scf.grid rasscf.grid --out diff.grid
computes the density difference (SCF − RASSCF) and writes it to
diff.grid. The shorthand flags --minus
and --plus are equivalent to
-a -1 and -a 1
respectively.
The simplest case requires both grid files to have the same mesh
(same Net= dimensions). If the two
calculations used the same coordinate frame but different mesh
resolutions, add --same-space: GV will
trilinearly resample the first grid onto the second grid’s mesh
before forming the linear combination.
If the two densities come from slightly different molecular
geometries (e.g. consecutive steps of a geometry optimisation or
points along an IRC path), use --align. GV
checks that both files contain the same atoms in the same order, verifies
that no atom has moved more than the displacement tolerance
(default 2 Å, overridden with
--align-tol), and then computes an optimal
rigid-body transformation (Kabsch rotation + translation) from the
paired atom positions. Grid2 is resampled onto grid1’s coordinate
frame using trilinear interpolation, the linear combination is formed,
and the result is written on grid1’s mesh with grid1’s atom
positions. The alignment RMSD is printed to stderr so you can check
whether the fit is reasonable:
gv --align --minus step_001.grid step_002.grid --out ddiff.grid
For the interaction-density workflow (comparing the density of a
complex AB to the sum of its fragments A and B in ghost-atom
calculations) the grids must share the same coordinate frame. Compute
the fragment sum first:
gv --plus A.grid B.grid --out sum.grid, then subtract
it from the complex:
gv --minus AB.grid sum.grid --out interaction.grid.
Electrostatic Potential (ESP) Surface
GV can compute and display an
electrostatic potential (ESP) surface: a Gaussian-blended van der
Waals isosurface colored by the Coulomb potential, with red for
electron-rich (negative) regions and blue for electron-poor (positive)
regions. The ESP is computed as
E(r) = ∑i qi / |r − ri|
where qi are point charges at the atomic positions.
Three sources of charges are supported.
From Molden charges (Mulliken or LoProp)
If a .molden file is loaded that contains
a [CHARGE] (MULLIKEN) or
[CHARGE] (LOPROP) section, the ESP
surface can be computed directly:
Right-click → ESP
surface → Compute from Molden charges
(native build).
In the browser build, use the Actions menu →
ESP surface (Molden charges).
LoProp charges (if present) are preferred over Mulliken charges
when both sections exist.
From an XYZ+charges file
A plain-text file with one atom per line in the format
N
comment
Element x y z charge
...
where coordinates are in Ångström and charges in
electron units (e), can be loaded via Right-click → ESP
surface → From XYZ+charges file (native) or the
Actions menu in the browser build (upload button).
From a Gaussian Cube EPOT file
A Gaussian Cube file (.cube) containing
an electrostatic potential grid — as produced by Gaussian,
ORCA, or similar programs — can be loaded via Right-click →
ESP surface → From EPOT grid (Cube format) or the
Actions menu in the browser build (upload button).
The atom positions from the currently loaded file are used for the
van der Waals surface; the cube grid values are interpolated onto the
surface vertices by trilinear interpolation.
Cube coordinates are converted from Bohr to Ångström and
values from e/Bohr to e/Å automatically.
The color range is auto-scaled from the cube data.
Generating an ESP grid from a Molden file (Python script)
The script molden2esp_lus.py (included in
the GV distribution) reads atom positions and Mulliken/LoProp charges
from a Molden file, computes the Coulomb ESP on a 3-D grid, and
writes a Luscus .lus file with
GridName= Electrostatic that can be
loaded into GV as a regular grid file for isosurface display:
python3 molden2esp_lus.py scf.molden esp.lus
python3 molden2esp_lus.py scf.molden esp.lus --step 0.2 --pad 3.0
The --step option sets the grid spacing in
Ångström (default 0.25) and --pad
sets the margin beyond the van der Waals radius of each atom
(default 3.0 Å). The script requires only the Python
standard library.
[PLACEHOLDER: screenshot — ESP surface on a small molecule; red region near electronegative atom (e.g. O), blue region near electropositive hydrogen; color bar or legend optional]
Controlling the ESP display
The color mapping uses three parameters (defined in
esp.c):
esp_max_value
— ESP magnitude (e/Å) at which the color reaches full
saturation (default 0.10).
esp_white_region
— ESP magnitude below which the surface appears white
(default 0.025).
esp_color_pos
— RGBA color for positive ESP (default blue,
0,0,1,0.7).
esp_color_neg
— RGBA color for negative ESP (default red,
1,0,0,0.7).
Use Show/Hide ESP surface to toggle visibility without
discarding the computed surface, and Clear ESP surface to
remove it. Loading a new file clears the ESP surface automatically.
order to make modifications of coordinates we have to select one,
two, three or four atoms. Selection is made by clicking on an atom.
The first selected atom is covered by blue-colored net, the following
selected atoms are covered by magenta-colored net. The number of
selected atoms determines the behavior of GV.
If only one atom is selected - any operations will refer to this
atom, if two atoms are selected - any operations will be done for the
bond, connecting these atoms, if three atoms are selected -
operations will be performed for the angle, and finally, four atoms
defines the dihedral angle. As a general rule - '+/-' changes the
value of selected object, PageUp/PageDown changes the property, = (or
F4) allows to set up the value. 
