Versions 3.x

Main view of the command panel and the rendering window showing pair measurements with path visualisation of a vacancy in silicon under tension 0.5% conditions. Another dialog display the bond length distribution in this simulation box of 215 silicon atoms.

V_sim uses two main windows, one to render the node set, and one with all the commands and the configuration tools. Look at the user guide for further details.

The rendering window receives some new hot keys:

• < Ctrl > + v is used to bring the orientation dialog chooser, where one can specify the camera orientation along axis, in box coordinates... This goes with a revamped camera menu with hot keys for prefered cameras. Prefered cameras are also now saved in the parameter file.
• < Ctrl > + f is used to show an information bar with a search field to highlight a node when one knows its id.
• n and p are used to load the 'next' or the 'previous' checked file in the browser list.

The colourisation can now display a legend for the varying parameter. When using the manual range for input normalisation, it is possible to restrict the colourisation to values in range only, having an easy way to colour only some relevant nodes.

The ab initio code BigDFT, doing electronic structure calculations over wavelets, received its own plug-in.

With it, V_Sim can read the compressed form of BigDFT wavefunctions directly from the density panel (either in plain text, Fortran binary or ETSF file format).

When activated, the parser of BigDFT can be used instead of the one of V_Sim for ASCII, xyz and Yaml file format. This allows to see the box as used by BigDFT natively and also to visualise the two wavelet grids used by the code.

This plug-in introduces also a new panel, where the user can launch a calculation on its own machine or connect to calculation running on a server. Data can be lively retrieved during the run (like the two highest occupied wavefunctions, the density) at each SCF step and displayed simply in V_Sim.

The SVG (and PDF) output received some upgrade. They are properly displaying dashed lines for binding between nodes (in wire mode, as in OpenGL). The point shape in atomic rendering in now also properly printed in SVG output. Nodes and lines partially visible are now properlly rendered.

V_Sim now registers its opened and saved files in the recent list of the GTK file chooser making desktop integration better.

Introduced by BigDFT, V_Sim now support natively (if libyaml is present on the system) the BigDFT Yaml structure file format. The use of Yaml makes this format very versatile and user friendly. It can store many additional information like forces, total energy...

For file formats that can store them, V_Sim can now display forces applied on atoms, without using the spin rendering mode. The Atomic rendering mode gets a new option to display forces natively with an automatic scaling or a manual one.

In this version, ASCII, xyz, XSF and Yaml file formats support this.

The pair dialog has been reworked a bit to allow to use several rendering mode for each pair. One can easily set-up a cylindrical pair rendering for bulk silicon distance and use a dashed line for some specific defect distance in the same silicon for instance.

The pair dialog has tabs now. The first one is still used to defined pairs between species. The second is used to plot a bond length distribution, i.e. the g(r) function.

The graphs shows the bobnd length distribution for a given species or for all, and can detail the distribution between different chemical species. On the shown example, the distribution is displayed for silicon atoms. Grey bars represent the distribution for all silicon atoms, while coloured lines represent the distribution for silicon with silicon (green) or silicon with hydrogen (white).

In addition, one can use this tool to display some information, like the number of neighbour in a certain distance range, or the mean length value in a certain range also.

Following the positions of atoms during a geometry evolution (saddle point search or geometry optimisation) is possible using the paths. The total energy of the system codes the colour projection on lines.

On the given screenshot, arrows have been added using Inkscape as post-processing.

The SVG and PDF exportation file formats have been extended. They support now:

• fog application;
• legend output;
• colourisation as defined in the data file tab;

Improvements of the coloured maps, adding marks in the legend for the iso-lines and creating identical iso-lines on all cutting planes. Internally, the rendering has been changed to use an adaptive mesh.

The quick pick with right click on a node in the rendering window can now print coordinates either in cartesian values or in reduced values, thanks to an option in the configuration tab.

Usage of GObject Introspection allows to script V_Sim in Python or other languages. A tab has been added to easily load and execute Python scripts. This capability is still experimental and requires last versions of GObject Introspection (> 1.9) and PyGObject (>2.28).

In this example, a new input file format is added to V_Sim to read CNT files from VASP.

Python module

Compiling a Python module from the source code of V_Sim enables the capability to call different V_Sim routines in Python.

On this example, a Python program reads an ABINIT input file, and for each dataset of this file, it can create directly in Python an object that will be given to V_Sim to render the given data:

O = v_sim.element("O", rgba=(1., 0.2, 0., 1.))
H = v_sim.element("H", rgba=(0.2, 0.4, 0.5, 0.3))

data = v_sim.data()
data.setPopulation({O:1, H:2})
data.addNode(O, (2.5, 2.5, 2))
data.addNode(H, (1.5, 2.5, 1))
data.addNode(H, (3.5, 2.5, 1))
data.setBox((5., 0., 5., 0., 0., 5.), True)

Geometry evolution

Doing an ab initio geometry relaxation or investigating a low energy path often requires to understand the moves of different atoms in the simulation box.

Checking a single box a load a new file will now highlight atom moves with arrow, visualising the direction and the amplitude of the moves between the previous file and the new one. For the most important moves, the actual distances between the two files are also printed.

Easy camera navigation

Using the 's' and the 'r' keys now enable the possibility to save and restore several camera settings. These settings are also selectable in the rendering window as a popup menu, clicking on the small magnifier ison in the right bottom corner.

Vibration and phonons

Thanks to the work of Jérémy Blanc, V_Sim can now animate vibrations in molecules or phonons in solids. A new tab has been introduced to list a set of phonons. One can navigate in them. The atoms can move accordingly to there vibration properties. In addition the moves can be represented by arrows.

Available screencasts:

• vibration in a molecule, OGG (8MB): vibrations.
• phonons in GeMn, OGG (30MB): phonons.

In solids, the imaginary part of the displacements and the q.r shift in taken into account.

Multiple coloured maps

The coloured map tab get several new capabilities:

• Several maps can be printed at once and the border of the maps are now smooth.
• The coloured scale can be linear or logarithmic.
• The maps can be exported into PDF or SVG for later use.

Measurements: distances and angles

In addition to the previous distance printing capabilities, it is possible to draw the angles. A convenient tool allows also to print at once all the first distances of a node and the relevant angles linking first neighbours.

Knowing about the physical unit

For the file formats that support units, one can switch between angstöms and bohr easily.

More surface tools

Several new tools have been designed to handle surfaces in a more detailled way. As an example, each surfaces has now a name or not. In the latter case, the resources of the surface are private to this surface (all changes do not affect the other surfaces). A special 'add button' in the panel has been designed to compute several surfaces at once (as in the build dialog). Finally the surface are now sensitive to the masking effect of planes and it is customizable per surface.

Preview in open dialog

Both both the atomic and the spin rendering methods, the opening dialog is available with a preview of the selected file. It shows the box and the nodes in the current state of the camera. The list of available elements is also displayed.

Smooth and edge

A rendering mode highlihgting polygons is available. It helps seeing planes and can be set on selected drawing elements (planes, surface but not nodes for instance).

It is possible to seen on this specific view the smooth cut produced by planes on surfaces. New polygons are created to complete the edge of the surfaces.

Background image

It is possible to set a background image over the uniform background colour. This image keep its scale ratio but its size is tuned to fit the viewing window.

An application for this capability is to super-impose microscopy images with atomistic modeling. The screenshot gives the example of a gold incommensurate boundary with a chevron reconstruction. The atomistic model is the stable configuration computed with a force field corresponding to the reconstruction. See the article published by F. Lançon, T. Radetic and U. Dahmen in Physical Review Letters, reference Vol. 89, n°8, p. 085502 (2002).

Recursive navigation

The browser panel has been modified to be able to list several directories at once and this is also used to show a recursive treeview of the file systems from one point.

Extended orientation chooser

Each time an orientation is required in V_Sim (as to set the camera view or to choose the plane normal vector), one can use a new dialog that propose three ways to select it. The first is the classical cartesian coordinates but the spherical system is also available. The last possibility is to choose the orientation in the box basis set as define by Miller's indexes for instance.

Periodic replication of the system

In addition to the periodic translations inside the super-cell, the box replication expand the system by copying the elements in the three space directions. The increase is smoothranging from only some percents of the initial size to five times de original size. All capabilities are also expanded, including planes, pairs and surfaces.

Further customisations for pairs

It is possible to declare more than one pair link with different distance criterions. This can be used to highlight multiple degrees of order in a system. For the wired pairs, a pattern can now be chosen. Finally, an 'auto-set' button is now available to compute the distances of first-neighbours.

Spins & atoms rendering

With this capability, atoms and spins can be rendered in the same time, allowing both spheres and arrows. A new option has been set to choose for the rendering of spin with null modulus : always drawn, nerver or using the atomic rendering instead.

Density representations

The iso-surface subpanel has been modified to allow to directly load scalar fields. Surfaces can be added, modified or removed on the fly. The name of each surfaces is also now editable.

Using plugins, densities can also be read from files conforming to specifications from Nanoquanta (see the ETSF page).

Nodes associated data

In the interactive dialog, informations on picked nodes are detailed in a table, showing associated data. Such informations are the colorisation informations for instance or the direction in the spin rendering method. For the former rendering method, values are editable on the fly.

Coloured map

A new subpanel allows to draw a cutting plane with a coloured map of a density. The plane is choosed from those defined in the plane subpanel and the scalar field is taken from the loaded files of the isosurfaces subpanel. Several shades are available and a legend is drawn. It represent the minimum and maximum value of the scalar field.

Printing distances measurements

Within the observe & pick dialog, picked distances are now printed directly on the rendering window. These labels are persistants which means that they connect the same atoms even if the rendered file is changed (at least if composition is equivalent between different files). This allows to spy on one or several distance evolution in a molecular dynamic for instance.

Command line

There are now more actions from the command line. It is possible, for instance, to draw some planes reading an XML file or directly apply some translations as soon as V_Sim is launched. All colorization funstionnalities have also ther own parameter in the command line. Use v_sim --help for complete list.

More talkative

The rendering window has been modify to show a status bar which shows some usefull informations such as picked distances or current action. An other line has been also added and it prints informations about the rendered file : number of nodes, description if the file format allow some.

Automatic colorization

The colorization subpanel has been reworked toward accessibility and for better easiness. Predefined shades has been added for instance proposing standard shades such as blue to red... Moreover, a checkbox asks V_Sim to automatically load a data file when a position file is rendered using its name as a search pattern. Finally a new tool allows to hide some atoms depending on the data contained in the data file. With such a functionality, it is easier to focus on atoms where data are relevant.

Planes drawing

This new subpanel is an interface to create planes. They are defined by a normal vector and their distance to the origin. Multiple planes can be drawn at a time. They can mask nodes on one of there size. When multiple planes are used, all nodes that are hidden by at least one plane are not drawn.

Spin rendering

It is now possible to draw arrows instead of spheres (i.e. drawing objects that are defined by their position and orientation in space). It can be usefull to represent spin values in magnetism area. The color is customizable and a specific mode allows V_Sim to colorize the arrows according to their orientation, as used in the screenshot.

Drawing sufaces

The source code of 'Visualize' program written by Luc Billard has been merge with V_Sim code to enable a surface drawing capability. This opens possibilities to draw electronic iso-density or complex surfaces boundaries... Moreover, an interface has been created to easily convert scalar fields to surfaces files (see their description).

Applying periodic translations

Within the pick/observe window, there is a new tool to apply translation values to the element in the box. On the screenshot, we can see the spin sphere translate to the border of the bounding box and cutted by a plane. Since the translation is periodic one, only input files with periodic boundaries definition can use the translation tool (see the formats page to know which input file is periodic or not).

Pairs management

The pairs dialog window has been changed since 2.x versions. From now on, color can be selected for each kind of pairs. A new way to render pairs is available: cylinders can be used instead of simple wires. The colors of cylinders can be user defined colors or they can share the same colors than the atoms they are linking together.

Browser subpanel

There is an option in the brwoser subpanel to automatically read the next selected file in the list at periodic intervals. The period can be chosen from 10ms (if computing power allows it) to several seconds. This is ideal function to follow a simple process in a molecular dynamic. Moreover the observe action is steal possible when playing files, allowing to change the point of view on the fly.

OpenGL subpanel

Some tuning of OpenGL option is now possible: the precision of drawing (number of polygons used) is customizable from 10% to 300% of normal rendering. The antialiasing of line can be activated. And finally, the rendering can be done in smooth polygons (normal), flat or wireframe.

Colorize subpanel

This is a new subpanel to colorize atoms from data of an external file. The data file has n columns and data is linearly combined to colorized the atoms in RGB or HSV mode.