• Gxsm at a glance
• Supported Instruments

Introduction

A example: The STM Image at the right shows a atomically resolved surface of a with about 2 Monolayers of Germanium covered Silicon 100 crystal surface. Brighter mean the ''atoms'' are at a higher layer. The structure made of overlapping ''balls'' looking like a mesh represents the local density of states - or just density of the electrons seen by the STM tip at the surface. The maxima can be interpreted as the positions of the atoms of the top layer... Gxsm is powerful, it is easy to extend via plug-ins, it is unlimited in data size... and it is a free and open source software hosted by SourceForge! It is based on the Linux Gtk+/Gnome development environment.

And it's free: Gxsm is licensed under the terms of the GNU General Public License (GPL).

Gxsm at a glance

• Support for STM, AFM, SPA-LEED, SARLS, and any other 2D (2D layered and multi-channel) data-acquisition method can be supported by Gxsm.

• The Gxsm core handles multiple channels of 2D (layered) data fields of arb. type and unlimited size and a grey-scale or false color view of 2D data image, using ''on the fly'' data transformation as there are:
  • ''Quick'': a line regression and subtraction is performed on each scan-line
  • ''Direct'': only contrast and brightness adjustments
  • ''Logarith.'': logarithmic scaling mode, almost used by diffraction methods
  • ''Horizontal'': automatic line average subtraction
  • ''Diff.'': view of X-derivative,
  • ''Periodic'': like ''Direct'' Mode, but grey-scale is applied modulo #grey-levels
  • More sophisticated background correction and data analysis methods are implemented as filters.

• Data presentation is by default a (grey or false color) image but it can be switchted to a profile view (1d), profile extraction on the fly... Or you can use a 3D shaded view (using MesaGL) which now offers a sophistacated scene setup.

• The ''high-level'' scan controller is now separated from the Gxsm core and is build as PlugIn, while the real-time ''low-level'' scanning process, data-acquisition and feedback loop (if needed), runs on the DSP - if present, else a dummy image is produced. The current scan-line, marked in red, can be viewed simultaneously as profile. (View->red Profile)

• Extremely flexible configuration of user settings and data acquisition and probe modes.
  • Easy to extend by Plug-ins, some examples of existing Plug-ins:
    • Math operations on 2D data:
    • Background correction methods
    • Image filtering 1D and 2D, including several Fourier transformation methods
    • Image analysis/statistics: histogram, step analysis, ...
    • Geometric transformations: scaling, rotation, affine, ...
    • and more, write and contribute your favorite math Plug-in for Gxsm! Don't be afraid, there is a step by step instruction tutorial and a math Plug-in generator, all you need to do is to add your math code!
  • Special datafile/formats import/export filters, (easy to extend via PlugIns):
    • a set of simple raw formats (.byt,.sht,.flt,...) see docu for details!
    • Grey Images in .pgm format (P5 type)
    • digital NanoScope data import (some versions)
    • Omicron Scala
    • WxSM (in preparation)
    • Park Scientific (AFM, basic import support)
    • Targa (.tga) export, in 8/16/24bits color depth
    • any NetCDF file containing a 2D data array
  • Special instrument control Plug-Ins:
    • a Scan Control Panel
    • SPM: DSP Control: Feedback and Scan Characteristics (Speed, ...)
    • SPM: Mover/slider and auto approach controls
    • SPM: flexible Probing: Spectroscopy (STS), Force-Distance Curves (AFM), using the DSP also Digital LockIn Probing (e.g. dI/dU (U)) is possible without any additional hardware! But not only SPM, I already ran our Quadrupole Mass Analyzer with it!
    • SPA-LEED: Peak Finder, Focus-Tool, Rate-Meter, Peak Intensity Monitor
    • SPA-LEED Control (used with SPA-LEED test module)
    • CCD control (very special)
  • NanoPlotter Plug-in: reads simple HPGL files and moves along the plot path using predefined DSP settings (U, I, Feedback Parameters, Speed, ...) for ''Pen-Up'' and ''Pen-Down'' movements. This was in principle already possible via the remote control and a script, but now it's much more convenient and user friendly! Even the path is shown ... can be modified, saved and re plotted!
  • A Plug-in categorizing mechanism automatically only loads the required Plug-Ins for the actual setup: E.g. no Hardware Control Plug-ins are loaded in ''offline'' Data Analysis Mode.
  • At the time there are more than 41 Plug-ins.
• Gxsm itself is hardware independent, that means a predefined command-like instruction/data exchange mechanism has to be served by a device driver (loadable kernel module). See hardware section for details!

• Scan parameter changing on the fly - you can modify the feedback parameters, change the scan speed or switch the tunneling voltage while scanning in between scan lines. For example: Imagine you are scanning a STM topography and current Image, the surface looks flat, then just change the feedback parameters to CP=0 and CI=1e-5 (something small) and now you are in constant height mode!

• On the fly, even while scanning is in progress, you can view profiles, extract data parts, re-scale - just do all you like!

• Remote Control Interface: The Gxsm scanning progress is fully scriptable by a special fifo-command interface: So you may use any language you like, I like perl, to put commands to Gxsm. This is extremely useful to program tricky and or long SPA-LEED scans.

• Cross Platform: works on Linux i386, PPC, others may work too.

• Gxsm takes full advantage of the NetCDF data format.

• Scan auto saving, session logging, Plug-in details browser, NC-View, PS-Printing and a Icon generator are available too.

• Included Add Ons:
• a digital real-time scope ''Goszi''
• a free Linux COFF loader to launch the DSP program on PC31 and PCI32 cards
• the required kernel modules
• DSP binary (precompiled) COFF files for STM and AFM, ask for more!
• A DSP status monitor, called ''lcd'' and as Gnome Applet ''dsp_applet''.

Supported Instruments

In August 2001 Gxsm supported the following seven instruments:

1. Scanning Tunneling Microscopy (STM)
2. Atomic Force Microscopy (AFM)
3. Scanning Angle Resolved Light Scattering (SARLS)
4. CCD-cameras (Percy's telescope)
5. Spot-Profile-Analysis of Low-Energy Electron Diffraction (SPA-LEED)
6. any similar method will work too

Computer-hardware support was originally limited to two signalprocessor-interfaceboards (DSP-boards) of the types PC31 and PCI32 manufactured by Innovative Integration. But the internal structure of Gxsm allowed for easy extendability to other hardware.

Knowing this, a new kernelmodule with a DSP-emulation thread was developed in January 2001 which allowes the use of non-DSP-interfaces. A hardware-free SPA-LEED simulation modules and a module for the Burr-Brown-Series were written.

The CCD-camera is controlled by a simple kernelmodule, which drives some hardware connected to the parallel port.

All hardware control is done via the /dev/pcdsp device (in Gxsm this devicename is configurable). Read/Write and IOControl operations control the opened device. This functionality was originally used fpr communication with the DSP-card. The driver (kernelmodule) has a high-level interface, including commands for autonomously scanning lines with successing data delivery.

The first part of this document describes the usage of the software. The last part describes its internal structure and step-by-step instructions for your own modifications of the X/Gxsm software.

Hint: In SPA-LEED mode we have a modified main window, displaying the SPA-LEED typical parameters and options.