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I was analyzing some force-distance curves using NanoScope Analysis and noticed unusual spacing between the horizontal scale data points.
The difference between data points was either 0, 0.167, or 0.333 nm in a seemingly random way. This seemed odd to me.
When I open the same file in Gwyddion, though, the spacing is a constant 0.1953 nm, which is consistent with my settings of 512 sampling rate and 100 nm sweep (100/512=0.1953).
The total length of the scan also comes out different in the two programs: 96.4 nm in NanoScope and 99.8 nm in Gwyddion.
Does anyone know which is correct or what is going on?
Thanks!
Scan performed on a D3100 system and Nanoscope software v7.30.
Analysis performed on NanoScope Analysis 1.40 (Build R2Sr1.83411) and Gwyddion 2.31.
Hi, which Nanoscope and which Gwyddion are you using? I've obtained force curves using Nanoscope III and V controler, but I can't open neither of them with Gwyddion 2.26. It gives me the following error:
Header field `@4:Ramp Begin DC Sample Bias' is missing
Do you have the @4:Ramp Begin DC Sample Bias line in your files?
Update: I saw that a new version of NanoScope Analysis was available after posting my question, so I updated the software; however, the issues discussed above remain unchanged.
Hello Luis,
I am using a D3100 Nanoscope V with Nanoscope software v7.30.
With Gwyddion 2.31 I have not had any trouble opening the force curve files.
I do not seem to have the header field you list.
I do have:
\@4:Ramp Begin Zsweep: V [Sens. Zsens] (0.005035400 V/LSB) 0 V
\@4:Ramp Begin: V [Sens. Zsens] (0.005035400 V/LSB) 0 V
\@2:DC Sample Bias: V [Sens. biassens] (0.0003051758 V/LSB) 0 V
\@3:DC Sample Bias: V [Sens. biassens] (0.0003051758 V/LSB) 0 V
Hello, tibs,
Could you please add your data files so that we can reproduce your problem?Go to your profile at the top right corner of the window and go to "my files" then. Upload your files in form of ZIP-files and add them to your posting via "Insert Media".
Best regards, Dietmar
Thank you, Dietmar.
Here are a few sample files:
force curves.zip
Man, your data looks terrible! This extreme noise is not normal. Also the fact that the Force increases at decreasing Z Sensor, so at increasing Separation, means you have got some serious problems. I have no experience with a D3100 system.
To me (as a non-specialist) it seems as if there is some problem with your laser point positioning. Could that be the case? You can see what my force curves look like here: Sah002-110 Bruch_008.zip (e.g. "Sah002-110 Bruch00002.008"). As you can clearly see they look completely different when compared with yours.
Hello Dietmar,
I agree the data is noisy, but at the moment I am more concerned if the software is correctly reading/plotting the deflection axis data as discussed in my original post.
By the way, I don't know what is the sign convention for the "Z sensor," but if I select either Deflection or Separation vs. "Z" (rather than "Z sensor") I get the expected response that you are talking about (i.e. force increases with decreasing separation); I don't think there is a serious problem in that regard, at least.
One last thing, are you measuring force curves in tapping mode or contact mode? I am using tapping mode.
Sorry, I meant to write that I am still concerned about the horizontal axis data spacing (which is Z sensor not deflection).
Dear tibs,
I looked again at all three of your plotted curves. In fact "only" two of the three curves start at negative Separation and go towards zero Separation. One of them - "m blank 2013-07-10.121" - shows at least positive Separation values as it should.
Nevertheless, the data is way too noisy to use it. And actually it is also way too noisy to be concerned about anything else. It seems as if the laser point was not perfectly aligned for your measurements. It might be that the machine had a hard time triggering and that this is the reason for several of your issues. This is definitely the first problem that you need to solve. The different spacings of Gwyddion and NanoscopeAnalysis might have different reasons and could also easily be a problem of Gwyddion. Try to export your data to a third software, this might answer your questions.
Regarding the mode of force curve gathering: There are many possibilities. The most common ones are simply ramp curves, Point-&-Shoot (which is "ramp" at given positions) and High-Speed Data Capture (HSDC). The mode you use for scanning doesn't matter as such, but it is important that you use an appropriate AFM probe. I use the RTESPA probe as it matches with the stiffness of my material. I you use too soft probes you won't obtain good curves.
Regards, Dietmar
So I figured out the difference between the z data:
In Nanoscope analysis I was looking at "Z sensor" data while Gwyddion was plotting "Z" data.
If I switch the X Data Type in Nanoscope Analysis from "Z sensor" to "Z" I get the same spacing and overall length as with Gwyddion.
Could someone please explain the difference between these data types?
The following is from the Multimode Picoforce manual; is "Low Voltage Z" the same thing as "Z" in the X Data Type pull down menu?
"Z SENSOR—the Z-position of the sample platform, the sensor represents the actual Zposition.
Low Voltage Z—the height signal sent to the Z-piezoelectric actuator (beforeamplification), which should correspond well with the height signal in closed loop, butnot be quite as accurate as the Z sensor in defining probe position vertically."
Finally, this may not be the correct forum, but does anyone know how to make Gwyddion plot "Z sensor" rather than "Z" data. It seems to auto default to plotting the "Z" data and I don't see how to switch it.
Now that is the reason, also for this strange negative Z values. So at least you found the problem.
I never get an output called "Z sensor". My output data is only the "deflection error". Might have to do with the way you run the machine. What's your probe properties (spring constant etc.)?
Regarding your last question: Why do you actually use Gwyddion for that? You just want to view X-Y-data and there are better programs for this special purpose. I would export the data using NanoscopeAnalysis (right click on the plot - export - XY data; watch out to export the curve you want to.
Dietmar
Z is the voltage signal applied to the piezo and z sensor is the actual movement of the piezo.
I guess you ramped in z open loop so your z signal is consistent and z sensor is discrete. It's because each step you give the piezo a constant voltage, the actual movement of the piezo is not the same and that's what z sensor reads.
Ang Li