# Gas station without pumps

## 2014 February 19

### Twelfth day of freshman design seminar

Filed under: freshman design seminar — gasstationwithoutpumps @ 23:12
Tags: , , ,

My counts of which days were which in the freshman design seminar were all messed, so three of my blog posts were misnamed:

date which day of class blog post
Mon 2014 Jan 6 1 First day of freshman design seminar
Wed 2014 Jan 8 2 Second day of freshman design seminar
Mon 2014 Jan 13 3 (Baskin lab tour) Third day of freshman design seminar
Wed 2014 Jan 15 4 Fourth day of freshman design seminar
Wed 2014 Jan 22 5 Fifth day of freshman design seminar
Mon 2014 Jan 27 6 Sixth day of freshman design seminar
Wed 2014 Jan 29 7 (Biomed lab tour) Biomed lab tours and online discussions
Mon 2014 Feb 3 8* Seventh day of freshman design seminar
Wed 2014 Feb 5 9 no post (ill and group tutor ran class)
Mon 2014 Feb 10 10* Ninth day of freshman design seminar
Wed 2014 Feb 12 11* Tenth day of freshman design seminar
Wed 2014 Feb 19 12 Twelfth day of freshman design seminar (this post)

Today we started by having the students turn in their Arduino programming homework, then start writing the program as a group. I told them that I particularly wanted those who had trouble with the assignment to provide input—I’m trying to get them to realize that questions and confusion are normal, and that the right action to take in college is to ask questions, rather than to hide ignorance.

This particular assignment was expected to be hard for them—I had not done the scaffolding for it that I had originally planned, but threw them into it with very little preparation. I told them that, but also that I was trying to get them used to looking things up and figuring them out, rather than waiting to be told exactly what to do. Again, I’m trying to get them out of the “regurgitate what the teacher said” mode that K–12 education has trained them into. If I accomplish nothing else this quarter, I hope to increase their willingness to ask questions (of their teachers and of the things they read).

We did get the program written, with some digressions into the difference between “==” and “=” in C++ and the convention in C and C++ that 0 is false and any other value is true. I also managed to work in the importance of good variable names to tell people what things meant, though this particular program doesn’t need any variables.  The students now have the notions of serial execution, conditional expressions, if-statements, digital I/O, serial communication (we had a digression into baud rate), and the Arduino setup/loop structure, which may be enough for their projects—they may also need analogRead(), which I should be sure to demo on Monday.

I then typed in the program we had created together and demoed it with Arduino. I had deliberately left in a bug that I had spotted (no space between the printing of the different fields), and the class spotted it and came up with a reasonable correction when the first output came out.

We only had about 10 minutes left, so I gave them feedback on their project proposals:

• Type homework for college classes!  Two of the groups had turned in hastily scribbled notes.
• Give explicit specifications for the project.  How big an incubator? How precisely does the temperature need to be controlled? How fast does temperature have to change for PCR? What temperatures are needed and how precisely? How many tubes need to be run through the PCR machine at once?  How much acceleration does the centrifuge need to produce? How precisely does the speed need to be controlled?
• Provide a block diagram giving all the components of the system (power supply, motor, fan, rotor, temperature sensor, … ) and lines showing the connections.  I talked about the importance of specifying the interfaces between components so that people could work simultaneously on different parts, and the need to renegotiate interfaces if the initial specification of them caused problems.

We talked a bit about prototyping—I want them to build something and learn enough to make an improved design, even if they don’t get a fully functional prototype.

For Monday, I assigned them the task of fleshing out the specifications for their project and producing a block diagram, filling in as many details as they could.  The group tutor is going to try to find time to meet with each group for an hour before then, to help them with flesh out their designs.

## 2014 February 18

### Still better I-V plot for Schottky diodes

Filed under: Circuits course,Data acquisition — gasstationwithoutpumps @ 00:32
Tags: , , ,

Last weekend I posted a voltage-versus-current curve for a 1N5817 Schottky diode, to confirm the theoretical formula $V = V_{T} \ln \left ( 1+ \frac{I_{C}}{I_{S}}\right)$, where IS is the saturation current of the diode, using the following setup

and measuring the results with an Arduino Leonardo.  I claimed that the resulting data fits the model well for over six decades (> 120dB):

Fitting over a wide range of currents is more robust than fitting over the narrower range that I can get with just one value for R2.
There is quantization error still on the voltages, but the overlapping current ranges give good data for most of the range. VT is now 26.1mV and IS is 0.91µA.
click to embiggen

I was a little dissatisfied at the low end, because of the low resolution of the Arduino analog-to-digital converter (only 10 bits).  This weekend I decided to repeat the measurements, but using a Freedom KL25Z board, which has a 16-bit ADC.  Of course, it doesn’t really get 16 bits of accuracy—the data sheet claims that when you use the hardware averaging of 32 samples in 16-bit differential mode (the most accurate) you get at least 12.8 equivalent bits and typically 14.5 equivalent bits. (For single-ended 16-bit, the effective number of bits is only guaranteed to be 12.2, and the typical is 13.9 bits.)  They claim a ±6.8LSB total unadjusted error.

My son helped me get the bare metal ARM system set up on my laptop, along with ADC and UART routines, so that I could write my own single-purpose data logger for this problem (he’s working on getting the KL25Z board integrated into the Arduino Data Logger, but it isn’t close to being ready yet).  My program used the longest sample times and hardware averaging of 32 samples, to get the most accurate conversions possible from the 16-bit ADC.  The first version of the program used differential inputs for the voltage across the diode (E20-E21), but single-ended readings (E21) for the voltage across the resistor.  I had to reduce the voltage for the test from 5v to 3.3v, because the KL25Z runs on 3.3v, not 5v. I got some rather weird results:

Two runs of measurement with R2=100Ω. The low-current measurements seem to be all noise.
click to embiggen

I could get decent measurement in the low-current range by using a larger resistor, so the problem was not noise in the measurement fixture or problems reading low differential voltages on the diode, but just with the small single-ended read for the current. It is pretty clear to me that the ADC does not work well when the input voltage results in less than about 50 counts.  (Note, that means that at the low end of the voltage range you only have about a 9.4-bit equivalent ADC.)

I modified the circuit to allow differential reading away from 0 for both the voltage across the diode and the voltage across the shunt resistor:

Adding an extra resistor ensured that the lowest voltage did not get too close to ground and I could use differential reads for both voltage (E20-E21) and current (E22-E23)/R2

This gave me a much cleaner reading, with problems only once the differential counts got below about 20:

Differential measurement with R2=100Ω. The low-current measurements have problems when the counts get small, but not nearly as severely as with the single-ended measurements.
click to embiggen

I replaced the 100Ω R2 resistor with a 15.56kΩ resistor (nominally 15kΩ), to extend to lower currents despite the noise in the ADC:

This plot extends the fit down to about 0.1µA, but only by adding an extra term—an offset to the voltage. I thought at first that overshoot to –11mV is an error in the analog-to-digital converter on the KL25Z, as I couldn’t see how my circuit could be back-biasing the diode.
Click to embiggen

I tried using larger resistors, but was unable to get any better data using them—I seem to be limited by the differential voltage measurement of the diode at the low end. I thought I might be able to improve the measurements by adding an instrumentation amp to increase the signal for low voltages.  But first I tried just hooking up a voltmeter, with no ADC or instrumentation amp connections.  When the voltage across R2 (100kΩ) is 0.31mV, the voltage across the diode plus R2 is only 0.05V, so there is -0.26mV across the diode.  The backwards voltage across the diode was not an artifact of the ADC!

I then tried looking at the voltage across the diode with my oscilloscope.  There is about 20mV of AC noise, independent of the DC voltage, until the diode has about 50mV across it (with the 15.5kΩ resistor for R2), by which time the noise has dropped to about 10mV (the Bitscope oscilloscope with the differential probe has a noise floor of about 3mV, if the two leads are connected together, so this is not just oscilloscope noise).  This noise seems to be white noise, not 60Hz hum pickup, so is probably coming from the diode.  This AC noise signal limits how accurately we can measure the DC current, and rectifying the noise could be the source of the mysterious “backwards” bias.

To reduce the noise, I put a 4.7µF ceramic capacitor in parallel with the diode, and redid all the measurements with 100Ω, 15.5kΩ, and 100kΩ resistors for R2.

Modified measurement circuit, adding a bypass capacitor to reduce AC noise on the diode and allow better DC measurement.

Now the signals are very clean down to nanoamp levels. I no longer need to add an offset to the voltage, as it is 0 to within the measurement repeatability. The noise from very small voltage differences for the 100Ω shunt resistor is still a bit of a problem, but that region is well covered by 15.5kΩ data. The curve was fit using just the 15.5kΩ and 100kΩ data, to avoid having to trim out the noise from the 100Ω data.
Click to embiggen

Lessons learned today:

• Higher-resolution ADCs do give smoother curves, with less digitization noise, but they aren’t a panacea for measurement problems. To get most of the resolution, I had to set the ADC to use long sample times and do a lot of averaging. I understand that Freescale Kinetis M series include 24-bit sigma-delta converters for higher precision at much lower speed (24 bits is 7 decimal digits), as well as the high-speed 16-bit successive-approximation converters. Unfortunately, they don’t have a low-cost development board for this series.
• Stay away from the bottom end of the ADC range on the KL25Z.  Scale single-ended inputs to have values at least 50, and differential inputs to have values at least 20.  There may be similar problems at the top end of the range, but I did not test for them.
I wondered if the problem may be switching from the large value for the voltage across the diode to the small voltage across the shunt resistor that was the problem. I tried putting in a dummy read between the voltage and the current reads, but that didn’t help at all. At first I thought that the low-count readings were good with the large shunt resistors, but this is probably an illusion: errors in the current measurement for small currents aren’t visible on the plot, because the voltage across the diode is not changing, and so large horizontal errors in the plot are not visible there.
• Watch out for AC noise when trying to measure DC parameters.  If there are semiconductor junctions around, the noise may be rectified to produce an unwanted DC signal.
• The differential ADC settings have a range of ±VDDA, not ±VDDA/2. This means that the least-significant bit step size is twice as big for differential inputs as for single-ended inputs. For some reason the Freescale documentation never bothers to express what the differential range is.
• Serial USB connections are a bit flakey—the Arduino serial monitor missed a byte about every 200–300 lines.  I looked for anomalous points on the plot, then commented out the lines that produced them—they were almost all explainable by one character having been missed by the serial monitor; e.g., I commented out “662401069     86      19” right after “660001069       865     17”,  because the last digit of the voltage (the second field) was missing.  The fields were a timestamp (in 24MHz ticks), voltage across the diode (in ADC units), and voltage across the shunt resistance (in ADC units).  [Actually, this was not a new lesson for me—I’ve had to do the same on almost all files collected from the Arduino serial monitor.  My son’s data logger code is better at not losing data, but it is still worthwhile to check for anomalies.]
• The 3.3v supply from the Freedom board is much cleaner than the 5v USB supply that I get from the Arduino (unless I use an external power supply with the Arduino), but I can only take about 10mA from the 3.3v supply before it begins to droop.  If I want  more than that, I’d better provide my own power supply (or at least my own LDO regulator from the USB 5v supply).

## 2014 February 15

### Freedom KL26Z board

Filed under: Circuits course — gasstationwithoutpumps @ 14:34
Tags: ,

I bought a Freedom KL26Z board this week, because I wanted another Freedom board, and the KL26Z has somewhat nicer peripherals (added magnetometer, light sensor, I2S interface) and only costs a a couple of bucks more. It should be fairly easy to add the KL26Z to the Data Logger software, once the KL25Z board is working with it.  We may have both working in time for the Spring Applied Circuits course.

Unfortunately, the board came with the same incompetently designed bootloader (by P&E Microcomputer Systems) as the KL25Z—you can’t load programs from Mac OS X, only from Windows machines (and not Windows 8, only Windows 7). They claim that this problem was fixed last year with a newer version of the OpenSDA software, but the board I just bought from DigiKey certainly doesn’t work with Mac OS X:

Board Name is: FRDM-KL26Z
MicroBoot Kernel Version is: 1.05
Application Version is: 0.00

You still need a Windows machine to load the OpenSDA software, so it is not that great a “fix” (if it even works). I’ll have to make a special trip up to campus to find an ancient Windows machine. When I do that, I might put on the MBED.org download software, which was working with Mac OS X (on the KL25Z boards) months before P&E claimed to have a fix. I’m assuming that the SDA interface is the same on the KL25Z and KL26Z boards, but I’m not certain of it (mbed has different download software for the KL46Z board, which makes me concerned that there are some board-specific differences).  I could try downloading the latest P&E Microcomputer Systems software and see if it works on the KL25Z board—if not I can go back to the mbed software on that board and wait for mbed to release KL26Z software.

I’m planning to use the bare-metal ARM software development kit, with the gnu gcc compiler, for future development on the KL25Z and KL26Z boards, rather than the mbed.org development tools, because the compiled code can be much smaller (less extra junk added in).  I’ve got the code installed on my Mac, but I’ve not tried running it yet. My son, who has gotten a few small programs working with the bare-metal ARM system using the KL25Z board, was going to help me set up my Makefiles this weekend (including a loader script that removes a lot of the stdio package if you aren’t using it—the default bare-metal ARM setup includes some fairly useless “assert” statements that add many kbytes to the downloaded programs). Unfortunately, there are a lot of different viruses circulating in Santa Cruz this winter, and he’s running a fever this weekend, so we’ll probably have to delay my getting bare-metal ARM working.

## 2014 February 13

### Tenth day of freshman design seminar

Filed under: freshman design seminar — gasstationwithoutpumps @ 17:22
Tags: , , ,

Yesterday’s class was originally planned to be an Arduino demo of analogRead() and Serial.print(), using either a pressure sensor or a phototransistor, but the class ended up going in a totally different direction.

At the beginning of class, I passed around a cheap vernier caliper and showed students how to measure the disposable cuvettes to 0.05mm precision. This was part of my continuing effort to expose students to simple tools that they should have seen in high school, but for the most part have not.

I started the class by collecting the proposals for design projects.  Since these were group efforts, there were only three proposals: a centrifuge, an incubator, and a PCR thermal cycler.  I’ve not read the proposals yet (I’m still under the weather, and ended up falling asleep last night right after dinner, and only waking up this morning barely in time to get to the department research seminar at noon), but I did read the titles in class, and started talking about what computer aspects there might be for each project.  The centrifuge is mainly a mechanical design, but a non-contact sensor (probably optical) for measuring the rotor speed would be useful—one might even want to include a motor speed control, but that depends on what they use for a motor. The other two designs both depend on regulating a temperature.  Important parameters include how tightly controlled the temperature has to be and how fast you have to move from one temperature to another.  An incubator generally needs to have a fairly fixed temperature, and only needs to respond to slow heat loss, except when the incubator is opened.  A PCR machine has to switch rapidly between three temperatures,  generally around 95° C, 50° C, and 75° C.

So we ended up talking about thermal control.  First I described the basic idea of having a “set point” and of simple on-off heater control, with high threshold and a low threshold.  We talked about temperature sensors, including the old-fashioned bimetal-strip thermostats, thermistors, thermocouples, and RTD sensors. I talked a little about how to choose among the different types (thermocouples for high temperature, RTD for high precision, thermistors for low cost and ease of interfacing).  I also mentioned semiconductor temperature sensors, which are used in a lot of integrated circuits (like CPUs and GPUs on their laptops), but are not very good for general temperature measurement.

We focused on thermistors as the simplest to use with the Arduino, and I showed them a data sheet for the NTCLE413E2103F520L thermistor we use in the Applied Circuits lab.  This lead to a discussion of how the thermistor resistance varies with temperature, and I showed them the Wikipedia page on thermistors, with its discussion of the Steinhart-Hart equation and the “B” parameterization of the formula.  I also explained what the B25/85 specification on the data sheet meant (measuring resistance at only 25° C and 85° C, and solving for B).

I then tried to get the class to come up with a circuit to convert resistance variation into voltage variation, but they were stumped. So I showed them a voltage divider and had them work out as a class what the output voltage was using just Ohms law. They were then able to see that replacing one resistor with a thermistor would allow them to see a voltage variation as a function of temperature. I told them about the first homework in the Applied Circuits course (figuring out the optimal value for the fixed resistor, to get the maximum change in voltage with temperature at a particular operating temperature), but did not assign the problem. Not everyone in the class has had calculus yet, and the problem really does require being able to differentiate and use the chain rule.

I ran out of time before doing anything with the Arduino! I did assign them an Arduino homework, though:

For Wednesday 2014 Feb 19 (no class Monday Feb 17), write an Arduino program that will report over the USB cable once every two seconds the status of pins 8, 9, and 10, whether that pin is high or low. The report should be viewable on the Arduino Serial Monitor. It should look something like

 8:HIGH 9: LOW 10: LOW
8: LOW 9:HIGH 10: LOW
8: LOW 9:HIGH 10: LOW
8: LOW 9: LOW 10: LOW

As a matter of common programming style, there should be a “block comment” at the beginning of every program telling what the program does (from a user’s standpoint, not how it works from a programmer’s standpoint), who wrote it, and when it was written. You may work on the programs in pairs (not larger groups), but the names of everyone who worked on

Turn in a printout of your program. This program is simple enough that I don’t need evidence of it working—for other class you may be asked to turn in the source code electronically, so that the graders can test the program, or provide input-output pairs that show evidence that the program is working correctly.

For those who find this program too easy, you can challenge yourself to do more ambitious programs:

• Accept characters from the USB serial line that change which pins you examine. (For example, getting the character ‘8’ with Serial.read() might turn on looking at pin 8, and getting ‘*’ might turn it off looking at pin 8.)
• Write a little control program that turns on the on-board LED (pin 13) when some combination of conditions is true and off when the conditions are false.

At the end of class, I had everyone use my wire strippers to cut and strip a few small pieces of wire, so that they could do the hardware portion of the Arduino programming.

## 2014 February 11

### Ninth day of freshman design seminar

Filed under: freshman design seminar — gasstationwithoutpumps @ 17:10
Tags: , , , , ,

The astute reader of this blog may notice that there was no “eighth day of freshman design seminar” post.  I was sick last Wednesday and unable to attend class, so I had the group tutor (a senior in bioengineering) take the class and have them discuss possible projects to take on.  I asked them to turn in proposals yesterday, but forgot to collect them—I’ll collect them tomorrow.  We’re about halfway through the course, so it is time for students to start on their projects.

I returned two homeworks yesterday: the colorimeter design and the RGB LED resistor sizing.

The colorimeter designs were not very good, lacking necessary details, but were somewhat better than previous spectrometer attempts. I think I’ll try reversing the order of those assignments in future, as the colorimeter is a simpler device. The biggest problem with the designs is that most of them were pieced together from web pages, with no citations.  Two of them were blatantly copied from Science Buddies, which has a decent design, but the students did not cite the source. I yelled “Cite your sources!” at the class, and explained that I could have flunked several of them out for plagiarism, and that in an upper-division course I would have. I hope they get the message, so that they don’t fail out later on. I decided not to prosecute academic integrity cases in this 2-unit, optional course, though I am making the science-buddy copyists redo the assignment.

I then explained to students the mistake I had made in the photodiode explanations (see Lying to my students) and corrected the understanding of the “open-circuit voltage” spec from the photodiode datasheets. I think that the students are a little more comfortable about finding things on datasheets now—I hope that lasts for them.

We then went over one of the RGB LED datasheets and did the resistor sizing for it.  About a third of the class had done a decent job on that assignment, and I cleared up the common mistakes:

• If a battery is used in a schematic, both ends need to be connected.  Other options are to use +5v and Gnd port symbols, or a +5V DC voltage source symbol.
• The LED diode must be forward biased (with a large current flow), and the triangular shape of the diode symbol shows which way conventional current flows.
• The voltage needed for determining the resistance is the voltage across the resistor, not the voltage across the diode, so it is 5v–VF, not VF.

I think I managed to get these points across—I relied fairly heavily on asking the students to do each step, so I’m pretty sure that at least half the class can now size a resistor for an LED.

Finally we could get to some new material. I wanted to show them how to program an Arduino, so we built up the standard blinking-LED first example for an Arduino.  To make it a little more interesting, I started with a true statement—I did not know whether the LED on pin 13 was hooked up with the anode or the cathode connected to pin 13.  We looked at the two possible circuits and how they would behave differently when the pin was high and when it was low.  I then explained “void setup()”, “void loop()”, and “pinMode(13,OUTPUT);”.  I had the students come up with the body of loop, feeding them the important constructs (digitalWrite and delay) only once they had expressed the action they wanted.  We ended up with a loop that help pin 13 high for a second and low for ¼ second.  After I typed in the program we had written, I showed them how to select the appropriate board type and download it to the Arduino.  The light blinked, and the students were able to figure out from the pattern of on and off that the LED was connected between pin 13 and GND (with a series resistor), with the anode towards pin 13.

I ran out of time and material at about the same time (a first for this quarter), and assigned the students to read about Arduino programming from the Arduino reference website, with particular attention to “if”, “while”, “pinMode”, “digitalWrite”, “digitalRead”, “analogRead”, and the timer functions.  I expect to go over some analogRead stuff in class tomorrow, and assign a small programming assignment over the weekend, probably using “Serial”.

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