Getting started in Simbody


I’m testing Simbody for mechanical system modeling, here are some quick notes.

VisualStudio 2016 setup

I followed the x64 VisualStudio instructions, placing the final installation in C:\Simbody. After creating a new C/C++ Win32 Console Application and a blank source file (to access the C/C++ options), I entered these project properties:

Configuration Properties | VC++ Directories | 
  Executable Directories = C:\Simbody\bin
Configuration Properties | C/C++ | All Options |
  Additional Include Directories = C:\Simbody\include
Configuration Properties | Linker | All Options |
  Additional Library Directories = C:\Simbody\lib
Configuration Properties | Linker | All Options |
  Additional Dependencies = libblas.lib;liblapack.lib;
  SimTKsimbody.lib (all in the lib directory)

I’m no expert on VS; the above work for me.

A basic check of the dynamics

Let’s model the elementary mass/spring/damper system and calculate the natural frequency and damping from the response:

See github and the many comments in verifyDynamics.cpp. Included there is a basic PositionReporter that writes positions into a given text file.

The values given in the figure allow calculation of the system’s response, with some relevant parameters being:

$\omega_n = \sqrt{\frac{K_{spring}}{M}} = 2.2361$ [rad/s]

$\zeta = \frac{C_{damp}}{2 \sqrt{K_{spring}M}}  = 0.0112 $ (underdamped)

$\omega_d = \omega_n \sqrt{1-\zeta^2} = 2.2359$ [rad/s]

Now, let’s measure these same parameters from the simulated response. Running verifyDyanmics.cpp produces a csv file with the x position written out every 0.1sec. Plotting this in Matlab gives:

The response is the black line, with blue x’s indicating the identified peaks and valleys. The dashpot causes the initial 10m/s velocity to decay exponentially, with the response envelope given by $A e^{-\zeta \omega_n t}$. If we measure the time between peaks or valleys, we find the damped time constant $t_d$, which is related to the damped natural frequency by:

$\omega_d = \frac{2\pi}{t_d} = 2.3639 $ versus $2.2359$ calculated above.

The above response also draws the envelope function, with the cyan giving the calculated envelope and the red dashed Matlab’s 1D exponential estimate.

So, this was a very simple check on Simbody’s physics and a good excuse to figure out how to easily move data out of Simbody.

PhD Preliminary Examination

I gave my prelim presentation this past January, recapping my work with Prof. Zinn on Interleaved Continuum-Rigid Manipulation. The presentation went well and I enjoyed the audience’s and committee’s questions, most of which centered on things that would be very fun to look at given infinite time. As I hope to graduate soon, I’ll only be able to look into a few of the most fundamental questions, saving others for later students. With that, here are links to my document and narrated slides, followed by the prelim’s abstract:

Preliminary Thesis [45MB PDF]

Slides [6.1MB PDF]

Prelim Presentation from Ben Conrad on Vimeo. (and on YouTube)


Continuum manipulator compliance enables operation in delicate environments at the cost of challenging actuation and control. In the case of catheter ablation of atrial fibrillation, the compliance of the continuum backbone lends an inherent safety to the device. This inherent safety frustrates attempts at precise, accurate, and fast control, limiting their use to simple, static positioning tasks. This preliminary work develops Interleaved Continuum-Rigid Manipulation, by which the hysteretic nonlinearities encountered in tendon-actuated continuum manipulators are compensated by discrete rigid joints located between continuum sections. The rigid joints introduce actuation redundancy, which an interleaved controller may use to avoid continuum nonlinearities and dynamic excitations, or to prefer particular configurations that may improve task accuracy, permit greater end-effector forces, or avoid environment obstacles. Two experimental systems explore the potential of these joints to 1) correct for actuation nonlinearities and enhance manipulator performance and 2) increase the manipulator’s dexterous workspace. These experiments also expose important design and control observations that were not apparent in the general robotic and continuum literature.

LED Christmas Lights

For any given product, it is always interesting to see which aspects are improved and which languish.  Engadget’s recommendation of the best LED and incandescent Christmas lights highlighted this; the difference between the LED and incandescent strands is almost entirely restricted to the bulb (and associated electronic driver).

LED Christmas light (top) versus incandescent (bottom)

Looking carefully at the above picture, the incandescent bulb can be removed from the socket while the continuous mold line (lying exactly between the socket’s two flat sides) suggests that the LED bulb cannot be removed.  Assuming this, I’d wager that the LED bulb is first connected to the wires and then the socket molded around this connection.  The socket length and design, then, serve no functional purpose beyond fulfilling the consumer’s expectation.

A simple machine to make LED Christmas lights. From left; a spool of multistrand, multiconductor wire passes between two vertical-alignment rollers, through a wire-puller (drive), and into the LED inserter. LEDs fall from the vertical hopper into a bit and are driven by the pneumatic cylinder into the wire, such that their leads pierce the wire and making electrical contact. Exiting the wire, the leads are bent against the wire in the same manner as a stapler curls the staple on the back of the paper. This prototype does not encase the LEDs, so after the press the light strand is wound around a spool for packaging.
LEDs can be inserted directly into the wire, then encapsulated in plastic/rubber for electrical isolation.

LED Christmas lights were just coming to the market during my senior year in high school.  My senior project focused on the attachment of the bulb to the wire, where I realized that the increase in bulb quality (incandescent to LED) and associated decrease in bulb failure lessened the need for consumer-replaceable bulbs.  So, I designed a light strand where the LEDs were directly inserted into the wire and also a machine to construct these strands.

Removing the socket results in a more compact light strand which should be cheaper to produce (less material and elimination of a dedicated electrical assembly) and less visually-intrusive because the ‘socket’ has been substantially reduced (Christmas light strands are green to blend in with the tree).  Electrical contact is maintained without soldering by the compliance of the wire, much as a nail driven into wood is retained by forces from the compressed fibers.

I’ve learned much in the ten years since this project, but this idea remains relevant and would be fun to revisit.  I built this project in the context of the Szmanda science scholarship, so my paper and presentation highlight the energy efficiency of LED lights against traditional incandescents:

Bike Helmet Head Light

I enjoy biking into Engineering every day and though not much of a problem today, the summer solstice, I like to see and be seen throughout the darker times.  I quite like my Planet Bike Blaze, a compact 2W bike light and its warble flash mode, but it’s somewhat difficult to interface to my helmet.  So, this past weekend I finally replaced the fishing line version with a 3D printed pan/tilt mount.

Helmet pan/tilt light mount
Helmet pan/tilt light mount

Continue reading “Bike Helmet Head Light”

PDF Tools I Use

PDFs are a staple of academia and industry, but they’re neigh-intolerable without the following:

  • Foxit Reader – I’ve used Foxit for years; it’s plain better than Adobe, allowing all sorts of commenting, highlighting, and manipulation tools that Adobe restricted.
  • PDF XChange – I was first encouraged to it by Docear and find it as capable as Foxit.  Recently I needed to OCR a scanned book; Foxit doesn’t have this in their free version but PDF XChange does, so it’s nice to have multiple tools.
  • Both of the preceding allow you to replace the document colors; pure inversion of white & black is an improvement, but I typically reduce the contrast by choosing a ~50% gray background and black text.  Without this change you end up staring at a 200W light bulb all day…
  • PDF reDirect – This is a pdf printer with a gui.  The gui makes it easy to batch combine and/or re-order pages in pdfs.  So as long as we have to communicate in PDF, this is a useful utility.
  • …and some things have to be done by ghostschript (Unix).  Four lines of python, a call to gs, and a secured PDF no longer prevents highlighting and commenting.

And because 1000s of PDFs in a hierarchy of folders is a huge pain, I use both Mendeley Desktop and Docear to manage organize the library.  I’m not content with either: Mendeley is owned by Elsevier, so it should be avoided, Docear is open source, having lots of feature requests and understaffed (volunteer) developers.  I’ll keep Mendeley around until Docear has a good cross-library pdf text search.  I love how visual Docear can be, I just wish it was able to auto-categorize.  Some of the most useful views are the most tedious to create by hand: consider a web showing who cited whom – the info is in the .bib and in the DOI/Google Scholar link but isn’t currently brought in and presented.  Since Docear’s open source and written in Java, I should be able to see how this might be done…perhaps this summer.



Electron Beam FreeForm Fabrication — IN SPACE

In the last post I described the basics Electron Beam FreeForm Fabrication (EBF3), here’s why I’m excited about it:

Let’s walk through this process:

Metallic Refuse

Life and research aboard the ISS requires a lot of supplies and results in good amounts of waste.  This is the most expensive garbage in the world, and, due to the restricted lab and living space, includes completed experiments and spent supply ships along with the more obvious packaging, clothing, food, and other waste. Given the nature of space exploration, this waste components of this waste are known absolutely and excellent candidates for in-orbit recycling.  Used Progress and other supply ships, having arrived at station, could likely be stripped of components and structures that are not required for their reentry garbage truck function and again recycled into new components and structures.  Though accompanied by greater risk, ISS (or some other manned or unmanned station) could also serve as a destination for end-of-life satellites as the only place where there residual in-orbit material value may be captured.

Garbage, Meet Recycler

If you introduce a metal into an electric field sufficient to overcome the intermetallic bonds, those bonds will break, freeing electrically-charged ions from the donor.  This plasmification is the basis for vacuum deposition, but what if the donor is not a pure metal but rather some alloy?  What if the donor is something like the aluminized mylar found in space (-age) blankets?

The second part of this step is an external electromagnetic field, as commonly found in mass spectrometers.  If the plasma is accelerated by an electric field and then encounters a magnetic field, the ions will arc according to the strength of the field and their mass.  With the electric and magnetic fields coarsely tuned according to the known properties of the garbage, its component atoms can be sorted into atomically-pure stacks.

Sorted Feedstock

These atomically-pure stacks are highly valuable, due to their purity and location in earth orbit, as long as there is a process by which they can be made into something new.

Feedstock, Meet Printer

The same combination of electric and magnetic fields used to recycle garbage can be 3D printed into new components and structures.  By selectively introducing atomically-pure feedstock into the same electron beam used for plasmification and guiding the plasma via the same magnetic field, a part could be build layer-upon-layer.  This is essentially EBF3, though instead of a translating build platform the platform could be stationary and the beam scanned across the part by varying the magnetic fields.  (Though for alloying a translating stage or translating emitter might be required…)

3D Printed, Variable Alloy Components…In Space

3D printing metallic components in space would be a game changer; it would allow recycling of substantial fractions of today’s orbital garbage into new components that equal or rival their terrestrially-produced counterparts.  Further, the cycle described could also be applied to asteroidal and other in-space resources.  I don’t know what technology Deep Space Industries envisions…

…but I can’t see why EBF3 would not meet their needs.


I’ve spent 500 words describing this concept, but it seems to be worth much more study.  While the individual elements of the described cycle exist terrestrially (and mass spectrometry has been used on many robotic space missions) they have not been integrated into a single apparatus.

Many questions accompany this concept; I hope to explore some of these going forward (as posts, and perhaps more formally), and, more than that, answer why MadeInSpace is on the ISS rather this…

Electron Beam FreeForm Fabrication (EBF3)

There are many cool things happening in 3D printing these days, but the technique I’m most excited about, electron beam freeform fabrication (EBF3), has received very little coverage.  So in this and following posts, I want to describe the basics of this technique and some of the cases where I think it is the ideal manufacturing technology.

Printing in plastic is easy.  Heat some PLA or ABS to 300-400F and squirt it out of a small nozzel while tracing the outlines of your part.  Alternately, selectively shine a UV light source on some UV-cure epoxy and you have a stereolithography machine.  These two techniques, finally free from patent protection, are responsible for virtually all of the media buzz in 3D printing.

While these technologies accomplish the basic aim of converting a CAD design into a dimensional prototype, few of these additively-produced prototypes can withstand loadings similar to those a traditionally-machined part (even when machined from the same plastic, let alone metal versus printed plastic).  Not every application needs this durability, but it is the greatest limitation of every 3D printer you’ve probably heard of.

Printing in metal is expensive; in contrast to the great variety of Kickstarted $300-3,000 consumer/prosumer printers, MatterFab made news this past summer with the announcement of a metal-printer targeted at $100,000.  This printer, and it’s million-dollar-plus competitors, uses a kilowatt-class laser to melt particles in a metal powder together, forming a solid part.  Depending on the scan speed, laser intensity, and material addition rate, this method (referred to as laser-engineered net shaping – LENS – and metal laser sintering) can produce fully-dense parts with material properties similar to those of cast or annealed parts.  Since melting the metallic powder depends on the relationship between the laser wavelength and intensity and the powder’s melting point and absorbtivity, machine cost and material selection are closely related.  Common configurations have difficulty producing aluminum, titanium-aluminide, tungsten, magnetic alloys, and others.   These difficulties are easily explained by considering the reflectivity of some common metals versus common laser wavelengths:

Reflectivity of common metals and common laser wavelengths. HPLD stands for high-powered laser diode. Chart courtesy Kennedy, Byrne, and Collins, 2004.
Reflectivity of common metals and common laser wavelengths. HPLD stands for high-powered laser diode. Chart courtesy Kennedy, Byrne, and Collins, 2004.

Similar to LENS, Electron Beam Freeform Fabrication (EBF3) directly melts metallic materials to form a fully dense part, though using an electron beam rather than a laser. EBF3 commonly uses a stationary electron beam and a multi-degree-of-freedom positioning system to build parts layer-by-layer. As shown below, the electron beam is focused at a particular point, melting any co-located materials. Introducing new material into this region – by a wire feeder – increases the volume of this pool. Indexing the positioning system causes the pool to move, leaving behind newly deposited material. Adding a second wire feeder enables in-pool alloying and the production of functional gradients (varying the alloy along the part). Most EBF3 systems operate inside a vacuum chamber to both prevent the surrounding environment from attenuating the electron beam, which also eliminate the prospect of part contamination.

Left: Schematic representation of electron beam freeform fabrication (EBF3), courtesy Taminger & Hafley, 2008. Right: An EBF3 machine at NASA Langley, courtesy of Bird & Hibberd, 2009.
Left: Schematic representation of electron beam freeform fabrication (EBF3), courtesy Taminger & Hafley, 2008. Right: An EBF3 machine at NASA Langley, courtesy of Bird & Hibberd, 2009.

Along with the prospect of metal-agnostic (or more so than LENS), studies from an EBF3 research group at NASA Langley indicate that resulting parts are stronger than wrought and tempered alloys:

Comparison of EBF3-produced Al 2219 to Al sheet and plate from Taminger & Hafley, 2008. ‘Typical’ refers to conventionally-produced wrought and tempered sheet and plate properties. Of note, the ‘As-deposited’ specimen has greater strength than the wrought and a T62-tempered EBF3 deposit outperforms a conventional T62 alloy.
Comparison of EBF3-produced Al 2219 to Al sheet and plate from Taminger & Hafley, 2008. ‘Typical’ refers to conventionally-produced wrought and tempered sheet and plate properties. Of note, the ‘As-deposited’ specimen has greater strength than the wrought and a T62-tempered EBF3 deposit outperforms a conventional T62 alloy.

In addition to producing parts with commendable material strength, EBF3 is a fast process. Able to trade resolution for speed, EBF3 has been demonstrated at deposition rates of 178 to 594 cm3/hr (11-36 in3/hr) in Al 2219 and 434 cm3/hr (26.5 in3/hr) in Ti-6-4 [Taminger & Hafley, 2008]. As a point of comparison, a representative laser-based system deposits at 8 to 33 cm3/hr (0.5 – 2 in3/hr) [Taminger & Hafley, 2010].  The electron beam is also more efficient at delivering energy to melt pool, at approximately 95%, than a laser process, which might see 10% efficiency due to losses in the laser, beam transmission losses, and the naturally high reflectivity of most metals [Taminger & Hafley, 2010].

According to Lori Garver (NASA Deputy Administrator through 2013), EBF3 is used in fabricating the titanium spars for use in the F-35 Joint Strike Fighter; some more mundane results are below:

Parts produced in Taminger & Hafley, 2008: a) a TI-6-4 wind tunnel model, b) a square box of Al 2219, c) an Al 2219 airfoil, d) an Al 2219 mixer nozzle, e) an Al 2219 converging/diverging nozzle, f) a Ti-6-4 guy wire fitting, g) a Ti-6-4 inlet duct, and h) a Ti-6-4 truss node.
Parts produced in Taminger & Hafley, 2008: a) a TI-6-4 wind tunnel model, b) a square box of Al 2219, c) an Al 2219 airfoil, d) an Al 2219 mixer nozzle, e) an Al 2219 converging/diverging nozzle, f) a Ti-6-4 guy wire fitting, g) a Ti-6-4 inlet duct, and h) a Ti-6-4 truss node.

The significant disadvantage of EBF3 is poorer control of the part surface quality than plastic and LENS printers. EBF3 part resolution is essentially limited by the feed wire diameter, but this diameter dependence has not been demonstrated in the literature.  Given the commercial availability of LENS techniques, the majority of the community has focused on understanding EBF3 and its unique alloying ability.  EBF3‘s selling point of printing with high strength alloys places the focus on accurate alloy production; applications demanding these alloys are sufficiently advanced (and costly) to delay interest in higher resolution.

EBF3 also requires an evacuated build environment, on the order of 1×10-4 Torr, adding an appreciable degree of complexity to any EBF3 (terrestrial) system [Taminger & Hafley, 2008].  Davé’s original 1995 description mentions that use of a high-energy electron beam (>500keV) can eliminate the need for vacuum, though such a device will be accompanied by its own complexities in generating large potentials. The literature has apparently not yet considered this variation.

Producing spars for the F35 is nice, but to me the killer application for EBF3 is not terrestrial, but in-space.  In the next post I’ll lay out why I think EBF3 is the ideal in-space manufacturing technology.

Pandora Bounties

I’ve used Pandora for many years and its selection is persistently limited in some genres of music I’d like to hear more of.  So given this, why can’t it offer bounties for creation of new music?

In my experience, liking or disliking more than every fourth track quickly leads their algorithm to overfit and play the same collection of, say, 50 songs without any variety.  This leads to user fatigue and consumption elsewhere.  As each station is essentially trying to learn what subgenre you enjoy, many users may end up with essentially the same overfit station and Pandora can tell how long they persist under the repetition before leaving for another source.  These statistics give Pandora a reasonable way to set the music-creation bounties, as they can be viewed as a projection of future earnings once the music has been created.

More importantly, this idea creates what should be a central element of Pandora’s business plan, that is to better inform artists what music is in demand.  Nostalgic artists are free to cling to the idea that they only produce what moves the heart, but for practically-minded and emerging artists, this program would give them some basic criteria to shoot for.

Works submitted for each particular bounty could then be introduced into the stations of previously-frustrated users, with the bounty winner determined by likes or plays over a set trial period.  (An element of this would be notifying users that Pandora has found new music for their station, encouraging them to give it another try.)

These works needn’t be new, as the bounty could incentivize retired musicians to enroll their music in Pandora’s catalog where rightsholder discovery may have prevented their prior inclusion.  Newly-created works would benefit both the artist and Pandora, as made-for-Pandora works could be recorded with significantly less or no label involvement, allowing Pandora to give artists all of the streaming fees (they could also be treated as works-for-hire, though this might reduce participation).