From b30f14749f90a8291ea95d48329efe20339dd66b Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Sat, 24 Apr 2021 17:03:00 -0500
Subject: rough merge of content from operation instructions

---
 .../wpp-fabrication-operation.tex                  | 480 +++++++++++++++++++++
 1 file changed, 480 insertions(+)
 create mode 100644 fabrication-and-operation-instructions/wpp-fabrication-operation.tex

(limited to 'fabrication-and-operation-instructions/wpp-fabrication-operation.tex')

diff --git a/fabrication-and-operation-instructions/wpp-fabrication-operation.tex b/fabrication-and-operation-instructions/wpp-fabrication-operation.tex
new file mode 100644
index 0000000..f301d73
--- /dev/null
+++ b/fabrication-and-operation-instructions/wpp-fabrication-operation.tex
@@ -0,0 +1,480 @@
+%% document
+\documentclass[11pt]{article}
+\usepackage[letterpaper, portrait, margin=0.75in]{geometry}
+\usepackage{setspace}
+\usepackage{color}
+
+% text
+\usepackage[utf8]{inputenc}
+\setlength\parindent{0pt}
+\setlength{\parskip}{1em}
+\renewcommand{\familydefault}{\sfdefault}
+\newcommand{\RomanNumeral}[1]{\textrm{\uppercase\expandafter{\romannumeral #1\relax}}}
+
+% math
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage[cm]{sfmath}
+\usepackage{commath}
+\usepackage{multirow}
+\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
+
+% graphics
+\usepackage{graphics}
+\usepackage{graphicx}
+\usepackage{epsfig}
+\usepackage{epstopdf}
+\usepackage{xpatch}
+\usepackage{pdfpages}
+\usepackage{float}
+
+% each section begins new page
+\let\stdsection\section
+\renewcommand\section{\clearpage\stdsection}
+
+% hyperref
+\usepackage[colorlinks=true, linkcolor=black, urlcolor=blue, citecolor=black, anchorcolor=black]{hyperref}
+\usepackage[all]{hypcap}  % helps hyperref work properly
+
+
+
+\usepackage[shortlabels]{enumitem}
+\setlist[enumerate, 1]{nosep}
+\setlist[enumerate, 2]{nosep, topsep=-5ex}
+\setlist[enumerate, 3]{nosep, topsep=-5ex}
+\setlist[enumerate, 4]{nosep, topsep=-5ex}
+\setlist[itemize, 1]{nosep}
+\setlist[itemize, 2]{nosep, topsep=-5ex}
+\setlist[itemize, 3]{nosep, topsep=-5ex}
+\setlist[itemize, 4]{nosep, topsep=-5ex}
+
+% bibliography
+\usepackage[numbers]{natbib}
+
+% title
+\title{Wisconsin Photoreactor Platform\\Fabrication and Operation Guide}
+\author{
+  Philip Lampkin \\
+  Blaise J. Thompson \\
+  Samuel H. Gellman
+  }
+\date{\today}
+
+\begin{document}
+
+\maketitle
+
+\includegraphics[width=\textwidth]{"../coverart.png"}
+
+\tableofcontents
+
+\section{Introduction}
+
+The Wisconsin Photo-Reactor (WPR) is made to be easily assembled.
+This document is meant to help chemists accomplish this assembly.
+Each reactor has two major components requiring detailed custom assembly:
+
+\begin{itemize}
+  \item The 3D printed enclosure, described in \autoref{SEC:enclosure}
+  \item The drive electronics, described in \autoref{SEC:electronics}
+\end{itemize}
+
+With these two major components complete, assembly of the WPR is relatively straight-forward.
+Details of final assembly are described in \autoref{SEC:assembly}.
+
+Throughout this document we refer to an online repository containing source and design files.
+This repository appears at \url{https://github.com/uw-madison-chem-shops/wisconsin-photoreactor}.
+This repository contains everything including the source for this very document.
+
+A working WPR is made up of many separate commercially available parts.
+This guide assumes that you have already done the work of procuring those parts.
+The online repository contains several README files with detailed part numbers and suggested vendors.
+
+The WPR is a living project.
+We welcome and encourage duplication and modification of our designs and documentation.
+If you notice problems or omissions within this assembly document, please consider opening an issue or pull request.
+
+TODO: FIGURE 1 FROM OPERATION GUIDE
+
+A WPP device consists of a base, reaction module and reactor driver (Figure 1).
+The base houses the photon source and cooling fan.
+The reaction module is comprised of a reflective reaction chamber and rigid vessel holder.
+A digital driver board, analog driver board or simple circuit integrating a commercial light emitting diode (LED) driver can be fitted to the base to drive the reactor.
+Each component is highly versatile, and apparatus assembly is fully modular (Figure 1B).
+
+Through variation of each component, one can quickly produce bespoke WPP devices to meet specific research needs.
+Configurational variations are easily documented for later reproduction.
+Detailed below are instructions for configuration and documentation of each component in a WPP apparatus.
+
+\section{Fabrication}
+
+\subsection{Photon Source} \label{SEC:photon-source}
+
+TODO: FIGURE 2 FROM OPERATION GUIDE
+
+The WPP architecture utilizes industry standard 20 mm LED star circuit boards mounted with 3 high-intensity LEDs to deliver photons to photoreactions (Figure 2A).
+These LED star boards are commercially available or can be easily fabricated (see fabrication guide).
+The range of wavelengths provided by a LED star depends upon the emission profile of the mounted LEDs.
+Through variation of the LED star integrated into a base (Figure 2B), the user can control the wavelengths of light delivered by the photon source to a reaction vessel.
+See fabrication guide for LED star installation instructions.
+
+\subsection{3D Printed Enclosure} \label{SEC:enclosure}
+
+\includegraphics[width=\textwidth]{"./3dp-coverat.jpg"}
+
+A WPP reaction module consists of a reaction chamber and vessel holder.
+By modifying chamber height and adjusting holder geometry, one can produce modules compatible with reaction vessels of various types and sizes.
+Template reaction chamber and vessel holder CAD designs are provided in the project repository.
+CAD designs and 3D-printable models for modules compatible with 1-, 4-, 8- and 24-mL vials are also provided in the repository (Figure 3A—B).
+
+A single reaction module can offer multiple layouts for reaction vessel placement.
+For the provided modules, two vessel placement configurations exist.
+First, the single reaction configuration, where one vessel is placed in the center of the module directly above the photon source (Figure 3C).
+This configuration exposes one vessel to maximum light intensity.
+Second, the multiple reaction configuration, where multiple vessels are placed in a circle around the photon source (Figure 3D).
+This configuration exposes each vessel to less light relative to the single reaction configuration but provides equivalent exposure to each vessel.
+Through variation of the reaction module, the user can configure the reaction vessel type, size and placement within a WPP apparatus.
+
+The body of the WPR is made up of three main pieces:
+
+\begin{itemize}
+    \item Base, containing LEDs, fan, and drive electronics.
+    \item Top plate accepting reaction vials.
+    \item Chamber walls spacing the top plate at the appropriate distance away from the base.
+\end{itemize}
+
+The WPR base is the same for all reactors.
+Look within the repository in the subdirectory ``photoreactor-base'' to find design and production files to produce the WPR base.
+You will also need to print a cable anchor, see files in that same directory.
+
+The top plate and chamber height must be specified for the particular reaction vessels used.
+Four examples for different vial sizes are pictured above.
+Look within the repository in the subdirectory ``photoreactor-tops'' to find existing designs.
+We encourage you to design your own if none of these suit your application.
+Consider adding your new designs to repository so that others may benefit from your design efforts.
+
+When interacting with the design files in our online repository you will see several different filetypes.
+We have designed the WPR enclosure using Fusion 360, and have included those f3d design files for those that wish to extend or modify the designs.
+Interacting with f3d files will require a Fusion 360 license.
+You will also find stl files in the online repository.
+These are common 3D-model exchange files which can be viewed using any 3D modeling program.
+In fact, GitHub itself has a built in stl viewer which you may use to inspect our designs.
+
+There are many options for getting your enclosures printed.
+We recommend white PLA as a material, although any white material should work---we have also used ABS.
+If you are printing yourself, follow the instructions provided by your printer to produce slices and program your printer.
+Note that you will need support material for the base.
+Any company or shop offering 3D printing as a service should be able to accept our stl files without further modification.
+
+We have succesfully printed using the following printers:
+
+\begin{itemize}
+  \item Ender 3
+  \item Stratasys uPrint SE Plus
+  \item Ultimaker 3
+\end{itemize}
+
+Once your parts are done you may need to remove extra bonding material with a razor blade or exacto-knife.
+The three pieces of your reactor should fit together snugly and securely.
+
+\clearpage
+
+\begin{center}
+  \includegraphics[width=0.5\textwidth]{"./heat-insert.jpg"}
+\end{center}
+
+Each WPR base contains seven threaded heat inserts.
+These allow components such as the drive circuit board to rigidly attach to the base via machine screws.
+Use a soldering iron to carefully heat these while pushing them into their cavities.
+
+\subsection{Electronics} \label{SEC:electronics}
+
+\includegraphics[width=\textwidth]{"./electronics-coverart.jpg"}
+
+The WPR incorporates small circuit boards controlling the incorporated LED and fan.
+We refer to these small boards as ``drivers''.
+There are two types available: the ``analog-driver'' and ``digital-driver''.
+Refer to the associated directories in the online repository for design files for each of these.
+
+Both drivers are built around Mean Well's LDD-1000L LED driver module.
+This module delivers constant current up to one amp.
+The current delivered can be controlled electronically in several different ways.
+WPR users wishing to understand this design should refer to Mean Well's datasheet.
+
+The analog-driver circuit is made to be as simple as possible.
+The circuit accepts DC 12 V through a barrel jack.
+A small knob is used to adjust light intensity.
+Fan speed is not adjustable.
+Refer to \autoref{SEC:analog-driver} for analog-driver assembly instructions and further explanation.
+
+The digital-driver circuit is made to be incorporated into an I$^2$C-based digital control system.
+In addition to power, these boards have 4-pin connectors to carry the I$^2$C serial data.
+The digital-driver is pictured above, without any connectors attached.
+Refer to \autoref{SEC:digital-driver} for digital-driver assembly instructions and further explanation.
+
+When interacting with the design files in our online repository you will see several different filetypes.
+These circuit boards were designed using KiCad, a free and open source electronics CAD software.
+All KiCad files are contained within the ``kicad'' subdirectories.
+You may modify and extend these designs however you like.
+
+Those wishing to reproduce our designs should refer to the gerber subdirectory.
+Within the gerber directory you will find zip files for each separate version of the PCB.
+You may upload these zip files to PCB manufacturers when ordering copies of our designs.
+
+A WPP device can be driven using a digital driver circuit board, an analog driver circuit board or a simple electronic circuit with a commercial LED driver (Figure 4).
+Digital and analog driver board fabrication instructions are provided in the fabrication guide.
+All provide power to the cooling fan and constant current to the LEDs.
+All utilize 1000 mA forward current LED drivers. Each driver provides different configurational abilities.
+
+\clearpage
+\subsubsection{Analog Driver} \label{SEC:analog-driver}
+
+The analog driver circuit is meant to be as simple as possible while still allowing for reproducible LED intensity control.
+To this end, the number of components has been minimized as much as possible.
+A full schematic of the analog circuit appears at the end of this section.
+A bill of materials appears within the README of the online repository.
+
+Through use of the analog driver board, one can control WPP device light intensity.
+This control is achieved through adjustment of the board-mounted potentiometer.
+No software is required, and multiple WPP reactors can be connected in series to a single power source (Figure 6A).
+However, fan speed isn’t adjustable and is maintained at maximum.
+Relative light intensity can be determined using the analog driver board test points and a multimeter (Figure 6B-D).
+The measured voltage can then be converted to relative light intensity using the values in Table 3.
+These values are derived from the manufacturer’s datasheet for the analog board’s LED driver.
+See the fabrication guide for more details.
+
+TODO: TABLE 3 FROM OPERATION GUIDE
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./bare-pcb.jpg"}
+\end{center}
+
+Your PCB manufacturer will send you a bare board, as seen above.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./surface-mount.jpg"}
+\end{center}
+
+Begin by adding the surface mount components.
+Recommend thin solder, e.g. 0.015''.
+The LED does have a polarity---ensure that the small green line points towards ground (left).
+Once done your board should look like the above.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./connectors.jpg"}
+\end{center}
+
+Next, add the connectors and the potentiometer knob.
+From now on we recommend standard gage solder, e.g. 0.031''.
+Once done your board should look like the above.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./barrels-tested.jpg"}
+\end{center}
+
+Next, add the barrel jacks and the test points.
+With these added you may plug in your board for the first time.
+You should see your power indicator LED illuminate.
+You should also be able to adjust the DC control voltage relative to ground by turning the knob, as shown above.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./pcb-driver.jpg"}
+\end{center}
+
+Finally, add the Mean Well LED driver.
+Note that this component goes on the back of the PCB, as shown above.
+
+\includepdf[landscape=true]{"../analog-driver-board/driver.pdf"}
+
+\subsubsection{Digital Driver} \label{SEC:digital-driver}
+
+The digital driver circuit can be controlled from a computer or some other digital device.
+We built our driver to work over I2C, consistent with an emerging standard for many ``maker'' products.
+While the physical connectors may be different, our digital circuit is compatible with the following systems.
+
+\begin{itemize}
+  \item \href{https://learn.adafruit.com/introducing-adafruit-stemma-qt}{Adafruit STEMMA}
+  \item \href{https://www.sparkfun.com/qwiic}{Sparkfun Qwiic}
+  \item \href{https://www.seeedstudio.com/category/Grove-c-1003.html}{Seeed Grove}
+\end{itemize}
+
+Through use of the digital driver board, one can control WPP device light intensity and fan speed.
+This control is achieved by connecting a control unit, like an Arduino Uno, to the digital driver board using custom software.
+Multiple WPP devices with digital driver boards can be connected to a single control unit and power supply (Figure 5).
+Open-source software for interfacing digital driver boards and Arduino Uno control units is provided in the project repository.
+Instructions for implementing this software and controlling WPP devices using it are in the fabrication guide.
+Other I2C peripherals can be connected to digital driver boards to expand functionality, but software must be produced to interface with them.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./digital-wired.jpg"}
+\end{center}
+
+Each digital driver is based around an ATtiny85 microcontroller acting as an I2C peripheral.
+Multiple digital driver boards may be ``networked'' together onto one I2C bus by simply daisy-chaining the boards together, as shown above.
+In such a use-case you must choose a unique I2C address for each ATtiny85 peripheral.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./redboard.jpg"}
+\end{center}
+
+There are many ways to interface with the I2C bus.
+We have used a SparkFun RedBoard, pictured above.
+You may find an example within the online repository that dynamically controls both the LED intensity and fan speed.
+
+\includepdf[landscape=true]{"../digital-driver-board/driver.pdf"}
+
+\subsubsection{Simple Driver} \label{SEC:simple-driver}
+
+TODO: FIGURE 7 FROM OPERATION GUIDE
+
+The LED driver circuit shown in Figure 6 is the simplest way to drive a WPP apparatus.
+Neither light intensity nor fan speed can be configured when using the simple LED driver circuit.
+Both are maintained at maximum power.
+However, no circuit board fabrication is required, and any commercial 1000 mA LED driver can be used.
+
+\subsection{Assembly} \label{SEC:assembly}
+
+\includegraphics[width=\textwidth]{"./assembly-coverart.jpg"}
+
+Once 3D printing is done and PCBs have been filled, WPR assembly is fairly straight-forward.
+The various electronic components must be installed into the base (pictured above), as described in \autoref{SEC:base}.
+Reflective coating must be added to the chamber walls, as described in \autoref{SEC:top}.
+After these final steps, your WPR is ready for synthesis!
+
+\clearpage
+\subsubsection{Base} \label{SEC:base}
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./bare-led.jpg"}
+\end{center}
+
+If possible, it's best to order your LEDs pre-attached to an ``LED star'' heat sink.
+Otherwise you may order bare LED stars and discrete LEDs.
+Either way, you will have a filled LED star as pictured above.
+In this example we are using LED Supply part number 07007-PL000-F.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./soldered-led.jpg"}
+\end{center}
+
+Start by soldering leads onto your LED star, using the red positive black negative convention.
+Soldering here may be challenging, as the LED star itself will resist your efforts to heat it.
+Adding some lead-based solder may help, due to the lower melting point.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./tap-heatsink.jpg"}
+\end{center}
+
+The aluminum heatsinks arrive preformed but without any tapping.
+Tap the heatsink for imperial 4-40 machine screws.
+We used thread-forming tap: OSG 1400105300 with a pneumatic ``air-tapper'' (pictured above), but you may do this by hand if you wish.
+You will need to tap just two of the innermost holes.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./led-and-heatsink.jpg"}
+\end{center}
+
+Install the LED star and heatsink with wires facing towards printed hole.
+Use 1/4'' screws.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./mounted-fan.jpg"}
+\end{center}
+
+Install the fan.
+Pay special attention to the orientation of the fan, including the location of the cord.
+Use 3/4'' screws here.
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./cable-tie.jpg"}
+\end{center}
+
+Install the cable anchor using a 1/4'' screw.
+Use a zip tie to capture the fan cord, as shown above.
+
+\clearpage
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./driver-on-base.jpg"}
+\end{center}
+
+Install the driver board using the threaded standoffs.
+Plug the LED and fan into the board.
+Pay special attention to the orientation of the fan connector.
+You should now be ready to test your base---remember to use proper eye protection!
+
+\clearpage
+\subsubsection{Top} \label{SEC:top}
+
+\begin{center}
+  \includegraphics[width=\textwidth/2]{"./reflector.jpg"}
+\end{center}
+
+Simply cut the reflective material to line the chamber.
+It's good to leave overlap around the interior, as shown.
+Remove the backing and stick the material to the chamber walls.
+
+\section{Operation}
+
+Once a WPP apparatus is configured with the desired photon source, reaction module and reactor driver, it can be used to drive photoreactions.
+
+TODO: FIGURE 8 FROM OPERATION GUIDE
+
+To conduct a photoreaction using a WPP device, an assembled apparatus should be placed on a lab stir plate, to provide reaction mixture stirring, and reaction vessels should be inserted into the apparatus in the desired layout (Figure 8).
+The 130 by 130 mm footprint of the WPP architecture is compatible with typical stir plates.
+A standard 12 V power supply can then be plugged into the reactor driver to turn on the device and start reaction.
+A single 12V 2 A power supply is sufficient to drive 2 WPP devices simultaneously.
+A switch can be installed between the WPP apparatus and power supply to provide power switching.
+
+Reaction and photon source cooling is provided by the computer fan integrated into the base.
+Additional cooling can be achieved through placement of fans above the WPP apparatus or by placing a WPP device on a stir plate within in a refrigerator or cold room.
+
+Once finished, the WPP apparatus can be switched off by simply unplugging it and disassembled for storage.
+
+\section{Documentation}
+
+Users should report the following for each photon source used:
+
+    (1) Max emission wavelength for LEDs.
+    (2) Manufacturer and part number for LEDs.
+    (3) Supplier and part number for LED star (if commercial).
+
+This information enables precise reproduction of WPP photon sources. Characterization of a photon source’s emission profile using a spectrometer is recommended but not required for reproduction. Emission profiles for commercial LEDs are supplied in part datasheets provided by manufacturers. A list of WPP-compatible LED stars exhibiting emission profiles across the visible range is provided in the project repository.
+
+Users should provide and report the following for each module used:
+
+    (1) Original CAD designs for both module parts.
+    (2) 3D-printable models for both module parts.
+    (3) Photos of each reaction vessel placement configuration.
+    (4) Manufacturer and part number for reaction vessel.
+
+These provisions enable precise reproduction of reaction modules. Documenting the height a vessel is held above the photon source is recommended but not required for reaction module reproduction. All reaction modules provided in the project repository hold vessels a standardized 7 mm above the photon source.
+
+Users should report the following when an analog driver board is used:
+
+    (1) Measured test point voltage.
+    (2) Relative intensity at which LEDs are driven (0 to 100%).
+
+These provisions enable precise reproduction of reaction conditions for transformations carried out using WPP devices fitted with analog driver boards.
+
+Users should provide and document the following when a digital driver board is used:
+
+    (1) Software used to operate the digital driver board, control unit and any other peripherals.
+    (2) Relative intensity at which LEDs are driven (0 to 100%).
+    (3) Relative fan speed (0 to 100%).
+
+These provisions enable precise reproduction of reaction conditions for transformations carried out using WPP devices fitted with digital driver boards
+
+Users should report the following when a simple LED driver circuit is used:
+
+    (1) Manufacturer and part number for LED driver.
+
+This information enables reproduction WPP devices fitted with the simple LED driver circuit.
+
+\section{Safety}
+
+WPP reactors utilize high-intensity light emitting diodes (LED) that can cause eye damage if proper safety precautions are not observed.
+Light-filtering safety glasses should be worn whenever a WPP apparatus photon source is powered.
+Care must be taken to use safety glasses protective against the specific emission wavelengths of the photon source.
+
+\end{document}
-- 
cgit v1.2.3

