rough merge of content from operation instructions

3 files changed, 144 insertions, 12 deletions

diff --git a/README.md b/README.md
index d12c754..bc35514 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ Care must be taken to use safety glasses protective against the specific emissio
 ## Frabication and Operation Instructions
 
 This repository contains detailed instructions for fabrication, operation and documentation of WPP devices.
-Please see [wpp-assembly.pdf](./assembly-instructions/wpp-assembly.pdf)
+Please see [wpp-fabrication-operation.pdf](./fabrication-and-operation-instructions/wpp-fabrication-operation.tex)
 
 ## Enclosure
 
diff --git a/fabrication-and-operation-instructions/wpr-assembly.pdf b/fabrication-and-operation-instructions/wpp-fabrication-operation.pdf
index df4123c..af212e8 100644
--- a/fabrication-and-operation-instructions/wpr-assembly.pdf
+++ b/fabrication-and-operation-instructions/wpp-fabrication-operation.pdf
diff --git a/fabrication-and-operation-instructions/wpr-assembly.tex b/fabrication-and-operation-instructions/wpp-fabrication-operation.tex
index 6b1c070..f301d73 100644
--- a/fabrication-and-operation-instructions/wpr-assembly.tex
+++ b/fabrication-and-operation-instructions/wpp-fabrication-operation.tex
@@ -52,7 +52,7 @@
 \usepackage[numbers]{natbib}
 
 % title
-\title{Wisconsin Photoreactor \\ Assembly Instructions}
+\title{Wisconsin Photoreactor Platform\\Fabrication and Operation Guide}
 \author{
   Philip Lampkin \\
   Blaise J. Thompson \\
@@ -64,7 +64,7 @@
 
 \maketitle
 
-\includegraphics[width=\textwidth]{"../coverart.jpg"}
+\includegraphics[width=\textwidth]{"../coverart.png"}
 
 \tableofcontents
 
@@ -94,10 +94,47 @@ 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.
 
-\section{3D Printed Enclosure} \label{SEC:enclosure}
+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}
@@ -150,7 +187,7 @@ 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.
 
-\section{Electronics} \label{SEC:electronics}
+\subsection{Electronics} \label{SEC:electronics}
 
 \includegraphics[width=\textwidth]{"./electronics-coverart.jpg"}
 
@@ -184,14 +221,30 @@ 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
-\subsection{Analog} \label{SEC:analog-driver}
+\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}
@@ -231,9 +284,9 @@ You should also be able to adjust the DC control voltage relative to ground by t
 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/driver.pdf"}
+\includepdf[landscape=true]{"../analog-driver-board/driver.pdf"}
 
-\subsection{Digital} \label{SEC:digital-driver}
+\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.
@@ -245,6 +298,13 @@ While the physical connectors may be different, our digital circuit is compatibl
   \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}
@@ -261,9 +321,18 @@ 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/driver.pdf"}
+\includepdf[landscape=true]{"../digital-driver-board/driver.pdf"}
+
+\subsubsection{Simple Driver} \label{SEC:simple-driver}
+
+TODO: FIGURE 7 FROM OPERATION GUIDE
 
-\section{Assembly} \label{SEC:assembly}
+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"}
 
@@ -273,7 +342,7 @@ Reflective coating must be added to the chamber walls, as described in \autoref{
 After these final steps, your WPR is ready for synthesis!
 
 \clearpage
-\subsection{Base} \label{SEC:base}
+\subsubsection{Base} \label{SEC:base}
 
 \begin{center}
   \includegraphics[width=\textwidth/2]{"./bare-led.jpg"}
@@ -335,7 +404,7 @@ 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
-\subsection{Top} \label{SEC:top}
+\subsubsection{Top} \label{SEC:top}
 
 \begin{center}
   \includegraphics[width=\textwidth/2]{"./reflector.jpg"}
@@ -345,4 +414,67 @@ 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}