@highrayzh, Great questions!
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The YAM in this paper is the actual scheme developed by Yamartino (1993). The predecessor to CMAQ (MAQSIP) and initial versions of CMAQ had multiple advection schemes as noted in that paper. Each of these schemes was tested thoroughly using idealized and real test cases. The PPM scheme was more frequently used because of monotonicity (unlike YAM and BOT), positive-definite characteristics, mass-conserving characteristics, use with irregular grid spacing (unlike say ASD), and computational performance across a variety of tests (idealized and 3D model based). Over time, other schemes were dropped because of maintenance costs for little-to-none used options.
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The “yamo” scheme misnomer, came to be about when Bob Yamartino proposed the minor edits to PPM to the EPA. The edits themselves were causing various issues so starting v5.3, we decided the costs outweigh the benefits. For the official release note see CMAQ/DOCS/Release_Notes/CMAQv5.3_PPM.md at 5.3.3 · USEPA/CMAQ · GitHub