Re-review of “S2P3-R(v1.0): a framework for efficient regional modeling of physical and biological structures and processes in shelf seas” by Marsh, Hickman and Sharples.
The authors have done a nice job with their edits of the manuscript, which has been considerably improved. In particular, I feel that their final paragraph is an excellent summary of the modeling framework they are presenting. However I still have issues with a few of the authors’ points, which do need further attention.
(1) On lines 69-72 the authors state in the revised manuscript: “S2P3 has not been extensively used and tested across real transects or in regions where 1D (vertical) processes are dominant, such that the model can be appropriately used for investigating time evolving 3D structures.” In my opinion, it is misleading to imply that S2P3-R can be used to investigate time-evolving 3D structures. As I understand it, the modeling framework essentially involves running many many model implementations in 1D at sites that are ~1 km apart. Thus S2P3 can help us understand how vertical processes vary in the horizontal, but this is fundamentally different from helping us understand 3D processes. The authors do say “3D structures” and not “3D processes”, but I feel it is likely that this point will be misinterpreted by readers. Thus I feel the authors need to make it clearer to the reader that this modeling framework: (1) does not provide a tool to examine 3D processes, but rather provides a tool to look at how vertical processes vary in horizontal space and (2) should only be used in regions where horizontal processes (such as horizontal advection) are known to be weak. Both of these points must be added to the abstract.
(2) It would be very helpful for readers and potential future users of the framework if the authors could recommend quantitative methods for determining if a region is characterized by weak horizontal advection, and thus suitable for this modeling framework. For example, the authors state: “1D (vertical) processes dominate 2D (horizontal) processes across much of the shelf seas, where we have the observations necessary for a co-evaluation of these processes.” I feel that this is an important component of the manuscript, and that this quantitative co-evaluation of vertical vs. horizontal processes should be included in the manuscript.
(3) I disagree with the statement that “the 1D approach is however valid for testing, against suitable observations of evolving physical structures, the extent to which advection may be important”(lines 696-698). Just as the authors state in their response document, the model-data discrepancy in Fig. 4 could be due to the missing horizontal processes, or it could be due to the relatively simple description of phytoplankton physiology. A 1D model framework cannot be used to determine the importance of horizontal processes simply be assessing model-data mismatch. There are multiple other potential explanations for model-data mismatch.
(4) I recommend removing almost all usage of “3D” within the manuscript, except where the authors are stating that this is not a 3D model. The overuse of “3D” makes it seem to the reader as if 3D processes are being modeled, but of course they are not. Similarly “2D” should be removed and replaced with “horizontal” to avoid unnecessary confusion. (In many situations “2D” represents x-z variability, not x-y variability.)
Specific comments:
Abstract – Change line 15-16 to: “…can be efficiently used to study the horizontal variability of vertical processes in shelf seas or other regions where horizontal advection is negligible, such as in the tidal mixing fronts that develop…”
Line 52 – word missing (to?)
Lind 70-71 – this sounds as if S2P3 has been extensively used in regions where 1D vertical processes are not dominant? I’m not sure this is what the authors intend to say here, but if it is, references are needed.
Line 72 – change to “used for investigating the horizontal variability of 1D structures”
Line 73 – simply remove “3D” or change to “to efficiently model the horizontal variability of physical and biological structures in shelf seas”
Line 75 – change to “facilitated the simulation of vertical processes and their horizontal variability in real-time…”
Line 465 – if the model overestimates the observations by a factor of two at most depths as stated in the text, I disagree with the statement that “the model reproduces the observations”.
Line 622 – should be “complement”.
Line 626 – remove 1D and 2D and parentheses
Line 635 – replace “unprecedented” with “high”. Some coupled 3D biological-physical models are run in estuaries and continental shelves (e.g. FVCOM) at resolution as high as a few hundreds of meters. Physical models are routinely run at resolutions as high as 50m (http://www.sciencedirect.com/science/article/pii/S007966111400130X) The horizontal resolution used here is not unprecedented in terms of 3D modeling.
Line 637 – remove “3D”
Line 645 – remove “(hence expensive)”. Evidence of this is not provided. If a 3D model is already set up and running, it would actually be more expensive to develop a new 1D model framework.
Line 653 – again, this resolution is not unprecedented.
Line 654 – but if massively parallel computing resources were available, why not actually run a 3D model that includes horizontal processes? Even if it takes a week to run instead of a few minutes, in terms of the total amount of time it takes to complete a research project, the run-time of a high resolution 3D model is typically quite small. The true benefit of this framework is that it can be used by those who do not have access to, or the knowledge of how to use, parallel computing resources.
Line 657 – what is meant by “temperature structures”? The word structure is used frequently throughout the manuscript, but it is a rather confusing terminology. Replace “3D temperature structures” with “Temperature distributions”
Line 697 – I disagree, as noted above. Please remove this paragraph.
Line 700-708 – very nice final paragraph! |