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add seperate page for cellular automata and physics update summary
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2 changes: 2 additions & 0 deletions physics/docs/ccpp_doxyfile
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# Note: If this tag is empty the current directory is searched.

INPUT = pdftxt/mainpage.txt \
pdftxt/ccppv7_phy_updates.txt \
pdftxt/all_schemes_list.txt \
pdftxt/GFS_v16_suite.txt \
pdftxt/GFS_v17_HR3_suite.txt \
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pdftxt/GFS_OZPHYS.txt \
pdftxt/GFS_H2OPHYS.txt \
pdftxt/GFS_SAMFdeep.txt \
pdftxt/GFS_CAUTOMATA.txt \
pdftxt/GFS_SAMFshal.txt \
pdftxt/GFDL_cloud.txt \
pdftxt/NSSLMICRO.txt \
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55 changes: 54 additions & 1 deletion physics/docs/library.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Man Zhang at 2024-06-27 13:18:41 -0600
%% Created for Man Zhang at 2024-07-02 13:44:09 -0600
%% Saved with string encoding Unicode (UTF-8)
@article{han_2021,
author = {J. Han, J. Peng, W. Li, W. Wang, Z. Zhang, F. Yang and W. Zheng},
date-added = {2024-07-02 13:49:10 -0600},
date-modified = {2024-07-02 13:49:10 -0600},
doi = {10.25923/CYBH-W893},
publisher = {National Centers for Environmental Prediction (U.S.)},
title = {Updates in the NCEP GFS Cumulus Convection, Vertical Turbulent Mixing, and Surface Layer Physics},
url = {https://repository.library.noaa.gov/view/noaa/33881},
year = {2021}}



@article{Han_2024,
author = {Han, Jongil and Peng, Jiayi and Li, Wei and Wang, Weiguo and Zhang, Zhan and Yang, Fanglin and Zheng, Weizhong},
date-added = {2024-07-02 13:44:05 -0600},
date-modified = {2024-07-02 13:44:05 -0600},
doi = {10.1175/waf-d-23-0134.1},
issn = {1520-0434},
journal = {Weather and Forecasting},
month = apr,
number = {4},
pages = {679{\^a}€“688},
publisher = {American Meteorological Society},
title = {Updates in the NCEP GFS PBL and Convection Models with Environmental Wind Shear Effect and Modified Entrainment and Detrainment Rates and Their Impacts on the GFS Hurricane and CAPE Forecasts},
url = {http://dx.doi.org/10.1175/WAF-D-23-0134.1},
volume = {39},
year = {2024},
bdsk-url-1 = {http://dx.doi.org/10.1175/WAF-D-23-0134.1}}

@article{Bengtsson_et_al_2020,
abstract = {Abstract In the atmosphere, convection can organize from smaller scale updrafts into more coherent structures on various scales. In bulk-plume cumulus convection parameterizations, this type of organization has to be represented in terms of how the resolved flow would ``feel'' convection if more coherent structures were present on the subgrid. This type of subgrid organization acts as building blocks for larger scale tropical convective organization known to modulate local and remote weather. In this work a parameterization for subgrid (and cross-grid) organization in a bulk-plume convection scheme is proposed using the stochastic, self-organizing, properties of cellular automata (CA). We investigate the effects of using a CA which can interact with three different components of the bulk-plume scheme that modulate convective activity: entrainment, triggering, and closure. The impacts of the revised schemes are studied in terms of the model's ability to organize convectively coupled equatorial waves (CCEWs). The differing impacts of adopting the stochastic CA scheme, as compared to the widely used Stochastically Perturbed Physics Tendency (SPPT) scheme, are also assessed. Results show that with the CA scheme, precipitation is more spatially and temporally organized, and there is a systematic shift in equatorial wave phase speed not seen with SPPT. Previous studies have noted a linear relationship between Gross Moist Stability (GMS) and Kelvin wave phase speed. Analysis of GMS in this study shows an increase in Kelvin wave phase speed and an increase in GMS with the CA scheme, which is tied to a shift from large-scale precipitation to convective precipitation.},
author = {Bengtsson, Lisa and Dias, Juliana and Tulich, Stefan and Gehne, Maria and Bao, Jian-Wen},
doi = {https://doi.org/10.1029/2020MS002260},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020MS002260},
journal = {Journal of Advances in Modeling Earth Systems},
keywords = {cellular automata, cumulus convection, convective organization, stochastic physics},
note = {e2020MS002260 2020MS002260},
number = {1},
pages = {e2020MS002260},
title = {A Stochastic Parameterization of Organized Tropical Convection Using Cellular Automata for Global Forecasts in NOAA's Unified Forecast System},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020MS002260},
volume = {13},
year = {2021},
bdsk-url-1 = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020MS002260},
bdsk-url-2 = {https://doi.org/10.1029/2020MS002260}}

@article{Han_et_al_2022,
author = {J. Han, F. Yang, R. Montuoro, W. Li, R. Sun},
date-added = {2024-07-02 11:17:39 -0600},
date-modified = {2024-07-02 11:20:58 -0600},
institution = {NCEP Office Note 506},
title = {Implementation of a positive definite mass-flux scheme and a method for removing the negative tracers in the NCEP GFS planetary boundary layer and cumulus convection scheme},
year = {2022}}

@article{xu_and_randall_1996,
author = {Xu, Kuan-Man and Randall, David A.},
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143 changes: 143 additions & 0 deletions physics/docs/pdftxt/GFS_CAUTOMATA.txt
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/**
\page cellular_automata Cellular Automata Stochastic Convective Organization Scheme

\b Scientific \b Background

Cumulus clouds in the atmosphere can organize into a variety of sizes, ranging
from small fair‐weather cumulus clouds, rain showers and thunderstorms, to
larger scale weather systems. In weather and climate models, such organization
is traditionally not well-represented as the motions associated with cumulus
clouds are generally too small to be resolved by the numerical model.
In this scheme we use a stochastic cellular automaton (CA), a mathematical
model often used to describe self‐organizing behavior in physical systems to
represent the effects of convective organization. The scheme addresses the
effect of convective organization in a bulk-plume cumulus convection
parameterizations (saSAS), where this type of organization has to be
represented in terms of how the resolved flow would “feel” convection if
more coherent structures were present on the subgrid.

In addition, for longer range forecasts (seasonal, decadal, climate),
the relevance of stochastic cumulus convection in numerical models can also
be discussed in terms of noise induced forcing. As an example, on the
time scale of organized convectively coupled waves, the small scale individual
convective plumes grow and decay so rapidly that they are not predictable
on time-scales longer than a few hours, whereas the organized larger scale
convectively coupled wave envelope can have a deterministic limit of
predictability of about two weeks. Thus, for longer range forecasts,
individual convective plumes can be viewed as stochastic noise - they can
have an impact on the convectively coupled waves (due to noise forcing),
but they are not predictable on their own. By providing the CA with a
stochastic initialization, the effect of stochastic cumulus convection
is also represented by the scheme.

The scientific motivation for the scheme, the CA rulesets explored, and
the impact on convectively coupled equatorial waves can be found in the
following references; Bengtsson et al. 2011 \cite Bengtsson_2011,
Bengtsson et al. 2013 \cite bengtsson_et_al_2013,
Bengtsson and Kornich (2016) \cite bengtsson_and_kornich_2016,
Bengtsson et al 2019 \cite Bengtsson_2019,
and Bengtsson et al. 2021 \cite bengtsson_et_al_2021.

\b Technical \b remarks

The CA source code is located in the stochastic physics submodule in
the ufs-weather-model: https://github.com/noaa-psd/stochastic_physics .
In the UFS Weather Model, the main call to the CA routines are made
from FV3/stochastic_physics_driver.F90.

There are currently two options to evolve the CA (can be done simultaneously);
(\p ca_global) a large scale global pattern which evolves the ruleset according
to game of life with cell history, or (\p ca_sgs) a sub-grid scale pattern
which is conditioned on a forcing from the atmospheric model. The two options
are controlled by namelist and are evolved in cellular_automata_globa.F90
and cellular_automata_sgs.F90 respectively. Both approaches use the main
CA module update_ca.F90 to evolve the CA in time. Since the CA needs to know
about its neighborhood it uses the halo information to gather the state
in adjacent MPI domains and/or adjacent cube sphere interfaces.

\b The \p ca_sgs \b option - \b Coupled \b to \b saSAS \b cumulus \b convection \b scheme

The evolution of the CA is an extension to the automaton family known as “Generations,”
which in turn is based on the “Game of Life”(Chopard & Droz, 1998 \cite Chopard_1998)
but adds cell history to the rule set. It is a deterministic CA ruleset, initialized
with Gaussian white noise. Thus, when used in an ensemble system, each ensemble
member can provide a different seed to the random number generator governing
the initial state to then generate a different evolution for each member.
By cell history we refer to newborn cells being given a “lifetime,”τ,
that is incrementally reduced by 1 each time step where the rules are not met,
in contrast to going directly from 1 to 0. The CA is conditioned on a
forcing from the host model through the lifetime variable τ such that:

\f[
\tau =N\left( \frac{\int_{l=1}^{l=top}E\frac{dp }{g} }{\max\left( \int_{l=1}^{l=top} E\frac{d p}{g}\right)} \right)
\f]

here, N is an integer that when multiplied by the model time-step represents
a physical time scale, such that τ is longer in regions where the forcing is larger,
E is the vertically integrated convective rain evaporation from the
saSAS cumulus convection scheme stored in Coupling%condition. The denominator is
the maximum value of the forcing in the global domain. While the grid-scale
forcing in practice could be any two-dimensional field, we choose here
to set it as the vertically integrated subgrid rain evaporation amount,
serving as an indicator of geographical regions where enhanced subgrid
organization may arise through convective cold-pools.

The CA is evolved on a finer grid than the numerical prediction
host model (size controlled by namelist), and can be either coarse
grained back to the host model grid as a fraction, or (in case of \p nca_plumes = .true.)
give back the maximum number of connected “plumes” (represented by
connected CA cells), and their associated size within each numerical
prediction host model grid-box. nca_plumes is default true and the
maximum cluster size is passed to the saSAS cumulus convection scheme
in the Coupling%ca_deep container.

Depending on the activated namelist options, the CA can feed back to
the saSAS convection scheme via the entrainment (\p ca_entr), closure
(\p ca_closure) or convective initiation (\p ca_trigger) in the following way:

- Entrainment (\p ca_entr): In entraining plume model bulk mass-flux schemes,
the upward mass-flux is typically parameterized as a function of environmental
air being entrained into the rising plume (as well as parcel properties at
cloud base). The fractional entrainment is described as a function of the
plume radius. Larger thermals (plumes) have smaller fractional entrainment,
which is a consequence of the fact that larger areas have relatively smaller
perimeters. In this scheme, the assumption is that subgrid organization will
lead to a few larger plumes rather than several smaller plumes, such that
the grid-box average fractional entrainment is reduced. Thus, after
the CA is updated, we count the number of plumes, and their associated
size within each NWP grid-box (\p nca_plumes = true). If the largest
cluster of cells found on the subgrid is larger than a set radius, then the
fractional entrainment rate is reduced at that grid-point by 30%
(selected based on experimentation)

- Triggering (\p ca_trigger): In NWP models physical processes are parameterized
in columns, and the horizontal interaction between physical processes takes
place only through advection and diffusion. As the CA can organize clusters
across adjacent NWP model grid-boxes, the method offers a novel approach to
enhance the probability of triggering of convection in nearby areas,
representing subgrid fluctuations in temperature and humidity, and triggering
in premoistened regions if convection is triggered in a cluster. The
stochastic nature of the CA may enhance organization in different
directions within the grid-box, and across grid-boxes, depending on the
initial seed. If the model is run as an ensemble, the convection scheme's
stochastic triggering function can help to improve uncertainty estimates
associated with subgrid fluctuations of temperature and humidity and
randomness in organization. In this work, model grid boxes in which the
CA's largest connecting plume exceeds a given threshold will be considered
as candidates for convective activation, in addition to saSAS’s current
triggering criteria.

- Closure (\p ca_closure): We assume that convection that organizes into
plumes with larger radii tends to cover a larger area fraction of the
grid-box and thereby acts to enhance the cloud base mass flux. In this
coupling strategy, we again count the number of plumes (represented by
connected cellular automaton cells), and their associated size within
each NWP grid-box. If the largest cluster of cells found on the subgrid
is larger than a set radius, then the cloud base mass-flux is enhanced in
that grid-box by 25% (selected based on experimentation). This option is
being revisited by reformulating the entire closure using a prognostic
evolution of the updraft area fraction, and is in its current formulation
not recommended.


*/
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