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107 changes: 55 additions & 52 deletions docs/source/citations/kpp.bib
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Expand Up @@ -59,6 +59,7 @@ @string{fpe
@string{gbc ={Global Biogeochem. Cycles}}
@string{gca ={Geochim. Cosmochim. Acta}}
@string{geot ={Geothermics}}
@string{gmd ={Geosci. Model Dev.}}
@string{gra ={Geophys. Res. Abstr.}}
@string{grl ={Geophys. Res. Lett.}}
@string{hca ={Helv. Chim. Acta}}
Expand All @@ -72,6 +73,7 @@ @string{jac
@string{jacs ={J. Am. Chem. Soc.}}
@string{jafc ={J. Agric. Food Chem.}}
@string{jam ={J. Appl. Meteorol.}}
@string{james ={J. Adv. Model. Earth Syst.}}
@string{japca ={J. Air. Pollut. Control Assoc.}}
@string{jappl ={J. Appl. Chem.}}
@string{jas ={J. Aerosol Sci.}}
Expand All @@ -84,6 +86,7 @@ @string{jcej
@string{jchro ={J. Chromatogr.}}
@string{jchroa ={J. Chromatogr. A}}
@string{jchros ={J. Chromatogr. Sci.}}
@string{jcompp ={J. Comput. Phys.}}
@string{jcp ={J. Chem. Phys.}}
@string{jcs ={J. Chem. Soc.}}
@string{jcsa ={J. Chem. Soc. A}}
Expand Down Expand Up @@ -152,7 +155,6 @@ @string{zn
@string{zpc ={Z. Phys. Chem.}}
@techreport{2002:Curtis-Sweetenham,
keyword = {facsimile},
author = {A. R. Curtis and W. P. Sweetenham},
title = {Facsimile/Chekmat User's Manual},
institution = {Computer Science and Systems Division, Harwell Lab.,
Expand All @@ -162,7 +164,6 @@ @techreport{2002:Curtis-Sweetenham
}

@article{2002:vonGlasow,
keyword = {model and MBL and Br2},
author = {R. {von Glasow} and R. Sander and A. Bott and P. J. Crutzen},
title = {Modeling halogen chemistry in the marine boundary layer.
1. {C}loud-free MBL},
Expand All @@ -174,36 +175,34 @@ @article{2002:vonGlasow
}

@article{2003:vonKuhlmann,
keyword = {model},
author = {R. von Kuhlmann and M. G. Lawrence and P. J. Crutzen and P. J.
Rasch},
title = {A model for studies of tropospheric ozone and nonmethane
hydrocarbons: Model description and ozone results},
journal = {jgr},
journal = jgr,
volume = {108D},
doi = {10.1029/2002JD002893},
year = {2003}
}

@article{2003:Djouad,
keyword = {model},
author = {R. Djouad and B. Sportisse and N. Audiffren},
title = {Reduction of multiphase atmospheric chemistry},
journal = {jac},
journal = jac,
volume = {46},
pages = {131-157},
DOI = {10.1023/A:1026067610565},
year = {2003}
}

@article{2004:IUPAC,
keyword = {iupac and data-tables and rate-const},
author = {R. Atkinson and D. L. Baulch and R. A. Cox and J. N.
Crowley and R. F. Hampson and R. G. Hynes and M. E.
Jenkin and M. J. Rossi and J. Troe},
title = {Evaluated kinetic and photochemical data for
atmospheric chemistry: Volume I -- gas phase reactions
of O_x, HO_x, NO_x, and SO_x species},
journal = {acp},
atmospheric chemistry: Volume {I} -- gas phase reactions
of {Ox}, {HOx}, {NOx}, and {SOx} species},
journal = acp,
volume = {4},
pages = {1461-1738},
doi = {10.5194/ACP-4-1461-2004},
Expand All @@ -214,24 +213,25 @@ @article{2004:Lehmann
author = {R. Lehmann},
title = {An algorithm for the determination of all significant pathways
in chemical reaction systems},
journal = {jac},
journal = jac,
volume = {47},
pages = {45-78},
DOI = {10.1023/B:JOCH.0000012284.28801.B1},
year = {2004}
}

@article{2005:Sander_et_al,
author = {R. Sander and A. Kerkweg and P. J\"ockel and J. Lelieveld},
title = {Technical Note: The new comprehensive atmospheric chemistry
module {MECCA}},
journal = {acp},
journal = acp,
volume = {5},
pages = {445-450},
DOI = {10.5194/ACP-5-445-2005},
year = {2005}
}

@article{2003:Trentman,
keyword = {kpp},
author = {J. Trentmann and M. O. Andreae and H.-F. Graf},
title = {Chemical processes in a young biomass-burning plume},
journal = jgr,
Expand All @@ -241,15 +241,14 @@ @article{2003:Trentman
}

@article{2003:Tang,
keyword = {kpp},
author = {Y. Tang and G. R. Carmichael and I. Uno and J.-H. Woo and G.
Kurata and B. Lefer and R. E. Shetter and H. Huang and
B. E. Anderson and M. A. Avery and A. D. Clarke and D. R.
Blake},
title = {Impacts of aerosols and clouds on photolysis frequencies and
photochemistry during TRACE-P: 2. Three-dimensional study using
a regional chemical transport model},
journal = {jgr},
journal = jgr,
volume = {108D},
doi = {10.1029/2002JD003100},
year = {2003}
Expand All @@ -258,32 +257,34 @@ @article{2003:Tang
@article{2003:Sandu_Daescu_and_Carmichael,
author = {A. Sandu and D. Daescu and G. R. Carmichael},
title = {Direct and adjoint sensitivity analysis of chemical kinetic
systems with KPP: I -- Theory and software tools},
journal = {ae},
systems with {KPP}: {I} -- Theory and software tools},
journal = ae,
volume = {37},
pages = {5083-5096},
DOI = {10.1016/J.ATMOSENV.2003.08.019},
year = {2003}
}

@article{2003:Daescu_Sandu_and_Carmichael,
author = {D. Daescu and A. Sandu and G. R. Carmichael},
title = {Direct and adjoint sensitivity analysis of chemical kinetic
systems with KPP: II -- Validation and numerical experiments},
journal = {ae},
systems with {KPP}: {II} -- Validation and numerical experiments},
journal = ae,
volume = {37},
pages = {5097-5114},
DOI = {10.1016/J.ATMOSENV.2003.08.020},
year = {2003}
}

@mastersthesis{1996:Damian-Iordache,
author = {V. Damian-Iordache},
title = {KPP -- Chemistry simulation development environment},
title = {{KPP} -- Chemistry simulation development environment},
school = {University of Iowa, USA},
year = {1996}
}

@book{1991:Hairer_and_Wanner
author = {E.~ Hairer and G.~ Wanner},
author = {E. Hairer and G. Wanner},
title = {Solving Ordinary Differential Equations II.
Stiff and Differential-Algebraic Problems},
publisher = {Springer-Verlag, Berlin},
Expand All @@ -295,11 +296,12 @@ @book{1996:Hairer_and_Wanner
title = {Solving Ordinary Differential Equations II. Stiff and
Differential-Algebraic Problems},
publisher = {Springer-Verlag},
DOI = {10.1007/978-3-642-05221-7},
year = {1996}
}

@book{1993:Hairer_Norsett_and_Wanner,
author = {E.~ Hairer and S.P.~ Norsett and G.~ Wanner},
author = {E. Hairer and S. P. Norsett and G. Wanner},
title = {Solving Ordinary Differential Equations I. Nonstiff Problems.},
publisher = {Springer-Verlag, Berlin},
year = {1993}
Expand All @@ -310,9 +312,10 @@ @article{2002:Damian_et_al
Carmichael},
title = {The kinetic preprocessor {KPP} -- a software environment for
solving chemical kinetics},
journal = {cce},
journal = cce,
volume = {26},
pages = {1567-1579},
DOI = {10.1016/S0098-1354(02)00128-X},
year = {2002}
}

Expand All @@ -321,9 +324,10 @@ @article{1997:Sandu_et_al_1
and F. A. Potra and D. Dabdub and J. H. Seinfeld},
title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry
problems--{I}. implicit vs explicit},
journal = {ae},
journal = ae,
volume = {31},
pages = {3151-3166},
DOI = {10.1016/S1352-2310(97)00059-9},
year = {1997}
}

Expand All @@ -332,16 +336,17 @@ @article{1997:Sandu_et_al_2
R. Carmichael and F. A. Potra},
title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry
problems {II}: {R}osenbrock solvers},
journal = {ae},
journal = ae,
volume = {31},
pages = {3459-3472},
DOI = {10.1016/S1352-2310(97)83212-8},
year = {1997}
}

@techreport{1995:KPP_User_Guide,
author = {V. Damian and A. Sandu and M. Damian and G. R. Carmichael
and F. A. Potra},
title = {KPP -- A symbolic preprocessor for chemistry kinetics --
title = {{KPP} -- A symbolic preprocessor for chemistry kinetics --
User's guide},
type = {Technical report},
institution = {The University of Iowa, Iowa City, IA 52246},
Expand All @@ -352,14 +357,14 @@ @article{1996:Sandu_et_al
author = {A. Sandu and F. A. Potra and V. Damian and G. R. Carmichael},
title = {Efficient implementation of fully implicit methods for
atmospheric chemistry},
journal = {jcompp},
journal = jcompp,
volume = {129},
pages = {101-110},
year = {1996}
}

@article{1986:Leis86a,
author = {J.R. Leis and M.A. Kramer},
author = {J. R. Leis and M. A. Kramer},
title = {ODESSA -- An Ordinary Differential Equation Solver
with Explicit Simultaneous Sensitivity Analysis},
journal = {ACM Transactions on Mathematical Software},
Expand All @@ -379,16 +384,16 @@ @book{1993:LSODE
}

@article{1989:VODE,
author = {P.N.~ Brown and G.D.~ Byrne and A.C.~ Hindmarsh},
title = {VODE: A Variable Step ODE Solver},
author = {P. N. Brown and G. D. Byrne and A. C. Hindmarsh},
title = {{VODE}: A Variable Step ODE Solver},
journal = {SIAM J. Sci. Stat. Comput.},
volume = {10},
year = {1989},
pages = {1038--1051}
}

@article{1999:Verwer,
author = {J.~ Verwer and E.J.~Spee and J. G.~ Blom and W.~ Hunsdorfer},
author = {J. Verwer and E. J. Spee and J. G. Blom and W. Hunsdorfer},
title = {A second order Rosenbrock method applied to photochemical
dispersion problems},
journal = {SIAM Journal on Scientific Computing},
Expand All @@ -398,42 +403,40 @@ @article{1999:Verwer
}

@article{2010:Santillana_et_al,
author = {M. Santillana~ and P.~ {Le Sager} and D.J.~ Jacob and
M.P.~ Brenner},
author = {M. Santillana and P. {Le Sager} and D. J. Jacob and
M. P. Brenner},
title = {An adaptive reduction algorithm for efficient chemical
calculations in global atmospheric chemistry models},
journal = {Atmospheric Environment},
journal = ae,
volume = {44},
number = {35},
pages = {4426-4431},
year = {2010},
issn = {1352-2310},
doi = {https://doi.org/10.1016/j.atmosenv.2010.07.044},
url = {https://www.sciencedirect.com/science/article/pii/S1352231010006242}
doi = {10.1016/j.atmosenv.2010.07.044}
}

@article{2020:Shen_et_al,
author = {L.~ Shen and D.J.~ Jacob and M.~ Santillana and X.~ Wang and
W.~ Chen},
author = {L. Shen and D. J. Jacob and M. Santillana and X. Wang and
W. Chen},
title = {An adaptive method for speeding up the numerical integration
of chemical mechanisms in atmospheric chemistry models:
application to GEOS-Chem version 12.0.0},
journal = {Geoscientific Model Development},
application to {GEOS-Chem} version 12.0.0},
journal = gmd,
volume = {13},
year = {2020},
number = {5},
pages = {2475--2486},
url = {https://gmd.copernicus.org/articles/13/2475/2020/},
doi = {10.5194/gmd-13-2475-2020}
doi = {10.5194/gmd-13-2475-2020},
year = {2020}
}

@article{2022:Lin_et_al,
author = {H.~ Lin and M.S.~ Long and R.~ Sander and A.~ Sandu and
R.M.~ Yantosca and L.A.~ Estrada and L.~ Shen and D.J.~ Jacob},
title = {An adaptive auto-reduction solver for speeding up integration
of chemical kinetics in atmospheric chemistry models:
implementation and evaluation within the Kinetic
Pre-Processor (KPP) version 3.0.0},
journal = {Journal of Advances in Modeling Earth Systems},
year = {in prep, 2022.}
author = {H. Lin and M. S. Long and R. Sander and A. Sandu and R.
M. Yantosca and L. A. Estrada and L. Shen and D. J.
Jacob},
title = {An adaptive auto-reduction solver for speeding up
integration of chemical kinetics in atmospheric
chemistry models: implementation and evaluation within
the Kinetic Pre-Processor ({KPP}) version 3.0.0},
journal = james,
year = {in prep., 2022}
}
4 changes: 2 additions & 2 deletions docs/source/conf.py
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Expand Up @@ -53,7 +53,7 @@ class RefStyle(UnsrtStyle):
default_name_style = LastFirst
default_sort_style = None
default_label_style = LabelStyle

def __init__(self):
super().__init__()
self.abbreviate_names = True
Expand Down Expand Up @@ -111,7 +111,7 @@ def format_web_refs(self, e):

latex_theme = "howto"
latex_logo = "_static/kpp-logo.png"
latex_show_pagerefs = True
#latex_show_pagerefs = True
latex_show_urls = "footnote"

latex_elements = {
Expand Down
6 changes: 3 additions & 3 deletions docs/source/getting_started/00_revision_history.rst
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Expand Up @@ -37,7 +37,7 @@ is currently still in preparation.
which all use the temperature from the :code:`temp` variable in
:file:`ROOT_Global.f90`. Alternatively, it is possible to copy the
old functions into a separate file and make them available via
:code:`F90_RCONST`.
:ref:`f90-RCONST`.

.. _kpp260:

Expand Down Expand Up @@ -127,7 +127,7 @@ NOTE: Contains KPP Modifications specific to GEOS-Chem:
KPP 2.3.1_gc
============

NOTE: KPP modifications specific to GEOS-Chem:
NOTE: KPP modifications specific to GEOS-Chem

ALSO NOTE: ReadTheDocs documentation has been updated in :ref:`kpp250`
to remove GEOS-Chem specific information.
Expand Down Expand Up @@ -266,7 +266,7 @@ KPP 2.1
=======

- Fortran90 output has been available since the preliminary version
“1.1-f90-alpha12” provided in :cite:`2005:Sander_et_al`.
“1.1-f90-alpha12” provided in :cite:t:`2005:Sander_et_al`.

- Matlab is a new target language (see Sect. `4.4 <#sec:matlab>`__).

Expand Down

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