more dois added, :cite:t: introduced

docs/source/citations/kpp.bib

@@ -194,6 +194,7 @@ @article{2003:Djouad
  journal      = jac,
  volume       = {46},
  pages        = {131-157},
+ DOI          = {10.1023/A:1026067610565},
  year         = {2003}
 }
 
@@ -219,6 +220,7 @@ @article{2004:Lehmann
  journal      = jac,
  volume       = {47},
  pages        = {45-78},
+ DOI          = {10.1023/B:JOCH.0000012284.28801.B1},
  year         = {2004}
 }
 
@@ -229,6 +231,7 @@ @article{2005:Sander_et_al
  journal      = acp,
  volume       = {5},
  pages        = {445-450},
+ DOI          = {10.5194/ACP-5-445-2005},
  year         = {2005}
 }
 
@@ -264,6 +267,7 @@ @article{2003:Sandu_Daescu_and_Carmichael
  journal      = ae,
  volume       = {37},
  pages        = {5083-5096},
+ DOI          = {10.1016/J.ATMOSENV.2003.08.019},
  year         = {2003}
 }
 
@@ -274,6 +278,7 @@ @article{2003:Daescu_Sandu_and_Carmichael
  journal      = ae,
  volume       = {37},
  pages        = {5097-5114},
+ DOI          = {10.1016/J.ATMOSENV.2003.08.020},
  year         = {2003}
 }
 
@@ -285,7 +290,7 @@ @mastersthesis{1996:Damian-Iordache
 }
 
 @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},
@@ -297,11 +302,12 @@ @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}
@@ -315,6 +321,7 @@ @article{2002:Damian_et_al
  journal      = cce,
  volume       = {26},
  pages        = {1567-1579},
+ DOI          = {10.1016/S0098-1354(02)00128-X},
  year         = {2002}
 }
 
@@ -326,6 +333,7 @@ @article{1997:Sandu_et_al_1
  journal      = ae,
  volume       = {31},
  pages        = {3151-3166},
+ DOI          = {10.1016/S1352-2310(97)00059-9},
  year         = {1997}
 }
 
@@ -337,6 +345,7 @@ @article{1997:Sandu_et_al_2
  journal      = ae,
  volume       = {31},
  pages        = {3459-3472},
+ DOI          = {10.1016/S1352-2310(97)83212-8},
  year         = {1997}
 }
 
@@ -361,7 +370,7 @@ @article{1996:Sandu_et_al
 }
 
 @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},
@@ -381,7 +390,7 @@ @book{1993:LSODE
 }
 
 @article{1989:VODE,
- author       = {P.N.~ Brown and G.D.~ Byrne and A.C.~ Hindmarsh},
+ 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},
@@ -390,7 +399,7 @@ @article{1989:VODE
 }
 
 @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},
@@ -400,8 +409,8 @@ @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   = ae,
@@ -410,13 +419,13 @@ @article{2010:Santillana_et_al
     pages     = {4426-4431},
     year      = {2010},
     issn      = {1352-2310},
-    doi       = {https://doi.org/10.1016/j.atmosenv.2010.07.044},
+    doi       = {10.1016/j.atmosenv.2010.07.044},
     url       = {https://www.sciencedirect.com/science/article/pii/S1352231010006242}
 }
 
 @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},
@@ -430,12 +439,12 @@ @article{2020:Shen_et_al
 }
 
 @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},
+ 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}
+ year         = {in prep., 2022}
 }

docs/source/getting_started/00_revision_history.rst

@@ -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>`__).
 

docs/source/tech_info/07_numerical_methods.rst

@@ -104,7 +104,7 @@ Rosenbrock methods
 **Integrator file:** :file:`int/rosenbrock.f90`
 
 An :math:`s`-stage Rosenbrock method (cf. Section IV.7 in
-:cite:`1991:Hairer_and_Wanner`) computes the next-step solution by the
+:cite:t:`1991:Hairer_and_Wanner`) computes the next-step solution by the
 formulas
 
 .. _alt-rosenbrock:
@@ -343,15 +343,15 @@ Rosenbrock with mechanism auto-reduction
 
 **Integrator file:** :file:`int/rosenbrock_autoreduce.f90`
 
-Mechanism auto-reduction (described in :cite:`2022:Lin_et_al`) expands
-previous work by :cite:`2020:Shen_et_al`,
-:cite:`2010:Santillana_et_al` to a computationally efficient
-implementation in KPP, avoiding memory re-allocation, re-compile of
-the code, and on-the-fly mechanism reduction based on dynamically
-determined  production and loss rate thresholds.
+Mechanism auto-reduction (described in :cite:t:`2022:Lin_et_al`) expands
+previous work by :cite:t:`2020:Shen_et_al` and
+:cite:t:`2010:Santillana_et_al` to a computationally efficient
+implementation in KPP, avoiding memory re-allocation, re-compile of the
+code, and on-the-fly mechanism reduction based on dynamically determined
+production and loss rate thresholds.
 
 We define a threshold :math:`\delta` which can be fixed (as in
-:cite:`2010:Santillana_et_al`) or determined by the production and
+:cite:t:`2010:Santillana_et_al`) or determined by the production and
 loss rates of a "target species" scaled by a factor
 
 .. math::
@@ -380,7 +380,7 @@ Runge-Kutta (aka RK) methods
 ============================
 
 A general :math:`s`-stage Runge-Kutta method is defined as (see
-Section II.1 of :cite:`1993:Hairer_Norsett_and_Wanner`)
+Section II.1 of :cite:t:`1993:Hairer_Norsett_and_Wanner`)
 
 .. math::
 
@@ -420,7 +420,7 @@ RADAU5
 
 This Runge-Kutta method of order 5 based on RADAU-IIA quadrature
 is stiffly accurate. The KPP implementation follows the original
-implementation of :cite:`1991:Hairer_and_Wanner`, Section IV.10. While
+implementation of :cite:t:`1991:Hairer_and_Wanner`, Section IV.10. While
 RADAU5 is relatively expensive (when compared to the Rosenbrock
 methods), it is more robust and is useful to obtain accurate reference
 solutions.
@@ -430,7 +430,7 @@ SDIRK
 **Integrator file:** :file:`int/sdirk.f90`,
 
 SDIRK is an L-stable, singly-diagonally-implicit Runge-Kutta method. The
-implementation is based on :cite:`1991:Hairer_and_Wanner`. Several
+implementation is based on :cite:t:`1991:Hairer_and_Wanner`. Several
 variants are available:
 
   - Sdirk 2a, 2b: 2 stages, order 2
@@ -442,15 +442,15 @@ SDIRK4
 **Integrator file:** :file:`int/sdirk4.f90`
 
 SDIRK4 is an L-stable, singly-diagonally-implicit Runge-Kutta method
-of order 4. The implementation is based on :cite:`1991:Hairer_and_Wanner`.
+of order 4. The implementation is based on :cite:t:`1991:Hairer_and_Wanner`.
 
 SEULEX
 ------
 **Integrator file:** :file:`int/seulex.f90`
 
 SEULEX is a variable  order stiff extrapolation code able to produce
 highly accurate solutions. The KPP implementation is based on the
-implementation of :cite:`1991:Hairer_and_Wanner`.
+implementation of :cite:t:`1991:Hairer_and_Wanner`.
 
 .. _rk-tlm:
 
@@ -511,7 +511,7 @@ Backward differentiation formulas
 
 Backward differentiation formulas (BDF) are linear multistep methods
 with excellent stability properties for the integration of chemical
-systems (cf. :cite:`1991:Hairer_and_Wanner`, Section V.1). The
+systems (cf. :cite:t:`1991:Hairer_and_Wanner`, Section V.1). The
 :math:`k`-step BDF method reads
 
 .. math::

docs/source/using_kpp/04_input_for_kpp.rst

@@ -746,7 +746,7 @@ Reordering of the species is performed in order to minimize the fill-in
 during the LU factorization, and therefore preserve the sparsity
 structure and increase efficiency. The reordering is done using a
 diagonal markowitz algorithm. The details are explained in
-:cite:`1996:Sandu_et_al`. The default is :command:`ON`.
+:cite:t:`1996:Sandu_et_al`. The default is :command:`ON`.
 :command:`OFF` means that KPP does not reorder the species. The order
 of the variables is the order in which the species are
 declared in the :command:`#DEFVAR` section.

docs/source/using_kpp/05_output_from_kpp.rst

@@ -668,7 +668,7 @@ in-place LU factorization :math:`P` as computed by and perform sparse
 backward and forward substitutions (using :math:`P` or its
 transpose). The sparse linear algebra routines :code:`KppDecomp` and
 :code:`KppSolve` are extremely efficient, as shown by
-:cite:`1996:Sandu_et_al`.
+:cite:t:`1996:Sandu_et_al`.
 
 .. _Stoichiom-and-StoichiomSP: