diff --git a/CHANGELOG.md b/CHANGELOG.md index a5b34b3a0..027adda2d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,14 @@ # AtChem2 - CHANGELOG +## v1.2.1 (January 2021) + +- new environment variable `ASA` (aerosol surface area) +- fix bug in the C-binding for `gfortran` version 9 and above +- remove tabs from the configuration files +- update the Travis configuration file +- tidy the comments and printout messages of various source files +- update the manual + ## v1.2 (May 2020) - implement argument parser and named arguments for the `atchem2` executable @@ -20,7 +29,7 @@ - new script to set the version of AtChem2 before a release (`tools/version.sh`) - minor improvements to the install procedure - move the example chemical mechanism file to the `mcm`/ directory, and add a minimal .fac file (`mechanism_skel.fac`) -- tidy and improve comments of various source files and scripts +- tidy and improve comments in various source files and scripts - minor fixes and updates ## v1.1.1 (January 2019) diff --git a/doc/AtChem2-Manual.pdf b/doc/AtChem2-Manual.pdf index 1744e11f0..daf87ef67 100644 Binary files a/doc/AtChem2-Manual.pdf and b/doc/AtChem2-Manual.pdf differ diff --git a/doc/latex/AtChem2-Manual.tex b/doc/latex/AtChem2-Manual.tex index e9893dd30..cb82730f8 100644 --- a/doc/latex/AtChem2-Manual.tex +++ b/doc/latex/AtChem2-Manual.tex @@ -51,7 +51,7 @@ \hspace{0.05\textwidth} % Box for the title page text \parbox[b]{0.75\textwidth}{ - {\Huge\bfseries AtChem2\\[0.5\baselineskip] v1.3-dev}\\[2\baselineskip] % Title + {\Huge\bfseries AtChem2\\[0.5\baselineskip] v1.2.1}\\[2\baselineskip] % Title {\LARGE\textit{User Manual}}\\[4\baselineskip] % Subtitle {\Large\textsc{R. Sommariva\\S. Cox}} % Author(s) \vspace{0.5\textheight}\\ diff --git a/doc/latex/Installation.tex b/doc/latex/Installation.tex index f21b6f604..58b862c0a 100644 --- a/doc/latex/Installation.tex +++ b/doc/latex/Installation.tex @@ -22,12 +22,12 @@ \section{Requirements} \label{sec:requirements} \begin{itemize} \item Fortran -- the model compiles with GNU \texttt{gfortran} - (version 4.8.5) and with Intel \texttt{ifort} (version 17.0)\\ + (version 4.8 and above) and with Intel \texttt{ifort} (version 17.0)\\ $\hookrightarrow$ default compiler: \texttt{gfortran} \item Python~\footnote{All Python scripts used in AtChem2 work equally - with Python v2 and v3. Support for Python v2 may be removed in - future versions of AtChem2.} -\item cmake + with Python v2 and v3. Support for Python v2 will be removed in + future versions of AtChem2.} +\item make and cmake \item Ruby (optional) \end{itemize} @@ -38,9 +38,9 @@ \section{Requirements} \label{sec:requirements} AtChem2 has the following dependencies: \begin{itemize} +\item BLAS and LAPACK \item CVODE \item openlibm -\item BLAS and LAPACK \item numdiff (optional) \item FRUIT (optional) \end{itemize} @@ -99,9 +99,10 @@ \section{Dependencies} \label{sec:dependencies} anywhere and given any name. In this manual, the \depdir\ is assumed to be: \texttt{\$HOME/atchem-lib/}. -Before installing the dependencies, make sure that a Fortran compiler, -Python, cmake and (optionally) Ruby are installed on the operating -system, as explained in Sect.~\ref{sec:requirements}. +Before installing the dependencies, make sure that a Fortran compiler +(e.g., \texttt{gfortran}), Python, make, cmake and (optionally) Ruby +are installed on the operating system, as explained in +Sect.~\ref{sec:requirements}. \subsection{Required dependencies} \label{subsec:required-dependencies} diff --git a/src/atchem2.f90 b/src/atchem2.f90 index 7d02437f6..3b0571085 100644 --- a/src/atchem2.f90 +++ b/src/atchem2.f90 @@ -150,7 +150,7 @@ end subroutine FCVFUN rout(:) = -1.0_DP rpar(:) = -1.0_DP - write (*, '(A)') 'AtChem2 v1.3-dev' + write (*, '(A)') 'AtChem2 v1.2.1' write (*,*) write (*, '(A)') '-------------' write (*, '(A)') ' Directories' diff --git a/tools/version.sh b/tools/version.sh index 6014fc3e7..bd4145ae1 100755 --- a/tools/version.sh +++ b/tools/version.sh @@ -14,8 +14,8 @@ # # N.B.: the script MUST be run from the main directory of AtChem2. -VERS_OLD="v1.2" -VERS_NEW="v1.3-dev" +VERS_OLD="v1.3-dev" +VERS_NEW="v1.2.1" find ./ -type f ! -name "version.sh" -print | xargs perl -pi -e "s/$VERS_OLD/$VERS_NEW/g" diff --git a/travis/tests/firstorder/firstorder.out.cmp b/travis/tests/firstorder/firstorder.out.cmp index ab87eb236..6c5f2d86e 100644 --- a/travis/tests/firstorder/firstorder.out.cmp +++ b/travis/tests/firstorder/firstorder.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/secondorder/secondorder.out.cmp b/travis/tests/secondorder/secondorder.out.cmp index a04bc4bac..ebb8c0862 100644 --- a/travis/tests/secondorder/secondorder.out.cmp +++ b/travis/tests/secondorder/secondorder.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short/short.out.cmp b/travis/tests/short/short.out.cmp index 377552876..4dbd1f488 100644 --- a/travis/tests/short/short.out.cmp +++ b/travis/tests/short/short.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_dense/short_dense.out.cmp b/travis/tests/short_dense/short_dense.out.cmp index f6d80ba17..bbbb248eb 100644 --- a/travis/tests/short_dense/short_dense.out.cmp +++ b/travis/tests/short_dense/short_dense.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_end_of_day/short_end_of_day.out.cmp b/travis/tests/short_end_of_day/short_end_of_day.out.cmp index bbc4fb39b..a9e2fd4ec 100644 --- a/travis/tests/short_end_of_day/short_end_of_day.out.cmp +++ b/travis/tests/short_end_of_day/short_end_of_day.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_ext1/short_ext1.out.cmp b/travis/tests/short_ext1/short_ext1.out.cmp index 95f0b7757..49633cec4 100644 --- a/travis/tests/short_ext1/short_ext1.out.cmp +++ b/travis/tests/short_ext1/short_ext1.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_ext2/short_ext2.out.cmp b/travis/tests/short_ext2/short_ext2.out.cmp index 1b1c73751..0e38d59b3 100644 --- a/travis/tests/short_ext2/short_ext2.out.cmp +++ b/travis/tests/short_ext2/short_ext2.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_ext3/short_ext3.out.cmp b/travis/tests/short_ext3/short_ext3.out.cmp index 04093e8ba..260ba59c2 100644 --- a/travis/tests/short_ext3/short_ext3.out.cmp +++ b/travis/tests/short_ext3/short_ext3.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_ext4/short_ext4.out.cmp b/travis/tests/short_ext4/short_ext4.out.cmp index c3ffaf215..e953eef5c 100644 --- a/travis/tests/short_ext4/short_ext4.out.cmp +++ b/travis/tests/short_ext4/short_ext4.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/short_no_pre/short_no_pre.out.cmp b/travis/tests/short_no_pre/short_no_pre.out.cmp index ffeb6f197..db7c679dc 100644 --- a/travis/tests/short_no_pre/short_no_pre.out.cmp +++ b/travis/tests/short_no_pre/short_no_pre.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp b/travis/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp index 5ec21338f..2246c3d34 100644 --- a/travis/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp +++ b/travis/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp b/travis/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp index 95355cc31..6a2b6bbb6 100644 --- a/travis/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp +++ b/travis/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_no/spec_yes_env_no.out.cmp b/travis/tests/spec_yes_env_no/spec_yes_env_no.out.cmp index b29922a3e..264425932 100644 --- a/travis/tests/spec_yes_env_no/spec_yes_env_no.out.cmp +++ b/travis/tests/spec_yes_env_no/spec_yes_env_no.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp b/travis/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp index 5ce101581..66ba5a31d 100644 --- a/travis/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp +++ b/travis/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp b/travis/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp index f20445cdc..acecf8fe3 100644 --- a/travis/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp +++ b/travis/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp b/travis/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp index 4b7b1087e..0e67e376e 100644 --- a/travis/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp +++ b/travis/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp b/travis/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp index 432967e95..47e8fd3eb 100644 --- a/travis/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp +++ b/travis/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp b/travis/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp index 2eddfba10..9c36a4521 100644 --- a/travis/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp +++ b/travis/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp b/travis/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp index 01fb87b43..0a9674227 100644 --- a/travis/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp +++ b/travis/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories diff --git a/travis/tests/static/static.out.cmp b/travis/tests/static/static.out.cmp index 1c8643fda..c3c78b540 100644 --- a/travis/tests/static/static.out.cmp +++ b/travis/tests/static/static.out.cmp @@ -1,4 +1,4 @@ -AtChem2 v1.3-dev +AtChem2 v1.2.1 ------------- Directories