Merge branch 'master' of github.com:uaf-arctic-eco-modeling/dvm-dos-tem into reorg3

Author: tobeycarman

CITATION.cff

@@ -1,19 +1,23 @@
-# cff-version: 1.2.0
+cff-version: 1.2.0
 title: "DVMDOSTEM"
 
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
+message: "If you use this software, please cite using the metadata in this file."
 type: software
+
 identifiers:
-  - type: doi
+  - description: "The Zenodo concept DOI of DVMDOSTEM. Use the Concept DOI representing all versions in citations when it is desirable to cite an evolving research artifact, without being specific about the version."
+    type: doi
     value: 10.5281/zenodo.4281497
-    description: "Latest release of DVMDOSTEM software"
+
+  - description: "The GitHub release URL."
+    type: url
+    value: "https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem/releases/tag/v0.8.3"
+
 repository-code: "https://uaf-arctic-eco-modeling/dvm-dos-tem"
 url: >-
   https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/index.html#
 abstract: >-
-  `DVMDOSTEM` is an advanced process-based terrestrial
+  DVMDOSTEM is an advanced process-based terrestrial
   ecosystem model (TEM) designed to study ecosystem responses to climate changes
   and disturbances. It has a particular focus on permafrost regions (i.e. regions
   characterized by soils that stay partially frozen all year round for at
@@ -30,105 +34,54 @@ keywords:
   - Tundra
 license: MIT
 authors:
-  - family-names: "Carman"
-    given-names: "Tobey B"
-    orcid: "https://orcid.org/0000-0003-4617-4674"
-    affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
-
-  - family-names: "Genet"
+  - family-names: "Genet" # Wildfire, calibration, scientific direction, 
     given-names: "Hélène"
     orcid: "https://orcid.org/0000-0003-4537-9563"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "Rutter"
-    given-names: "Ruth A"
-    orcid: "https://orcid.org/0009-0009-7043-6081"
-    affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
-
-  - family-names: "Jafarov"
-    given-names: "Elchin"
-    orcid: "https://orcid.org/0000-0002-8310-3261"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Euskirchen"
+  - family-names: "Euskirchen" # DVM, scientific direction
     given-names: "Eugénie"
     orcid: "https://orcid.org/0000-0002-0848-4295"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "Maglio"
-    given-names: "Ben"
-    orcid: "https://orcid.org/0000-0002-1948-0177"
+  - family-names: "McGuire" # TEM, scientific direction
+    given-names: "A. D."
+    orcid: "https://orcid.org/0000-0003-4646-0750"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "Clein"
-    given-names: "Joy"
-    orcid: "https://orcid.org/0000-0002-2816-5312"
+  - family-names: "Carman" # Software development and maintenance
+    given-names: "Tobey B."
+    orcid: "https://orcid.org/0000-0003-4617-4674"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "Briones"
-    given-names: "Valeria"
-    orcid: "https://orcid.org/0000-0002-5649-851X"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Mullen"
-    given-names: "Andrew L"
-    orcid: "https://orcid.org/0000-0002-9127-9996"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Greaves"
-    given-names: "Heather"
-    orcid: "https://orcid.org/0000-0002-8800-019X"
+  - family-names: "Rutter" # Software development and maintenance
+    given-names: "Ruth A."
+    orcid: "https://orcid.org/0009-0009-7043-6081"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "McGuire"
-    given-names: "A. D."
-    orcid: "https://orcid.org/0000-0003-4646-0750"
+  - family-names: "Clein" # Calibration
+    given-names: "Joy"
+    orcid: "https://orcid.org/0000-0002-2816-5312"
     affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
 
-  - family-names: "Yuan"
+  - family-names: "Yuan" # Merging DVM, DOS, and TEM
     given-names: "Fengming"
     orcid: "https://orcid.org/0000-0003-0910-5231"
     affiliation: "Environmental Science Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"
 
-  - family-names: "Chang"
-    given-names: "Chu-Chun"
-    orcid: "https://orcid.org/0000-0002-2971-2349"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Rady"
-    given-names: "Joshua M."
-    orcid: "https://orcid.org/0000-0002-7806-136X"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Teber"
-    given-names: "Doğukan"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Rogers"
-    given-names: "Brendan M"
-    orcid: "https://orcid.org/0000-0001-6711-8466"
-    affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
-
-  - family-names: "Smith"
-    given-names: "Trevor"
+  - family-names: "Jafarov" # Calibration
+    given-names: "Elchin"
     affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
+    orcid: "https://orcid.org/0000-0002-8310-3261"
 
-  - family-names: "Mevenkamp"
-    given-names: "Hannah"
-    orcid: "https://orcid.org/0000-0002-7241-5374"
-    affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
-
-  - family-names: "Lara"
-    given-names: "Mark J"
-    orcid: "https://orcid.org/0000-0002-4670-7031"
-    affiliation: "Department(s) of Plant Biology and Geography, University of Illinois Urbana-Champaign, Urbana, IL 61801"
+  - family-names: "Yi" # DOS
+    given-names: "Shuhua"
+    orcid: "https://orcid.org/0000-0003-4932-8237"
+    affiliation: "Laboratory of Herbage Improvement And Agro-ecosystem, Lanzhou University, Lanzhou 730000, Gansu Province, P.R. China"
 
-  - family-names: "Zhuang"
+  - family-names: "Zhuang" # TEM
     given-names: "Qianlai"
     orcid: "https://orcid.org/0000-0002-4536-9851"
     affiliation: "Department of Earth, Atmospheric, and Planetary Science, Purdue University, West Lafayette IN 47907 USA"
 
-  - family-names: "Yi"
-    given-names: "Shuhua"
-    affiliation: "School of Geographic Sciences, Nantong University, Nantong Jiangsu, 226019 P.R. China"
 

Dockerfile

@@ -46,7 +46,7 @@ ARG GID=1000
 
 # === IMAGE FOR GENERAL C++ DEVELOPMENT =======================================
 # General development tools, compilers, text editors, etc
-FROM ubuntu:focal AS cpp-dev
+FROM ubuntu:jammy AS cpp-dev
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y --fix-missing && apt-get install -y \
     build-essential \
@@ -110,7 +110,7 @@ RUN apt-get update --fix-missing -y && apt-get install -y \
     libreadline-dev \
     libsqlite3-dev \
     llvm \
-    python-openssl \
+    python3-openssl \
     tk-dev \
     wget \
     xz-utils \
@@ -237,7 +237,7 @@ USER $UNAME
 # A container run from this images will need to have data supplied (i.e. one or
 # more mounted volumes) in order to run dvmdostem.
 #
-FROM ubuntu:focal AS dvmdostem-run
+FROM ubuntu:jammy AS dvmdostem-run
 ARG UNAME
 ARG UID
 ARG GID

Dockerfile-mapping-support

@@ -7,6 +7,9 @@ ARG UNAME=develop
 ARG UID=1000
 ARG GID=1000
 
+# Should try this updated image at some point...
+#FROM ghcr.io/osgeo/gdal:ubuntu-full-3.11.0
+
 # need this for netCDF
 FROM osgeo/gdal:ubuntu-full-3.2.2
 

HOWTO_RELEASE.md

@@ -39,8 +39,12 @@
    go back to step 1. You will need to delete the tag created in step 3 so that
    you can re-create it.
 
-5. Bump the version number in `docs_src/sphinx/sources/conf.py, commit the
-   change and then build the docs:
+5. Bump version numbers:
+  -  in `docs_src/sphinx/sources/conf.py `, and
+  -  in the `CITATION.cff` file, specifically under the
+     `identifiers.description` for the Github release URL.
+
+  Then commit the changes and build the docs:
 
          ```
          $ docker compose exec --workdir /work/docs_src/sphinx \

config/config.js

@@ -123,6 +123,7 @@
   },
 
   "model_settings": {
+    "cell_timelimit": 120, //Run time limit per cell in seconds. 0 for no limit.
     "dynamic_lai": 1,                   // from model (1) or from input (0)
     "baseline_start": 1901,  //start year for baseline EQ climate
     "baseline_end": 1931     //end year for baseline EQ climate

config/output_spec.csv

@@ -51,6 +51,7 @@ LFVC,Litterfall C from vascular PFTs,g/m2/time,,,invalid,,,invalid,double,
 LFVN,Litterfall N from vascular PFTs,g/m2/time,,,invalid,,,invalid,double,
 LWCLAYER,LWC by layer,m3/m3,,,invalid,invalid,invalid,forced,double,
 MINEC,Mineral SOM C,g/m2,,,invalid,invalid,invalid,invalid,double,
+MOSSDEATHC,Dead moss C,g/m2,,,,invalid,invalid,invalid,double,
 MOSSDZ,Moss thickness,m,,invalid,invalid,invalid,invalid,invalid,double,
 NDRAIN,N losses from drainage (AVLN),g/m2/time,invalid,invalid,invalid,invalid,invalid,invalid,double,
 NETNMIN,Soil net N mineralization,g/m2/time,,,invalid,invalid,invalid,,double,

docs_src/sphinx/source/conf.py

@@ -25,8 +25,8 @@
 author = 'Tobey Carman, Ruth Rutter, Helene Genet, Eugenie Euskirchen'
 
 # The full version, including alpha/beta/rc tags
-release = 'v0.8.1'
-version = 'v0.8.1'
+release = 'v0.8.3'
+version = 'v0.8.3'
 
 
 # -- General configuration ---------------------------------------------------

include/CohortLookup.h

@@ -208,6 +208,7 @@ class CohortLookup {
 
   // Q10 and soil moisture factors for Rh
   double rhq10;
+  double rhmoistfrozen;
   double moistmin;
   double moistopt;
   double moistmax;

include/ModelData.h

@@ -113,6 +113,9 @@ class ModelData {
   bool dynamic_LAI; // True: calculate LAI as a function of vegc, False: use static_lai from CohortLookup 
   bool useseverity; // using fire severity inputs
 
+  int cell_timelimit; //Time limit in seconds for cell computation time
+  time_t cell_stime; //Start time per cell. Move to Runner?
+
   bool outSiteDay;
 
   bool get_envmodule();

include/TEMUtilityFunctions.h

@@ -33,6 +33,19 @@ extern src::severity_logger< severity_level > glg;
 
 namespace temutil {
 
+  class TEMException : public std::exception {};
+
+  class NetCDFDefineModeException : public TEMException {
+  public:
+      const char* what() const noexcept override {
+          return "NetCDF define mode exception.";
+      }
+  };
+
+  class CellTimeExceeded : public TEMException {};
+
+
+
   /** A 'predicate' function that can be used with std::remove_if(..)
 
    Intended to be used with STL containers, so requirements on T are