JGCRI · cahartin · Jan 5, 2018 · Jan 19, 2016 · Jan 20, 2016 · Jan 20, 2016
diff --git a/.gitignore b/.gitignore
@@ -53,6 +53,7 @@ Run Test Cases
 Debug
 libs
 project_files/visual_studio/
+project_files/VS/*.*
 libs/
 *.kdev4
 

diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,38 @@
+# Build Hector on Travis CI
+# BBL January 2017
+# See https://travis-ci.org/bpbond/hector
+
+language: cpp
+
+compiler:
+  - clang
+  - gcc
+
+branches:
+  only:
+  - master
+  - rc1.2
+
+before_script:
+ - export BOOSTVERSION=1_62_0
+ - export BOOSTVERDIR=1.62.0
+ - wget http://downloads.sourceforge.net/project/boost/boost/${BOOSTVERDIR}/boost_${BOOSTVERSION}.tar.bz2\?r\=\&ts\=1435589970\&use_mirror\=garr -O /tmp/boost.tar.bz2
+ - tar jxf /tmp/boost.tar.bz2
+ - mv boost_$BOOSTVERSION $PWD/boost-trunk
+ - export BOOSTROOT="$PWD/boost-trunk"
+
+ - cd $BOOSTROOT
+ - ./bootstrap.sh --with-libraries=filesystem 
+ - ./b2
+ - cd $TRAVIS_BUILD_DIR
+
+# Code above is necessary because Travis's default Boost is 1_46_0
+# which doesn't include odeint and other stuff. Otherwise, we could
+# simple use the following lines:
+#  - sudo apt-get update -qq
+#  - sudo apt-get install libboost-dev libboost-filesystem-dev libboost-system-dev
+
+script: 
+ - make hector
+ - ./test_hector.sh ./source/hector 
+
diff --git a/README.md b/README.md
@@ -1,4 +1,6 @@
-hector
+[![Build Status](https://travis-ci.org/JGCRI/hector.svg?branch=master)](https://travis-ci.org/JGCRI/hector)
+
+Hector
 ======
 
 This is the repository for **Hector**, an open source, object-oriented, simple global climate carbon-cycle model. It  runs essentially instantaneously while still representing the most critical global scale earth system processes, and is one of a class of models heavily used for for emulating complex climate models and uncertainty analyses. For example, Hector's global temperature rise for the RCP 8.5 scenario, compared to observations and other model results, looks like this:
@@ -8,3 +10,12 @@ This is the repository for **Hector**, an open source, object-oriented, simple g
 The primary source of Hector model documentation is the Github [wiki](https://github.com/JGCRI/hector/wiki); please note that the wiki documents are included in the repository, but you'll need to use `git clone --recursive` to get them installed locally. The code is also well documented with [Doxygen](http://doxygen.org)-style comments. A formal model description paper ([Hartin et al. 2015](http://www.geosci-model-dev.net/8/939/2015/gmd-8-939-2015.html)) documents its science internals and performance relative to observed data, the [CMIP5](http://cmip-pcmdi.llnl.gov/cmip5/) archive, and the reduced-complexity [MAGICC](http://www.magicc.org) model.
 
 This work is supported by the [Integrated Assessment Research Program](http://science.energy.gov/ber/research/cesd/integrated-assessment-of-global-climate-change/) of the Office of Science, U.S. Department of Energy. The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830.
+
+## Tools and Software That Work with Hector
+
+* [GCAM](https://github.com/JGCRI/gcam-core): Hector can be used as
+  the climate component in the GCAM integrated assessment model.  
+* [pyhector](https://github.com/openclimatedata/pyhector): a python
+  interface to Hector.  
+
+
diff --git a/headers/components/bc_component.hpp b/headers/components/bc_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef BLACK_CARBON_COMPONENT_H
 #define BLACK_CARBON_COMPONENT_H

diff --git a/headers/components/ch4_component.hpp b/headers/components/ch4_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 
 #ifndef CH4_COMPONENT_H
@@ -86,4 +76,3 @@ class CH4Component : public IModelComponent {
 }
 
 #endif // CH4_COMPONENT_H
-
diff --git a/headers/components/component_data.hpp b/headers/components/component_data.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef COMPONENT_DATA_H
 #define COMPONENT_DATA_H
@@ -200,12 +190,6 @@
 #define D_TEMP_LL               "Temp_LL"
 #define D_SPINUP_CHEM           "spinup_chem"
 
-#define D_HEAT_FLUX             "heatflux"
-#define D_HEAT_UPTAKE_EFF       "kappa"
-#define D_MAX_HEAT_UPTAKE_EFF   "k_max"
-#define D_KAPPA50_TEMP          "t_mid"
-#define D_MIN_HEAT_UPTAKE_EFF   "k_min"
-#define D_SLOPE_HEAT_UPTAKE_EFF  "slope"
 //#define D_SPECIFIC_HEAT			"cp"
 
 #define D_CO3_LL				"CO3_LL"
@@ -265,6 +249,14 @@
 #define D_SO2I_B                "so2i_b"
 #define D_OC_B                  "oc_b"
 #define D_BC_B                  "bc_b"
+
+// temperature component
+#define D_DIFFUSIVITY           "diff"
+#define D_AERO_SCALE            "alpha"
+#define D_FLUX_MIXED            "flux_mixed"
+#define D_FLUX_INTERIOR         "flux_interior"
+#define D_HEAT_FLUX             "heatflux"
+
 // ------------------- messages being passed between components -------------------------
 
 #define M_GETDATA               "getData"

diff --git a/headers/components/component_names.hpp b/headers/components/component_names.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef COMPONENT_NAMES_H
 #define COMPONENT_NAMES_H
@@ -36,6 +26,7 @@
 #define OH_COMPONENT_NAME   "OH"
 #define N2O_COMPONENT_NAME "N2O"
 #define TEMPERATURE_COMPONENT_NAME "temperature"
+
 #define OCEAN_COMPONENT_NAME "ocean"
 #define ONELINEOCEAN_COMPONENT_NAME "onelineocean"
 
@@ -110,4 +101,3 @@
 #define DUMMY_COMPONENT_NAME "dummy-component"
 
 #endif
-
diff --git a/headers/components/dummy_model_component.hpp b/headers/components/dummy_model_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef DUMMY_MODEL_COMPONENT_H
 #define DUMMY_MODEL_COMPONENT_H

diff --git a/headers/components/forcing_component.hpp b/headers/components/forcing_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef FORCING_COMPONENT_H
 #define FORCING_COMPONENT_H

diff --git a/headers/components/halocarbon_component.hpp b/headers/components/halocarbon_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef HALOCARBON_COMPONENT_HPP
 #define HALOCARBON_COMPONENT_HPP

diff --git a/headers/components/imodel_component.hpp b/headers/components/imodel_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef IMODEL_COMPONENT_H
 #define IMODEL_COMPONENT_H

diff --git a/headers/components/n2o_component.hpp b/headers/components/n2o_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef N2O_COMPONENT_H
 #define N2O_COMPONENT_H

diff --git a/headers/components/o3_component.hpp b/headers/components/o3_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef OZONE_COMPONENT_H
 #define OZONE_COMPONENT_H

diff --git a/headers/components/oc_component.hpp b/headers/components/oc_component.hpp
@@ -1,18 +1,8 @@
 /* Hector -- A Simple Climate Model
    Copyright (C) 2014-2015  Battelle Memorial Institute
 
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License, version 2 as
-   published by the Free Software Foundation.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License along
-   with this program; if not, write to the Free Software Foundation, Inc.,
-   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+   Please see the accompanying file LICENSE.md for additional licensing
+   information.
 */
 #ifndef ORGANIC_CARBON_COMPONENT_H
 #define ORGANIC_CARBON_COMPONENT_H