Merge pull request #532 from jhamman/master

doc updates for VIC 4.2.d

docs/Development/CurrentVersion.md

@@ -1,10 +1,11 @@
 # Current Version of VIC Model
 
-## Current Version: 4.2.c [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.22307.svg)](http://dx.doi.org/10.5281/zenodo.22307)
+## Current Version: 4.2.d
 
-The current version of VIC is 4.2.c, a minor bug fix update to 4.2.  4.2 is itself a minor release in the VIC 4 development track.  The release prior to 4.2 was VIC 4.1.2.m.
 
-Here we provide a brief description of the features of 4.2 (and hotfixes 4.2.a-4.2.c) and differences between 4.2 and previous versions.
+The current version of VIC is 4.2.d, a minor bug fix update to 4.2.  4.2 is itself a minor release in the VIC 4 development track.  The release prior to 4.2 was VIC 4.1.2.m.
+
+Here we provide a brief description of the features of 4.2 (and hotfixes 4.2.a-4.2.d) and differences between 4.2 and previous versions.
 
 ## Summary of new features
 

docs/Development/VersionSummaries.md

@@ -4,7 +4,7 @@ The tables below compare features (and bug fixes) of current and previous versio
 
 * * *
 
-## VIC 4.2 (hotfix 4.2.c)
+## VIC 4.2 (hotfix 4.2.d)
 
 * **Partial Vegetation Cover**
     *   Accounts for gaps in vegetative cover, through which bare soil evaporation can occur In terms of radiation attenuation and turbulence, the bare soil between plants is treated like understory, rather than a large open area of bare soil.
@@ -49,16 +49,22 @@ The tables below compare features (and bug fixes) of current and previous versio
     *   Removed SUN1999 albedo option
     *   Require JULY_TAVG_SUPPLIED=TRUE when COMPUTE_TREELINE=TRUE
 
-## Bug Fixes in VIC 4.2.a-4.2.c
+## Bug Fixes in VIC 4.2.a-4.2.d
+
+* **Fixed uninitialized dmy struct when writing binary output when OUTPUT_FORCE is True**
+    *   Previously, the `dmy_struct` was not allocated or initializaed when `OUTPUT_FORCE == TRUE` and the output format is binary.  This fix corrects this bug.
+
+* **Fixed uninitialized vegetation albedo when VEGPARAM_LAI is False**
+    *   Previously, some vegetation parameters were left uninitialized when `VEGPARAM_LAI == FALSE`.  This bug has been corrected.
 
 * **Fixed uninitialized bare soil albedo**
     *   Previously, bare_albedo was unset for the bare soil case (`iveg!=Nveg`). This fix sets the bare_albedo to the global variable value of `BARE_SOIL_ALBEDO`.
 
 * **Cleanup of frozen soil option constraints**
     *   Removed hardcoded, behind the scenes checks for the `EXP_TRANS` and `NO_FLUX` global parameter values for case of `QUICK_SOLVE=TRUE` in `calc_surf_energy_bal`.
 
-* **Fixed memory error in `initialize_atmos` when OUTPUT_FORCE = TRUE* **
-    *   Previously, access to unitialized elements of the veg_con and veg_hist structure was attempted when OUTPUT_FORCE = TRUE, causing a memory error and the model to crash.  This fix sets these elements inside a `if (!options.OUTPUT_FORCE)` block allowing the OUTPUT_FORCE option to work as expected.
+* **Fixed memory error in `initialize_atmos` when OUTPUT_FORCE = TRUE ***
+    *   Previously, access to uninitialized elements of the veg_con and veg_hist structure was attempted when OUTPUT_FORCE = TRUE, causing a memory error and the model to crash.  This fix sets these elements inside a `if (!options.OUTPUT_FORCE)` block allowing the OUTPUT_FORCE option to work as expected.
 
 * **Documented how VIC 4.2 needs user to specify veg_lib and veg_param files when OUTPUT_FORCE = TRUE**
     *   Prior to release 4.2, a user could run VIC in OUTPUT_FORCE mode with only a soil parameter file and forcing files.  This functionality is now broken as of release 4.2 and will not be fixed.  Users must either supply veg_lib and veg_parameter files (which the user is likely to have anyway) or use the standalone forcing disaggregator under cevelopment for use with release 5.0.  The documentation was updated to describe this issue as of release 4.2.c.

docs/index.md

@@ -1,10 +1,11 @@
 # Variable Infiltration Capacity (VIC) Macroscale Hydrologic Model
 
-[![Build Status](https://travis-ci.org/UW-Hydro/VIC.png?branch=develop)](https://travis-ci.org/UW-Hydro/VIC) [![VIC Users Listserve](https://img.shields.io/badge/VIC%20Users%20Listserve-Active-blue.svg)](https://mailman.u.washington.edu/mailman/listinfo/vic_users) [![Join the chat at https://gitter.im/UW-Hydro/VIC](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/UW-Hydro/VIC?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![GitHub license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://raw.githubusercontent.com/UW-Hydro/VIC/master/LICENSE.txt) [![Documentation Status](https://readthedocs.org/projects/vic/badge/?version=latest)](http://vic.readthedocs.org/en/latest/) [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.22307.svg)](http://dx.doi.org/10.5281/zenodo.22307)
+[![Build Status](https://travis-ci.org/UW-Hydro/VIC.png?branch=develop)](https://travis-ci.org/UW-Hydro/VIC) [![VIC Users Listserve](https://img.shields.io/badge/VIC%20Users%20Listserve-Active-blue.svg)](https://mailman.u.washington.edu/mailman/listinfo/vic_users) [![Join the chat at https://gitter.im/UW-Hydro/VIC](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/UW-Hydro/VIC?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![GitHub license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://raw.githubusercontent.com/UW-Hydro/VIC/master/LICENSE.txt) [![Documentation Status](https://readthedocs.org/projects/vic/badge/?version=latest)](http://vic.readthedocs.org/en/latest/)
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.56057.svg)](http://dx.doi.org/10.5281/zenodo.56057)
 
 VIC ([Liang et al., 1994](Documentation/References.md)) is a macroscale hydrologic model that solves full water and energy balances, originally developed by Xu Liang at the University of Washington.  VIC is a research model and in its various forms it has been applied to most of the major river basins around the world, as well as [globally](links.md). The VIC model is distributed under the [GNU GPL v2.0](http://www.gnu.org/licenses/gpl-2.0.html) license. If you make use of this model, please acknowledge the appropriate references listed on the [references](Documentation/References.md) page. These should include [Liang et al., 1994](Documentation/References.md) plus any references relevant to the features you are using, which are cited in the feature descriptions on the [Model Overview](Overview/ModelOverview.md) page.
 
-Development and maintenance of the current official version of the VIC model is led by the [UW Hydro | Computational Hydrology group](http://www.hydro.washington.edu) in the [Department of Civil and Environmental Engineering](http://www.ce.washington.edu) at the [University of Washington](http://www.washington.edu). Every new application addresses new problems and conditions that the model may not currently be able to handle, and as such the model is always under development. The VIC model is an open source development project, which means that contributions are welcome, including to the VIC documentation. 
+Development and maintenance of the current official version of the VIC model is led by the [UW Hydro | Computational Hydrology group](http://www.hydro.washington.edu) in the [Department of Civil and Environmental Engineering](http://www.ce.washington.edu) at the [University of Washington](http://www.washington.edu). Every new application addresses new problems and conditions that the model may not currently be able to handle, and as such the model is always under development. The VIC model is an open source development project, which means that contributions are welcome, including to the VIC documentation.
 
 All development activity is coordinated via the [VIC github page](https://github.com/UW-Hydro/VIC), where you can also find all archived, current, beta, and development versions of the model.
 

readme.md

@@ -7,7 +7,8 @@
 | VIC Users Listserve    | [![VIC Users Listserve](https://img.shields.io/badge/VIC%20Users%20Listserve-Active-blue.svg)](https://mailman.u.washington.edu/mailman/listinfo/vic_users)                                              |
 | Developers Gitter Room | [![Join the chat at https://gitter.im/UW-Hydro/VIC](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/UW-Hydro/VIC?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) |
 | License                | [![GitHub license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://raw.githubusercontent.com/UW-Hydro/VIC/master/LICENSE.txt)                                                              |
-| Current Release DOI    | [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.35302.svg)](http://dx.doi.org/10.5281/zenodo.35302) |
+| Current Release DOI    | 
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.56057.svg)](http://dx.doi.org/10.5281/zenodo.56057) |
 
 ----------
 

src/global.h

@@ -22,7 +22,7 @@
   2013-Dec-27 Removed QUICK_FS option.					TJB
   2014-May-20 Added ref_veg_vegcover.					TJB
 **********************************************************************/
-char *version = "4.2.c 2015-December-12";
+char *version = "4.2.d 2015-June-20";
 char *optstring = "g:vo";
 int flag;