updating the main readme with some notes about the cal. version...
Merge branch 'master' of github.com:ua-snap/dvm-dos-tem
Manually Grabbed patch from fengming's master branch.

Fengming's Note:
two bugs found when doing calibration
(1) in Runner.cpp, setupid(). Gridid associated ids previously were
messed up with independent data ids.
(2) in CohortLookup.cpp. The leading whitespaces before 'CMT??' will
cause error in reading parameters and initial values for each 'CMT'
type.
Manually grabbed patch from Fengming's master.

Fengming's Note:
A bug in vegetation_bgc.cpp for maintenance resp.
This was introduced in the very beginning, but forgot taking it out. It
affects effectively adjusting 'KRB' for reasonable NPP during
calibration. So must be corrected.
Grab latest calibration codes from aeshna (4-22-2013).
Merge branch 'fm-april-updates' into devel

This collects the latest work from Fengming. Still needing to undertake
more or less a manual process for this because Fengming's master is farily
out of date from the ua-snap master.

Changes to the extrapolation version (main calculator code) were manually
added by examining the most recent commit on Fengming's master branch.

Changes to the calibration version were manually retrieved from aeshna
(because Fengming's github repo does not contain any of the calibration
version, updated to that code must be gotten from aeshna).
Updating the main README
updating main readme...
Refactor the parsing of community codes into a utility function.
Grab one more updated file from aeshna (5-8-2013).

Missed this file on the recent updates. The GUI was running
painfully slow and throwing an error about negative ice/water in
various layers.

This file appears to FIX that, and the program runs at expected speed now.
Merge pull request #24 from tobeycarman/devel

Updating the ua-snap devel branch with latest code

This merge brings in a bunch of recent work, mainly from Fengming, but also some minor updates by me (Tobey). I have still been having to incorporate Fengming's work more or less by hand to make the commits and history readable. Here are the notes, compiled from emails and commit messages, of what I think this pull request addresses.

Namely:

 * vegetation_bgc.cpp. 'rm' (maintenance respiration) had a temporary setting which not removed after testing.
 * in Runner.cpp:: setupIDs(). grid-level ids for a grid are messed up with their record numbers for each dataset.
 * leading 'white space' issue in searching 'CMT??' in reading parameters/default initial conditions.

 * dead moss layer is separated as a horizon with different decomposition rate (to be calibrated), which previously was same as litter decomposition rate;
 * environmental module (biophysical processes) has been rewritten for soil thermal/hydrological processes. Previously there are yearly oscillation of thermal properties, and this update is supposed to be improve in this 

 * Continued refactoring of cmt_bgcsoil.txt reading code
 * Updating the extrapolation and calibration codes to reflect the most recent code in /home/stuff/fengming/TEMmodules/DVMDOSTEM/ on aeshna (This includes the changes listed above; process is explained in more details in some of the past commit messages)
 * General improvements to the README
2 bugs relevant to ID and CMTxx lookup

There are still 2 more bugs relevant to IDs searching and CMTxx lookup:
(1) runner.cpp. If no matching ID found in those data files, no checking
and no error message when model quits.
(2) CohortLookup.cpp. If blank line(s) in those parameter files, and
CMTxx lookup reaches the end of files (i.e., no match found), model
would crash without error message.
Merge pull request #28 from fmyuan/devel

2 bugs relevant to ID and CMTxx lookup
eclipse IDE files put in .gitignore

I use Eclipse IDE to develop and debug codes. It generates a lot of
setting and debug information. They are not put into github.
a variable added to 'RestartData'

soil layer 'FROZEN' added to 'RestartData'. Originally it's derived from
'FROZENFRAC', which appears not accurate and causes some error message
when initial mode is 'restart'.

A more fully clear-up added in 'Runner::runmode2' (exactly same as in
runmode3). This will completely correct data messing when new cohort
runs.
bug fixes and restart i/o for spatial mode

(1) bugs in 'ed' -'sois': soil layer 'frozen' needs to add
(2) for spatial-mode: monthly restart is not read from file anymore, but
from a deque for all grids (or cohorts).
(3) spatial-mode calling loops: year, month, and cohort are in one, as
Alec suggested.

N.B. my testing on cygwin shows memory leak - needs re-check.
changing wildfire.cpp so there is a oneseverity = 5 (flood)
Actually delete old netcdf files - preferable to use the system supplied version!
Removing unnecessary files from calibration/config
work on calibration build.xml.