Update .bzrignore for my automated backup
1. Bug fix in multiple_scatter.f90.  One variable was not initialised correctly. 
2. Added several diagnostic variables to the output.
1.  Intermediate commit, to avoid losing stuff.  The goal is to make the output in ED more
    standard:
    
    a. Name conventions:
       i.   FMEAN: sub-daily means (the old AVG or MEAN variables).  AVG variables that
                   were not sub-daily means retained the old name.
       ii.  DMEAN: daily means
       iii. MMEAN: monthly mean
       iv.  MMSQU: monthly mean sum of squares 
       v.   QMEAN: mean diel
       vi.  QMSQU: mean sum of squares by hour of day
      
      2. The means are now for the native level (cohort, patch or site), plus polygon-level
         They all get a suffix: (_CO for cohorts, _PA for patches, _SI for sites, _PY for
         polygons).  Metadata are also available
      
      3. Biomass variables at polygon are split by DBH and PFT.  The total and total by 
         PFT or by DBH can be found by aggregating these variables accordingly.  They can be also
         determined using the cohort-, patch-, or site-level variables.
      
      4. BRAMS, and some R scripts aren't tested yet, but they will be soon. 

2.  Some classification variables that did not make sense to exist at the  polygon-level 
    (e.g. soil texture, soil colour) were deleted and only the site-level was kept.  

3.  Minor bug fixes in fusion, particularly with mortality.  Fast means are now part of
    the patch/cohort dynamics because they are written to the output after the 
    dynamics.
1. Added a few scripts that are useful for controlling massive simulations (thousands of
   runs).
   a. make_joborder.r - It helps creating the joborder.txt.
   b. read_monthly.r  - It reads the monthly mean files but it doesn't create anything
   c. run_monthly.sh  - script to call read_monthly.r for all simulations (useful for 
                        crontab)
   d. plot.status.r   - suggested script to plot stuff for the runs, but it is not a 
                        general script, you will probably need to adjust it for each
                        group of runs.

2. Changed ed_state_vars.f90 so it only writes fmean, dmean, mmean, qmean variables to 
   history if it makes sense to do so.  For example, there is no need to write daily means
   to history unless history files are written more often than once a day. 

3. Updated some R scripts to be able to read the new output variables.
Minor bug fixes on BRAMS, so it also works with the new variables.
1.  Updated the script to compare hourly results at high resolution
2.  Fixed a big on make_joborder.r, in case soil texture is one of the varying variables,
    sand and clay fraction are overwritten.  Soil texture = 0 means site level, in case 
    it is needed.
3.  Added a new flag for MAXPATCH: if it is -1 or 1, it will force the fusion down to
    one patch for each land use type.
1. Various changes in the post-processing shell and R scripts.  I don't remember all of 
   them, most are minor, just to conform to the new variable names, and also to allow 
   transparent background (easier to use in presentations where the background is not 
   white).
2. Added a new function, that creates POV-Ray representations of the plant community.
3. Added the option of turning off the site-, patch- and cohort-level means (which make the
   output considerably larger).
1. Minor bug fixes in the heat capacity of soils and vegetation
2. Minor bug fix: mmean_broot wasn't being updated.
3. Updates of many R scripts
4. Included many utility R scripts
Merging of Marcos' r321 commits.
See report 81ml321rapid.pdf  for details and tests.

From Marcos' Line:
revno: 321
committer: Marcos Longo <mlongo@fas.harvard.edu>
branch nick: EDBRAMS
timestamp: Sat 2012-10-20 19:53:58 -0400
message:
  1. Bug fix in multiple_scatter.f90.  One variable was not initialised correctly. 
  2. Added several diagnostic variables to the output.
Local (on mainline) modification, added $FFILEOUT prefixes to the super-high frequency thermodynamic output files.
This is necessary for running multiple sites in the test suit.
This commit migrates MLO r322-r327.  
Description of Changes: Committers Fixes: Fixed bug in fmean carbon values and some py accounting variables. revno: 327: 1 Minor bug fixes in the heat capacity of soils and vegetation. 2 Minor bug fix: mmean broot wasn’t being updated. 3 Updates of many R scripts. 4 Included many utility R scripts. revno: 326 1. Various changes in the post-processing shell and R scripts. 2. Added POV-Ray representations of the plant community. 3. Added the option of turning off the site-, patch- and cohort-level means (which make the output considerably larger). revno: 325: 1. Updated R scripts. 2. Added a new flag for MAXPATCH: if it is -1 or 1, it will force the fusion down to one patch for each land use type. revno: 324: Minor bug fixes on BRAMS, so it also works with the new variables. revno: 323: 1. Added R scripts 2. Changed ed state vars.f90 so it only writes fmean, dmean, mmean, qmean variables to history if it makes sense to do so. revno: 322: 1. Intermediate commit, to avoid losing stuff. New output standards. 2. Minor bug fixes in fusion, particularly with mortality. Fast means are now part of the patch/cohort dynamics because they are written to the output after the dynamics.
Minor bug fixes applied by RGK as well.
move from bazaar to git