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Merge gridded_code into master#375

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chaukap merged 176 commits intomasterDrylandEcology/STEPWAT2:masterfrom gridded_codeDrylandEcology/STEPWAT2:gridded_codeCopy head branch name to clipboardDec 2, 2019

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Commits on Apr 4, 2019

• (issue #256) moved RandSeed() calls to right before runGrid()

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• (issue #251) removed unneeded call to free_all_sxw_memory

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Commits on Apr 6, 2019

• (Issue #254) Remove xgrow and veg_prod_type

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Commits on Apr 7, 2019

• Prototyped CellType struct, created ST_stats.h

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Commits on Apr 10, 2019

• Moved randseed to former location, added randseed calls to ST_grid.c

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Commits on Apr 11, 2019

• Compress sxw.c variables into struct.

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• Issue #259 Added SXW variables to CellType struct

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• Issue #253 removed readme.txt from testing.sagebrush.master folder

  

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Commits on Apr 12, 2019

• Changed name of new sxw struct (issue #267)

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Commits on Apr 14, 2019

• (issue #271) changed global variables to pointers

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Commits on Apr 15, 2019

• Issue #271 added dealloc_Globals() function to be called at the end of the program

  

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Commits on Apr 17, 2019

• issue #271 move SOILWAT head to my branch

  

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Commits on Apr 18, 2019

• Created allocate_gridCells and load_cell functions

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• Changed _Ppt, _Dist, _Temp to pointers

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Commits on Apr 22, 2019

• (issue #274) created stat_Copy_Accumulators function

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Commits on Apr 23, 2019

• (issue #278) Made transp_window a pointer

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• (issue #279) added .vscode to the gitignore

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• (issue #728) added deallocation function to sxw.c

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• (issue #280) changed SXW and SXWResources to pointers

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Commits on Apr 24, 2019

• (issue #247) updated SOILWAT head

  

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• Added call to stat_Copy_Accumulators in load_cell.

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• Created and implemented new copy_sxw_variables funciton

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• (issue #277) changed name of copy_sxw function in ST_grid.c

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Commits on Apr 25, 2019

• (issue #280) removed unused SXW reference in ST_stats.c

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• (issue #281) restructured variable _SomeKillage

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• (issue #281) added _SomeKillage to deallocate_Globals function

  

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Commits on Apr 30, 2019

• Moved allocate_gridCells into _init_grid_inputs

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Commits on May 1, 2019

• (issue #286) reordered init functions

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• Moved local variable declarations to the top, moved function description

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Commits on May 7, 2019

• Added SoilType struct to CellType.

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Commits on May 9, 2019

• Added init Species struct to CellType struct

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Commits on May 14, 2019

• Continued work on RunGrid()

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• Made RunGrid more similar to main

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• Resolved conflict for PR #297

  

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• Resolved incompatibility resulting from merging master into this branch

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Commits on May 17, 2019

• Removed load_spinup_cell call and renamed a variable

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• Merge remote-tracking branch 'origin/gridded_code' into gridded_code

  

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• Changed structure and function calls of _run_spinup

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Commits on May 20, 2019

• Removed assignment of Globals->nCells

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• Addressed comment made on commit d278849

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Commits on May 22, 2019

• Overhauled _init_stepwat_inputs

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• (Issue #305) Merge master (clean_code_lowpriority) into gridded_code

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• (Issue #305) Uncomment gridded code

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• (Issue #306) Multiple changes (read description)

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• (Issue #306) Change where _resource_cur is initialized

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Commits on May 23, 2019

• (Issue #283) Implement grid file and directory enum

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• Spinup now uses the requested species

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• Created unload_cell function.

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• Implemented unload_cell.

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• Removed UseSeedDispersal and DuringSpinup from unload_cell

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• Uncommented Species and RGroup from load_cell

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• (Issue #285) Move reading maxrgroupspecies.in outside parm_Initialize

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• (Issue #307) Create struct for truly global variables

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• (Issue #285) Allow maxrgroupspecies.in to be read

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Commits on May 24, 2019

• Removed _copy_species from ST_grid.c

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Commits on May 25, 2019

• (Issue #285) Overhaul _read_disturbances_in

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Commits on May 26, 2019

• Revert "(Issue #285) Overhaul _read_disturbances_in"

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Commits on May 28, 2019

• (Issue #284) Make RGroup and Species work correctly in gridded mode

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• Addressed typo in commit 873a2f5

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Commits on May 29, 2019

• (Issues #285 #286) Break up _init_grid_inputs

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Commits on May 30, 2019

• (Issue #285) Overhaul _init_grid_inputs

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• (Issue #285) Overhaul _read_disturbances_in

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• (Issue #285) Overhaul _read_init_species

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• (Issue #285) Overhaul _read_soils_in

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Commits on May 31, 2019

• (Issue #285) Overhaul _read_seed_dispersal_in

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• (Issue #285) Overhaul _init_grid_globals

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• (Issue #285) Fixed bugs in _read_seed_dispersal_in

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Commits on Jun 3, 2019

• Fixed some issues with SXW initialization

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• Removed references to Globals without loading a cell

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• Added someKillage to cellType

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Commits on Jun 4, 2019

• Added function to allocate gridCell accumulators

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• Moved printing general info to RunGrid

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• Changes _load_cell call in RunGrid, updated Spinup

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• SXW_Reset(void) -> SXW_Reset(char* SOILWAT_file)

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Commits on Jun 5, 2019

• Moved runModelYears, runModelIterations, nCells and randseed

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• Merging master into girdded_code

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Commits on Jun 6, 2019

• Updated _set_sd_lyppt to use gridCells

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Commits on Jun 7, 2019

• Removed _set_sd_lyppt entirely (issue #287)

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• Corrected 1-indexing issues (issue #287)

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• Uncommented _do_seed_dispersal

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• Removed strange values from grid_disturbances.csv

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Commits on Jun 9, 2019

• (Issue #309) Convert _do_seed_dispersal to use gridCells

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• (Issue #309) Remove H and VT from grid_seed_dispersal.in

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Commits on Jun 10, 2019

• Merged master into gridded_code (#320)

  

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• Resolved errors introduced while merging pull request #320

  

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Commits on Jun 12, 2019

• (Issue #309) Forgot to replace grid_Disturb[i] with RGroup[0]

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• Stat output fixed to point of completion

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• Continued work on all cell average function

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• partially overhauled _free_grid_memory

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Commits on Jun 14, 2019

• (issue #310) corrected misstyped assignment

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Commits on Jun 17, 2019

• Compressed all global deallocation into one function

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• Sealed up memory leaks

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• Removed references to load_sxw_memory from ST_grid

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Commits on Jun 18, 2019

• (Issues #300 #301) Add _kill_maxage

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• (Issues #287 #301) Add _kill_maxage

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• Merge remote-tracking branch 'origin/gridded_code' into gridded_code

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Commits on Jun 19, 2019

• Added standard deviation calculation.

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Commits on Jun 21, 2019

• Corrected deallocation of mySeedDispersal->prob

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• Removed a few deprecated functions

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• Reset SXW for all grid cells

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• Fixed historical weather file not being used.

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Commits on Jun 24, 2019

• Removed unnecessary Mem_free call (issue #327)

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Commits on Jun 26, 2019

• Modified initialization parameters

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Commits on Jul 3, 2019

• Created methods for saving and loading the spinup conditions.

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Commits on Jul 5, 2019

• Continued work on Spinup (issue #300)

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• removed use_spinup column from grid_initSpecies.csv

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• Updated grid_disturbances.in

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Commits on Jul 8, 2019

• Removed unused functions (issue #311)

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• Corrected some compiler warnings

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• Overhauled progress bar

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• Removed old progress bar and improved new one.

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Commits on Jul 9, 2019

• Added two new functions related to Initialization

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• Modified general info printed to terminal

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• Changed some variable names to make them more ambigous

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Commits on Jul 13, 2019

• (issue #252) Removed cheatgrass parameters from grid_disturbances.csv

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• (issue #343) created a input parameter for spinup years.

  

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• (issue #344) moved VW to species.in.

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• (issue #344) added VW column header to species.in

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• Combined grid_seed_dispersal.in and grid_setup.in (issue #351)

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Commits on Jul 15, 2019

• Removed unused variables deprecated by merging grid_seed_dispersal and grid_setup

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• Removed deprecated function _read_a_float.

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• Continued work on the Initialization process. (issue #342)

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• Removed deprecated summary at the top of the file

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• Reviewed parameter initialization functions and made small changes.

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• Removed deprecated functions and removed unnecessary declarations

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Commits on Jul 16, 2019

• Added a blocker to seed dispersal. (issue #326)

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• First attempt at fixing _init_seed_dispersal

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• Introduced a "sender" variable to improve code readability

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Commits on Jul 17, 2019

• (issue #312) Improved function and variable descriptions

  

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• Moved functionallity from _run_spinup to runInitialization

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Commits on Jul 18, 2019

• Separated initialization from ST_grid and added header files (Large commit)

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Commits on Jul 19, 2019

• (issue #359) Created progress bar .c and .h files.

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Commits on Jul 22, 2019

• Addressed comment on commit f7faa9d

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• Created seed dispersal module (.c and .h files)

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• Added some documentation to the ST_seedDispersal files.

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• Addressing comments on commit c23e288

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• Sealed additional memory leaks (issue #322)

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• Added input parameter for individual cell output (issue #360)

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• Hard-coded UseSeedDispersal to FALSE

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• Added function to calculate average mortality (issue #361)

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• Resolved some compiler warnings

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• (issue #369) removed mort_EndOfYear form spinup

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• Issue #367 modified SoilType struct to match SOILWAT better

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• Overhauled soil layer swapping (issue #367)

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• updated SOILWAT head to latest commit on Bugfix_247

  

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• #374 overhauled grid_soils.csv

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• Addressed seg faults in copy_ functions

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• Merged pull request #373

  

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• Updated SOILWAT2 head to latest commit on Bugfix_247

  

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• #372 Located bug causing non-gridded mode to crash

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• Addressing comments on pull request #375

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• Multiple changes to ST_stats.

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• Added error check to _read_soils_in

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• Removed spaces between grid_soils.csv entries

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• Addressing comments on PR #375

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• Addressing comments on PR #375

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• Resolved merge conflict for PR #382

  

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• Addressing comments on PR #375

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• Removed unused includes and fixed a typo

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• Removed unused print satements and redundancies

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• Removed commented-out code

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• Removed commented-out statements

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• Added back a print statement in ST_main.c

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• Small changes requested in PR #375

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• Addressing comments on pull request #375

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• Addressing comments on pull request #375

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• Addressing comments on pull request #375

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• Continued addressing comments on pull request #375

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• Addressed more comments on pull request #375

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• Modified two comments as discussed in pull request #375

  

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• Reduced number of cells specified in grid input CSVs

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• Improved documentation of unusual code in runGrid()

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• Updated sw_src to latest commit on Bugfix_247_STEPWAT_compatability

  

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• Merge branch 'master' into gridded_code

  

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• Updated ST_params.c To work with gridded mode.

  

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• Update SOILWAT2 head

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