{"push_id":711746880,"size":68,"distinct_size":0,"ref":"refs/heads/master","head":"7b0eec21b8830805dac98660787aa0c8fe7df5ae","before":"1892b3e200482469ea616dac90279a814269e442","commits":[{"sha":"5f27ef308c71f68ccc6e4cfbb350aed98a8596a5","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"My first commit using git.  Bringing most of the 2014 changes...\n\nShort story.  ED: added a few tweaks/controls for mortality and reproduction, and changed\nthe disturbance routines so disturbance types are more descriptive, and forestry is now\nconsistent with the disturbance rates.  ED/BRAMS: the model can now be compiled without\nMPI.  BRAMS: created a LEAF-4 that looks very similar to big leaf ED, and fixed CARMA for\nshortwave.  Ramspost: fixed a bunch of things, added more variables.\n\nLong story.\n1. ED\n   a. Changed minimum height for reproduction for tropical trees, based on\n      Wright, S. J. et al. 2005: Reproductive size thresholds in tropical trees:\n         variation among individuals, species and forests.  J. Trop. Ecol. 21, 307--315,\n         doi:10.1017/S0266467405002294\n   b. Bug fix in growth_balive, living tissues wouldn't be built again when\n      phenology_status was zero (leaves fully flushed).\n   c. Changed minimum reproduction size so that seed_rain actually works.\n   d. Bug fix in rk4_derivs.f90, a call for qslif8 was incorrectly passing specific\n      humidity instead of pressure\n   e. Density-dependent mortality: Single maximum carbon balance, assumed to be equal to\n      plant at the top of the canopy and no soil water limitation.  Added an offset for\n      negative carbon balance mortality, so rates don't start hiking before reaching\n      negative carbon balance.\n   f. Changed compilation instruction files so it allows to compile the code with two\n      different levels of optimisation.  This dramatically reduces compilation times for\n      ed_state_vars.f90 and average_utils.f90 using ifort-13.  Old include.mk.opt files\n      should still work.\n   g. Added include that works with Embrapa computers.\n   h. Disturbance routines:\n      i.   Changed the land use classes in ED.  Now there are 6 categories\n           1 -- Agriculture (cropland/pasture, still not split)\n           2 -- Forest plantation\n           3 -- Tree fall\n           4 -- Fire\n           5 -- Abandonment\n           6 -- Logged\n\n           This eliminated some redundant variables, such as plantation,\n           nat_dist_type, nat_disturbance_rate since these patches are tracked and\n           can coexist in the same site.\n\n      ii.  Simplified the forestry routines.  Now the files in forestry.f90 only\n           determine the rates and harvested area.\n      iii. Harvesting now takes the minimum DBH into account for all logging.  The\n           minimum is set a the land use file as before, but now it is also used\n           during logging with biomass target (aka George Hurtt's files).\n      iv.  Bug fix in disturbance.  Now if the disturbed patch would become too\n           small, the entire patch is disturbed, so it preserves total area.\n      v.   Disturbance rate in the output is now consistent with the patch\n           creation.  This wasn't true for logging.\n      vi.  Patch fusion now allows different disturbance types to be fused as long\n           as they are sufficiently old.\n      vii. Disturbance rates are now updated annually, to ensure that the rates are\n           consistent with patch dynamics.\n\n   i. Fixed utils_c.c so the string length is consistent with the rest of the\n      code.  I had to hardcode the length, so this will likely happen again if\n      str_len is changed.\n   j.  Increased the maximum number of files so the model is able to handle\n       the harmonised land use data sets.\n   k.  Some other minor bug fixes, I don't remember all of them.\n\n2. ED + BRAMS\n   a. Turned all files that use mpi into F90.  This allows the code to be compiled without\n      MPI support.  I had to do this to be able to compile at USP, I couldn't have a\n      consistent set of HDF5 + MPI with the same compiler.  Somehow gfortran didn't want\n      to compile MPI, and ifort didn't want to compile HDF5.\n   b. Added several components of the vegetation water and energy cycle to BRAMS output. I\n      haven't tested with ED-BRAMS yet, so beware that this may need some fixes in the\n      future.\n\n3. BRAMS.\n   a.  Radiation.  Vegetation radiation is now solved using two-stream, based on\n       ED-2.2 (check my dissertation).  It assumes 6 layers for numerical stability.\n       Some of the parameters were borrowed from CLM-4.\n   b.  Transpiration/photosynthesis: sun and shade leaves were determined from CLM-4\n       formulation, and the photosynthesis for each of the 2 layers are solved using\n       the ED-2.2 method (check my dissertation).\n   c.  Root and growth respiration: similar to ED-2.2, root biomass is estimated to be\n       the same as the leaf biomass.\n   d.  Heterotrophic respiration: the dependence on soil moisture and temperature is the\n       same as ED-2.2.  The maximum rate is defined after\n       Reichstein, M. et al. 2003: Modelling temporal and large-scale spatial variability\n       of soil respiration from soil water availability, temperature and vegetation\n       productivity indices. Global Biogeochem. Cycles, 17(4), 1104,\n       doi:10.10292003GB002035\n   e.  Heat capacity is now based on biomass, like in ED-2.2.  The SLA profile was taken\n       from CLM-4.\n   f.  Thermal conductance and fluxes between snowy ground were updated to what is done\n       in ED.\n   g.  IADVEC=2 is now saving fluxes properly and STILT runs with IADVEC=2 are conserving\n       mass.\n   h.  CARMA is now working for shortwave radiation, and results are much more realistic\n       than Harrington.  Cumulus feedback is also working with CARMA, and CARMA now\n       calculates the direct/diffuse components of PAR and NIR.\n   i.  LEAF-3/LEAF-4 have time steps for vegetation.\n   j.  Additional variables to reduce nudging near the surface.\n   k.  New RAMSIN variable to decide whether to search for LOU recursively or not.\n\n4. Ramspost\n  a.  Several new variables needed for the USP/LNCC project.\n  b.  Several bug fixes in Ramspost, now Ramspost is working for pressure level\n      coordinates and all vorticities and divergence are working.\n  c.  Categorical variables such as soil texture and vegetation class are now reprojected\n      using nearest neighbour instead of horizontal interpolation.\n  d.  Removed \"entry\" methods to define sub-routines.  All sub-routines are now defined as\n      independent sub-routines.\n\n5. R scripts\n   a.  Several bug fixes, updates, etc.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/5f27ef308c71f68ccc6e4cfbb350aed98a8596a5"},{"sha":"1ed606661ed86fd55fe7e0a85ca9396d3eead164","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Added more ignore rules","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/1ed606661ed86fd55fe7e0a85ca9396d3eead164"},{"sha":"e7863173147a70c361beb9ec996f8ab33478eaac","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Bug fixes in fusion, plus save different solutions from photosynthesis\n\n1.  Minor bug fixes in fuse/fiss (Ctrl+C/Ctrl+V type).  Extended Ryan's LAI fix to all\n    variables, and applied to wood.  A minor change is that now rlai/dlai are relative\n    weights so they work for both large and small LAI.\n2.  Save all three photosynthesis answers (light-limited, RuBP-limited, CO2-limited) to\n    the output.  No real change to the code, although the three cases are always solved\n    now.\n3.  Update on R scripts.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/e7863173147a70c361beb9ec996f8ab33478eaac"},{"sha":"53953f9b6bbce0b580da8c4fa3f908ad58edf0b0","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Minor fixes on shell scripts, no change in the code.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/53953f9b6bbce0b580da8c4fa3f908ad58edf0b0"},{"sha":"0e7032b0327e28debc3e3aec145bee6c2678830e","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Minor fixes to shell and R scripts.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/0e7032b0327e28debc3e3aec145bee6c2678830e"},{"sha":"5f2390029ff46321fd52d34169373db1ded2216b","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Minor changes to some R scripts","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/5f2390029ff46321fd52d34169373db1ded2216b"},{"sha":"9751469ac1d19d010f99b92aefbdb3b56f22078c","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Bug fixes in BRAMS Makefile.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/9751469ac1d19d010f99b92aefbdb3b56f22078c"},{"sha":"3a9142108eca9c7fd758f516e275426be703f067","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Updates to some R files.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/3a9142108eca9c7fd758f516e275426be703f067"},{"sha":"259e9959b0aa16848b2927dc2269e122796c0be3","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Bug fix in boolean.utils.r","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/259e9959b0aa16848b2927dc2269e122796c0be3"},{"sha":"55161e6ddd29e7bf5b494bedbe9cb64436f624c3","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1.  Bug fix on long term dynamics.  There were a few cases in which leaf internal energy\n    became inconsistent with leaf temperature, causing the integrator to crash at the\n    beginning of the month.\n2.  Added a quick routine that checks if the situation described above happens.  By\n    default this option is turned off, but it can be easily turned on for debugging\n3.  Merged two quick fixes from Christine Rollinson, although I am about to merge with the\n    updated mainline","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/55161e6ddd29e7bf5b494bedbe9cb64436f624c3"},{"sha":"a25c69d21e3e5c2b40a4a21a7adc6ec4feb4ca66","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Merge https://github.com/EDmodel/ED2\nBrought the HDF5 bug fix","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/a25c69d21e3e5c2b40a4a21a7adc6ec4feb4ca66"},{"sha":"ae7b6276fb967fa1896a2e8647ce87cd31b3118a","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1.  Minor bug fix in ed_state_vars.F90, so light profile QMEAN is included in the Q files.\n2.  Changes in R scripts and aux shell scripts","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/ae7b6276fb967fa1896a2e8647ce87cd31b3118a"},{"sha":"25f2508d61fd2f96ab63185989777fa6deaf5bed","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Adding a file I forgot.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/25f2508d61fd2f96ab63185989777fa6deaf5bed"},{"sha":"3e31dd3396347244baa281678b1b59d07d2a05c9","author":{"email":"37b832a46b971769fdebe789bed07c88224c3581@lbl.gov","name":"Ryan Knox"},"message":"Merge pull request #42 from rgknox/master\n\nAdded CRs patch that calculates depth_available","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/3e31dd3396347244baa281678b1b59d07d2a05c9"},{"sha":"2706bb873bf04c2f7cc3d0c28ce42f29918e2846","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"Changes to some R scripts.  Committing before merging with master","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/2706bb873bf04c2f7cc3d0c28ce42f29918e2846"},{"sha":"70c397f68af0dedd95491b2a854a5a1cfd5f7e54","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1. Merge branch 'master' of https://github.com/EDmodel/ED2\n\nConflicts:\n\tED/src/driver/ed_driver.F90\n\tED/src/dynamics/canopy_struct_dynamics.f90\n\tED/src/dynamics/euler_driver.f90\n\tED/src/dynamics/farq_leuning.f90\n\tED/src/dynamics/growth_balive.f90\n\tED/src/dynamics/heun_driver.f90\n\tED/src/dynamics/hybrid_driver.f90\n\tED/src/dynamics/mortality.f90\n\tED/src/dynamics/radiate_driver.f90\n\tED/src/dynamics/rk4_derivs.F90\n\tED/src/dynamics/rk4_driver.F90\n\tED/src/memory/ed_state_vars.F90\n\tED/src/utils/fuse_fiss_utils.f90\n\tED/src/utils/update_derived_props.f90\n\n2. Removed the case in which small patches had disturbance adjusted to eliminate the\n   patch.\n\n3. Preparing to test","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/70c397f68af0dedd95491b2a854a5a1cfd5f7e54"},{"sha":"27fe9d931ae6fcc68081f6c44ac693b6fb11d647","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1.  average_utils: Changed integration of mean squares, to avoid underflow\n2.  fuse_2_cohorts: Defined relative weights based on nplant, to avoid underflows when\n    nplant is very small.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/27fe9d931ae6fcc68081f6c44ac693b6fb11d647"},{"sha":"b13aac247c024867fba486b750c0f25bb76f94e4","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1. Updated R scripts","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/b13aac247c024867fba486b750c0f25bb76f94e4"},{"sha":"3dc26a3bd46495f79212ea2ba25cd222f7895e03","author":{"email":"3fcb11aa1ce3f32085821d400bf4a117aec4ab62@gmail.com","name":"Marcos Longo"},"message":"1. Removed the extra rshort_s from h_flux_s and replaced mzg by ksn, following discussions\n   with Ryan Knox and Christy Rollinson.","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/3dc26a3bd46495f79212ea2ba25cd222f7895e03"},{"sha":"f388538ceed5c0ae9cd421f9c2459986229c6a46","author":{"email":"ee5f6a71ae0a80cd6b9b846b0e9e20d6f282ecc2@gmail.com","name":"DanielNScott"},"message":"- updated edmain to give parallelization info for OMP as well as MPI.\n- updated utils_c.c to include a cpu-number checking function.\n- fixed some wrong labelling and misleading variable names in seed_dispersal()","distinct":false,"url":"https://api.github.com/repos/LEAF-BoiseState/ED2/commits/f388538ceed5c0ae9cd421f9c2459986229c6a46"}]}