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stable_r17.0.0

GACODE stable_r17.0.0
@smithsp smithsp tagged this 12 Jan 07:50 
* Added an official LICENSE.txt
* shared/EXPRO moved to gapy/EXPRO
* shared/GEO moved to gapy/src
* Expanded gapy python tools
* Various and sundry CGYRO changes
* Cleaned up some GYRO code
* NEO
  * NEO can use PETSC, SUPERLU, or CUDA
  * NEO regression cases 14, 15, 17, 20 changed definition of accepted answer
* Changed API
  - input.gyro
    - Added
      - EXTRA_PRINT_FLAG
      - SDLNTDR
      - SDLNTDR_2...SDLNTDR_5
      - SDLNTDR_ELECTRON
      - SDLNNDR
      - SDLNNDR_2...SDLNTDR_5
      - SDLNNDR_ELECTRON
      - SOURCE_METHOD
    - Deprecated
      - AMP_PHI_STUDY
      - EXPLICIT_DAMP_ELEC
      - FLUXAVE_WINDOW
      - KILL_E_DRIFT_FLAG
      - KILL_I_DRIFT_FLAG
      - KILL_I_PARALLEL_FLAG
      - LOCK_TI_FLAG
      - NINT_ORB_DO
      - NINT_ORB_S
      - NONLINEAR_TRANSFER_FLAG
      - NONUNIFORM_GRID_FLAG
      - NU_I_KROOK
      - N_MUMPS_MAX
      - N_STUDY
      - PLOT_FILTER
      - Q_SCALE
      - RADIAL_GRID_OFFSET
      - REINTEGRATE_FLAG
      - SOURCE_FLAG
      - SPARSE_METHOD
      - S_GRID
      - TRAPDIFF_FLAG
      - TRUNCATION_METHOD
      - VELOCITY_OUTPUT_FLAG
    - Changed (Deprecated-> New)
      - SOURCE_FLAG-> SOURCE_METHOD
      - DOPPLER_SCALE-> GAMMA_E_SCALE
      - PGAMMA-> GAMMA_P
      - PGAMMA_SCALE-> GAMMA_P_SCALE
  - input.neo
    - Added
      - USE_CUDA
      - USE_PETSC
  - input.tgyro
    - Deprecated
      - TGYRO_SEARCH_WEIGHT
      - LOC_HE_FEEDBACK_FLAG
* PLATFORMs
  - Added
    - SWIP
    - SUMMITDEV_GPU
    - STAMPEDE2_SKX_IFORT
    - GASUMMIT_GPU
    - CORI_KNL_HT2_MKL
    - CORI_KNL_HT2_MKLHT
* profiles_gen
  - Cleaned up OMFIT interface
  - Removed -gmerge CLI option
  - Removed -ions CLI option
  - Removed -plot CLI option
  - Added -RMIN CLI option
  - Added -RMAX CLI option
  - -cer CLI option takes an argument
  - Corrected sign error of radiated power for ONETWO statefile
  - Improved diagnostic printing
* python
  - cgyro's data_plot_single changed CLI to include
    - theta as angle to plot for plot_types: rcorr_phi, ky_phi, kxky_phi, kx_phi,
    - diss for plot_type: ky_flux, kx_phi
  - removed cgyro_dump_flux.py
  - new cgyro/cgyro_plot_fluct_mpi.py
  - new cgyro/plot_rt.py
  - new cgyro/vis_torcut.py
  - new cgyro/vis_wheel.py
  - gacodefuncs.py
    - new specmap function (get symbol from m and z)
    - new tag_helper function (get nicely formatted label from tag, m, z)
    - new time_vector function (convert string time index to numeric range)
    - new theta_index function (get index from theta and theta_plot)
    - new mkfile function (get basename and extension from filename)
  - indentation of gyro/data_plot.py and gyro/data.py changed to 3 spaces
  - handle new gyro binary format output files
  - gyroData stores simulation directory in .dir (was .dirname)
  - gyro/data_plot_single.py has new CLI arguments
  - gyro/fluctuation2d.py must be run in the directory with the GYRO results
  - removed gyro/text_diff.py
  - neo/data.py improved GEO parsing
  - trace.py new file for doing python based fourier mapping of flux surfaces
  - cgyro regression cases are run as part of the standard regression tests*
* TGYRO
  - Fixed evolution with particle evolution flag set to 2
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