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DCBLSoares case (dry and "moist")#30

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meyerbe wants to merge 583 commits intopressel:masterfrom meyerbe:master

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Commits on Jul 19, 2016

print statements in 4th decomp SA, MA schemes
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problem NetCDFIO_Fields changes
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debugging
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debugging
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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debugging
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debugging
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debugging
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debugging
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print statement
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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debugging
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Commits on Jul 20, 2016

changing to upstream Thermodynamics.pyx, ThermodynamicsSA.pyx/pxd, thermodynamics_sa.h
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VisOutput back to upstream (no numbering of files at same time)
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adding Pa.barrier() to Simulation3d.pyx
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adding Pa.barrier() to Simulation3d.pyx
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checking if Sim.StatsIO.close_files is the problem
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checking if Sim.force_io is the problem
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debugging
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debugging
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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debugging ThermodynamicsSA
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setting all equal to upstream
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back: Grid.pyx
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back: ParallelMPI comments, Radiation empty lines
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back: Microphysics, print statements
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Commits on Jul 21, 2016

back: Restart, Leerzeichen
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back: Timepstepping (print statements)
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back: PrognosticVariables (print statement)
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back: DiagnosticVariables (print statement)
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back: Surface (Soares Case, Leerzeichen, Print statements)
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back: Forcing (Soares Case, Print statements)
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back: ReferenceState (Print statements)
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back: Initialization (Soares Case)
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back: SGS and sgs.h (const Viscosity conditioned )
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back: SGS (print statement)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: VisualizationOutput (adding self.count, option for different path)
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back: NetCDFIO (print statement, comments)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: Simulation (print SGS)
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back: VisualizationOutput (adding self.count, option for different path)
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back: NetCDFIO (print statement, comments)
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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back: ConditionalStatistics (print statement, comments)
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back: Thermodynamics (print statement)
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back: MomentumAdvection.pyx (print statement)
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back: ThermodynamicsSA.pyx (only print statement)
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back: ThermodynamicsSA.pyx (adding debug_tend module)
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back: thermodynamics_sa.h (changes in eos_c)
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back: thermodynamics_sa.h (adding eos_c_refstate)
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back: thermodynamics_sa.h (modifying eos_c_update)
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back: momentum_advection_central.h (print statements), momentum_advection.h (inluding other *_ql.h files, comments)
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back: momentum_advection.h (including nex cases)
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revert to upstream: NetCDFIO.pyx/pxd
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back: scalar_advection.h (include ql cases)
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back: Grid.pyx (comment)
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back: NetCDFIO.pyx (only comments)
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back: NetCDFIO.pxd (only comments)
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back: Surface.pyx (nur Leerzeichen)
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back: Timestepping.pyx (comments)
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Commits on Jul 22, 2016

back: ThermodynamicsSA.pyx (including eos_c_refstate)
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back: Simulation3d.pyx (importing and initializing StochasticNoise)
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back: Simulation3d.pyx (importing and initializing StochasticNoise)
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back: Simulation3d.pyx (only importing StochasticNoise (not initializing))
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back: Simulation3d.pyx (only importing os)
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back: Simulation3d.pyx (only importing SN)
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back: Simulation3d.pyx (not importing SN)
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back: Simulation3d.pyx (adding modules check_nans, output_nan_arrays)
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back: Simulation3d.pyx (adding only modules check_nans)
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back: Simulation3d.pyx (using modules check_nans, debug_tend)
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back: Simulation3d.pyx (print statements)
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back: Simulation3d.pyx (self.output_path)
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back: Simulation3d.pyx (self.force_io(self.Pa))
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back: Simulation3d.pyx (adding self.output_nan)
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back: Simulation3d.pyx (comments)
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back: ConditionalStatistics.pyx (adding NanStatistics class --> commented out)
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back: ThermodynamicsSA.pyx (setting eos_c --> eos_c_refstate for ReferenceState initialisation; eos_c_update normal iteration loop)
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back: thermodynamics_sa.h (including isnan-testing and option for no-loop sat adjustment (not activated))
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back: thermodynamics_sa.h and ThermodynamicsSA.pyx (eos_update including int n_nan)
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back: ThermodynamicsSA.pyx (forgot to comment some lines out)
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back: NetCDFIO.pyx (comment out everything)
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back: NetCDFIO.pyx (print statement)
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Commits on Jul 23, 2016

adding nan output to SA, MA 4th decomp ql
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print statement
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print statement
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changing Thermodynamics to new scheme (no iteration in eos_update)
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Commits on Jul 28, 2016

changing thermodynamics to old scheme
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changing Thermodynamics to old scheme; comments about Thermodynamics
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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DCBL Soares moist: turning Sfc LHF off
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Commits on Jul 29, 2016

take away some 'debug_tend' and print statements
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Commits on Aug 8, 2016

print statements
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print statements
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print statements
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adding passive scalar 'scal' in DCBL_moist
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debug passive scalar 'phi'; changing debug_tend output
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Commits on Aug 9, 2016

Merge branch 'master' of https://github.com/pressel/pycles into devel_ql
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changing passive scalar 'phi' to be initialized in Tracer.pyx and Initialization.pyx
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including tracer dictionary in generate-namelist.py
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output T_max if w_tend = nan
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Vis output of phi; print statements
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print t max
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generate_namelist: adding max T value for CC lookup table (DCBLSoares_moist)
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print statement temp
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print statement temp
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print statement temp
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debug 'debug_tend', loop ijk_max
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print statement
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Commits on Aug 10, 2016

print statement
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Commits on Aug 12, 2016

print statement
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LHF on
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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print statement
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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print statement
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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debugging tracers (deleting clean_up module)
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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Commits on Aug 15, 2016

print statement
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Commits on Aug 18, 2016

print statement
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print statement
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print statement
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print statement
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initializing mean fields in ql MA weno5; free one more vector in ql SA weno5
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ql SA weno5: initializing mean fields to zero; changing flux computation to be more efficient
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ql SA weno5: upwinding based on total velocity and not on velocity fluctuations
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ql MA weno5: upwinding based on total velocity and not on velocity fluctuations
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Commits on Aug 19, 2016

print statements
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adding 'debug_tend to ThermodynamicsDry'
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Commits on Sep 27, 2016

print statements
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Commits on Oct 5, 2016

changing StableBubble into yz-plane bcs. of VisualizationOutput
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modifying bubble stable case
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adding 'v' to Vis Output
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Commits on Oct 7, 2016

Merge branch 'master' of https://github.com/pressel/pycles into devel_ql
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if statement for moist/dry thermodynamics in VisualizationOutput
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change initialization of tracer to be variable
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Commits on Oct 10, 2016

test: output fields every time-step
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print statements
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print statements
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Commits on Oct 11, 2016

adding smooth transition for tracer initialisation
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Commits on Oct 13, 2016

print statements Sim
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print statements Sim
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print statements Sim
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print statements Sim
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cdef qt_varshift, ql_varshift in Sim.debug_tend
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adding Sim.plot_figure
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removing Sim.plot_figure
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changing kmax of tracers Soares
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debug
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smoothing initial BOMEX profile
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Commits on Oct 17, 2016

changing dz for tracer initialization (dz=50 --> dz= 250)
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changing dz for tracer initialization (dk=5 --> dk= 50)
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print
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Commits on Oct 18, 2016

changing inital profile for tracer in DCBL Soares
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Commits on Oct 20, 2016

adding post processing files
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Commits on Oct 21, 2016

adding Vis_fields.py: Visualisation from fields; EddyField_output.py: computing eddy fields and output as nc-fields; Compatibility.py: first draft to test compatibility according to Christoph Schär
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adding output from LES fields
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debug divergence of correlations
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debug plotting
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adding phi-contours in contourf-plot of other field
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optimising
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Commits on Oct 24, 2016

adding new plotting module for fields with contours
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Commits on Nov 29, 2016

merge upstream
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modifing the saturation adjustment scheme (tested for BOMEX QL, 4th order, UniformViscosity EV=1.2, t>=1900s)
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Commits on Nov 30, 2016

further correction of eos_c: constrain T_2 by 350 K
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Commits on Dec 1, 2016

sat. adjustment: adding conditon qv_star_1 > 0.0
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sat. adjustment: adding T2 output
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print statements
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Commits on Jul 23, 2017

new modification in thermodynmaics_sa.h to handle temperatures above the boiling temperature
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print statement
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Commits on Jul 25, 2017

merging conflict
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Merge branch 'devel_ql' of https://github.com/meyerbe/pycles into devel_ql
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print statements
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plotting
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read in changed; computation wphi_div
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thermodynamics_sa.h: modification 4, for T_2>T_boil
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merge conflict
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Commits on Jul 26, 2017

changes in default setting of DCBLSoares for stochastic noise
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Surface.pyx: adapting to upstream; trying to fix problem in Soares case
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Initialization: change tracer initialisation in DCBLSoares case to whole domain
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Commits on Jul 27, 2017

Commits on Jun 22, 2018

merging upstream changes
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Commits on Jun 25, 2018

finishing merging of upstream (minor commenting changes)
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Fixing merging issues in Surface (Soares) and Tracers (PV.add_variable)
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fixing merging issues
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Commits on Jun 26, 2018

Starting ColdPoolDry case: namelist, Initialization, Forcing, Surface
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Commits on Jun 28, 2018

Changing Initialization ColdPoolDry
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merging changes due to upstream changes from devel_ql
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merging changes due to upstream changes from devel_ql - 2
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Commits on Jun 29, 2018

merging changes due to upstream changes from devel_ql - 3
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merging changes due to upstream changes from devel_ql - 4
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merging changes due to upstream changes from devel_ql - 5
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Commits on Jul 12, 2018

VisOutput: changes upstream; refactoring
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Commits on Jul 18, 2018

Changing Initialization ColdPoolDry to constant background entropy
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Commits on Aug 6, 2018

adding cold pool dry double 2d case; changing namelist of cold pool
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Commits on Aug 11, 2018

Vis.py: adding min time, adding limits on levels; extending color bar
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Commits on Aug 13, 2018

VisualizationOutput: changing exception statement in VisualizationOutput to not output if qt not in PV; exception wasnt caught before
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Commits on Aug 15, 2018

adding ColdPoolDry_double_3D case; incl. option for initial noise on theta
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Commits on Aug 17, 2018

adding triple ColdPool 3D case
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Commits on Aug 20, 2018

Merge branch 'devel_ql' of https://github.com/meyerbe/pycles
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adding Cold Pool case; merging upstream; conditional Viscosity SGS case; resolving merging problems bcs of Soares case
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Commits on Dec 24, 2019

update CP initialization as used for PE scaling and collisions

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resolving merging conflict, updating CP namelists0

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adding stable CP case

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adding CP surface scheme

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adding CP surface scheme

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resolving merging conflicts

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undo merging with devel_ql branch: remove ql-advection schemes

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Commits on Sep 4, 2020

fixing Merging conflicts
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