Comments
This is the radial electric field shear and is a global term (can’t be treated in a local simulation)
It it zeroed automatically in a linear simulation
DEFAULT = 0.0
See discussion on plasma rotation
Definition
+The ballooning angle parameter \(\mathrm{PX0} = \theta_0/(2\pi)\).
+Comments
+DEFAULT = 0.0
This is used only for linear simulations.
The most unstable linear mode is normally at \(\mathrm{PX0} = 0\).
Choose \(0 \le \mathrm{PX0} < 1\).
Definition
diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html index 5e09bdb..9689da4 100644 --- a/docs/gyro/gyro_history.html +++ b/docs/gyro/gyro_history.html @@ -236,7 +236,7 @@This is false for realistic core tokamak parameters. The so-called parallel nonlinearity (a velocity-space nonlinearity which is formally one order smaller in \(\rho_*\) than other terms in the gyrokinetic equations) is only one of several small terms commonly neglected in the standard operation of gyrokinetic codes. GYRO has shown [CWPC06] that the parallel nonlinearity has no statistically significant effect on the diagnosed transport when rho_* < 0.01. Moreover, the parallel nonlinearity has nothing whatsoever to do with the entropy paradox or with producing steady-states of turbulence. To be clear the parallel nonlinearity (related to the nonlinear Landau damping and to wave-particle trapping) is the physical origin of a small turbulent heating source. GYRO is the first code to diagnostically calculate this heating [HW06].
+This is false for realistic core tokamak parameters. The so-called parallel nonlinearity (a velocity-space nonlinearity which is formally one order smaller in \(\rho_*\) than other terms in the gyrokinetic equations) is only one of several small terms commonly neglected in the standard operation of gyrokinetic codes. GYRO has shown [CWPC06] that the parallel nonlinearity has no statistically significant effect on the diagnosed transport when \(\rho_* < 0.01\). Moreover, the parallel nonlinearity has nothing whatsoever to do with the entropy paradox or with producing steady-states of turbulence. To be clear the parallel nonlinearity (related to the nonlinear Landau damping and to wave-particle trapping) is the physical origin of a small turbulent heating source. GYRO is the first code to diagnostically calculate this heating [HW06].
Description
+Mass and charge of all species
+Format
+Rectangular array of ASCII data:
+cols: \(2 \times \mathtt{N\_SPECIES}\)
For each species \(\sigma\):
++++
+- +
\(m_\sigma/m_\mathrm{norm}\): species mass (we suggest always taking deuterium as the normalizing mass)
- +
\(z_\sigma\): species charge
Description
diff --git a/docs/objects.inv b/docs/objects.inv index 850f828..8ce935c 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/searchindex.js b/docs/searchindex.js index ee0b542..d6cd43d 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["build", "cgyro", "cgyro/FAQ", "cgyro/cgyro_cori", "cgyro/cgyro_list", "cgyro/cgyro_table", "cgyro/cgyro_titan", "cgyro/outputs", "cgyro/running_cases", "download", "geometry", "gyro", "gyro/gyro_gallery", "gyro/gyro_history", "gyro/gyro_list", "gyro/gyro_table", "gyro/gyro_vv", "index", "input_gacode", "license", "misc", "neo", "neo/neo_list", "neo/neo_table", "neo/outputs", "prgen", "rotation", "setup", "shortfall", "tglf", "tglf/tglf_list", "tglf/tglf_output_list", "tglf/tglf_table", "tgyro", "tgyro/equations", "tgyro/output", "tgyro/plot", "tgyro/scenarios", "tgyro/solver", "tgyro/tgyro_list", "tgyro/tgyro_table", "workshop", "zreferences"], "filenames": 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"ZMAG": [[4, "zmag"]], "Tabular list for input.cgyro": [[5, "tabular-list-for-input-cgyro"]], "Plasma shape/geometry": [[5, "id1"]], "Advanced shape parameters": [[5, "id2"]], "Control parameters": [[5, "id3"], [15, "id1"]], "Fields": [[5, "id4"]], "Numerical Resolution": [[5, "id5"]], "Numerical Dissipation": [[5, "id6"]], "Time Stepping": [[5, "id7"]], "Species-related parameters": [[5, "id8"]], "Collisions": [[5, "id9"]], "Rotation physics": [[5, "id10"], [23, "id5"]], "Global-spectral parameters": [[5, "id11"]], "Output file control": [[5, "id12"]], "Running CGYRO on OLCF Titan (deprecated)": [[6, "running-cgyro-on-olcf-titan-deprecated"]], "Titan capabilities": [[6, "titan-capabilities"]], "Titan Platform File": [[6, "titan-platform-file"]], "Memory vs speed tradeoff in collisional term": [[6, "memory-vs-speed-tradeoff-in-collisional-term"]], "CGYRO output files": [[7, "cgyro-output-files"]], "Time-independent output": [[7, "id1"]], "Common time-dependent output": [[7, "id2"]], "Restart data": [[7, "id3"]], "Output Normalization": [[7, "output-normalization"]], "Quick-start example": [[8, "quick-start-example"]], "Command-line usage": [[8, "command-line-usage"]], "Batch submission": [[8, "batch-submission"]], "Download and user agreement": [[9, "download-and-user-agreement"]], "Appropriate References": [[9, "id6"], [42, "id144"]], "Source code": [[9, "source-code"]], "Repository access": [[9, "repository-access"]], "FLUX-SURFACE GEOMETRY": [[10, "flux-surface-geometry"]], "Coordinates": [[10, "coordinates"]], "Bounding-box method": [[10, "bounding-box-method"]], "Effective field": [[10, "effective-field"]], "Equilibria": [[10, "equilibria"]], "Table of geometry parameters": [[10, "table-of-geometry-parameters"]], "Magnetic field orientation": [[10, "magnetic-field-orientation"]], "GYRO": [[11, "gyro"]], "Quick links": [[11, "quick-links"], [21, "quick-links"], [29, "quick-links"], [33, "quick-links"]], "Gallery of classic GYRO images (circa 2003)": [[12, "gallery-of-classic-gyro-images-circa-2003"]], "Gyrokinetic Simulation in the 2000s": [[13, "gyrokinetic-simulation-in-the-2000s"]], "Prehistory": [[13, "prehistory"]], "Design History": [[13, "design-history"]], "Yearly Publication Synopsis": [[13, "yearly-publication-synopsis"]], "2002": [[13, "id20"]], "2003": [[13, "id22"]], "2004": [[13, "id25"]], "2005": [[13, "id33"]], "2006": [[13, "id40"]], "2007": [[13, "id49"]], "2008": [[13, "id59"]], "2009": [[13, "id63"]], "A Computational Science and User Perspective": [[13, "a-computational-science-and-user-perspective"]], "Urban Legends": [[13, "urban-legends"]], "UL1: The local gyroBohm limit of global codes differs from local codes": [[13, "ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes"]], "UL2: Full torus simulations are necessary to correctly compute the local transport": [[13, "ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport"]], "UL3: Eulerian codes have inadequate velocity-space resolution": [[13, "ul3-eulerian-codes-have-inadequate-velocity-space-resolution"]], "UL4: The parallel nonlinearity can have a dramatic effect on the transport": [[13, "ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport"]], "Alphabetical list for input.gyro": [[14, "alphabetical-list-for-input-gyro"]], "AMP_PHI_N": [[14, "amp-phi-n"]], "Tabular list for input.gyro": [[15, "tabular-list-for-input-gyro"]], "GYRO verification and validation (pre 2010)": [[16, "gyro-verification-and-validation-pre-2010"]], "Verification Studies": [[16, "verification-studies"]], "Cyclone Base Case with Adiabatic Electrons (2001)": [[16, "cyclone-base-case-with-adiabatic-electrons-2001"]], "Local limit of Global Simulations (2004)": [[16, "local-limit-of-global-simulations-2004"]], "Gyrokinetic Simulation of Impurities (2004)": [[16, "gyrokinetic-simulation-of-impurities-2004"]], "Electron Temperature Gradient Turbulence (2006)": [[16, "electron-temperature-gradient-turbulence-2006"]], "Energetic particle transport coefficients (2009)": [[16, "energetic-particle-transport-coefficients-2009"]], "Compressional Electromagnetic Perturbations (2010)": [[16, "compressional-electromagnetic-perturbations-2010"]], "GYRO Validation Abstracts": [[16, "gyro-validation-abstracts"]], "Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data": [[16, "comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data"]], "Comparison of GYRO synthetic diagnostic results with C-Mod PCI data": [[16, "comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data"]], "Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer data in Tore Supra": [[16, "comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra"]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[16, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "The General Atomics GACODE Suite": [[17, "the-general-atomics-gacode-suite"]], "Running GACODE": [[17, "running-gacode"]], "Geometry": [[17, "geometry"]], "Plasma Rotation": [[17, "plasma-rotation"]], "Equilibrium and Profiles": [[17, "equilibrium-and-profiles"]], "Software": [[17, null]], "Codes": [[17, null]], "Physics": [[17, null]], "input.gacode": [[18, "input-gacode"]], "File structure": [[18, "id3"]], "GACODE License": [[19, "gacode-license"]], "Miscellaneous": [[20, "miscellaneous"]], "NEO": [[21, "neo"]], "Data output": [[21, "data-output"]], "Alphabetical list for input.neo": [[22, "alphabetical-list-for-input-neo"]], "ANISO_MODEL_*": [[22, "aniso-model"]], "BETA_STAR": [[22, "beta-star"]], "DLNNDRE_ADE": [[22, "dlnndre-ade"]], "DLNTDR_PARA_*": [[22, "dlntdr-para"]], "DLNTDR_PERP_*": [[22, "dlntdr-perp"]], "DLNTDRE_ADE": [[22, "dlntdre-ade"]], "DPHI0DR": [[22, "dphi0dr"]], "EPAR0": [[22, "epar0"]], "EPAR0_SPITZER": [[22, "epar0-spitzer"]], "GEO_NY": [[22, "geo-ny"]], "GEO_YIN": [[22, "geo-yin"]], "NE_ADE": [[22, "ne-ade"]], "NU_1": [[22, "nu-1"]], "OMEGA_ROT": [[22, "omega-rot"]], "OMEGA_ROT_DERIV": [[22, "omega-rot-deriv"]], "PROFILE_DLNNDR_*_SCALE": [[22, "profile-dlnndr-scale"]], "PROFILE_DLNTDR_*_SCALE": [[22, "profile-dlntdr-scale"]], "PROFILE_EQUILIBRIUM_MODEL": [[22, "profile-equilibrium-model"]], "PROFILE_ERAD0_MODEL": [[22, "profile-erad0-model"]], "RHO_STAR": [[22, "rho-star"]], "RMAJ_OVER_A": [[22, "rmaj-over-a"]], "RMIN_OVER_A": [[22, "rmin-over-a"]], "RMIN_OVER_A_2": [[22, "rmin-over-a-2"]], "S_ZMAG": [[22, "s-zmag"]], "SHEAR": [[22, "shear"]], "SIM_MODEL": [[22, "sim-model"]], "SPITZER_MODEL": [[22, "spitzer-model"]], "TE_ADE": [[22, "te-ade"]], "TEMP_PARA_*": [[22, "temp-para"]], "TEMP_PERP_*": [[22, "temp-perp"]], "THREED_MODEL": [[22, "threed-model"]], "THREED_EXB_MODEL": [[22, "threed-exb-model"]], "THREED_EXB_DPHI0DR": [[22, "threed-exb-dphi0dr"]], "ZMAG_OVER_A": [[22, "zmag-over-a"]], "Parameters for input.neo": [[23, "parameters-for-input-neo"]], "Numerical resolution": [[23, "id1"]], "Plasma equilibrium/geometry": [[23, "id2"]], "General models": [[23, "id3"]], "Profile models": [[23, "id4"]], "Nonaxisymmetric effects": [[23, "id6"]], "Species-dependent parameters": [[23, "id7"]], "Extra subroutine interface parameters": [[23, "extra-subroutine-interface-parameters"]], "NEO Output Files": [[24, "neo-output-files"]], "Standard output files": [[24, "standard-output-files"]], "Experimental profiles output files": [[24, "experimental-profiles-output-files"]], "Rotation output files": [[24, "rotation-output-files"]], "Subroutine output": [[24, "subroutine-output"]], "Detailed description of NEO output files": [[24, "detailed-description-of-neo-output-files"]], "out.neo.equil": [[24, "out-neo-equil"]], "out.neo.exp_norm": [[24, "out-neo-exp-norm"]], "out.neo.f": [[24, "out-neo-f"]], "out.neo.grid": [[24, "out-neo-grid"]], "out.neo.phi": [[24, "out-neo-phi"]], "out.neo.rotation": [[24, "out-neo-rotation"]], "out.neo.theory": [[24, "out-neo-theory"]], "out.neo.theory_nclass": [[24, "out-neo-theory-nclass"]], "out.neo.transport": [[24, "out-neo-transport"]], "out.neo.transport_exp": [[24, "out-neo-transport-exp"]], "out.neo.transport_flux": [[24, "out-neo-transport-flux"]], "out.neo.transport_gv": [[24, "out-neo-transport-gv"]], "out.neo.vel": [[24, "out-neo-vel"]], "out.neo.vel_fourier": [[24, "out-neo-vel-fourier"]], "profiles_gen": [[25, "profiles-gen"]], "History and Overview": [[25, "history-and-overview"]], "PLASMA ROTATION THEORY": [[26, "plasma-rotation-theory"]], "Physical considerations": [[26, "physical-considerations"]], "Sonic rotation formalism": [[26, "sonic-rotation-formalism"]], "The rotation profile": [[26, "the-rotation-profile"]], "Input parameters": [[26, "input-parameters"]], "Theoretical basis for sonic rotation": [[26, "theoretical-basis-for-sonic-rotation"]], "Connection to experimental data": [[26, "connection-to-experimental-data"]], "Consistency with force balance": [[26, "consistency-with-force-balance"]], "Environment setup": [[27, "environment-setup"]], "NERSC PERLMUTTER (CPU)": [[27, "nersc-perlmutter-cpu"]], "NERSC PERLMUTTER (GPU)": [[27, "nersc-perlmutter-gpu"]], "GA OMEGA": [[27, "ga-omega"]], "DIII-D L-mode shortfall": [[28, "diii-d-l-mode-shortfall"]], "Key publications and presentations": [[28, "key-publications-and-presentations"]], "EXPERIMENTAL profiles": [[28, "experimental-profiles"]], "GYRO results": [[28, "gyro-results"]], "GKW results (added 25-jan-2013)": [[28, "gkw-results-added-25-jan-2013"]], "Cross-code benchmarking results": [[28, "cross-code-benchmarking-results"]], "Acknowledgments": [[28, "acknowledgments"]], "TGLF": [[29, "tglf"]], "References: TGLF saturation models": [[29, "id9"]], "References: TGLF validation against experimental data": [[29, "id10"]], "Alphabetical list for input.tglf": [[30, "alphabetical-list-for-input-tglf"]], "ADIABATIC_ELEC": [[30, "adiabatic-elec"]], "ALPHA_E": [[30, "alpha-e"]], "ALPHA_ZF": [[30, "alpha-zf"]], "ALPHA_MACH": [[30, "alpha-mach"]], "ALPHA_P": [[30, "alpha-p"]], "ALPHA_QUENCH": [[30, "alpha-quench"]], "ALPHA_SA": [[30, "alpha-sa"]], "AS_1": [[30, "as-1"]], "BETAE": [[30, "betae"]], "B_MODEL_SA": [[30, "b-model-sa"]], "DEBYE": [[30, "debye"]], "DEBYE_FACTOR": [[30, "debye-factor"]], "DELTA_LOC": [[30, "delta-loc"]], "DRMAJDX_LOC": [[30, "drmajdx-loc"]], "DRMINDX_LOC": [[30, "drmindx-loc"]], "DZMAJDX_LOC": [[30, "dzmajdx-loc"]], "ETG_FACTOR": [[30, "etg-factor"]], "FILTER": [[30, "filter"]], "FIND_WIDTH": [[30, "find-width"]], "FT_MODEL_SA": [[30, "ft-model-sa"]], "GCHAT": [[30, "gchat"]], "GEOMETRY_FLAG": [[30, "geometry-flag"]], "GHAT": [[30, "ghat"]], "GRADB_FACTOR": [[30, "gradb-factor"]], "IBRANCH": [[30, "ibranch"]], "IFLUX": [[30, "iflux"]], "KAPPA_LOC": [[30, "kappa-loc"]], "KX0_LOC": [[30, "kx0-loc"]], "KYGRID_MODEL": [[30, "kygrid-model"]], "LINSKER_FACTOR": [[30, "linsker-factor"]], "MASS_1": [[30, "mass-1"]], "NBASIS_MAX": [[30, "nbasis-max"]], "NBASIS_MIN": [[30, "nbasis-min"]], "NEW_EIKONAL": [[30, "new-eikonal"]], "NKY": [[30, "nky"]], "NMODES": [[30, "nmodes"]], "NS": [[30, "ns"]], "NWIDTH": [[30, "nwidth"]], "NXGRID": [[30, "nxgrid"]], "PARK": [[30, "park"]], "P_PRIME_LOC": [[30, "p-prime-loc"]], "Q_LOC": [[30, "q-loc"]], "Q_PRIME_LOC": [[30, "q-prime-loc"]], "Q_SA": [[30, "q-sa"]], "RLNS_1": [[30, "rlns-1"]], "RLTS_1": [[30, "rlts-1"]], "RMAJ_LOC": [[30, "rmaj-loc"]], "RMAJ_SA": [[30, "rmaj-sa"]], "RMIN_LOC": [[30, "rmin-loc"]], "RMIN_SA": [[30, "rmin-sa"]], "SAT_RULE": [[30, "sat-rule"]], "SHAT_SA": [[30, "shat-sa"]], "SIGN_BT": [[30, "sign-bt"]], "SIGN_IT": [[30, "sign-it"]], "S_DELTA_LOC": [[30, "s-delta-loc"]], "S_KAPPA_LOC": [[30, "s-kappa-loc"]], "S_ZETA_LOC": [[30, "s-zeta-loc"]], "TAUS_1": [[30, "taus-1"]], "THETA0_SA": [[30, "theta0-sa"]], "THETA_TRAPPED": [[30, "theta-trapped"]], "UNITS": [[30, "units"]], "USE_BISECTION": [[30, "use-bisection"]], "USE_BPAR": [[30, "use-bpar"]], "USE_BPER": [[30, "use-bper"]], "USE_INBOARD_DETRAPPED": [[30, "use-inboard-detrapped"]], "USE_MHD_RULE": [[30, "use-mhd-rule"]], "USE_TRANSPORT_MODEL": [[30, "use-transport-model"]], "VEXB": [[30, "vexb"]], "VEXB_SHEAR": [[30, "vexb-shear"]], "VPAR_1": [[30, "vpar-1"]], "VPAR_MODEL": [[30, "vpar-model"]], "VPAR_SHEAR_1": [[30, "vpar-shear-1"]], "VPAR_SHEAR_MODEL": [[30, "vpar-shear-model"]], "WD_ZERO": [[30, "wd-zero"]], "WIDTH": [[30, "width"]], "WIDTH_MIN": [[30, "width-min"]], "WRITE_WAVEFUNCTION_FLAG": [[30, "write-wavefunction-flag"]], "XNUE": [[30, "xnue"]], "XNU_FACTOR": [[30, "xnu-factor"]], "XNU_MODEL": [[30, "xnu-model"]], "XWELL_SA": [[30, "xwell-sa"]], "ZEFF": [[30, "zeff"]], "ZETA_LOC": [[30, "zeta-loc"]], "ZMAJ_LOC": [[30, "zmaj-loc"]], "ZS_1": [[30, "zs-1"]], "Alphabetical list for out.tglf files": [[31, "alphabetical-list-for-out-tglf-files"]], "density_spectrum": [[31, 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interface, and plotting": [[33, "data-output-python-interface-and-plotting"]], "Transport equations and solution": [[33, "transport-equations-and-solution"]], "Equations solved in TGYRO": [[34, "equations-solved-in-tgyro"]], "Density Transport": [[34, "density-transport"]], "Density fluxes and sources": [[34, "id2"]], "Energy Transport": [[34, "energy-transport"]], "Energy fluxes and sources": [[34, "id3"]], "Momentum Transport": [[34, "momentum-transport"]], "Momentum fluxes and sources": [[34, "id4"]], "Connection of Fluxes to Powers": [[34, "connection-of-fluxes-to-powers"]], "OUTPUT": [[35, "output"]], "PLOT": [[36, "plot"]], "Scenarios and connection to energy sources": [[37, "scenarios-and-connection-to-energy-sources"]], "TGYRO solver algorithm": [[38, "tgyro-solver-algorithm"]], "Formulation": [[38, "formulation"]], "Some comments regarding units": [[38, "some-comments-regarding-units"]], "Solution strategy": [[38, "solution-strategy"]], "Formulation on a discrete grid": [[38, 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"2002": [[11, "id20"]], "2003": [[11, "id22"]], "2004": [[11, "id25"]], "2005": [[11, "id33"]], "2006": [[11, "id40"]], "2007": [[11, "id49"]], "2008": [[11, "id59"]], "2009": [[11, "id63"]], "A Computational Science and User Perspective": [[11, "a-computational-science-and-user-perspective"]], "Urban Legends": [[11, "urban-legends"]], "UL1: The local gyroBohm limit of global codes differs from local codes": [[11, "ul1-the-local-gyrobohm-limit-of-global-codes-differs-from-local-codes"]], "UL2: Full torus simulations are necessary to correctly compute the local transport": [[11, "ul2-full-torus-simulations-are-necessary-to-correctly-compute-the-local-transport"]], "UL3: Eulerian codes have inadequate velocity-space resolution": [[11, "ul3-eulerian-codes-have-inadequate-velocity-space-resolution"]], "UL4: The parallel nonlinearity can have a dramatic effect on the transport": [[11, "ul4-the-parallel-nonlinearity-can-have-a-dramatic-effect-on-the-transport"]], "Alphabetical list for input.gyro": [[12, "alphabetical-list-for-input-gyro"]], "AMP_PHI_N": [[12, "amp-phi-n"]], "Tabular list for input.gyro": [[13, "tabular-list-for-input-gyro"]], "GYRO verification and validation (pre 2010)": [[14, "gyro-verification-and-validation-pre-2010"]], "Verification Studies": [[14, "verification-studies"]], "Cyclone Base Case with Adiabatic Electrons (2001)": [[14, "cyclone-base-case-with-adiabatic-electrons-2001"]], "Local limit of Global Simulations (2004)": [[14, "local-limit-of-global-simulations-2004"]], "Gyrokinetic Simulation of Impurities (2004)": [[14, "gyrokinetic-simulation-of-impurities-2004"]], "Electron Temperature Gradient Turbulence (2006)": [[14, "electron-temperature-gradient-turbulence-2006"]], "Energetic particle transport coefficients (2009)": [[14, "energetic-particle-transport-coefficients-2009"]], "Compressional Electromagnetic Perturbations (2010)": [[14, "compressional-electromagnetic-perturbations-2010"]], "GYRO Validation Abstracts": [[14, "gyro-validation-abstracts"]], "Comparison of GYRO synthetic diagnostic results with DIII-D BES and CER data": [[14, "comparison-of-gyro-synthetic-diagnostic-results-with-diii-d-bes-and-cer-data"]], "Comparison of GYRO synthetic diagnostic results with C-Mod PCI data": [[14, "comparison-of-gyro-synthetic-diagnostic-results-with-c-mod-pci-data"]], "Comparison of GYRO simulations with fast-sweeping and Doppler reflectometer data in Tore Supra": [[14, "comparison-of-gyro-simulations-with-fast-sweeping-and-doppler-reflectometer-data-in-tore-supra"]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[14, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "The General Atomics GACODE Suite": [[15, "the-general-atomics-gacode-suite"]], "Running GACODE": [[15, "running-gacode"]], "Geometry": [[15, "geometry"]], "Plasma Rotation": [[15, "plasma-rotation"]], "Equilibrium and Profiles": [[15, "equilibrium-and-profiles"]], "Software": [[15, null]], "Codes": [[15, null]], "Physics": [[15, null]], "input.gacode": [[16, "input-gacode"]], "File structure": [[16, "id3"]], "GACODE License": [[17, "gacode-license"]], "Miscellaneous": [[18, "miscellaneous"]], "NEO": [[19, "neo"]], "Data output": [[19, "data-output"]], "Alphabetical list for input.neo": [[20, "alphabetical-list-for-input-neo"]], "ANISO_MODEL_*": [[20, "aniso-model"]], "BETA_STAR": [[20, "beta-star"]], "DLNNDRE_ADE": [[20, "dlnndre-ade"]], "DLNTDR_PARA_*": [[20, "dlntdr-para"]], "DLNTDR_PERP_*": [[20, "dlntdr-perp"]], "DLNTDRE_ADE": [[20, "dlntdre-ade"]], "DPHI0DR": [[20, "dphi0dr"]], "EPAR0": [[20, "epar0"]], "EPAR0_SPITZER": [[20, "epar0-spitzer"]], "GEO_NY": [[20, "geo-ny"]], "GEO_YIN": [[20, "geo-yin"]], "NE_ADE": [[20, "ne-ade"]], "NU_1": [[20, "nu-1"]], "OMEGA_ROT": [[20, "omega-rot"]], "OMEGA_ROT_DERIV": [[20, "omega-rot-deriv"]], "PROFILE_DLNNDR_*_SCALE": [[20, "profile-dlnndr-scale"]], "PROFILE_DLNTDR_*_SCALE": [[20, "profile-dlntdr-scale"]], "PROFILE_EQUILIBRIUM_MODEL": [[20, "profile-equilibrium-model"]], "PROFILE_ERAD0_MODEL": [[20, "profile-erad0-model"]], "RHO_STAR": [[20, "rho-star"]], "RMAJ_OVER_A": [[20, "rmaj-over-a"]], "RMIN_OVER_A": [[20, "rmin-over-a"]], "RMIN_OVER_A_2": [[20, "rmin-over-a-2"]], "S_ZMAG": [[20, "s-zmag"]], "SHEAR": [[20, "shear"]], "SIM_MODEL": [[20, "sim-model"]], "SPITZER_MODEL": [[20, "spitzer-model"]], "TE_ADE": [[20, "te-ade"]], "TEMP_PARA_*": [[20, "temp-para"]], "TEMP_PERP_*": [[20, "temp-perp"]], "THREED_MODEL": [[20, "threed-model"]], "THREED_EXB_MODEL": [[20, "threed-exb-model"]], "THREED_EXB_DPHI0DR": [[20, "threed-exb-dphi0dr"]], "ZMAG_OVER_A": [[20, "zmag-over-a"]], "Parameters for input.neo": [[21, "parameters-for-input-neo"]], "Numerical resolution": [[21, "id1"]], "Plasma equilibrium/geometry": [[21, "id2"]], "General models": [[21, "id3"]], "Profile models": [[21, "id4"]], "Nonaxisymmetric effects": [[21, "id6"]], "Species-dependent parameters": [[21, "id7"]], "Extra subroutine interface parameters": [[21, "extra-subroutine-interface-parameters"]], "NEO Output Files": [[22, "neo-output-files"]], "Standard output files": [[22, "standard-output-files"]], "Experimental profiles output files": [[22, "experimental-profiles-output-files"]], "Rotation output files": [[22, "rotation-output-files"]], "Subroutine output": [[22, "subroutine-output"]], "Detailed description of NEO output files": [[22, "detailed-description-of-neo-output-files"]], "out.neo.equil": [[22, "out-neo-equil"]], "out.neo.exp_norm": [[22, "out-neo-exp-norm"]], "out.neo.f": [[22, "out-neo-f"]], "out.neo.grid": [[22, "out-neo-grid"]], "out.neo.phi": [[22, "out-neo-phi"]], "out.neo.rotation": [[22, "out-neo-rotation"]], "out.neo.species": [[22, "out-neo-species"]], "out.neo.theory": [[22, "out-neo-theory"]], "out.neo.theory_nclass": [[22, "out-neo-theory-nclass"]], "out.neo.transport": [[22, "out-neo-transport"]], "out.neo.transport_exp": [[22, "out-neo-transport-exp"]], "out.neo.transport_flux": [[22, "out-neo-transport-flux"]], "out.neo.transport_gv": [[22, "out-neo-transport-gv"]], "out.neo.vel": [[22, "out-neo-vel"]], "out.neo.vel_fourier": [[22, "out-neo-vel-fourier"]], "profiles_gen": [[23, "profiles-gen"]], "History and Overview": [[23, "history-and-overview"]], "PLASMA ROTATION THEORY": [[24, "plasma-rotation-theory"]], "Physical considerations": [[24, "physical-considerations"]], "Sonic rotation formalism": [[24, "sonic-rotation-formalism"]], "The rotation profile": [[24, "the-rotation-profile"]], "Input parameters": [[24, "input-parameters"]], "Theoretical basis for sonic rotation": [[24, "theoretical-basis-for-sonic-rotation"]], "Connection to experimental data": [[24, "connection-to-experimental-data"]], "Consistency with force balance": [[24, "consistency-with-force-balance"]], "Environment setup": [[25, "environment-setup"]], "NERSC PERLMUTTER (CPU)": [[25, "nersc-perlmutter-cpu"]], "NERSC PERLMUTTER (GPU)": [[25, "nersc-perlmutter-gpu"]], "GA OMEGA": [[25, "ga-omega"]], "DIII-D L-mode shortfall": [[26, "diii-d-l-mode-shortfall"]], "Key publications and presentations": [[26, "key-publications-and-presentations"]], "EXPERIMENTAL profiles": [[26, "experimental-profiles"]], "GYRO results": [[26, "gyro-results"]], "GKW results (added 25-jan-2013)": [[26, "gkw-results-added-25-jan-2013"]], "Cross-code benchmarking results": [[26, "cross-code-benchmarking-results"]], "Acknowledgments": [[26, "acknowledgments"]], "TGLF": [[27, "tglf"]], "References: TGLF saturation models": [[27, "id9"]], "References: TGLF validation against experimental data": [[27, "id10"]], "Alphabetical list for input.tglf": [[28, "alphabetical-list-for-input-tglf"]], "ADIABATIC_ELEC": [[28, "adiabatic-elec"]], "ALPHA_E": [[28, "alpha-e"]], "ALPHA_ZF": [[28, "alpha-zf"]], "ALPHA_MACH": [[28, "alpha-mach"]], "ALPHA_P": [[28, "alpha-p"]], "ALPHA_QUENCH": [[28, "alpha-quench"]], "ALPHA_SA": [[28, "alpha-sa"]], "AS_1": [[28, "as-1"]], "BETAE": [[28, "betae"]], "B_MODEL_SA": [[28, "b-model-sa"]], "DEBYE": [[28, "debye"]], "DEBYE_FACTOR": [[28, "debye-factor"]], "DELTA_LOC": [[28, "delta-loc"]], "DRMAJDX_LOC": [[28, "drmajdx-loc"]], "DRMINDX_LOC": [[28, "drmindx-loc"]], "DZMAJDX_LOC": [[28, "dzmajdx-loc"]], "ETG_FACTOR": [[28, "etg-factor"]], "FILTER": [[28, "filter"]], "FIND_WIDTH": [[28, "find-width"]], "FT_MODEL_SA": [[28, "ft-model-sa"]], "GCHAT": [[28, "gchat"]], "GEOMETRY_FLAG": [[28, "geometry-flag"]], "GHAT": [[28, "ghat"]], "GRADB_FACTOR": [[28, "gradb-factor"]], "IBRANCH": [[28, "ibranch"]], "IFLUX": [[28, "iflux"]], "KAPPA_LOC": [[28, "kappa-loc"]], "KX0_LOC": [[28, "kx0-loc"]], "KYGRID_MODEL": [[28, "kygrid-model"]], "LINSKER_FACTOR": [[28, "linsker-factor"]], "MASS_1": [[28, "mass-1"]], "NBASIS_MAX": [[28, "nbasis-max"]], "NBASIS_MIN": [[28, "nbasis-min"]], "NEW_EIKONAL": [[28, "new-eikonal"]], "NKY": [[28, "nky"]], "NMODES": [[28, "nmodes"]], "NS": [[28, "ns"]], "NWIDTH": [[28, "nwidth"]], "NXGRID": [[28, "nxgrid"]], "PARK": [[28, "park"]], "P_PRIME_LOC": [[28, "p-prime-loc"]], "Q_LOC": [[28, "q-loc"]], "Q_PRIME_LOC": [[28, "q-prime-loc"]], "Q_SA": [[28, "q-sa"]], "RLNS_1": [[28, "rlns-1"]], "RLTS_1": [[28, "rlts-1"]], "RMAJ_LOC": [[28, "rmaj-loc"]], "RMAJ_SA": [[28, "rmaj-sa"]], "RMIN_LOC": [[28, "rmin-loc"]], "RMIN_SA": [[28, "rmin-sa"]], "SAT_RULE": [[28, "sat-rule"]], "SHAT_SA": [[28, "shat-sa"]], "SIGN_BT": [[28, "sign-bt"]], "SIGN_IT": [[28, "sign-it"]], "S_DELTA_LOC": [[28, "s-delta-loc"]], "S_KAPPA_LOC": [[28, "s-kappa-loc"]], "S_ZETA_LOC": [[28, "s-zeta-loc"]], "TAUS_1": [[28, "taus-1"]], "THETA0_SA": [[28, "theta0-sa"]], "THETA_TRAPPED": [[28, "theta-trapped"]], "UNITS": [[28, "units"]], "USE_BISECTION": [[28, "use-bisection"]], "USE_BPAR": [[28, "use-bpar"]], "USE_BPER": [[28, "use-bper"]], "USE_INBOARD_DETRAPPED": [[28, "use-inboard-detrapped"]], "USE_MHD_RULE": [[28, "use-mhd-rule"]], "USE_TRANSPORT_MODEL": [[28, "use-transport-model"]], "VEXB": [[28, "vexb"]], "VEXB_SHEAR": [[28, "vexb-shear"]], "VPAR_1": [[28, "vpar-1"]], "VPAR_MODEL": [[28, "vpar-model"]], "VPAR_SHEAR_1": [[28, "vpar-shear-1"]], "VPAR_SHEAR_MODEL": [[28, "vpar-shear-model"]], "WD_ZERO": [[28, "wd-zero"]], "WIDTH": [[28, "width"]], "WIDTH_MIN": [[28, "width-min"]], "WRITE_WAVEFUNCTION_FLAG": [[28, "write-wavefunction-flag"]], "XNUE": [[28, "xnue"]], "XNU_FACTOR": [[28, "xnu-factor"]], "XNU_MODEL": [[28, "xnu-model"]], "XWELL_SA": [[28, "xwell-sa"]], "ZEFF": [[28, "zeff"]], "ZETA_LOC": [[28, "zeta-loc"]], "ZMAJ_LOC": [[28, "zmaj-loc"]], "ZS_1": [[28, "zs-1"]], "Alphabetical list for out.tglf files": [[29, "alphabetical-list-for-out-tglf-files"]], "density_spectrum": [[29, "density-spectrum"]], "eigenvalue_spectrum": [[29, "eigenvalue-spectrum"]], "field_spectrum": [[29, "field-spectrum"]], "intensity_spectrum": [[29, "intensity-spectrum"]], "nsts_crossphase_spectrum": [[29, "nsts-crossphase-spectrum"]], "QL_flux_spectrum": [[29, "ql-flux-spectrum"]], "sat_geo_spectrum": [[29, "sat-geo-spectrum"]], "scalar_saturation_parameters": [[29, "scalar-saturation-parameters"]], "spectral_shift": [[29, "spectral-shift"]], "sum_flux_spectrum": [[29, "sum-flux-spectrum"]], "temperature_spectrum": [[29, "temperature-spectrum"]], "Table of inputs and outputs": [[30, "table-of-inputs-and-outputs"]], "Control": [[30, "id1"]], "Species Vectors": [[30, "id2"]], "Gaussian width parameters": [[30, "id3"]], "Miller geometry parameters": [[30, "id4"]], "s-alpha geometry parameters": [[30, "id5"]], "Change-at-your-own-risk parameters": [[30, "id6"]], "TGLF output parameters": [[30, "id7"]], "TGLF output files": [[30, "id8"]], "TGYRO": [[31, "tgyro"]], "Data output, python interface, and plotting": [[31, "data-output-python-interface-and-plotting"]], "Transport equations and solution": [[31, "transport-equations-and-solution"]], "Equations solved in TGYRO": [[32, "equations-solved-in-tgyro"]], "Density Transport": [[32, "density-transport"]], "Density fluxes and sources": [[32, "id2"]], "Energy Transport": [[32, "energy-transport"]], "Energy fluxes and sources": [[32, "id3"]], "Momentum Transport": [[32, "momentum-transport"]], "Momentum fluxes and sources": [[32, "id4"]], "Connection of Fluxes to Powers": [[32, "connection-of-fluxes-to-powers"]], "OUTPUT": [[33, "output"]], "PLOT": [[34, "plot"]], "Scenarios and connection to energy sources": [[35, "scenarios-and-connection-to-energy-sources"]], "TGYRO solver algorithm": [[36, "tgyro-solver-algorithm"]], "Formulation": [[36, "formulation"]], "Some comments regarding units": [[36, "some-comments-regarding-units"]], "Solution strategy": [[36, "solution-strategy"]], "Formulation on a discrete grid": [[36, "formulation-on-a-discrete-grid"]], "Computation of the Jacobian": [[36, "computation-of-the-jacobian"]], "input.tgyro Alphabetical List": [[37, "input-tgyro-alphabetical-list"]], "LOC_BETAE_SCALE": [[37, "loc-betae-scale"]], "TGYRO_DEN_METHOD*": [[37, "tgyro-den-method"]], "LOC_DX": [[37, "loc-dx"]], "LOC_DX_MAX": [[37, "loc-dx-max"]], "LOC_ER_FEEDBACK_FLAG": [[37, "loc-er-feedback-flag"]], "LOC_EVOLVE_GRAD_ONLY_FLAG": [[37, "loc-evolve-grad-only-flag"]], "LOC_HE_FEEDBACK_FLAG": [[37, "loc-he-feedback-flag"]], "TGYRO_ITERATION_METHOD": [[37, "tgyro-iteration-method"]], "LOC_LOCK_PROFILE_FLAG": [[37, "loc-lock-profile-flag"]], "TGYRO_MODE": [[37, "tgyro-mode"]], "TGYRO_NEO_METHOD": [[37, "tgyro-neo-method"]], "TGYRO_RELAX_ITERATIONS": [[37, "tgyro-relax-iterations"]], "LOC_RELAX": [[37, "loc-relax"]], "LOC_RESIDUAL_METHOD": [[37, "loc-residual-method"]], "LOC_RESTART_FLAG": [[37, "loc-restart-flag"]], "LOC_SCENARIO": [[37, "loc-scenario"]], "TGYRO_THERM_FLAG*": [[37, "tgyro-therm-flag"]], "LOC_TE_FEEDBACK_FLAG": [[37, "loc-te-feedback-flag"]], "LOC_TI_FEEDBACK_FLAG": [[37, "loc-ti-feedback-flag"]], "TGYRO_WRITE_PROFILES_FLAG": [[37, "tgyro-write-profiles-flag"]], "input.tgyro Tabular List": [[38, "input-tgyro-tabular-list"]], "High-level control": [[38, "id1"]], "Iteration control": [[38, "id2"]], "Profile Feedback Control": [[38, "id3"]], "Physics Control": [[38, "id4"]], "Species Parameters": [[38, "id5"]], "CGYRO Workshop 2022": [[39, "cgyro-workshop-2022"]], "AGENDA": [[39, "agenda"]], "References": [[40, "references"]]}, "indexentries": {}}) \ No newline at end of file diff --git a/html/src/cgyro.rst b/html/src/cgyro.rst index 3b936aa..0d6638d 100644 --- a/html/src/cgyro.rst +++ b/html/src/cgyro.rst @@ -85,8 +85,6 @@ Running Cases ------------- * :doc:`running cases