From ab82e4d3e04313dd605145bf1831feb636dc681c Mon Sep 17 00:00:00 2001 From: Jeff Candy Date: Wed, 24 Apr 2024 17:09:59 -0700 Subject: [PATCH] Documentation updates --- docs/.buildinfo | 2 +- docs/build.html | 2 +- docs/build/pre_linux.html | 2 +- docs/build/pre_osx.html | 2 +- docs/cgyro.html | 2 +- docs/cgyro/FAQ.html | 2 +- docs/cgyro/cgyro_list.html | 45 ++++++++++++++++++++++++++++---- docs/cgyro/cgyro_table.html | 2 +- docs/cgyro/outputs.html | 2 +- docs/cgyro/running_cases.html | 2 +- docs/download.html | 2 +- docs/genindex.html | 6 ++--- docs/geometry.html | 2 +- docs/gyro.html | 3 ++- docs/gyro/gyro_gallery.html | 2 +- docs/gyro/gyro_history.html | 2 +- docs/gyro/gyro_list.html | 2 +- docs/gyro/gyro_table.html | 2 +- docs/gyro/gyro_vv.html | 2 +- docs/index.html | 7 ++--- docs/input_gacode.html | 2 +- docs/license.html | 2 +- docs/misc.html | 3 ++- docs/neo.html | 2 +- docs/neo/neo_list.html | 2 +- docs/neo/neo_table.html | 2 +- docs/neo/outputs.html | 2 +- docs/objects.inv | Bin 10891 -> 10889 bytes docs/prgen.html | 2 +- docs/rotation.html | 2 +- docs/search.html | 6 ++--- docs/searchindex.js | 2 +- docs/setup.html | 20 +++++++------- docs/shortfall.html | 2 +- docs/tglf.html | 2 +- docs/tglf/tglf_list.html | 2 +- docs/tglf/tglf_output_list.html | 2 +- docs/tglf/tglf_table.html | 2 +- docs/tgyro.html | 3 ++- docs/tgyro/equations.html | 2 +- docs/tgyro/output.html | 2 +- docs/tgyro/plot.html | 2 +- docs/tgyro/scenarios.html | 2 +- docs/tgyro/solver.html | 2 +- docs/tgyro/tgyro_list.html | 2 +- docs/tgyro/tgyro_table.html | 2 +- docs/workshop.html | 2 +- docs/zreferences.html | 2 +- html/requirements.txt | 5 ++++ html/src/cgyro/cgyro_list.rst | 43 ++++++++++++++++++++++++++++-- html/src/setup.rst | 14 +++++----- 51 files changed, 158 insertions(+), 75 deletions(-) create mode 100644 html/requirements.txt diff --git a/docs/.buildinfo b/docs/.buildinfo index e3188be..2598f27 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: ac567936f247f9e80da7ea843cbae49f +config: 711f83b3aa3bbab10fa381c061ae4e28 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build.html b/docs/build.html index 34baf82..2810ea2 100644 --- a/docs/build.html +++ b/docs/build.html @@ -18,7 +18,7 @@ - + diff --git a/docs/build/pre_linux.html b/docs/build/pre_linux.html index fa57450..d7b1c0f 100644 --- a/docs/build/pre_linux.html +++ b/docs/build/pre_linux.html @@ -18,7 +18,7 @@ - + diff --git a/docs/build/pre_osx.html b/docs/build/pre_osx.html index 68ab765..eec1f0a 100644 --- a/docs/build/pre_osx.html +++ b/docs/build/pre_osx.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgyro.html b/docs/cgyro.html index 59e358e..91ecd08 100644 --- a/docs/cgyro.html +++ b/docs/cgyro.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgyro/FAQ.html b/docs/cgyro/FAQ.html index 2625fad..72972fa 100644 --- a/docs/cgyro/FAQ.html +++ b/docs/cgyro/FAQ.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html index d8c3bf0..c3d5411 100644 --- a/docs/cgyro/cgyro_list.html +++ b/docs/cgyro/cgyro_list.html @@ -7,7 +7,7 @@ Alphabetical list for input.cgyro — GACODE - + @@ -18,9 +18,9 @@ - + - + @@ -413,9 +413,13 @@

Alphabetical list for input.cgyro

DZMAG

Definition

-

Rate of change of plasma elevation:

+

The derivative of the elevation:

-\[a \frac{\partial Z_0(r)}{\partial r} \; .\]
+\[\frac{\partial Z_0(r)}{\partial r} \; .\] +

Comments

+
@@ -864,6 +868,12 @@

Alphabetical list for input.cgyro

PRINT_STEP

Definition

+

Frequency of simulation data output.

+

Comments

+
    +

  • DEFAULT = 100

    • +

  • If PRINT_STEP=100, simulation data will be output after every 100 timesteps

    • +

@@ -924,6 +934,14 @@

Alphabetical list for input.cgyro

RESTART_STEP

+

Definition

+

Frequency of restart file generation

+

Comments

+
    +

  • DEFAULT = 10

    • +

  • If PRINT_STEP=100 and RESTART_STEP=10, simulation data will be output once every 100 timesteps and restart +data will be output once every 1000 timesteps (i.e., once every 10 data outputs)

    • +

RMIN

@@ -1252,11 +1270,28 @@

Alphabetical list for input.cgyro

ZF_TEST_MODE

Definition

+

Toggle test for time-evolution of a single \(k_x\) mode (the classic zonal flow test).

+

Choices

+
    +

  • ZF_TEST_MODE = 0: No test (default)

    • +

  • ZF_TEST_MODE = 1: Trigger test

    • +
+

Comments

+
    +

  • DEFAULT = 0

    • +

  • The standard test is to evolve a single radial mode (N_RADIAL=1)

    • +

  • If N_RADIAL > 1, multiple independent modes will be evolved with \(k_x \rho = 2\pi p/L\) where \(1 \le p \le\) N_RADIAL

    • +

ZMAG

Definition

+

The ratio \(Z_0(r)/a\), where \(Z_0\) is the elevation and \(a\) is the radius of the LCFS.

+

Comments

+
    +

  • DEFAULT = 0.0

    • +

Return to table of inputs

diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html index 1929484..9ad305e 100644 --- a/docs/cgyro/cgyro_table.html +++ b/docs/cgyro/cgyro_table.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgyro/outputs.html b/docs/cgyro/outputs.html index c106de5..b4d85ef 100644 --- a/docs/cgyro/outputs.html +++ b/docs/cgyro/outputs.html @@ -18,7 +18,7 @@ - + diff --git a/docs/cgyro/running_cases.html b/docs/cgyro/running_cases.html index 80054a6..062eefc 100644 --- a/docs/cgyro/running_cases.html +++ b/docs/cgyro/running_cases.html @@ -18,7 +18,7 @@ - + diff --git a/docs/download.html b/docs/download.html index 5cee942..8644e26 100644 --- a/docs/download.html +++ b/docs/download.html @@ -18,7 +18,7 @@ - + diff --git a/docs/genindex.html b/docs/genindex.html index e99508b..02c173c 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -6,7 +6,7 @@ Index — GACODE - + @@ -17,9 +17,9 @@ - + - + diff --git a/docs/geometry.html b/docs/geometry.html index 6607afc..763f871 100644 --- a/docs/geometry.html +++ b/docs/geometry.html @@ -18,7 +18,7 @@ - + diff --git a/docs/gyro.html b/docs/gyro.html index 6868f7c..0b5df4d 100644 --- a/docs/gyro.html +++ b/docs/gyro.html @@ -18,9 +18,10 @@ - + + diff --git a/docs/gyro/gyro_gallery.html b/docs/gyro/gyro_gallery.html index 2f763fa..1112495 100644 --- a/docs/gyro/gyro_gallery.html +++ b/docs/gyro/gyro_gallery.html @@ -18,7 +18,7 @@ - + diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html index 9689da4..a0d376e 100644 --- a/docs/gyro/gyro_history.html +++ b/docs/gyro/gyro_history.html @@ -18,7 +18,7 @@ - + diff --git a/docs/gyro/gyro_list.html b/docs/gyro/gyro_list.html index 71320ba..3571083 100644 --- a/docs/gyro/gyro_list.html +++ b/docs/gyro/gyro_list.html @@ -18,7 +18,7 @@ - + diff --git a/docs/gyro/gyro_table.html b/docs/gyro/gyro_table.html index 09b402a..82f5f78 100644 --- a/docs/gyro/gyro_table.html +++ b/docs/gyro/gyro_table.html @@ -18,7 +18,7 @@ - + diff --git a/docs/gyro/gyro_vv.html b/docs/gyro/gyro_vv.html index 584a255..309a92a 100644 --- a/docs/gyro/gyro_vv.html +++ b/docs/gyro/gyro_vv.html @@ -18,7 +18,7 @@ - + diff --git a/docs/index.html b/docs/index.html index bd2333e..ad1e041 100644 --- a/docs/index.html +++ b/docs/index.html @@ -7,7 +7,7 @@ The General Atomics GACODE Suite — GACODE - + @@ -18,9 +18,10 @@ - + - + + diff --git a/docs/input_gacode.html b/docs/input_gacode.html index fcf7781..59ee2d4 100644 --- a/docs/input_gacode.html +++ b/docs/input_gacode.html @@ -18,7 +18,7 @@ - + diff --git a/docs/license.html b/docs/license.html index 923a34b..b73e7df 100644 --- a/docs/license.html +++ b/docs/license.html @@ -18,7 +18,7 @@ - + diff --git a/docs/misc.html b/docs/misc.html index f904b08..48129d7 100644 --- a/docs/misc.html +++ b/docs/misc.html @@ -18,9 +18,10 @@ - + + diff --git a/docs/neo.html b/docs/neo.html index aac03eb..8f9307b 100644 --- a/docs/neo.html +++ b/docs/neo.html @@ -18,7 +18,7 @@ - + diff --git a/docs/neo/neo_list.html 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"gamma-e-scale"]], "GAMMA_P": [[5, "gamma-p"]], "GAMMA_P_SCALE": [[5, "gamma-p-scale"]], "GPU_BIGMEM_FLAG": [[5, "gpu-bigmem-flag"]], "H_PRINT_FLAG": [[5, "h-print-flag"]], "IPCCW": [[5, "ipccw"], [22, "ipccw"]], "KAPPA": [[5, "kappa"], [22, "kappa"]], "GFLUX_PRINT_FLAG": [[5, "gflux-print-flag"]], "KY": [[5, "ky"], [30, "ky"]], "LAMBDA_DEBYE": [[5, "lambda-debye"]], "LAMBDA_DEBYE_SCALE": [[5, "lambda-debye-scale"]], "MACH": [[5, "mach"]], "MACH_SCALE": [[5, "mach-scale"]], "MASS_*": [[5, "mass"], [22, "mass"]], "MAX_TIME": [[5, "max-time"]], "MOMENT_PRINT_FLAG": [[5, "moment-print-flag"]], "MPI_RANK_ORDER": [[5, "mpi-rank-order"]], "NONLINEAR_FLAG": [[5, "nonlinear-flag"]], "N_FIELD": [[5, "n-field"]], "N_GLOBAL": [[5, "n-global"]], "NU_GLOBAL": [[5, "nu-global"]], "NUP_RADIAL": [[5, "nup-radial"]], "UP_THETA": [[5, "up-theta"]], "NUP_THETA": [[5, "nup-theta"]], "UP_ALPHA": [[5, "up-alpha"]], "NUP_ALPHA": [[5, "nup-alpha"]], "NU_EE": [[5, "nu-ee"]], "N_RADIAL": [[5, "n-radial"], [22, "n-radial"]], "N_THETA": [[5, "n-theta"], [22, "n-theta"]], "N_XI": [[5, "n-xi"], [22, "n-xi"]], "N_ENERGY": [[5, "n-energy"], [22, "n-energy"]], "N_TOROIDAL": [[5, "n-toroidal"]], "N_SPECIES": [[5, "n-species"], [22, "n-species"]], "PRINT_STEP": [[5, "print-step"]], "PROFILE_MODEL": [[5, "profile-model"], [22, "profile-model"]], "PX0": [[5, "px0"]], "Q": [[5, "q"], [22, "q"]], "QUASINEUTRAL_FLAG": [[5, "quasineutral-flag"]], "RESTART_STEP": [[5, "restart-step"]], "RMIN": [[5, "rmin"]], "RMAJ": [[5, "rmaj"]], "ROTATION_MODEL": [[5, "rotation-model"], [22, "rotation-model"]], "S": [[5, "s"]], "SHIFT": [[5, "shift"], [22, "shift"]], "SHAPE_COS0": [[5, "shape-cos0"], [22, "shape-cos0"]], "SHAPE_S_COS0": [[5, "shape-s-cos0"], [22, "shape-s-cos0"]], "SHAPE_COS1": [[5, "shape-cos1"], [22, "shape-cos1"]], "SHAPE_S_COS1": [[5, "shape-s-cos1"], [22, "shape-s-cos1"]], "SHAPE_COS2": [[5, "shape-cos2"], [22, "shape-cos2"]], "SHAPE_S_COS2": [[5, "shape-s-cos2"], [22, "shape-s-cos2"]], "SHAPE_COS3": [[5, "shape-cos3"], [22, "shape-cos3"]], "SHAPE_S_COS3": [[5, "shape-s-cos3"], [22, "shape-s-cos3"]], "SHAPE_SIN3": [[5, "shape-sin3"], [22, "shape-sin3"]], "SHAPE_S_SIN3": [[5, "shape-s-sin3"], [22, "shape-s-sin3"]], "SILENT_FLAG": [[5, "silent-flag"], [22, "silent-flag"]], "S_DELTA": [[5, "s-delta"], [22, "s-delta"]], "S_KAPPA": [[5, "s-kappa"], [22, "s-kappa"]], "S_ZETA": [[5, "s-zeta"], [22, "s-zeta"]], "TEMP_*": [[5, "temp"], [22, "temp"]], "THETA_PLOT": [[5, "theta-plot"]], "UDSYMMETRY_FLAG": [[5, "udsymmetry-flag"]], "UP_RADIAL": [[5, "up-radial"]], "UPWIND_SINGLE_FLAG": [[5, "upwind-single-flag"]], "VELOCITY_ORDER": [[5, "velocity-order"]], "Z_*": [[5, "z"], [22, "z"]], "Z_EFF": [[5, "z-eff"]], "Z_EFF_METHOD": [[5, "z-eff-method"]], "ZETA": [[5, "zeta"], [22, "zeta"]], "ZF_TEST_MODE": [[5, "zf-test-mode"]], "ZMAG": [[5, "zmag"]], "Tabular list for input.cgyro": [[6, "tabular-list-for-input-cgyro"]], "Plasma shape/geometry": [[6, "id1"]], "Advanced shape parameters": [[6, "id2"]], "Control parameters": [[6, "id3"], [15, "id1"]], "Fields": [[6, "id4"]], "Numerical Resolution": [[6, "id5"]], "Numerical Dissipation": [[6, "id6"]], "Time Stepping": [[6, "id7"]], "Species-related parameters": [[6, "id8"]], "Collisions": [[6, "id9"]], "Rotation physics": [[6, "id10"], [23, "id5"]], "Global-spectral parameters": [[6, "id11"]], "Output file control": [[6, "id12"]], "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"]], "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.species": [[24, "out-neo-species"]], "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, "density-spectrum"]], "eigenvalue_spectrum": [[31, "eigenvalue-spectrum"]], "field_spectrum": [[31, "field-spectrum"]], "intensity_spectrum": [[31, "intensity-spectrum"]], "nsts_crossphase_spectrum": [[31, "nsts-crossphase-spectrum"]], "QL_flux_spectrum": [[31, "ql-flux-spectrum"]], "sat_geo_spectrum": [[31, "sat-geo-spectrum"]], "scalar_saturation_parameters": [[31, "scalar-saturation-parameters"]], "spectral_shift": [[31, "spectral-shift"]], "sum_flux_spectrum": [[31, "sum-flux-spectrum"]], "temperature_spectrum": [[31, "temperature-spectrum"]], "Table of inputs and outputs": [[32, "table-of-inputs-and-outputs"]], "Control": [[32, "id1"]], "Species Vectors": [[32, "id2"]], "Gaussian width parameters": [[32, "id3"]], "Miller geometry parameters": [[32, "id4"]], "s-alpha geometry parameters": [[32, "id5"]], "Change-at-your-own-risk parameters": [[32, "id6"]], "TGLF output parameters": [[32, "id7"]], "TGLF output files": [[32, "id8"]], "TGYRO": [[33, "tgyro"]], "Data output, python 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, "formulation-on-a-discrete-grid"]], "Computation of the Jacobian": [[38, "computation-of-the-jacobian"]], "input.tgyro Alphabetical List": [[39, "input-tgyro-alphabetical-list"]], "LOC_BETAE_SCALE": [[39, "loc-betae-scale"]], "TGYRO_DEN_METHOD*": [[39, "tgyro-den-method"]], "LOC_DX": [[39, "loc-dx"]], "LOC_DX_MAX": [[39, "loc-dx-max"]], "LOC_ER_FEEDBACK_FLAG": [[39, "loc-er-feedback-flag"]], "LOC_EVOLVE_GRAD_ONLY_FLAG": [[39, "loc-evolve-grad-only-flag"]], "LOC_HE_FEEDBACK_FLAG": [[39, "loc-he-feedback-flag"]], 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[5, 10, 18, 22], "z_1": [5, 22], "z_2": [5, 22], "z_3": [5, 22], "z_a": 26, "z_c": 16, "z_e": 38, "z_eff": 18, "z_i": 38, "zeeland": 42, "zeff": [17, 32], "zeng": 42, "zero": [5, 13, 22, 30, 32, 39], "zeroth": [22, 24, 26, 39], "zeta": [6, 10, 17, 18, 23, 30, 32], "zeta_loc": [17, 32], "zf": 30, "zf_test_mod": 6, "zhang": 42, "zhu": 42, "zmag": [6, 10, 18], "zmag_over_a": [10, 17, 23], "zmaj_loc": [17, 32], "zonal": [5, 6, 13, 30, 42], "zoom": 41, "zs_1": [17, 32], "\u03b1": 42}, "titles": ["Build from sources", "Ubuntu/Mint", "OSX Sonoma", "CGYRO", "FAQ", "Alphabetical list for input.cgyro", "Tabular list for input.cgyro", "CGYRO output files", "Running Cases", "Download and user agreement", "FLUX-SURFACE GEOMETRY", "GYRO", "Gallery of classic GYRO images (circa 2003)", "Gyrokinetic Simulation in the 2000s", "Alphabetical list for input.gyro", "Tabular list for input.gyro", "GYRO verification and validation (pre 2010)", "The General Atomics GACODE Suite", "input.gacode", "GACODE License", "Miscellaneous", "NEO", "Alphabetical list for input.neo", "Parameters for input.neo", "NEO Output Files", "profiles_gen", "PLASMA ROTATION THEORY", "Environment setup", "DIII-D L-mode shortfall", "TGLF", "Alphabetical list for input.tglf", "Alphabetical list for out.tglf files", "Table of inputs and outputs", "TGYRO", "Equations solved in TGYRO", "OUTPUT", "PLOT", "Scenarios and connection to energy sources", "TGYRO solver algorithm", "input.tgyro Alphabetical List", "input.tgyro Tabular List", "CGYRO Workshop 2022", "References"], "titleterms": {"": [5, 32], "2000": 13, "2001": 16, "2002": 13, "2003": [12, 13], "2004": [13, 16], "2005": 13, "2006": [13, 16], "2007": 13, "2008": 13, "2009": [13, 16], "2010": 16, "2013": 28, "2022": 41, "25": 28, "A": 13, "BES": 16, "The": [13, 17, 26], "_scale": 22, "abstract": 16, "access": 9, "acknowledg": 28, "ad": 28, "adiabat": 16, "adiabatic_elec": 30, "advanc": 6, "against": 29, "agenda": 41, "agreement": 9, "algorithm": 38, "alpha": 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"turbul": 16, "ubuntu": 1, "udsymmetry_flag": 5, "ul1": 13, "ul2": 13, "ul3": 13, "ul4": 13, "unit": [30, 38], "up_alpha": 5, "up_radi": 5, "up_theta": 5, "upwind_single_flag": 5, "urban": 13, "usag": 8, "use_bisect": 30, "use_bp": 30, "use_bpar": 30, "use_inboard_detrap": 30, "use_mhd_rul": 30, "use_transport_model": 30, "user": [9, 13], "valid": [16, 29], "variabl": 0, "vector": 32, "vel": 24, "vel_fouri": 24, "veloc": 13, "velocity_ord": 5, "verif": 16, "vexb": 30, "vexb_shear": 30, "vpar_1": 30, "vpar_model": 30, "vpar_shear_1": 30, "vpar_shear_model": 30, "wd_zero": 30, "width": [30, 32], "width_min": 30, "workshop": 41, "write_wavefunction_flag": 30, "xnu_factor": 30, "xnu_model": 30, "xnue": 30, "xwell_sa": 30, "yearli": 13, "your": 32, "z_": [5, 22], "z_eff": 5, "z_eff_method": 5, "zeff": 30, "zeta": [5, 22], "zeta_loc": 30, "zf_test_mod": 5, "zmag": 5, "zmag_over_a": 22, "zmaj_loc": 30, "zs_1": 30}}) \ No newline at end of file diff --git a/docs/setup.html b/docs/setup.html index 1d3de85..b29cc5e 100644 --- a/docs/setup.html +++ b/docs/setup.html @@ -7,7 +7,7 @@ Environment setup — GACODE - + @@ -18,9 +18,9 @@ - + - + @@ -114,7 +114,7 @@

NERSC PERLMUTTER (CPU)

Sample job layout (32 MPI, 8 OMP) = 1 node, 59 min wall-clock time:

-
$ gacode_qsub -code cgyro -n 32 -nomp 8 -repo atom -w 00:59:00
+
$ gacode_qsub -code cgyro -n 32 -nomp 8 -repo atom -w 59
 

 

 

@@ -131,24 +131,24 @@ 
NERSC PERLMUTTER (GPU)
-

Sample job layout (16 MPI, 8 OMP) = (1 node, 4 GPU) 59 min wall-clock time:

-
$ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom -w 00:59:00
+
Sample job layout (16 MPI, 16 OMP) = (2 nodes, 8 GPUs) 59 min wall-clock time:

+
$ gacode_qsub -code cgyro -n 16 -nomp 16 -repo atom -w 59
 

 

 

 
Important

-
Perlmutter GPU has 4 GPUs and 128 logical cores per node (8 OMP * 16 MPI)

+
Perlmutter GPU has 4 GPUs and 128 logical cores per node

 

 

 
Important

-
Better to set TOROIDALS_PER_PROC > 1 in input.cgyro and use -nomp 32

+
Use ONLY either -nomp 16 (2 MPI/GPU) or -nomp 32 (1 MPI/GPU)

 

 
 

 
GA OMEGA

 
To run in a dedicated GACODE environment, add these lines to .bashrc:

-
export GACODE_PLATFORM=IRIS
-export GACODE_ROOT=/fusion/projects/theory/gacode
+
export GACODE_PLATFORM=OMEGA_INTEL
+export GACODE_ROOT=/fusion/projects/theory/shared/gacode
 . ${GACODE_ROOT}/shared/bin/gacode_setup
 . ${GACODE_ROOT}/platform/env/env.${GACODE_PLATFORM}
 

diff --git a/docs/shortfall.html b/docs/shortfall.html
index 6909ea2..517e646 100644
--- a/docs/shortfall.html
+++ b/docs/shortfall.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tglf.html b/docs/tglf.html
index 29ca659..77dad5c 100644
--- a/docs/tglf.html
+++ b/docs/tglf.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tglf/tglf_list.html b/docs/tglf/tglf_list.html
index 88ba9ef..4bb3e7a 100644
--- a/docs/tglf/tglf_list.html
+++ b/docs/tglf/tglf_list.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tglf/tglf_output_list.html b/docs/tglf/tglf_output_list.html
index a27c478..ee1f0c8 100644
--- a/docs/tglf/tglf_output_list.html
+++ b/docs/tglf/tglf_output_list.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tglf/tglf_table.html b/docs/tglf/tglf_table.html
index 836d582..fd33d9b 100644
--- a/docs/tglf/tglf_table.html
+++ b/docs/tglf/tglf_table.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tgyro.html b/docs/tgyro.html
index c8d7dee..cbfed4e 100644
--- a/docs/tgyro.html
+++ b/docs/tgyro.html
@@ -18,9 +18,10 @@
         
         
         
-        
+        
         
         
+        
     
     
     
diff --git a/docs/tgyro/equations.html b/docs/tgyro/equations.html
index ebbb5fb..d3fef85 100644
--- a/docs/tgyro/equations.html
+++ b/docs/tgyro/equations.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tgyro/output.html b/docs/tgyro/output.html
index 5ee40e6..a762ba2 100644
--- a/docs/tgyro/output.html
+++ b/docs/tgyro/output.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
     
diff --git a/docs/tgyro/plot.html b/docs/tgyro/plot.html
index 57a0496..d23aff9 100644
--- a/docs/tgyro/plot.html
+++ b/docs/tgyro/plot.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
     
diff --git a/docs/tgyro/scenarios.html b/docs/tgyro/scenarios.html
index 1150515..9146e52 100644
--- a/docs/tgyro/scenarios.html
+++ b/docs/tgyro/scenarios.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tgyro/solver.html b/docs/tgyro/solver.html
index 570a14d..4fdfcef 100644
--- a/docs/tgyro/solver.html
+++ b/docs/tgyro/solver.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tgyro/tgyro_list.html b/docs/tgyro/tgyro_list.html
index 0f43364..488e5f0 100644
--- a/docs/tgyro/tgyro_list.html
+++ b/docs/tgyro/tgyro_list.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/tgyro/tgyro_table.html b/docs/tgyro/tgyro_table.html
index d9efdbe..404c040 100644
--- a/docs/tgyro/tgyro_table.html
+++ b/docs/tgyro/tgyro_table.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
         
diff --git a/docs/workshop.html b/docs/workshop.html
index 1ee01a5..edbe228 100644
--- a/docs/workshop.html
+++ b/docs/workshop.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
     
diff --git a/docs/zreferences.html b/docs/zreferences.html
index b39945c..b5945d7 100644
--- a/docs/zreferences.html
+++ b/docs/zreferences.html
@@ -18,7 +18,7 @@
         
         
         
-        
+        
         
         
     
diff --git a/html/requirements.txt b/html/requirements.txt
new file mode 100644
index 0000000..07b6a7d
--- /dev/null
+++ b/html/requirements.txt
@@ -0,0 +1,5 @@
+sphinx
+sphinxcontrib.bibtex
+sphinxcontrib.contentui
+fluiddyn
+sphinx_rtd_theme
diff --git a/html/src/cgyro/cgyro_list.rst b/html/src/cgyro/cgyro_list.rst
index 2bf0ef1..1d7c041 100644
--- a/html/src/cgyro/cgyro_list.rst
+++ b/html/src/cgyro/cgyro_list.rst
@@ -440,11 +440,14 @@ DZMAG
 
 **Definition**
 
-Rate of change of plasma elevation:
+The derivative of the elevation:
 
 .. math::
-   a \frac{\partial Z_0(r)}{\partial r} \; .
+   \frac{\partial Z_0(r)}{\partial r} \; .
 
+**Comments**
+
+- DEFAULT = 0.0
 
 ----
 
@@ -1088,6 +1091,13 @@ PRINT_STEP
 
 **Definition**
 
+Frequency of simulation data output.
+
+**Comments**
+
+- DEFAULT = 100
+- If PRINT_STEP=100, simulation data will be output after every 100 timesteps
+
 ----
 
 .. _cgyro_profile_model:
@@ -1171,6 +1181,16 @@ Enforce quasineutrality when using experimental profiles.
 RESTART_STEP
 ------------
 
+**Definition**
+
+Frequency of restart file generation
+
+**Comments**
+
+- DEFAULT = 10
+- If PRINT_STEP=100 and RESTART_STEP=10, simulation data will be output once every 100 timesteps and restart
+  data will be output once every 1000 timesteps (i.e., once every 10 data outputs)
+
 .. _cgyro_rmin:
 
 RMIN
@@ -1638,6 +1658,19 @@ ZF_TEST_MODE
 
 **Definition**
 
+Toggle test for time-evolution of a single :math:`k_x` mode (the classic zonal flow test).
+
+**Choices**
+
+- ZF_TEST_MODE = 0: No test (default)
+- ZF_TEST_MODE = 1: Trigger test
+
+**Comments**
+
+- DEFAULT = 0
+- The standard test is to evolve a single radial mode (N_RADIAL=1)
+- If N_RADIAL > 1, multiple independent modes will be evolved with :math:`k_x \rho = 2\pi p/L` where :math:`1 \le p \le` N_RADIAL 
+
 ----
 
 .. _cgyro_zmag:
@@ -1647,6 +1680,12 @@ ZMAG
 
 **Definition**
 
+The ratio :math:`Z_0(r)/a`, where :math:`Z_0` is the :doc:`elevation <../geometry>` and :math:`a` is the radius of the LCFS.
+
+**Comments**
+
+- DEFAULT = 0.0
+
 ----
 
 
diff --git a/html/src/setup.rst b/html/src/setup.rst
index aa4cc4d..469b84d 100644
--- a/html/src/setup.rst
+++ b/html/src/setup.rst
@@ -16,7 +16,7 @@ Add the following lines to ``.bashrc``::
   
 Sample job layout (32 MPI, 8 OMP) = 1 node, 59 min wall-clock time::
 
-  $ gacode_qsub -code cgyro -n 32 -nomp 8 -repo atom -w 00:59:00
+  $ gacode_qsub -code cgyro -n 32 -nomp 8 -repo atom -w 59
 
 .. important::
    Perlmutter CPU has 256 logical cores per node (8 OMP * 32 MPI)
@@ -31,23 +31,23 @@ Add the following lines to ``.bashrc``::
   . ${GACODE_ROOT}/shared/bin/gacode_setup
   . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
 
-Sample job layout (16 MPI, 8 OMP) = (1 node, 4 GPU) 59 min wall-clock time::
+Sample job layout (16 MPI, 16 OMP) = (2 nodes, 8 GPUs) 59 min wall-clock time::
 
-  $ gacode_qsub -code cgyro -n 16 -nomp 8 -repo atom -w 00:59:00
+  $ gacode_qsub -code cgyro -n 16 -nomp 16 -repo atom -w 59
 
 .. important::
-   Perlmutter GPU has 4 GPUs and 128 logical cores per node (8 OMP * 16 MPI)
+   Perlmutter GPU has 4 GPUs and 128 logical cores per node
 
 .. important::
-   Better to set TOROIDALS_PER_PROC > 1 in input.cgyro and use -nomp 32
+   Use ONLY either -nomp 16 (2 MPI/GPU) or -nomp 32 (1 MPI/GPU)
 
 GA OMEGA
 --------
 
 To run in a **dedicated GACODE environment**, add these lines to ``.bashrc``::
 
-  export GACODE_PLATFORM=IRIS
-  export GACODE_ROOT=/fusion/projects/theory/gacode
+  export GACODE_PLATFORM=OMEGA_INTEL
+  export GACODE_ROOT=/fusion/projects/theory/shared/gacode
   . ${GACODE_ROOT}/shared/bin/gacode_setup
   . ${GACODE_ROOT}/platform/env/env.${GACODE_PLATFORM}