From 9f764f123905b959889b02264c9f434338c383c5 Mon Sep 17 00:00:00 2001 From: Jeff Candy Date: Tue, 16 Jan 2024 09:11:45 -0800 Subject: [PATCH] trying push again --- docs/build.html | 56 ++++++++++++++++++-------------- docs/cgyro.html | 4 +-- docs/cgyro/FAQ.html | 4 +-- docs/cgyro/cgyro_cori.html | 4 +-- docs/cgyro/cgyro_list.html | 4 +-- docs/cgyro/cgyro_table.html | 4 +-- docs/cgyro/cgyro_titan.html | 4 +-- docs/cgyro/outputs.html | 4 +-- docs/cgyro/running_cases.html | 4 +-- docs/download.html | 4 +-- docs/genindex.html | 4 +-- docs/geometry.html | 4 +-- docs/gyro.html | 4 +-- docs/gyro/gyro_gallery.html | 4 +-- docs/gyro/gyro_history.html | 4 +-- docs/gyro/gyro_list.html | 4 +-- docs/gyro/gyro_table.html | 4 +-- docs/gyro/gyro_vv.html | 4 +-- docs/index.html | 6 ++-- docs/input_gacode.html | 4 +-- docs/license.html | 4 +-- docs/misc.html | 4 +-- docs/neo.html | 4 +-- docs/neo/neo_list.html | 4 +-- docs/neo/neo_table.html | 4 +-- docs/neo/outputs.html | 4 +-- docs/objects.inv | Bin 11069 -> 11107 bytes docs/prgen.html | 7 ++-- docs/rotation.html | 4 +-- docs/search.html | 4 +-- docs/searchindex.js | 2 +- docs/setup.html | 4 +-- docs/shortfall.html | 4 +-- docs/tglf.html | 4 +-- docs/tglf/tglf_list.html | 4 +-- docs/tglf/tglf_output_list.html | 4 +-- docs/tglf/tglf_table.html | 4 +-- docs/tgyro.html | 4 +-- docs/tgyro/equations.html | 4 +-- docs/tgyro/output.html | 4 +-- docs/tgyro/plot.html | 4 +-- docs/tgyro/scenarios.html | 4 +-- docs/tgyro/solver.html | 4 +-- docs/tgyro/tgyro_list.html | 4 +-- docs/tgyro/tgyro_table.html | 4 +-- docs/workshop.html | 4 +-- docs/zreferences.html | 4 +-- 47 files changed, 124 insertions(+), 115 deletions(-) diff --git a/docs/build.html b/docs/build.html index b6dcc2a..e322b72 100644 --- a/docs/build.html +++ b/docs/build.html @@ -7,7 +7,7 @@ Build from sources — GACODE - + @@ -20,7 +20,7 @@ - + @@ -54,7 +54,9 @@
  • Environment setup
  • Build from sources
    • @@ -110,37 +112,43 @@

    Prerequisites -

    Environment variables

    -

    First, you need to locate a suitable platform, or make your own platform files. After cloning the repository, you can query the existing platforms using:

    +
    +

    Concept of platform files

    +

    In order to compile the full GACODE package on a new machine, platform files must be created. You can use existing ones or create your own. After cloning the repository, you can query the existing platforms using:

    $ ./gacode/shared/bin/gacode_platforms
    -

    In order to compile the full GACODE package on a new machine, platform files must be created. Let’s imagine you have a new laptop, and you want this platform to be known as MY_PC. In this case you’ll need these lines in your shell RC file:

    -
    export GACODE_PLATFORM=MY_PC
-export GACODE_ROOT=$HOME/gacode
-. $GACODE_ROOT/shared/bin/gacode_setup
-
    -
    -

    Then you must create the following files:

    -
      -

    1. Machine-specific compilation options:

      -
      $GACODE_ROOT/platform/build/make.inc.MY_PC
+
      To create new platform files (say, for a new platform MINE) then copy/edit the following files:
      
+
      $GACODE_ROOT/platform/build/make.inc.MINE
+$GACODE_ROOT/platform/exec/exec.MINE
+$GACODE_ROOT/platform/env/env.MINE (if needed)
 
      
 
      
-
      2. -

    2. Parallel execution command syntax:

      -
      $GACODE_ROOT/platform/exec/exec.MY_PC
+
      Numerous templates for each of these files can be found in the specific folders, and most often there will be an existing machine files that is almost exactly what you need
      
+
    +
    +

    Environment variables

    +

    To use your new platform files, enter the following lines in your shell RC file:

    +
    export GACODE_PLATFORM=MINE
+export GACODE_ROOT=$HOME/gacode
+. $GACODE_ROOT/shared/bin/gacode_setup
+. $GACODE_ROOT/platform/env/env.MINE (if needed)
    - -

  • Any module load commands (optional) go here:

    -
    $GACODE_ROOT/platform/env/env.MY_PC
+
    • +
    +

    OpenBLAS

    +

    When building with gfortran, we recommend using OpenBLAS. It is important to build with single-threaded settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:

    +
    FC=gfortran
+BINARY=64
+USE_THREAD=0
+NUM_THREADS=1
+NO_SHARED=1
+NO_CBLAS=1
+NO_LAPACKE=1
    - - -

    Numerous templates for each of these files can be found in the specific folders, and most often there will be an existing machine files that is almost exactly what you need. So, the strategy is to copy a similar machine file to your new one, and tweak as required.

    +

    You can find an example of linking to OpenBLAS in platform/build/make.inc.MINT.

    Building

    diff --git a/docs/cgyro.html b/docs/cgyro.html index 1a75d3a..724f9f2 100644 --- a/docs/cgyro.html +++ b/docs/cgyro.html @@ -7,7 +7,7 @@ CGYRO — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/FAQ.html b/docs/cgyro/FAQ.html index edb42df..2625fad 100644 --- a/docs/cgyro/FAQ.html +++ b/docs/cgyro/FAQ.html @@ -7,7 +7,7 @@ FAQ — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/cgyro_cori.html b/docs/cgyro/cgyro_cori.html index 1ba76dd..842a143 100644 --- a/docs/cgyro/cgyro_cori.html +++ b/docs/cgyro/cgyro_cori.html @@ -7,7 +7,7 @@ Running CGYRO on NERSC Cori — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html index fd1cf5f..937455e 100644 --- a/docs/cgyro/cgyro_list.html +++ b/docs/cgyro/cgyro_list.html @@ -7,7 +7,7 @@ Alphabetical list for input.cgyro — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html index 9c0ff70..1929484 100644 --- a/docs/cgyro/cgyro_table.html +++ b/docs/cgyro/cgyro_table.html @@ -7,7 +7,7 @@ Tabular list for input.cgyro — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/cgyro_titan.html b/docs/cgyro/cgyro_titan.html index c3c7af0..b7f4065 100644 --- a/docs/cgyro/cgyro_titan.html +++ b/docs/cgyro/cgyro_titan.html @@ -7,7 +7,7 @@ Running CGYRO on OLCF Titan (deprecated) — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/outputs.html b/docs/cgyro/outputs.html index a14caac..c106de5 100644 --- a/docs/cgyro/outputs.html +++ b/docs/cgyro/outputs.html @@ -7,7 +7,7 @@ CGYRO output files — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/cgyro/running_cases.html b/docs/cgyro/running_cases.html index 6ecbb94..80054a6 100644 --- a/docs/cgyro/running_cases.html +++ b/docs/cgyro/running_cases.html @@ -7,7 +7,7 @@ Running Cases — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/download.html b/docs/download.html index 20985ad..5cee942 100644 --- a/docs/download.html +++ b/docs/download.html @@ -7,7 +7,7 @@ Download and user agreement — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/genindex.html b/docs/genindex.html index 1d157f7..e99508b 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -6,7 +6,7 @@ Index — GACODE - + @@ -19,7 +19,7 @@ - + diff --git a/docs/geometry.html b/docs/geometry.html index fa84bd8..6607afc 100644 --- a/docs/geometry.html +++ b/docs/geometry.html @@ -7,7 +7,7 @@ FLUX-SURFACE GEOMETRY — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro.html b/docs/gyro.html index 54c6713..6868f7c 100644 --- a/docs/gyro.html +++ b/docs/gyro.html @@ -7,7 +7,7 @@ GYRO — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro/gyro_gallery.html b/docs/gyro/gyro_gallery.html index 1a13317..2f763fa 100644 --- a/docs/gyro/gyro_gallery.html +++ b/docs/gyro/gyro_gallery.html @@ -7,7 +7,7 @@ Gallery of classic GYRO images (circa 2003) — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html index 0935066..5e09bdb 100644 --- a/docs/gyro/gyro_history.html +++ b/docs/gyro/gyro_history.html @@ -7,7 +7,7 @@ Gyrokinetic Simulation in the 2000s — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro/gyro_list.html b/docs/gyro/gyro_list.html index b305f0c..71320ba 100644 --- a/docs/gyro/gyro_list.html +++ b/docs/gyro/gyro_list.html @@ -7,7 +7,7 @@ Alphabetical list for input.gyro — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro/gyro_table.html b/docs/gyro/gyro_table.html index a5a62e6..09b402a 100644 --- a/docs/gyro/gyro_table.html +++ b/docs/gyro/gyro_table.html @@ -7,7 +7,7 @@ Tabular list for input.gyro — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/gyro/gyro_vv.html b/docs/gyro/gyro_vv.html index 57491d2..584a255 100644 --- a/docs/gyro/gyro_vv.html +++ b/docs/gyro/gyro_vv.html @@ -7,7 +7,7 @@ GYRO verification and validation (pre 2010) — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 5aeb1d6..25c7149 100644 --- a/docs/index.html +++ b/docs/index.html @@ -7,7 +7,7 @@ The General Atomics GACODE Suite — GACODE - + @@ -20,7 +20,7 @@ - + @@ -135,7 +135,9 @@

    Equilibrium and ProfilesBuild from sources diff --git a/docs/input_gacode.html b/docs/input_gacode.html index 93b7284..fcf7781 100644 --- a/docs/input_gacode.html +++ b/docs/input_gacode.html @@ -7,7 +7,7 @@ input.gacode — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/license.html b/docs/license.html index 04e2104..923a34b 100644 --- a/docs/license.html +++ b/docs/license.html @@ -7,7 +7,7 @@ GACODE License — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/misc.html b/docs/misc.html index 1315802..f904b08 100644 --- a/docs/misc.html +++ b/docs/misc.html @@ -7,7 +7,7 @@ Miscellaneous — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/neo.html b/docs/neo.html index a82b579..aac03eb 100644 --- a/docs/neo.html +++ b/docs/neo.html @@ -7,7 +7,7 @@ NEO — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/neo/neo_list.html b/docs/neo/neo_list.html index 8647824..069e7f5 100644 --- a/docs/neo/neo_list.html +++ b/docs/neo/neo_list.html @@ -7,7 +7,7 @@ Alphabetical list for input.neo — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/neo/neo_table.html b/docs/neo/neo_table.html index 9c509d7..439b97c 100644 --- a/docs/neo/neo_table.html +++ b/docs/neo/neo_table.html @@ -7,7 +7,7 @@ Parameters for input.neo — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/neo/outputs.html b/docs/neo/outputs.html index fb8d103..8be5237 100644 --- a/docs/neo/outputs.html +++ b/docs/neo/outputs.html @@ -7,7 +7,7 @@ NEO Output Files — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/objects.inv b/docs/objects.inv index 9edf865dc0c9039ef8c672a8967c57889a13101a..850f828f02920d3937fb40cb954b60ed850c0a2b 100644 GIT binary patch delta 8080 zcmV;BA8+8jR^wK%8VrBgI^I|Kc_X#4KlM`}P)j4L5f-C9F4U6YK_zMchWLYA&cA(er;_c~~fCw29G9;v*r+Frh6EfuUuSEl{ zQ1^A+fI;1Wpw)i>Ppn{=4%&S+s1affMUi1GO+b-I+BVQMoRAnQ=>`&KQrwbPoz(4h zs{tZs8t3sEFzjK{Rs4^?e}PR>2F->QdmF9e|2d+yGHWFYR#Wsgid+k6ido+buE9R_3@%|)EUG$bhR% z9x`7X_q93=Ob{j^Lt=POe*$3@!Qu%fd|a+!w0V926rT9&n_$e#(CP%lm%;_Nv}53&37tFZbEEX^(-Llbck!Tu`tAJEN? 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    profiles_gen

    History and Overview

    -

    [DRAFT]

    -

    The initial motivation for profiles_gen (circa 2005) was to separate the source code required to read and process ONETWO profile data from the main GYRO code base. The rationale was that reading plasma profile and geometry data to calculate suitable inputs for gyrokinetic simulation was not the job of a gyrokinetic code. In the early days, global gyrokinetic simulation was done with artificial/model profiles, and only GYRO was attempting to use bonafide experimental inputs. So in the summer of 2005 it was decided to split the GYRO experimental profile handling into a new tool called iterdb_read. This morphed into the tool iterdb2gyro, which finally became profiles_gen in 2010. The conceptual motivation for profiles_gen was to provide a barrier between the challenges of experimental profile data formats and the standard (typically dimensionless) inputs for gyrokinetic (GYRO) and neoclassical (NEO) simulation. Also, in the pre-2010 period, it became clear that there was a need to standardize and improve geometry input, as ONETWO geometry data was of limited quality. This led to the idea of separating the profile date (typically from ONETWO or TRANSP) from the equilibrium shape data (from EFIT). By 2009 (?), the ability to specify both a “profile statefile” and an EFIT “gfile” was established. The output from profiles_gen creates a unique form for use with the other GACODE transport codes.

    +

    The initial motivation for profiles_gen (circa 2005) was to separate the source code required to read and process ONETWO profile data from the main GYRO code base. The rationale was that reading plasma profile and geometry data to calculate suitable inputs for gyrokinetic simulation was not the job of a gyrokinetic code. So in the summer of 2005 it was decided to split the GYRO experimental profile handling into a new tool called iterdb_read. This morphed into the tool iterdb2gyro, which finally became profiles_gen in 2010. The conceptual motivation for profiles_gen was to provide a barrier between the challenges of experimental profile data formats and the standard (typically dimensionless) inputs for gyrokinetic (GYRO) and neoclassical (NEO) simulation. Also, in the pre-2010 period, it became clear that there was a need to standardize and improve geometry input, as ONETWO geometry data was low quality. This led to the idea of separating the profile date (typically from ONETWO or TRANSP) from the equilibrium shape data (from EFIT). By 2010, the ability to specify both a “profile statefile” and an EFIT “gfile” was established. The output from profiles_gen creates a unique format for use with the other GACODE transport codes.

    diff --git a/docs/rotation.html b/docs/rotation.html index 4d77e6a..6929eec 100644 --- a/docs/rotation.html +++ b/docs/rotation.html @@ -7,7 +7,7 @@ PLASMA ROTATION THEORY — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/search.html b/docs/search.html index 665973b..ca38ff2 100644 --- a/docs/search.html +++ b/docs/search.html @@ -6,7 +6,7 @@ Search — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/searchindex.js b/docs/searchindex.js index 041e04a..ee0b542 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", 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"SHAPE_S_COS1": [[4, "shape-s-cos1"], [22, "shape-s-cos1"]], "SHAPE_COS2": [[4, "shape-cos2"], [22, "shape-cos2"]], "SHAPE_S_COS2": [[4, "shape-s-cos2"], [22, "shape-s-cos2"]], "SHAPE_COS3": [[4, "shape-cos3"], [22, "shape-cos3"]], "SHAPE_S_COS3": [[4, "shape-s-cos3"], [22, "shape-s-cos3"]], "SHAPE_SIN3": [[4, "shape-sin3"], [22, "shape-sin3"]], "SHAPE_S_SIN3": [[4, "shape-s-sin3"], [22, "shape-s-sin3"]], "SILENT_FLAG": [[4, "silent-flag"], [22, "silent-flag"]], "S_DELTA": [[4, "s-delta"], [22, "s-delta"]], "S_KAPPA": [[4, "s-kappa"], [22, "s-kappa"]], "S_ZETA": [[4, "s-zeta"], [22, "s-zeta"]], "TEMP_*": [[4, "temp"], [22, "temp"]], "THETA_PLOT": [[4, "theta-plot"]], "UDSYMMETRY_FLAG": [[4, "udsymmetry-flag"]], "UP_RADIAL": [[4, "up-radial"]], "UPWIND_SINGLE_FLAG": [[4, "upwind-single-flag"]], "VELOCITY_ORDER": [[4, "velocity-order"]], "Z_*": [[4, "z"], [22, "z"]], "Z_EFF": [[4, "z-eff"]], "Z_EFF_METHOD": [[4, "z-eff-method"]], "ZETA": [[4, "zeta"], [22, "zeta"]], "ZF_TEST_MODE": [[4, "zf-test-mode"]], "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, "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, 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"tgyro-relax-iterations"]], "LOC_RELAX": [[39, "loc-relax"]], "LOC_RESIDUAL_METHOD": [[39, "loc-residual-method"]], "LOC_RESTART_FLAG": [[39, "loc-restart-flag"]], "LOC_SCENARIO": [[39, "loc-scenario"]], "TGYRO_THERM_FLAG*": [[39, "tgyro-therm-flag"]], "LOC_TE_FEEDBACK_FLAG": [[39, "loc-te-feedback-flag"]], "LOC_TI_FEEDBACK_FLAG": [[39, "loc-ti-feedback-flag"]], "TGYRO_WRITE_PROFILES_FLAG": [[39, "tgyro-write-profiles-flag"]], "input.tgyro Tabular List": [[40, "input-tgyro-tabular-list"]], "High-level control": [[40, "id1"]], "Iteration control": [[40, "id2"]], "Profile Feedback Control": [[40, "id3"]], "Physics Control": [[40, "id4"]], "Species Parameters": [[40, "id5"]], "CGYRO Workshop 2022": [[41, "cgyro-workshop-2022"]], "AGENDA": [[41, "agenda"]], "References": [[42, "references"]]}, "indexentries": {}}) \ No newline at end of file diff --git a/docs/setup.html b/docs/setup.html index 7824b82..1d3de85 100644 --- a/docs/setup.html +++ b/docs/setup.html @@ -7,7 +7,7 @@ Environment setup — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/shortfall.html b/docs/shortfall.html index 7ea0ce8..6909ea2 100644 --- a/docs/shortfall.html +++ b/docs/shortfall.html @@ -7,7 +7,7 @@ DIII-D L-mode shortfall — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tglf.html b/docs/tglf.html index bc24661..29ca659 100644 --- a/docs/tglf.html +++ b/docs/tglf.html @@ -7,7 +7,7 @@ TGLF — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tglf/tglf_list.html b/docs/tglf/tglf_list.html index 5a2b207..88ba9ef 100644 --- a/docs/tglf/tglf_list.html +++ b/docs/tglf/tglf_list.html @@ -7,7 +7,7 @@ Alphabetical list for input.tglf — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tglf/tglf_output_list.html b/docs/tglf/tglf_output_list.html index 48fb3b1..a27c478 100644 --- a/docs/tglf/tglf_output_list.html +++ b/docs/tglf/tglf_output_list.html @@ -7,7 +7,7 @@ Alphabetical list for out.tglf files — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tglf/tglf_table.html b/docs/tglf/tglf_table.html index 584095e..836d582 100644 --- a/docs/tglf/tglf_table.html +++ b/docs/tglf/tglf_table.html @@ -7,7 +7,7 @@ Table of inputs and outputs — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro.html b/docs/tgyro.html index 54d4d5f..c8d7dee 100644 --- a/docs/tgyro.html +++ b/docs/tgyro.html @@ -7,7 +7,7 @@ TGYRO — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/equations.html b/docs/tgyro/equations.html index de98767..ebbb5fb 100644 --- a/docs/tgyro/equations.html +++ b/docs/tgyro/equations.html @@ -7,7 +7,7 @@ Equations solved in TGYRO — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/output.html b/docs/tgyro/output.html index 885e9aa..5ee40e6 100644 --- a/docs/tgyro/output.html +++ b/docs/tgyro/output.html @@ -7,7 +7,7 @@ OUTPUT — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/plot.html b/docs/tgyro/plot.html index 0526085..57a0496 100644 --- a/docs/tgyro/plot.html +++ b/docs/tgyro/plot.html @@ -7,7 +7,7 @@ PLOT — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/scenarios.html b/docs/tgyro/scenarios.html index c87263b..1150515 100644 --- a/docs/tgyro/scenarios.html +++ b/docs/tgyro/scenarios.html @@ -7,7 +7,7 @@ Scenarios and connection to energy sources — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/solver.html b/docs/tgyro/solver.html index 4a198b4..570a14d 100644 --- a/docs/tgyro/solver.html +++ b/docs/tgyro/solver.html @@ -7,7 +7,7 @@ TGYRO solver algorithm — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/tgyro_list.html b/docs/tgyro/tgyro_list.html index 40aac45..0f43364 100644 --- a/docs/tgyro/tgyro_list.html +++ b/docs/tgyro/tgyro_list.html @@ -7,7 +7,7 @@ input.tgyro Alphabetical List — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/tgyro/tgyro_table.html b/docs/tgyro/tgyro_table.html index 22613f0..d9efdbe 100644 --- a/docs/tgyro/tgyro_table.html +++ b/docs/tgyro/tgyro_table.html @@ -7,7 +7,7 @@ input.tgyro Tabular List — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/workshop.html b/docs/workshop.html index b06078f..1ee01a5 100644 --- a/docs/workshop.html +++ b/docs/workshop.html @@ -7,7 +7,7 @@ CGYRO Workshop 2022 — GACODE - + @@ -20,7 +20,7 @@ - + diff --git a/docs/zreferences.html b/docs/zreferences.html index 3f8d82b..b39945c 100644 --- a/docs/zreferences.html +++ b/docs/zreferences.html @@ -7,7 +7,7 @@ References — GACODE - + @@ -20,7 +20,7 @@ - +