From e555662ae0d160559d5242b238182f1155ab2d1a Mon Sep 17 00:00:00 2001 From: Jeff Candy Date: Thu, 21 Mar 2024 14:34:21 -0700 Subject: [PATCH] Updated PX0, removed some depecated files --- docs/cgyro.html | 2 - docs/cgyro/cgyro_list.html | 15 +++++ docs/gyro/gyro_history.html | 2 +- docs/index.html | 1 + docs/neo/outputs.html | 36 ++++++++++-- docs/objects.inv | Bin 11107 -> 10802 bytes docs/searchindex.js | 2 +- html/src/cgyro.rst | 2 - html/src/cgyro/cgyro_cori.rst | 85 ---------------------------- html/src/cgyro/cgyro_list.rst | 24 +++++++- html/src/cgyro/cgyro_titan.rst | 93 ------------------------------- html/src/cgyro/running_cases.rst | 1 - html/src/gyro/gyro_history.rst | 2 +- html/src/index.rst | 1 + html/src/neo/outputs.rst | 25 +++++++++ 15 files changed, 97 insertions(+), 194 deletions(-) delete mode 100644 html/src/cgyro/cgyro_cori.rst delete mode 100644 html/src/cgyro/cgyro_titan.rst diff --git a/docs/cgyro.html b/docs/cgyro.html index 724f9f2..59e358e 100644 --- a/docs/cgyro.html +++ b/docs/cgyro.html @@ -206,8 +206,6 @@

Normalization

diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html index 937455e..d8c3bf0 100644 --- a/docs/cgyro/cgyro_list.html +++ b/docs/cgyro/cgyro_list.html @@ -485,6 +485,8 @@

Alphabetical list for input.cgyro\(\mathbf{E}\times\mathbf{B}\) shearing rate \(\displaystyle \frac{a}{c_s} \gamma_E\).

Comments

 @@ -879,6 +881,19 @@

Alphabetical list for input.cgyro

+
+

PX0

+

Definition

+

The ballooning angle parameter \(\mathrm{PX0} = \theta_0/(2\pi)\).

+

Comments

+ +
+

Q

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 @@

UL3: Eulerian codes have inadequate velocity-space resolution

UL4: The parallel nonlinearity can have a dramatic effect on the transport

-

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].

+
+

out.neo.species

+

Description

+

Mass and charge of all species

+

Format

+

Rectangular array of ASCII data:

+ +
    +

  1. For each species \(\sigma\):

    +
    +
      +

    • \(m_\sigma/m_\mathrm{norm}\): species mass (we suggest always taking deuterium as the normalizing mass)

      • +

    • \(z_\sigma\): species charge

      • +
    +
    +
    2. +
+
+

out.neo.theory

Description

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The speed difference can be up to 20% at both extremes. - -.. note:: When running the jobs, you must use the same platform file that you used for building the executable. - -Balancing MPI Rank vs OMP -------------------------- - -When submitting a CGYRO job, you are asked to pick an MPI rank ( *-n* ) and the number of threads/process ( *-nomp* ). -The product will determine the amount of compute resources you will use. - -The recommended setting is to pick **nomp** to be 4. - -For jobs that use only a few nodes, **-nomp 2** may be better, and for really big runs, you may get a marginal speedup using **-nomp 8** or even **-nomp 16**. - -Trading speed vs efficiency ---------------------------- - -As with most HPC codes, CGYRO will run faster when using more compute resources (i.e. compute nodes). -However, like most HPC codes, the efficiency will generally decrease as you use more resources, too. -I.e. you will be able to get **less computation done with the same amount of allocation time**. - -Often, this is an expected tradeoff to get the desired results within a reasonable amount of time, -but it should be a conscious decision. -E.g. if you need the results of 8 independent simulations at once, and you do not care for partial results, -it will be more efficient to run them in parallel, each using 1/8th of the resources, -instead of running them sequentially using as many resources as possible for each. - -The actual speedup, and the related efficiency, depends on the actual input setup. -Below you can see the wallclock results doing a few steps for the very small *nl01*, the medium sized *nl03* and the large *nl04*. - -.. csv-table:: **nl01** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 2,38.4,1.0x,100% - 4,22.3,1.7x,86% - 8,12.3,3.1x,78% - 16,7.0,5.5x,69% - 32,5.2,7.4x,46% - 64,4.1,9.5x,30% - -.. csv-table:: **nl03** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 8,933,1.0x,100% - 16,489,1.9x,95% - 32,259,3.6x,90% - 64,152,6.1x,77% - 128,85,11x,68% - 256,57,16x,51% - -.. csv-table:: **nl04** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 128,154,1.0x,100% - 256,101,1.5x,76% - 512,57,2.7x,68% - 1024,37,4.2x,52% - - -Return to :doc:`top ` - - diff --git a/html/src/cgyro/cgyro_list.rst b/html/src/cgyro/cgyro_list.rst index 379beee..2bf0ef1 100644 --- a/html/src/cgyro/cgyro_list.rst +++ b/html/src/cgyro/cgyro_list.rst @@ -541,10 +541,12 @@ GAMMA_E **Definition** -Normalized :math:`\exb` shearing rate :math:`\displaystyle \frac{a}{c_s} \gamma_E`. +Normalized :math:`\exb` shearing rate :math:`\displaystyle \frac{a}{c_s} \gamma_E`. **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 :doc:`plasma rotation <../rotation>` @@ -1108,6 +1110,24 @@ Selector for profile data input. ---- +.. _cgyro_px0: + +PX0 +--- + +**Definition** + +The ballooning angle parameter :math:`\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 :math:`\mathrm{PX0} = 0`. +- Choose :math:`0 \le \mathrm{PX0} < 1`. + +---- + .. _cgyro_q: Q @@ -1122,7 +1142,7 @@ Safety factor, :math:`q`, of the flux surface. - DEFAULT = 2.0 - This is only active with :ref:`cgyro_equilibrium_model` = 2 (the Miller equilibrium model). - When experimental profiles are used (:ref:`cgyro_profile_model` = 2), the safety factor as a function of radius is read from :ref:`input.gacode` and the safety factor gradient is computed internally. - + ---- .. _cgyro_quasineutral_flag: diff --git a/html/src/cgyro/cgyro_titan.rst b/html/src/cgyro/cgyro_titan.rst deleted file mode 100644 index ce8e85a..0000000 --- a/html/src/cgyro/cgyro_titan.rst +++ /dev/null @@ -1,93 +0,0 @@ -Running CGYRO on OLCF Titan (deprecated) -======================================== - -ORNL Titan is one of the most popular GPU platforms on which to run CGYRO. -This document provides some guidance on how to best make use of its resources - -Titan capabilities ------------------- - -The bulk of the Titan compute power comes from the approximately 18k nodes, each hosting a single AMD Opteron CPU and a NVIDIA K20X GPU. -For our purposes, each Opteron provides 16 execution threads. -Each node is also equiped with 32 GB of CPU RAM and 5GB of GPU RAM. - -Titan Platform File -------------------- - -The recommended platform file is: - - * TITAN_PGI - -Memory vs speed tradeoff in collisional term --------------------------------------------- - -Unless you are using the simplified collision operator, i.e. **not COLLISION_MODEL=5**, -CGYRO will run that operator on CPU-only by default. -This choice has been made due to the significant memory cost of the other operators, -allowing simulations to run on a small number of nodes. - -This default choice does however significantly slow down the simulation. -To force the collisional operator to execute on the (much faster) GPU, set - - * GPU_BIGMEM_FLAG=1 - -The faster setup will require significantly more GPU memory. If your job fails with CUDA errors, try increasing the number of nodes being used. - - - -Balancing MPI Rank vs OMP -------------------------- - -When submitting a CGYRO job, you are asked to pick an MPI rank ( *-n* ) and the number of threads/process ( *-nomp* ). -The product will determine the amount of compute resources you will use. - -The recommended setting is to pick **nomp** to be 2. - -For really big runs, you can make use of more nodes by setting **-nomp 4** or even **-nomp 8**. - -Trading speed vs efficiency ---------------------------- - -As with most HPC codes, CGYRO will run faster when using more compute resources (i.e. compute nodes). -However, like most HPC codes, the efficiency will generally decrease as you use more resources, too. -I.e. you will be able to get **less computation done with the same amount of allocation time**. - -Often, this is an expected tradeoff to get the desired results within a reasonable amount of time, -but it should be a conscious decision. -E.g. if you need the results of 8 independent simulations at once, and you do not care for partial results, -it will be more efficient to run them in parallel, each using 1/8th of the resources, -instead of running them sequentially using as many resources as possible for each. - -The actual speedup, and the related efficiency, depends on the actual input setup. -Below you can see the wallclock results doing a few steps for the very small *nl01*, the medium sized *nl03* and the large *nl04*. - -.. csv-table:: **nl01** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 8,40,1.0x,100% - 16,20,2.0x,99% - 32,13,3.1x,78% - 64,7.9,5.1x,63% - 128,6.7,6.0x,38% - 256,5.5,7.3x,23% - -.. csv-table:: **nl03** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 64,366,1.0x,100% - 128,203,1.8x,90% - 256,149,2.5x,62% - 512,123,3.0x,37% - 1024,77,4.7x,30% - -.. csv-table:: **nl04** - :header: "#nodes","Wallclock time","Speedup","Efficiency" - - 1024,123,1.0x,100% - 2048,94,1.3x,65% - 4096,73,1.7x,42% - - -Return to :doc:`top ` - - diff --git a/html/src/cgyro/running_cases.rst b/html/src/cgyro/running_cases.rst index fb608f8..39503e8 100644 --- a/html/src/cgyro/running_cases.rst +++ b/html/src/cgyro/running_cases.rst @@ -4,7 +4,6 @@ Running Cases Quick-start example ------------------- - :: $ cgyro -g reg08 diff --git a/html/src/gyro/gyro_history.rst b/html/src/gyro/gyro_history.rst index 42cdf7d..85560a4 100644 --- a/html/src/gyro/gyro_history.rst +++ b/html/src/gyro/gyro_history.rst @@ -148,7 +148,7 @@ The truth is in fact quite the opposite. Published GYRO simulations are always UL4: The parallel nonlinearity can have a dramatic effect on the transport ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -This is false for realistic core tokamak parameters. The so-called parallel nonlinearity (a velocity-space nonlinearity which is formally one order smaller in :math:`\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 :cite:`candy:2006b` 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 :cite:`hinton:2006`. +This is false for realistic core tokamak parameters. The so-called parallel nonlinearity (a velocity-space nonlinearity which is formally one order smaller in :math:`\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 :cite:`candy:2006b` that the parallel nonlinearity has no statistically significant effect on the diagnosed transport when :math:`\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 :cite:`hinton:2006`. .. [1] Practically speaking, global simulations allow modest profile variation within the simulation domain, where local simulations consider fixed temperature, density, shape, etc. Even global simulations, however, must enforce the formal restrictions imposed by the gyrokinetic ordering. diff --git a/html/src/index.rst b/html/src/index.rst index 84d0f24..951506b 100644 --- a/html/src/index.rst +++ b/html/src/index.rst @@ -32,6 +32,7 @@ Equilibrium and Profiles GACODE software works with the :ref:`input.gacode` format. .. toctree:: + :maxdepth: 4 :caption: Software license diff --git a/html/src/neo/outputs.rst b/html/src/neo/outputs.rst index 155c3dc..59162f2 100644 --- a/html/src/neo/outputs.rst +++ b/html/src/neo/outputs.rst @@ -26,6 +26,7 @@ Standard output files :ref:`neo_out.neo.grid`, "Numerical grid parameters" :ref:`neo_out.neo.phi`, "Poloidal variation of first-order es potential" :ref:`neo_out.neo.theory`, "Neoclassical transport coefficients from analytic theory" + :ref:`neo_out.neo.species`, "Mass and charge of all species" :ref:`neo_out.neo.theory_nclass`, "Neoclassical transport coefficients from the NCLASS code" :ref:`neo_out.neo.transport`, "Neoclassical transport coefficients from DKE solve" :ref:`neo_out.neo.transport_flux`, "Neoclassical fluxes in GB units from DKE solve" @@ -284,6 +285,30 @@ For each :math:`\theta_j`, j=1..N_THETA .. =========================================================================================== +.. _neo_out.neo.species: + +out.neo.species +--------------- + +**Description** + +Mass and charge of all species + +**Format** + +Rectangular array of ASCII data: + +* cols: :math:`2 \times \nspec` + +1. For each species :math:`\sigma`: + + - :math:`m_\sigma/m_\nrm`: species mass (we suggest always taking deuterium as the normalizing mass) + - :math:`z_\sigma`: species charge + +----- + +.. =========================================================================================== + .. _neo_out.neo.theory: out.neo.theory