From 2a51684439c1fa80c8d285202fdecc3ada5eb761 Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@ucsd.edu>
Date: Thu, 18 Jul 2024 12:14:22 -0700
Subject: [PATCH] Add optimization related tab

---
 docs/cgyro/cgyro_table.html    |  43 ++++++++++++++++++++++++++-------
 docs/objects.inv               | Bin 10988 -> 11000 bytes
 docs/searchindex.js            |   2 +-
 html/src/cgyro/cgyro_table.rst |  15 ++++++++++--
 4 files changed, 48 insertions(+), 12 deletions(-)

diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html
index 96d0694..774f079 100644
--- a/docs/cgyro/cgyro_table.html
+++ b/docs/cgyro/cgyro_table.html
@@ -110,6 +110,7 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 <li><p><a class="reference internal" href="#tab-rotation"><span class="std std-ref">Rotation physics</span></a></p></li>
 <li><p><a class="reference internal" href="#tab-global"><span class="std std-ref">Global-spectral parameters</span></a></p></li>
 <li><p><a class="reference internal" href="#tab-output"><span class="std std-ref">Output file control</span></a></p></li>
+<li><p><a class="reference internal" href="#tab-optimization"><span class="std std-ref">Optimization related parameters</span></a></p></li>
 </ul>
 <span id="tab-shape"></span><table class="docutils align-default" id="id1">
 <caption><span class="caption-text"><strong>Plasma shape/geometry</strong></span><a class="headerlink" href="#id1" title="Link to this table"></a></caption>
@@ -421,11 +422,7 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 <td><p>Binormal spectral upwind order</p></td>
 <td><p>3</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-velocity-order"><span class="std std-ref">VELOCITY_ORDER</span></a></p></td>
-<td><p>What internal velocity order to use</p></td>
-<td><p>1</p></td>
-</tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-upwind-single-flag"><span class="std std-ref">UPWIND_SINGLE_FLAG</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-upwind-single-flag"><span class="std std-ref">UPWIND_SINGLE_FLAG</span></a></p></td>
 <td><p>Use reduced precision communication</p></td>
 <td><p>0</p></td>
 </tr>
@@ -565,10 +562,6 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 <td><p>Reduce Sugama memory use</p></td>
 <td><p>0</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-gpu-bigmem-flag"><span class="std std-ref">GPU_BIGMEM_FLAG</span></a></p></td>
-<td><p>Enable GPU offload</p></td>
-<td><p>1</p></td>
-</tr>
 </tbody>
 </table>
 <span id="tab-rotation"></span><table class="docutils align-default" id="id10">
@@ -671,6 +664,38 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 </tr>
 </tbody>
 </table>
+<span id="tab-optimization"></span><table class="docutils align-default" id="id13">
+<caption><span class="caption-text"><strong>Optimization related parameters</strong></span><a class="headerlink" href="#id13" title="Link to this table"></a></caption>
+<colgroup>
+<col style="width: 30.2%" />
+<col style="width: 58.1%" />
+<col style="width: 11.6%" />
+</colgroup>
+<thead>
+<tr class="row-odd"><th class="head"><p>input.cgyro parameter</p></th>
+<th class="head"><p>Short description</p></th>
+<th class="head"><p>Default</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-toroidals-per-proc"><span class="std std-ref">TOROIDALS_PER_PROC</span></a></p></td>
+<td><p>How many toroidal harmonics per MPI process</p></td>
+<td><p>1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-mpi-rank-order"><span class="std std-ref">MPI_RANK_ORDER</span></a></p></td>
+<td><p>Relative ordering of MPI ranks</p></td>
+<td><p>2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-velocity-order"><span class="std std-ref">VELOCITY_ORDER</span></a></p></td>
+<td><p>What internal velocity order to use</p></td>
+<td><p>1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-gpu-bigmem-flag"><span class="std std-ref">GPU_BIGMEM_FLAG</span></a></p></td>
+<td><p>Enable GPU offload when possible</p></td>
+<td><p>1</p></td>
+</tr>
+</tbody>
+</table>
 </section>
 
 
diff --git a/docs/objects.inv b/docs/objects.inv
index 0597aadd4ee3aa0f7c4ea75fd487aea9ad9b66ce..51c37cf2c865d32df23fce23faf4b1e6d75d307d 100644
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diff --git a/docs/searchindex.js b/docs/searchindex.js
index 8cee2eb..834623f 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
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for input.tglf": [[30, null]], "Alphabetical list for out.tglf files": [[31, null]], "Anomalous Transport in the DIII-D Tokamak Matched by Supercomputer Simulation": [[16, "anomalous-transport-in-the-diii-d-tokamak-matched-by-supercomputer-simulation"]], "Appropriate References": [[9, "id6"], [42, "id144"]], "BETAE": [[30, "betae"]], "BETAE_UNIT": [[5, "betae-unit"]], "BETAE_UNIT_SCALE": [[5, "betae-unit-scale"]], "BETA_STAR": [[22, "beta-star"]], "BETA_STAR_SCALE": [[5, "beta-star-scale"]], "BOX_SIZE": [[5, "box-size"]], "BTCCW": [[5, "btccw"], [22, "btccw"]], "B_MODEL_SA": [[30, "b-model-sa"]], "Batch submission": [[8, "batch-submission"]], "Bounding-box method": [[10, "bounding-box-method"]], "Brief description": [[3, "brief-description"]], "Build on your laptop": [[0, null]], "Building": [[0, "building"]], "CGYRO": [[3, null]], "CGYRO Normalization": [[3, "id8"]], "CGYRO Workshop 2022": [[41, null]], "CGYRO output files": [[7, null]], "COLLISION_ENE_DIFFUSION": [[5, 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"connect": [26, 34, 37], "consider": 26, "consist": 26, "control": [6, 15, 32, 40], "coordin": 10, "correctli": 13, "cpu": 27, "cross": 28, "cyclon": 16, "d": [16, 28], "data": [3, 7, 16, 21, 26, 29, 33], "deby": 30, "debye_factor": 30, "delta": [5, 22], "delta_loc": 30, "delta_t": 5, "delta_t_method": 5, "dens_": [5, 22], "densiti": 34, "density_spectrum": 31, "depend": [7, 23], "descript": [3, 24], "design": 13, "detail": 24, "diagnost": 16, "differ": 13, "diii": [16, 28], "discret": 38, "dissip": 6, "dlnndr_": [5, 22], "dlnndre_ad": 22, "dlntdr_": [5, 22], "dlntdr_para_": 22, "dlntdr_perp_": 22, "dlntdre_ad": 22, "doppler": 16, "download": 9, "dphi0dr": 22, "dramat": 13, "drmajdx_loc": 30, "drmindx_loc": 30, "dzmag": 5, "dzmajdx_loc": 30, "e_max": 5, "effect": [10, 13, 23], "eigenvalue_spectrum": 31, "electromagnet": 16, "electron": 16, "energet": 16, "energi": [34, 37], "environ": [0, 27], "epar0": 22, "epar0_spitz": 22, "equat": [33, 34], "equil": 24, "equilibria": 10, "equilibrium": [17, 23], "equilibrium_model": [5, 22], "error_tol": 5, "etg_factor": 30, "eulerian": 13, "exampl": 8, "exp_norm": 24, "experiment": [24, 26, 28, 29], "extra": 23, "f": 24, "faq": 4, "fast": 16, "feedback": 40, "field": [6, 10], "field_print_flag": 5, "field_spectrum": 31, "file": [0, 6, 7, 18, 24, 31, 32], "filter": 30, "find_width": 30, "first": 0, "flux": [10, 34], "forc": 26, "formal": 26, "formul": 38, "freq_tol": 5, "frequent": 3, "from": 13, "ft_model_sa": 30, "full": 13, "futur": 3, "ga": 27, "gacod": [17, 18, 19], "galleri": 12, "gamma_": 5, "gamma_e_scal": 5, "gamma_p": 5, "gamma_p_scal": 5, "gaussian": 32, "gchat": 30, "gener": [17, 23], "geo_ni": 22, "geo_yin": 22, "geometri": [6, 10, 17, 23, 32], "geometry_flag": 30, "gflux_print_flag": 5, "ghat": 30, "gkw": 28, "global": [6, 13, 16], "gpu": 27, "gpu_bigmem_flag": 5, "gradb_factor": 30, "gradient": 16, "grid": [24, 38], "gyro": [11, 12, 14, 15, 16, 28], "gyrobohm": 13, "gyrokinet": [13, 16], "h_print_flag": 5, "have": 13, "high": 40, "histori": [13, 25], "ibranch": 30, "iflux": 30, "imag": [3, 12], "impur": 16, "inadequ": 13, "independ": 7, "input": [3, 5, 6, 14, 15, 18, 21, 22, 23, 26, 30, 32, 33, 39, 40], "intensity_spectrum": 31, "interfac": [23, 33], "ipccw": [5, 22], "iter": 40, "jacobian": 38, "jan": 28, "kappa": [5, 22], "kappa_loc": 30, "kei": 28, "kx0_loc": 30, "ky": [5, 30], "kygrid_model": 30, "l": 28, "lambda_deby": 5, "lambda_debye_scal": 5, "laptop": 0, "legend": 13, "level": 40, "licens": 19, "limit": [13, 16], "line": 8, "link": [11, 21, 29, 33], "linsker_factor": 30, "list": [5, 6, 14, 15, 22, 30, 31, 39, 40], "loc_betae_scal": 39, "loc_dx": 39, "loc_dx_max": 39, "loc_er_feedback_flag": 39, "loc_evolve_grad_only_flag": 39, "loc_he_feedback_flag": 39, "loc_lock_profile_flag": 39, "loc_relax": 39, "loc_residual_method": 39, "loc_restart_flag": 39, "loc_scenario": 39, "loc_te_feedback_flag": 39, "loc_ti_feedback_flag": 39, "local": [13, 16], "mach": 5, "mach_scal": 5, "magnet": 10, "mass_": [5, 22], "mass_1": 30, "match": 16, "max_tim": 5, "method": 10, "miller": 32, "mint": 1, "miscellan": 20, "mod": 16, "mode": 28, "model": [23, 29], "moment_print_flag": 5, "momentum": 34, "mpi_rank_ord": 5, "n": 30, "n_energi": [5, 22], "n_field": 5, "n_global": 5, "n_radial": [5, 22], "n_speci": [5, 22], "n_theta": [5, 22], "n_toroid": 5, "n_xi": [5, 22], "nbasis_max": 30, "nbasis_min": 30, "ne_ad": 22, "necessari": 13, "neo": [21, 22, 23, 24], "nersc": 27, "new_eikon": 30, "nky": 30, "nmode": 30, "nonaxisymmetr": 23, "nonlinear": 13, "nonlinear_flag": 5, "normal": [3, 7, 21], "nsts_crossphase_spectrum": 31, "nu_1": 22, "nu_e": 5, "nu_glob": 5, "numer": [6, 23], "nup_alpha": 5, "nup_radi": 5, "nup_theta": 5, "nwidth": 30, "nxgrid": 30, "omega": 27, "omega_rot": 22, "omega_rot_deriv": 22, "openbla": 0, "optim": 6, "orient": 10, "osx": 2, "out": [24, 31], "output": [3, 6, 7, 21, 24, 32, 33, 35], "overview": [11, 18, 25, 28, 29, 33], "own": 32, "p_prime_loc": 30, "parallel": 13, "paramet": [6, 10, 15, 23, 26, 32, 40], "park": 30, "particl": 16, "past": 3, "pci": 16, "perlmutt": 27, "perspect": 13, "perturb": 16, "phi": 24, "physic": [6, 17, 23, 26, 40], "plasma": [6, 17, 23, 26], "platform": 0, "plot": [3, 33, 36], "power": 34, "pre": 16, "prebuilt": 27, "prehistori": 13, "present": 28, "print_step": 5, "profil": [17, 23, 24, 26, 28, 40], "profile_dlnndr_": 22, "profile_dlntdr_": 22, "profile_equilibrium_model": 22, "profile_erad0_model": 22, "profile_model": [5, 22], "profiles_gen": 25, "public": [13, 28], "px0": 5, "python": 33, "q": [5, 22], "q_loc": 30, "q_prime_loc": 30, "q_sa": 30, "ql_flux_spectrum": 31, "quasineutral_flag": 5, "question": 3, "quick": [8, 11, 21, 29, 33], "refer": [9, 29, 42], "reflectomet": 16, "regard": 38, "relat": 6, "repositori": 9, "resolut": [6, 13, 23], "restart": 7, "restart_step": 5, "result": [16, 28], "rho_star": 22, "risk": 32, "rlns_1": 30, "rlts_1": 30, "rmaj": 5, "rmaj_loc": 30, "rmaj_over_a": 22, "rmaj_sa": 30, "rmin": 5, "rmin_loc": 30, "rmin_over_a": 22, "rmin_over_a_2": 22, "rmin_sa": 30, "rotat": [6, 17, 23, 24, 26], "rotation_model": [5, 22], "run": [3, 8, 17], "s_delta": [5, 22], "s_delta_loc": 30, "s_kappa": [5, 22], "s_kappa_loc": 30, "s_zeta": [5, 22], "s_zeta_loc": 30, "s_zmag": 22, "sat_geo_spectrum": 31, "sat_rul": 30, "satur": 29, "scalar_saturation_paramet": 31, "scenario": 37, "scienc": 13, "shape": 6, "shape_cos0": [5, 22], "shape_cos1": [5, 22], "shape_cos2": [5, 22], "shape_cos3": [5, 22], "shape_s_cos0": [5, 22], "shape_s_cos1": [5, 22], "shape_s_cos2": [5, 22], "shape_s_cos3": [5, 22], "shape_s_sin3": [5, 22], "shape_sin3": [5, 22], "shat_sa": 30, "shear": 22, "shift": [5, 22], "shortfal": 28, "sign_bt": 30, "sign_it": 30, "silent_flag": [5, 22], "sim_model": 22, "simul": [3, 13, 16], "softwar": 17, "solut": [33, 38], "solv": 34, "solver": 38, "some": 38, "sonic": 26, "sonoma": 2, "sourc": [0, 3, 9, 34, 37], "space": 13, "speci": [6, 23, 24, 32, 40], "spectral": 6, "spectral_shift": 31, "spitzer_model": 22, "standard": 24, "start": 8, "step": [0, 6], "strategi": 38, "structur": 18, "studi": 16, "submiss": 8, "subroutin": [23, 24], "suit": 17, "sum_flux_spectrum": 31, "supercomput": 16, "supra": 16, "surfac": 10, "sweep": 16, "synopsi": 13, "synthet": 16, "tabl": [10, 32], "tabular": [6, 15, 40], "taus_1": 30, "te_ad": 22, "temp_": [5, 22], "temp_para_": 22, "temp_perp_": 22, "temperatur": 16, "temperature_spectrum": 31, "tglf": [29, 30, 31, 32], "tgyro": [33, 34, 38, 39, 40], "tgyro_den_method": 39, "tgyro_iteration_method": 39, "tgyro_mod": 39, "tgyro_neo_method": 39, "tgyro_relax_iter": 39, "tgyro_therm_flag": 39, "tgyro_write_profiles_flag": 39, "theoret": 26, "theori": [24, 26], "theory_nclass": 24, "theta0_sa": 30, "theta_plot": 5, "theta_trap": 30, "threed_exb_dphi0dr": 22, "threed_exb_model": 22, "threed_model": 22, "time": [6, 7], "tokamak": 16, "tore": 16, "toroidals_per_proc": 5, "toru": 13, "transport": [13, 16, 24, 33, 34], "transport_exp": 24, "transport_flux": 24, "transport_gv": 24, "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": [0, 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/html/src/cgyro/cgyro_table.rst b/html/src/cgyro/cgyro_table.rst
index b8ea9e4..cfd9f62 100644
--- a/html/src/cgyro/cgyro_table.rst
+++ b/html/src/cgyro/cgyro_table.rst
@@ -13,6 +13,7 @@ Tabular list for input.cgyro
 * :ref:`tab-rotation`
 * :ref:`tab-global`
 * :ref:`tab-output`
+* :ref:`tab-optimization`
 
 .. _tab-shape:
   
@@ -109,7 +110,6 @@ Tabular list for input.cgyro
    ":ref:`cgyro_nup_radial`", Radial spectral upwind order,3
    ":ref:`cgyro_nup_theta`", Poloidal upwind order,3
    ":ref:`cgyro_nup_alpha`", Binormal spectral upwind order,3
-   ":ref:`cgyro_velocity_order`", What internal velocity order to use,1
    ":ref:`cgyro_upwind_single_flag`", Use reduced precision communication,0
 
 .. _tab-time:
@@ -154,7 +154,6 @@ Tabular list for input.cgyro
    ":ref:`cgyro_collision_ene_diffusion`", Toggle energy diffusion,1
    ":ref:`cgyro_collision_kperp`", Toggle so-called FLR term, 0
    ":ref:`cgyro_collision_precision_mode`", Reduce Sugama memory use, 0
-   ":ref:`cgyro_gpu_bigmem_flag`", Enable GPU offload, 1
 
 .. _tab-rotation:
 
@@ -189,3 +188,15 @@ Tabular list for input.cgyro
    ":ref:`cgyro_moment_print_flag`", Output of density and energy moments, 0
    ":ref:`cgyro_gflux_print_flag`", Output of global flux profiles, 0
    ":ref:`cgyro_h_print_flag`", Output of distribution (single-mode only), 0
+
+.. _tab-optimization:
+
+.. csv-table:: **Optimization related parameters**
+   :header: "input.cgyro parameter", "Short description", "Default"
+   :widths: 13, 25, 5
+
+   ":ref:`cgyro_toroidals_per_proc`", How many toroidal harmonics per MPI process,1
+   ":ref:`cgyro_mpi_rank_order`", Relative ordering of MPI ranks,2
+   ":ref:`cgyro_velocity_order`", What internal velocity order to use,1
+   ":ref:`cgyro_gpu_bigmem_flag`", Enable GPU offload when possible, 1
+