1D diagnostics
--------------

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xgc.oneddiag.bp contains diagnostics of flux-surface averaged quantities.

**Remarks**

There are two radial discretizations in the 1D diagnostics:
one set by the input parameter ``sml_00_npsi`` and one set by the number of closed flux surfaces crossing the lower-field-side midplane (# |nbsp| flux |nbsp| surfaces).
There can be narrow flux surfaces that do not cross the lower-field-side midplane and these are not included in the default 1D diagnostics.

For neoclassical simulations (XGCa) it is advisable to calculate the proper flux-surface averaged fluxes by using the
`2D diagnostics <xgc_output_2D.html>`_, and either the node volumes in `Mesh <xgc_output_mesh.html>`_ or the flux-surface averaging matrix in `Matrix operations <xgc_output_matrix.html>`_. The reason is that the neoclassical fluxes are so small that it is important to accurately split the adiabatic and non-adiabatic parts of the distribution function.

'# outputs' below is '# of time steps.' The time steps are usually incremental, but a restart of simulations from checkpoint files will break this.
'step' will indicate the time steps of the simulation and 'time' will tell the physical time of the time step.

In the variable names, the prefix ``e_``, ``i_``, ``i2_``, tells the plasma species.
The suffixes of the plasma quantities are ``_1d`` or ``_df_1d``. ``_1d`` if for full-f quantities and ``_df_1d`` is for total-f quantities.
Full-f (``_1d``) quantities are usually noisy and do not include collision/source physics. 
These quantities are directly linked to marker particles.
Total-f (``_df_1d``) quantities are actual plasma quantities for total-f simulations.
For reduced delta-f simulations, ``_df_1d`` will give perturbed quantities, but not always - some of the variables are not adequate for reduced delta-f simulation.


.. centered:: **xgc.oneddiag.bp** |br| :smallbluegray:`Printed when: diag_1d_on=.true..` |nbsp| |nbsp| |nbsp| :smallbluegray:`Output frequency: diag_1d_period.`

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   * - *Output*
     - Dimension
     - Units
     - Description
   * - *cden00_1d*
     - # |nbsp| outputs :math:`\times` ``sml_00_npsi``
     - :math:`{\mathrm{m}}^{-3}`
     - charge density in psi00 (iden00_1d - eden00_1d)
   * - | *e_gc_density_1d*
       | *i_gc_density_1d*
       | *e_gc_density_df_1d*
       | *i_gc_density_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{m}}^{-3}`
     - Electron/Ion density of gyro-center. Note that the gyro-center density is close to the actual plasma density for electrons, but polarization density could be significantly large for ions and the gyro-center density plus the polarization density is the actual ion density. 
   * - | *e_gc_poloidal_flow_1d*
       | *i_gc_poloidal_flow_1d*
       | *e_gc_poloidal_flow_df_1d*
       | *i_gc_poloidal_flow_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{m/s}}`
     - Flux averaged poloidal flow of gyro-center. This differs from the poloidal flow by the diamagnetic flow. 
   * - | *e_gc_toroidal_flow_1d*
       | *i_gc_toroidal_flow_1d*
       | *e_gc_toroidal_flow_df_1d*
       | *i_gc_toroidal_flow_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{m/s}}`
     - Flux averaged toroidal flow of gyro-center. This differs from the toroidal flow by the diamagnetic flow. 
   * - | *e_grad_psi_sqr_1d*
       | *i_grad_psi_sqr_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{T^2/m^2}}`
     - Particle average of :math:`{\mathrm{|\nabla \psi|^2}}` for each flux surfaces. Roughly flux average of :math:`{\mathrm{|\nabla \psi|^2}}` This is usually used for converting :math:`{\mathrm{{\partial \psi}}` to :math:`{\mathrm{\partial r}}`
   * - | *e_grad_psi_sqr_df_1d*
       | *i_grad_psi_sqr_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - Units
     - Do not use these variables. Use '_1d' to get Flux average of :math:`{\mathrm{|\nabla \psi|^2}}`
   * - | *e_parallel_flow_1d*
       | *i_parallel_flow_1d*
       | *e_parallel_flow_df_1d*
       | *i_parallel_flow_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{m/s}}`
     - Parallel flow velocities
   * - | *e_parallel_mean_en_1d*
       | *i_parallel_mean_en_1d*
       | *e_parallel_mean_en_df_1d*
       | *i_parallel_mean_en_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{eV}}`
     - Parallel kinetic energy in eV. :math:`<0.5 m v^2>` For parallel temperature, mean flow energy should be subtracted.
   * - | *e_perp_temperature_1d*
       | *i_perp_temperature_1d*
       | *e_perp_temperature_df_1d*
       | *i_perp_temperature_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`\mathrm{eV}`
     - Perpendicular temperature :math:`<\mu B>`
   * - | *e_poloidal_ExB_flow_1d*
       | *i_poloidal_ExB_flow_1d*
       | *e_poloidal_ExB_flow_df_1d*
       | *i_poloidal_ExB_flow_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{m/s}}`
     - Particle average of poloidal flow by :math:`E \times B` drift.
   * - | *e_radial_en_flux_1d*
       | *i_radial_en_flux_1d*
       | *e_radial_en_flux_df_1d*
       | *i_radial_en_flux_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{JTm^2s^{-1}}}` 
     - Particle averaged radial energy flux in :math:`\psi` space. :math:`<E V \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (J m/s)'
   * - | *e_radial_en_flux_3db_1d*
       | *i_radial_en_flux_3db_1d*
       | *e_radial_en_flux_3db_df_1d*
       | *i_radial_en_flux_3db_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{JTm^2s^{-1}}}` 
     - Particle averaged radial energy flux by :math:`\delta B` in :math:`\psi` space. :math:`<E V_{\delta B} \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (J m/s)'
   * - | *e_radial_en_flux_ExB_1d*
       | *i_radial_en_flux_ExB_1d*
       | *e_radial_en_flux_ExB_df_1d*
       | *i_radial_en_flux_ExB_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{JTm^2s^{-1}}}` 
     - Particle averaged radial energy flux by :math:`E \times B` in :math:`\psi` space. :math:`<E V_{E \times B} \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (J m/s)'
   * - | *e_radial_flux_1d*
       | *i_radial_flux_1d*
       | *e_radial_flux_df_1d*
       | *i_radial_flux_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{Tm^2 s^{-1}}}` 
     - Particle averaged radial drift in :math:`\psi` space. :math:`<V \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (m/s)'
   * - | *e_radial_flux_3db_1d*
       | *i_radial_flux_3db_1d*
       | *e_radial_flux_3db_df_1d*
       | *i_radial_flux_3db_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{Tm^2 s^{-1}}}` 
     - Particle averaged radial drift by :math:`\delta B` in :math:`\psi` space. :math:`<V_{\delta B} \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (m/s)'
   * - | *e_radial_flux_ExB_1d*
       | *i_radial_flux_ExB_1d*
       | *e_radial_flux_ExB_df_1d*
       | *i_radial_flux_ExB_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{Tm^2 s^{-1}}}` 
     - Particle averaged radial drift by :math:`E \times B` in :math:`\psi` space. :math:`<V_{E \times B} \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (m/s)'
   * - | *e_radial_mom_flux_1d*
       | *i_radial_mom_flux_1d*
       | *e_radial_mom_flux_df_1d*
       | *i_radial_mom_flux_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{T m^3 s^{-2}}}` 
     - Particle averaged toroidal momentum flux in :math:`\psi` space. :math:`<V_{tor} V \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (m/s)'
   * - | *e_radial_mom_flux_ExB_1d*
       | *i_radial_mom_flux_ExB_1d*
       | *e_radial_mom_flux_ExB_df_1d*
       | *i_radial_mom_flux_ExB_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{T m^3 s^{-2}}}` 
     - Particle averaged toroidal momentum flux by :math:`E \times B` in :math:`\psi` space. :math:`<V_{tor} V_{E \times B} \cdot \nabla \psi>` Averaged :math:`\nabla \psi` is required to get radial flux in real space (m/s)'
   * - | *e_tor_angular_momentum_1d*
       | *i_tor_angular_momentum_1d*
       | *e_tor_angular_momentum_df_1d*
       | *i_tor_angular_momentum_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`\mathrm{m^2 s^{-1}}`
     - Toroidal angular momentum (without mass) < V_{tor} R >
   * - | *e_vpar_x_B_1d*
       | *i_vpar_x_B_1d*
       | *e_vpar_x_B_df_1d*
       | *i_vpar_x_B_df_1d*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`{\mathrm{T m s^{-1}}}` 
     - For bootstrap current :math:`<V_{||} B>`
   * - | *eden00_1d*
       | *iden00_1d*
     - # |nbsp| outputs :math:`\times` ``sml_00_npsi``
     - :math:`{\mathrm{m}}^{-3}`
     - perturbed density of electron/ion. Even though the suffixes are '_1d', these are total-f quantities for total-f simulations.
   * - *gsamples*
     - # |nbsp| outputs
     - N.A.
     - Radial array size of '00' variables
   * - *pot00_1d*
     - # |nbsp| outputs :math:`\times` ``sml_00_npsi``
     - V
     - Flux averaged electrostatic potential
   * - *psi*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - Normalized
     - Normalized poloidal magnetic flux at each output on each flux surface.
   * - *psi00*
     - # |nbsp| outputs :math:`\times` ``sml_00_npsi``
     - :math:`\mathrm{T m^2}`
     - Unnormalized poloidal magnetic flux at each output on each flux surface.
   * - *psi_mks*
     - | # |nbsp| outputs :math:`\times`
       | # |nbsp| flux |nbsp| surfaces
     - :math:`\mathrm{T m^2}`
     - Unnormalized poloidal magnetic flux at each output on each flux surface.
   * - *samples*
     - # |nbsp| outputs
     - N.A.
     - | # |nbsp| flux |nbsp| surfaces
   * - *step*
     - # |nbsp| outputs
     - Positive integer
     - (1, 2, ..., # |nbsp| outputs) :math:`\times` ``diag_1d_period``, i.e. the simulation time steps when the diagnostics are printed.
   * - *time*
     - # |nbsp| outputs
     - :math:`\mathrm{s}`
     - Simulation time at each output in seconds.
   * - *tindex*
     - # |nbsp| outputs
     - Positive integer
     - 1, 2, ..., # |nbsp| outputs

Usage example
~~~~~~~~~~~~~

.. image:: ./img/example_xgc_plot_2D_profile_time_evolution_trans.png
   :target: ./_images/example_xgc_plot_2D_profile_time_evolution_trans.png
   :alt: alt_text
	 
Time evolution of the radial profiles of flux-surface averaged density, temperature, and radial particle and energy fluxes.

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