logan-nc · Oct 24, 2026 · Oct 19, 2026 · Oct 19, 2026 · Oct 19, 2026 · Oct 19, 2026
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -3,3 +3,11 @@
 .. _DIIID_ideal_example:
 
 .. include:: examples/DIIID_ideal_example/README
+
+.. _DIIID_kinetic_example:
+
+.. include:: examples/DIIID_kinetic_example/README
+
+.. _DIIID_resistive_example:
+
+.. include:: examples/DIIID_resistive_example/README
diff --git a/docs/examples/DIIID_ideal_example/README b/docs/examples/DIIID_ideal_example/README
@@ -3,7 +3,7 @@ GPEC DIII-D Ideal Example
 
 This example uses a baseline DIII-D-like H-mode. The equilibrium is an artificial one made with TokaMaker to have 0D parameters matching typical DIII-D H-mode values, and the kinetic profiles are self-consistent with the equilibrium.
 
-Note that the coil and pentrc input namelists use relative paths to the package's data files. If you would like to run the example in a different location, you must update those paths appropriately.
+Note that the coil input namelist uses a relative path to the package's data files. If you would like to run the example in a different location, you must update that path appropriately.
 
 Following a typical workflow we first ``cd`` to the example's directory, then run DCON::
 
@@ -39,4 +39,4 @@ Finally, we run PENTRC to compute the neoclassical toroidal viscosity (NTV) torq
   PENTRC START => ...
   PENTRC STOP => Normal termination.
 
-The full (``fgar``) and trapped-only (``tgar``) torque calculations agree reasonably well, consistent with the expectation that banana-orbit particles dominate the nonambipolar transport. The reduced large-aspect-ratio (``rlar``) result typically differs significantly from the general-aspect-ratio calculations for shaped, high-beta H-mode plasmas.
+The full (``fgar``) and trapped-only (``tgar``) torque calculations agree reasonably well, consistent with the expectation that banana-orbit particles dominate the nonambipolar transport. The reduced large-aspect-ratio (``rlar``) result (enabled with ``rlar_flag=t``; off in this example) typically differs significantly from the general-aspect-ratio calculations for shaped, high-beta H-mode plasmas.
diff --git a/docs/examples/DIIID_kinetic_example/README b/docs/examples/DIIID_kinetic_example/README
@@ -30,4 +30,4 @@ Finally, we run PENTRC for the full neoclassical torque calculation::
   PENTRC START => ...
   PENTRC STOP => Normal termination.
 
-The full general-aspect-ratio (``fgar``) and trapped-only (``tgar``) torque results can be compared to assess the trapped-particle dominance. The ``data_dir`` in ``pentrc.in`` points to the precomputed special function matrix used by the reduced large-aspect-ratio (``rlar``) method, which serves as a cross-check.
+The full general-aspect-ratio (``fgar``) and trapped-only (``tgar``) torque results can be compared to assess the trapped-particle dominance. The ``data_dir`` in ``pentrc.in`` points to the precomputed special function matrix used by the reduced large-aspect-ratio (``rlar``) method, which can be enabled with ``rlar_flag=t`` as a cross-check.
diff --git a/docs/index.rst b/docs/index.rst
@@ -67,3 +67,5 @@ The GPEC repository contains a number of examples intended to provide both consi
 Example console commands and output are given below.
 
 - :ref:`DIII-D Ideal Example <DIIID_ideal_example>`
+- :ref:`DIII-D Kinetic Example <DIIID_kinetic_example>`
+- :ref:`DIII-D Resistive Example <DIIID_resistive_example>`
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -50,7 +50,7 @@ Important make targets
 ----------------------
 
 * all (default): build all main executables and libraries
-* allf: same as all but Fortran-only modules
+* allf: currently builds the same modules as all
 * clean: remove built objects and module files
 * clear: remove example outputs in docs/examples
 * realclean: deep clean including dependencies built into deps
@@ -82,7 +82,7 @@ netCDF libraries:
 * NETCDF_FORTRAN_HOME: preferred when C and Fortran installs are split
 * NETCDFHOME or NETCDF_DIR: netCDF installation prefix
 * NETCDFINC: netCDF include path
-* NETCDF_C_HOME or NETCDF_C_DIR: netCDF-C location if separate
+* NETCDF_C_HOME: netCDF-C location if separate
 
 Dependency install location:
 
@@ -180,8 +180,8 @@ Then build with::
 X11 (xdraw)
 ^^^^^^^^^^^
 
-If xdraw fails to link on macOS, ensure XQuartz is installed and add include
-and library paths in xdraw/makefile, for example::
+If xdraw fails to link on macOS, ensure XQuartz is installed and set
+X11_HOME (read by install/DEFAULTS.inc), for example::
 
     brew install libx11
     export X11_HOME=/opt/homebrew

diff --git a/docs/namelists.rst b/docs/namelists.rst
@@ -1,5 +1,5 @@
 
-Fully annotated namelist input files can be found in the $GPECHOME/input directory and any of the examples in $GPECHOME/docs/examples directories of any `public installation <installation>`.
+Fully annotated namelist input files can be found in the $GPECHOME/input directory and any of the examples in $GPECHOME/docs/examples directories of any :ref:`public installation <installation>`.
 
 The major input files requiring user interaction are as follows.
 
@@ -40,7 +40,7 @@ This namelist controls the MATCH code, including which DCON eigenfunction (sol_n
 The PENTRC Namelist
 ====================
 
-This namelist sets the inputs, controls the behavior, and determines the outputs of the GPEC code.
+This namelist sets the inputs, controls the behavior, and determines the outputs of the PENTRC code.
 
 .. include:: ../input/pentrc.in
    :literal:

diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -125,46 +125,46 @@ The binary GPEC outputs can be viewed using the commandxdraw filenamewhere filen
 Output Files
 ============
 
-The GPEC outputs are entirely specified by flags (bool types t or f) set in the GPEC_output section of GPEC.in. All outputs are ASCII files, and can be grouped into two major categories.
+The GPEC outputs are entirely specified by flags (bool types t or f) set in the gpec_output section of gpec.in. Outputs are written as ASCII tables (ascii_flag), xdraw binary files (bin_flag, bin_2d_flag) and netcdf files (netcdf_flag), and can be grouped into the categories below.
 
 ASCII File Outputs
 ------------------
 
-A number of the flag options in GPEC.in instruct GPEC to output ASCII file data. Some of these outputs are always available. Some, however, require a input error field instead of a hard coded harmonic_flag call. Both groups are listed in detail here.
+A number of the flag options in gpec.in instruct GPEC to output ASCII file data. Some of these outputs are always available. Some, however, require an external 3D field input (data_flag, coil_flag, harmonic_flag) or a single eigenmode (mode_flag). Both groups are listed in detail here.
 
 Outputs Always Available
 
-These GPEC outputs can always be obtained from a equil.bin file output from DCON.
+These GPEC outputs can always be obtained from a euler.bin file output from DCON.
 
-GPEC_response_n#.out
+gpec_response_n#.out
 
     **Flag** resp_flag
 
     **Info** Energy for DCON eigenmodes and stability indices. Eigenvalues and eigenvectors for vacuum and plasma inductance (virtual casing currents to fields), plasma permeability (external fields to total fields), and plasma reluctance.
 
-GPEC_singcoup_matrix_n#.out
+gpec_singcoup_matrix_n#.out
 
     **Flag** singcoup_flag
 
     **Info** The coupling matrix to resonant fields, coupling matrix to singular currents, and to island half-widths is given for each rational surface within the plasma (q=2, 3, etc) for each surface the real and imaginary coupling constants are given for each poloidal mode number on the control surface.
 
-GPEC_singcoup_svd_n#.out
+gpec_singcoup_svd_n#.out
 
     **Flag** singcoup_flag
 
-    **Info** The SVD singular values (s) and eigen vectors for each coupling matrix in GPEC_singcoup_matrix_n#.out. Large s corresponds to large amplification, with the largest (most important mode) listed at the top. The results should be dotted with the unweighted normal field spectrum to give physical meaning.
+    **Info** The SVD singular values (s) and eigen vectors for each coupling matrix in gpec_singcoup_matrix_n#.out. Large s corresponds to large amplification, with the largest (most important mode) listed at the top. The results should be dotted with the unweighted normal field spectrum to give physical meaning.
 
 Outputs Available When Error Field is Provided
 
-These outputs are only available when an external error field file is provided as an input to GPEC. This means GPEC.in must have the data_flag turned on and a infile specified.
+These outputs are only available when an external 3D field is provided as an input to GPEC. This means gpec.in must have data_flag (with an infile specified), coil_flag, harmonic_flag, or mode_flag turned on.
 
-GPEC_control_n#.out
+gpec_control_n#.out
 
-    **Flag** 
+    **Flag** none (always written with ascii_flag)
 
     **Info** The Plasma response for an external perturbation on the control surface. This includes the vacuum energy, surface energy, plasma energy, real and imaginary vacuum input \mathbf{B}_{in} and total field on plasma boundary\mathbf{B}_{out}as a function of poloidal mode number.
 
-GPEC_singfld_n#.out
+gpec_singfld_n#.out
 
     **Flag** singfld_flag
 
@@ -174,21 +174,21 @@ GPEC_singfld_n#.out
 
     **Info** Additional section showing the overlap field (Tesla) and overlap percentage for each eigenmode in the singcoup_svd output. See :ref:`coupling_overlap` for definitions.
 
-GPEC_pmod_n#.out
+gpec_pmodb_n#.out
 
     **Flag** pmodb_flag
 
-    **Info** Eulerian and Lagrangian \left|\mathbf{B}\right|(real and imaginary) for each poloidal mode number at each value of \Psi_{N} output. This output is necessary for NTV post processing.
+    **Info** Perturbed field strength (real and imaginary, Tesla) for each poloidal mode number at each value of \Psi_{N} output: the Eulerian \delta B (eulb), the Lagrangian \delta B of the displacement with zero \xi^\zeta in the working (jac_type) coordinates (lagb), B\nabla\cdot\xi_\perp (Bdivxprp) and the force-balance form of B\kappa\cdot\xi_\perp (Bkxprp). lagb is not the \xi_\perp-only Lagrangian \delta B; that is -(Bdivxprp+Bkxprp) up to the equilibrium force-balance residual. See :doc:`pmodb_gauge` before using these columns for NTV post processing.
 
-GPEC_xbnormal_n#.out
+gpec_xbnormal_n#.out
 
     **Flag** xbnormal_flag
 
-    **Info** The normal components of the displacement, magnetic field without the plasma response, and magnetic field with the plasma response included for each poloidal mode number at each value of \Psi_{N} output.??
+    **Info** The normal displacement (xno), the normal perturbed magnetic field (bno), and the Jacobian-weighted contravariant psi component of the perturbed field J\mathbf{B}\cdot\nabla\psi (bwp) for each poloidal mode number at each value of \Psi_{N} output.
 
-GPEC_*rzphi_n#.out
+gpec_*rzphi_n#.out
 
-A number of output files have a similar structure. Here the * in the file name is replaced by the appropriate leading letters of the corresponding flag. For example the xrzphi_flag for n=1 creates a GPEC_xrzphi_n1.out file. some common properties of these files are:
+A number of output files have a similar structure. Here the * in the file name is replaced by the appropriate leading letters of the corresponding flag. For example the xrzphi_flag for n=1 creates a gpec_xrzphi_n1.out file. some common properties of these files are:
 
 • real and imaginary components: Output files contain two dimensional data on an \left(r,z\right) grid for a single toroidal harmonic. To translate into three dimensions, perform the transformationB\left(r,z,\phi\right)=B_{real}\left(r,z\right)\cos\left(n\phi\right)+B_{imag}\left(r,z\right)\sin\left(n\phi\right)
 
@@ -211,17 +211,17 @@ A number of output files have a similar structure. Here the * in the file name i
 
     **Info** The false perturbed magnetic field in the vacuum region on the \left(r,z,\phi\right) grid calculated using the GPEC boundary surface current composed of both the vacuum component and the plasma response.
 
-    **Flag** vpbrzphi_flag
+    **Flag** pbrzphi_flag (writes gpec_vpbrzphi_n#.out)
 
     **Info** The true perturbed magnetic field in the vacuum region on the \left(r,z,\phi\right) grid due to the plasma response alone calculated from the plasma response surface condition.
 
     **Flag** vvbrzphi_flag
 
     **Info** The false perturbed magnetic field in the vacuum region on the \left(r,z,\phi\right) grid calculated using the GPEC boundary surface current from the external fields alone.
 
-    **Flag** ssbrzphi_flag
+    **Flag** vsbrzphi_flag (with ss_flag(i) selecting surfaces; requires singfld_flag)
 
-    **Info** The false perturbed magnetic field in the vacuum region on the \left(r,z,\phi\right) grid calculated using the GPEC boundary surface current from the external fields alone.
+    **Info** The vacuum field on the \left(r,z,\phi\right) grid due to the currents on the selected resonant surfaces.
 
 Energy Decomposition Outputs
 ----------------------------
@@ -281,7 +281,7 @@ pflux_re(im)_2d.bin
 
 bnormal_spectrum.bin
 
-    **Flag** bin_flag
+    **Flag** bin_2d_flag
 
     **Info** Surfmn type contours of the normal perturbed magnetic fields as a function of poloidal harmonic number and \Psi_{N}.