format and docs

Author: wilfonba

docs/documentation/case.md

@@ -408,6 +408,13 @@ Details of implementation of viscosity in MFC can be found in [Coralic (2015)](r
 | `surface_tension`      | Logical | Activate surface tension |
 | `viscous`              | Logical | Activate viscosity |
 | `hypoelasticity`       | Logical | Activate hypoelasticity* |
+| `igr`                  | Logical | Enable solution via information geometric regularization (IGR) [Cao (2024)](references.md) |
+| `igr_order`            | Integer | Order of reconstruction for IGR [3,5] |
+| `alf_factor`           | Real    | Alpha factor for IGR entropic pressure (default 10) |
+| `igr_pres_lim`         | Logical | Limit IGR pressure to avoid negative values (default F) |
+| `igr_iter_solver`      | Integer | Solution method for IGR elliptic solve [1] Jacobi [2] Gauss-Seidel |
+| `num_igr_iters`        | Integer | Number of iterations for for the IGR elliptic solve (default 2) |
+| `num_igr_warm_start_iters` | Integer | Number of iterations for the IGR elliptic solve at the first time step (defualt 50) |
 
 - \* Options that work only with `model_eqns = 2`.
 - † Options that work only with ``cyl_coord = 'F'``.
@@ -501,7 +508,7 @@ This option requires `weno_Re_flux` to be true because cell boundary values are
 | `type`*                | Integer | The geometry of the patch. [1]: Line [2]: Circle [3]: Rectangle |
 | `x[y,z]_centroid`*     | Real    | Centroid of the boundary patch in the x[y,z]-direction          |
 | `length_x[y,z]`*       | Real    | Length of the boundary patch in the x[y,z]-direction            |
-| `radius`*              | Real    | Radius of the boundary patch                                    |
+| `radiue`*              | Real    | Radius of the boundary patch                                    |
 *: These parameters should be prepended with `patch_bc(j)%` where $j$ is the patch index.
 
 Boundary condition patches can be used with the following boundary condition types:

docs/documentation/references.md

@@ -10,6 +10,8 @@
 
 - <a id="Bryngelson19">Bryngelson, S. H., Schmidmayer, K., Coralic, V., Meng, J. C., Maeda, K., and Colonius, T. (2019). Mfc: An open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver. arXiv preprint arXiv:1907.10512.</a>
 
+- <a id="Cao24">Cao A. and. Sch&auml;fer F. (2024). Information Geometric Regularization of the Barotropic Euler Equations. arXiv preprint arXiv:2308.14127.</a>
+
 - <a id="Chen22">Chen, S. S., Li, J. P., Li, Z., Yuan, W., & Gao, Z. H. (2022). Anti-dissipation pressure correction under low Mach numbers for Godunov-type schemes. Journal of Computational Physics, 456, 111027. </a>
 
 - <a id="Childs12">Childs, H., Brugger, E., Whitlock, B., Meredith, J., Ahern, S., Pugmire, D., Biagas, K., Miller, M., Harrison, C., Weber, G. H., Krishnan, H., Fogal, T., Sanderson, A., Garth, C., Bethel, E. W., Camp, D., R¨ubel, O., Durant, M., Favre, J. M., and Navr´atil, P. (2012). VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data. In High Performance Visualization–Enabling Extreme-Scale Scientific Insight, pages 357–372.</a>
@@ -62,4 +64,4 @@
 
 - <a id="Powell94">Powell, K. G. (1994). An approximate Riemann solver for magnetohydrodynamics: (That works in more than one dimension). In Upwind and high-resolution schemes (pp. 570-583). Springer.</a>
 
-- <a id="Cao19">Cao, S., Zhang, Y., Liao, D., Zhong, P., and Wang, K. G. (2019). Shock-induced damage and dynamic fracture in cylindrical bodies submerged in liquid. International Journal of Solids and Structures, 169:55–71. Elsevier.</a>
+- <a id="Cao19">Cao, S., Zhang, Y., Liao, D., Zhong, P., and Wang, K. G. (2019). Shock-induced damage and dynamic fracture in cylindrical bodies submerged in liquid. International Journal of Solids and Structures, 169:55–71. Elsevier.</a>

src/post_process/m_start_up.f90

@@ -473,7 +473,7 @@ impure subroutine s_save_data(t_step, varname, pres, c, H)
                         end do
                     end do
                 else
-                    q_sf(:,:,:) = q_cons_vf(adv_idx%end)%sf(x_beg:x_end, y_beg:y_end, z_beg:z_end)
+                    q_sf(:, :, :) = q_cons_vf(adv_idx%end)%sf(x_beg:x_end, y_beg:y_end, z_beg:z_end)
                 end if
                 write (varname, '(A,I0)') 'alpha', num_fluids
                 call s_write_variable_to_formatted_database_file(varname, t_step)

src/pre_process/include/3dHardcodedIC.fpp

@@ -86,12 +86,11 @@
 
         q_prim_vf(E_idx)%sf(i, j, k) = p_th*f_cut_on(r - r_th, eps_smooth)*f_cut_on(x_cc(i), eps_smooth) + p_am
 
-
     case (370)
         ! This hardcoded case extrudes a 2D profile to initialize a 3D simulation domain
         @: HardcodedReadValues()
 
-    ! Put your variable assignments here
+        ! Put your variable assignments here
     case default
         call s_int_to_str(patch_id, iStr)
         call s_mpi_abort("Invalid hcid specified for patch "//trim(iStr))

src/simulation/m_igr.fpp

@@ -122,40 +122,40 @@ contains
 
         #:if not MFC_CASE_OPTIMIZATION
             if (igr_order == 3) then
-                    vidxb = -1; vidxe = 2; 
-                    !$acc update device(vidxb, vidxe)
+                vidxb = -1; vidxe = 2; 
+                !$acc update device(vidxb, vidxe)
 
-                    @:ALLOCATE(coeff_L(0:2))
-                    coeff_L(0) = (2._wp/6._wp)
-                    coeff_L(1) = (5._wp/6._wp)
-                    coeff_L(2) = (-1._wp/6._wp)
-                    !$acc update device(coeff_L)
+                @:ALLOCATE(coeff_L(0:2))
+                coeff_L(0) = (2._wp/6._wp)
+                coeff_L(1) = (5._wp/6._wp)
+                coeff_L(2) = (-1._wp/6._wp)
+                !$acc update device(coeff_L)
 
-                    @:ALLOCATE(coeff_R(-1:1))
-                    coeff_R(1) = (2._wp/6._wp)
-                    coeff_R(0) = (5._wp/6._wp)
-                    coeff_R(-1) = (-1._wp/6._wp)
-                    !$acc update device(coeff_R)
+                @:ALLOCATE(coeff_R(-1:1))
+                coeff_R(1) = (2._wp/6._wp)
+                coeff_R(0) = (5._wp/6._wp)
+                coeff_R(-1) = (-1._wp/6._wp)
+                !$acc update device(coeff_R)
 
             elseif (igr_order == 5) then
-                    vidxb = -2; vidxe = 3; 
-                    !$acc update device(vidxb, vidxe)
-
-                    @:ALLOCATE(coeff_L(-1:3))
-                    coeff_L(-1) = (-3._wp/60._wp)
-                    coeff_L(0) = (27._wp/60._wp)
-                    coeff_L(1) = (47._wp/60._wp)
-                    coeff_L(2) = (-13._wp/60._wp)
-                    coeff_L(3) = (2._wp/60._wp)
-                    !$acc update device(coeff_L)
-
-                    @:ALLOCATE(coeff_R(-2:2))
-                    coeff_R(2) = (-3._wp/60._wp)
-                    coeff_R(1) = (27._wp/60._wp)
-                    coeff_R(0) = (47._wp/60._wp)
-                    coeff_R(-1) = (-13._wp/60._wp)
-                    coeff_R(-2) = (2._wp/60._wp)
-                    !$acc update device(coeff_R)
+                vidxb = -2; vidxe = 3; 
+                !$acc update device(vidxb, vidxe)
+
+                @:ALLOCATE(coeff_L(-1:3))
+                coeff_L(-1) = (-3._wp/60._wp)
+                coeff_L(0) = (27._wp/60._wp)
+                coeff_L(1) = (47._wp/60._wp)
+                coeff_L(2) = (-13._wp/60._wp)
+                coeff_L(3) = (2._wp/60._wp)
+                !$acc update device(coeff_L)
+
+                @:ALLOCATE(coeff_R(-2:2))
+                coeff_R(2) = (-3._wp/60._wp)
+                coeff_R(1) = (27._wp/60._wp)
+                coeff_R(0) = (47._wp/60._wp)
+                coeff_R(-1) = (-13._wp/60._wp)
+                coeff_R(-2) = (2._wp/60._wp)
+                !$acc update device(coeff_R)
             end if
         #:endif