MHD Hyperbolic Divergence Cleaning #1086
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| #!/usr/bin/env python3 | ||
| import json | ||
| import math | ||
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| # Configuring case dictionary | ||
| print( | ||
| json.dumps( | ||
| { | ||
| # Logistics | ||
| "run_time_info": "T", | ||
| # Computational Domain Parameters | ||
| "x_domain%beg": 0.0, | ||
| "x_domain%end": 1.0, | ||
| "y_domain%beg": 0.0, | ||
| "y_domain%end": 1.0, | ||
| "m": 399, | ||
| "n": 399, | ||
| "p": 0, | ||
| "dt": 0.0004, | ||
| "t_step_start": 0, | ||
| "t_step_stop": 375, | ||
| "t_step_save": 5, | ||
| # Simulation Algorithm Parameters | ||
| "num_patches": 1, | ||
| "model_eqns": 2, | ||
| "alt_soundspeed": "F", | ||
| "num_fluids": 1, | ||
| "mpp_lim": "F", | ||
| "mixture_err": "F", | ||
| "time_stepper": 3, | ||
| "weno_order": 5, | ||
| "mapped_weno": "T", | ||
| "weno_eps": 1.0e-6, | ||
| "null_weights": "F", | ||
| "mp_weno": "F", | ||
| "riemann_solver": 1, | ||
| "wave_speeds": 1, | ||
| "avg_state": 2, | ||
| "bc_x%beg": -1, | ||
| "bc_x%end": -1, | ||
| "bc_y%beg": -1, | ||
| "bc_y%end": -1, | ||
| # Formatted Database Files Structure Parameters | ||
| "format": 1, | ||
| "precision": 2, | ||
| "prim_vars_wrt": "T", | ||
| "rho_wrt": "T", | ||
| "parallel_io": "T", | ||
| # MHD | ||
| "mhd": "T", | ||
| "hyper_cleaning": "T", | ||
| "hyper_cleaning_speed": 2.5, | ||
| "hyper_cleaning_tau": 0.004, | ||
| # Patch 1 - 2D MHD Rotor Problem | ||
| # gamma = 1.4 | ||
| # Ambient medium (r > 0.1): | ||
| # rho = 1 | ||
| # p = 1 | ||
| # v = (0, 0, 0) | ||
| # B = (1, 0, 0) | ||
| # Rotor (r <= 0.1): | ||
| # rho = 10 | ||
| # v has angular velocity of 20 | ||
| "patch_icpp(1)%hcid": 252, | ||
| "patch_icpp(1)%geometry": 3, | ||
| "patch_icpp(1)%x_centroid": 0.5, | ||
| "patch_icpp(1)%y_centroid": 0.5, | ||
| "patch_icpp(1)%length_x": 1.0, | ||
| "patch_icpp(1)%length_y": 1.0, | ||
| "patch_icpp(1)%vel(1)": 0.0, | ||
| "patch_icpp(1)%vel(2)": 0.0, | ||
| "patch_icpp(1)%vel(3)": 0.0, | ||
| "patch_icpp(1)%pres": 1.0, | ||
| "patch_icpp(1)%Bx": 5.0 / math.sqrt(math.pi * 4.0), | ||
| "patch_icpp(1)%By": 0.0, | ||
| "patch_icpp(1)%Bz": 0.0, | ||
| "patch_icpp(1)%alpha_rho(1)": 1.0, | ||
| "patch_icpp(1)%alpha(1)": 1.0, | ||
| # Fluids Physical Parameters | ||
| "fluid_pp(1)%gamma": 1.0e00 / (1.4e00 - 1.0e00), | ||
| "fluid_pp(1)%pi_inf": 0.0, | ||
| } | ||
| ) | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -882,6 +882,7 @@ contains | |
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| if (cont_damage) qK_prim_vf(damage_idx)%sf(j, k, l) = qK_cons_vf(damage_idx)%sf(j, k, l) | ||
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| if (hyper_cleaning) qK_prim_vf(psi_idx)%sf(j, k, l) = qK_cons_vf(psi_idx)%sf(j, k, l) | ||
| #ifdef MFC_POST_PROCESS | ||
| if (bubbles_lagrange) qK_prim_vf(beta_idx)%sf(j, k, l) = qK_cons_vf(beta_idx)%sf(j, k, l) | ||
| #endif | ||
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@@ -1152,6 +1153,8 @@ contains | |
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| if (cont_damage) q_cons_vf(damage_idx)%sf(j, k, l) = q_prim_vf(damage_idx)%sf(j, k, l) | ||
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| if (hyper_cleaning) q_cons_vf(psi_idx)%sf(j, k, l) = q_prim_vf(psi_idx)%sf(j, k, l) | ||
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| end do | ||
| end do | ||
| end do | ||
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
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@@ -363,6 +363,9 @@ contains | |||||
| ! Damage state variable | ||||||
| if (cont_damage) dbvars = dbvars + 1 | ||||||
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| ! Hyperbolic cleaning for MHD | ||||||
| if (hyper_cleaning) dbvars = dbvars + 1 | ||||||
|
Contributor
There was a problem hiding this comment. Suggestion: The hyperbolic cleaning scalar is counted as an output variable whenever Severity Level: Major
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| if (hyper_cleaning) dbvars = dbvars + 1 | |
| if (mhd .and. hyper_cleaning) dbvars = dbvars + 1 |
Steps of Reproduction ✅
1. Configure a run that requests Binary formatted post-processing output (format == 2) and
enable hyperbolic cleaning while MHD is disabled. The dbvars counter is computed inside
s_initialize_data_output_module in src/post_process/m_data_output.fpp; the hyper_cleaning
increment is at the lines shown above (lines 366-367).
2. Start the application so that s_initialize_data_output_module runs and sets dbvars (the
code path that computes dbvars includes the two lines at 366-367). Because hyper_cleaning
is true, dbvars is incremented unconditionally at 367 even though mhd is false.
3. The code path that writes the Binary file header in s_open_formatted_database_file
(src/post_process/m_data_output.fpp) writes the declared number of variables into the file
header: write (dbfile) m, n, p, dbvars. This write uses the dbvars value computed above.
4. Later the routines that actually write per-variable binary blocks
(s_write_variable_to_formatted_database_file and related code in the same file) skip
MHD-related variables when mhd is false, so fewer variable blocks are emitted than the
header advertised. The result is a mismatch between header (contains extra hyper_cleaning
variable) and actual data blocks; binary readers or downstream post-processing will
mis-interpret file layout, causing corrupted reads or failures.Prompt for AI Agent 🤖
This is a comment left during a code review.
**Path:** src/post_process/m_data_output.fpp
**Line:** 367:367
**Comment:**
*Logic Error: The hyperbolic cleaning scalar is counted as an output variable whenever `hyper_cleaning` is true, even if MHD is disabled; this can make the declared number of binary output variables (`dbvars`) larger than the number actually written, corrupting the binary file layout for non‑MHD runs where `hyper_cleaning` might be (mis)enabled.
Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
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@@ -117,6 +117,7 @@ module m_global_parameters | |||||
| integer :: b_size !< Number of components in the b tensor | ||||||
| integer :: tensor_size !< Number of components in the nonsymmetric tensor | ||||||
| logical :: cont_damage !< Continuum damage modeling | ||||||
| logical :: hyper_cleaning !< Hyperbolic cleaning for MHD | ||||||
| logical :: igr !< enable IGR | ||||||
| integer :: igr_order !< IGR reconstruction order | ||||||
| logical, parameter :: chemistry = .${chemistry}$. !< Chemistry modeling | ||||||
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@@ -143,6 +144,7 @@ module m_global_parameters | |||||
| integer :: c_idx !< Index of color function | ||||||
| type(int_bounds_info) :: species_idx !< Indexes of first & last concentration eqns. | ||||||
| integer :: damage_idx !< Index of damage state variable (D) for continuum damage model | ||||||
| integer :: psi_idx !< Index of hyperbolic cleaning state variable for MHD | ||||||
| !> @} | ||||||
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| ! Cell Indices for the (local) interior points (O-m, O-n, 0-p). | ||||||
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@@ -407,6 +409,7 @@ contains | |||||
| b_size = dflt_int | ||||||
| tensor_size = dflt_int | ||||||
| cont_damage = .false. | ||||||
| hyper_cleaning = .false. | ||||||
| igr = .false. | ||||||
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| bc_x%beg = dflt_int; bc_x%end = dflt_int | ||||||
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@@ -812,6 +815,13 @@ contains | |||||
| damage_idx = dflt_int | ||||||
| end if | ||||||
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| if (hyper_cleaning) then | ||||||
|
Contributor
There was a problem hiding this comment. Suggestion: The hyperbolic cleaning variable is appended to the system state vector whenever Severity Level: Major
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| if (hyper_cleaning) then | |
| if (hyper_cleaning .and. mhd .and. n > 0) then |
Steps of Reproduction ✅
1. Configure a run where model_eqns selects the branch that executes the state-vector
annotation code in impure subroutine s_initialize_global_parameters_module (the large
routine that sets up cont_idx, mom_idx, B_idx, etc.). The psi_idx insertion block is at
lines 818..823 in that routine and will be executed when control reaches the sys_size
annotation logic inside the model_eqns handling.
2. Enable hyper_cleaning in the case input (so the module variable hyper_cleaning becomes
true by the time s_initialize_global_parameters_module runs). The module does not enforce
that hyper_cleaning implies mhd or multidimensional geometry anywhere in this file
(hyper_cleaning is an independent logical declared at line ~120).
3. With hyper_cleaning = .true. and mhd = .false. (or with a 1D run where n == 0), the
existing code at lines 818..823 will append psi_idx to sys_size even though the MHD state
(B_idx) or multidimensionality may not be present — changing the global sys_size and
therefore the expected state-vector layout.
4. The mismatch becomes observable when downstream code that assembles or solves the
system (or any IO/serialization expecting a specific ordering) assumes no psi state unless
MHD/multidimensionality is active. In practice this misconfiguration is realistic (user
sets hyper_cleaning without toggling mhd), so the current guardless insertion can produce
incorrect indexing. Guarding the insertion with ".and. mhd .and. n > 0" prevents adding
the psi field when MHD or multidimensional geometry is not active.Prompt for AI Agent 🤖
This is a comment left during a code review.
**Path:** src/post_process/m_global_parameters.fpp
**Line:** 818:818
**Comment:**
*Logic Error: The hyperbolic cleaning variable is appended to the system state vector whenever `hyper_cleaning` is true, regardless of whether MHD is enabled or the problem is multidimensional, which can create a state layout that does not match the assumptions of the MHD hyperbolic cleaning solver (implemented only for 2D/3D MHD), leading to inconsistent indexing and potential downstream runtime errors.
Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -105,7 +105,7 @@ contains | |
| & 'adv_n', 'ib', 'cfl_adap_dt', 'cfl_const_dt', 'cfl_dt', & | ||
| & 'surface_tension', 'hyperelasticity', 'bubbles_lagrange', & | ||
| & 'output_partial_domain', 'relativity', 'cont_damage', 'bc_io', & | ||
| & 'down_sample','fft_wrt', 'hyper_cleaning' ] | ||
| call MPI_BCAST(${VAR}$, 1, MPI_LOGICAL, 0, MPI_COMM_WORLD, ierr) | ||
| #:endfor | ||
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High-level Suggestion
Refactor the new hardcoded initial conditions in Fortran files like
2dHardcodedIC.fppinto configurable input files for the test cases. This improves modularity and separates test configuration from core logic. [High-level, importance: 6]Solution Walkthrough:
Before:
After: