Periodic Immersed Boundary Wrapping for Circular and Spherical Geometries #1117
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,141 @@ | ||
| import json | ||
| import math | ||
| import numpy as np | ||
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| gam_a = 1.4 | ||
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| # sphere diameter | ||
| D = 0.1 | ||
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| # circle density | ||
| rho_c = 200 | ||
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| # domain length | ||
| L = 10 * D | ||
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| # mach number | ||
| M = 1.2 | ||
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| # reynolds number | ||
| Re = 400.0 | ||
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| # pressure | ||
| P = 101325 | ||
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| # density | ||
| rho = 1.0 | ||
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| # fluid velocity | ||
| v1 = M * np.sqrt(gam_a * P / rho) | ||
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| # dynamic viscosity | ||
| mu = rho * v1 * D / Re | ||
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| dt = 1.0e-06 | ||
| Nt = 5000 | ||
| t_save = 20 | ||
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| # to fully resolve requires 40-60 cells across circle diameter | ||
| Nx = 511 | ||
| Ny = Nx | ||
| Nz = 0 | ||
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| # immersed boundary dictionary | ||
| ib_dict = {} | ||
| ib_dict.update( | ||
| { | ||
| f"patch_ib({1})%geometry": 2, | ||
| f"patch_ib({1})%x_centroid": 0.5 * L, | ||
| f"patch_ib({1})%y_centroid": 0.5 * L, | ||
| f"patch_ib({1})%radius": D / 2, | ||
| f"patch_ib({1})%slip": "F", | ||
| f"patch_ib({1})%moving_ibm": 0, | ||
| f"patch_ib({1})%mass": rho_c * np.pi * (D / 2.0) ** 2, | ||
| } | ||
| ) | ||
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| # Configuring case dictionary | ||
| case_dict = { | ||
| # Logistics | ||
| "run_time_info": "T", | ||
| # Computational Domain Parameters | ||
| # x direction | ||
| "x_domain%beg": -5.0 * D, | ||
| "x_domain%end": 5.0 * D, | ||
| # y direction | ||
| "y_domain%beg": -5.0 * D, | ||
| "y_domain%end": 5.0 * D, | ||
| "cyl_coord": "F", | ||
| "m": Nx, | ||
| "n": Ny, | ||
| "p": Nz, | ||
| "dt": dt, | ||
| "t_step_start": 0, | ||
| "t_step_stop": Nt, | ||
| "t_step_save": t_save, | ||
| # Simulation Algorithm Parameters | ||
| # Only one patch is necessary for one fluid | ||
| "num_patches": 1, | ||
| # Use the 5 equation model | ||
| "model_eqns": 2, | ||
| # 6 equations model does not need the K \div(u) term | ||
| "alt_soundspeed": "F", | ||
| # One fluids: air | ||
| "num_fluids": 1, | ||
| # time step | ||
| "mpp_lim": "F", | ||
| # Correct errors when computing speed of sound | ||
| "mixture_err": "T", | ||
| # Use TVD RK3 for time marching | ||
| "time_stepper": 3, | ||
| # Reconstruct the primitive variables to minimize spurious | ||
| # Use WENO5 | ||
| "weno_order": 5, | ||
| "weno_eps": 1.0e-14, | ||
| "weno_Re_flux": "T", | ||
| "weno_avg": "T", | ||
| "avg_state": 2, | ||
| "mapped_weno": "T", | ||
| "null_weights": "F", | ||
| "mp_weno": "T", | ||
| "riemann_solver": 2, | ||
| "wave_speeds": 1, | ||
| # periodic bc | ||
| "bc_x%beg": -1, | ||
| "bc_x%end": -1, | ||
| "bc_y%beg": -1, | ||
| "bc_y%end": -1, | ||
| # Set IB to True and add 1 patch for every sphere | ||
| "ib": "T", | ||
| "num_ibs": 1, | ||
| "viscous": "T", | ||
| # Formatted Database Files Structure Parameters | ||
| "format": 1, | ||
| "precision": 2, | ||
| "prim_vars_wrt": "T", | ||
| "E_wrt": "T", | ||
| "parallel_io": "T", | ||
| # Patch: square filled with air | ||
| "patch_icpp(1)%geometry": 3, | ||
| # Uniform properties, centroid is at the center of the domain | ||
| "patch_icpp(1)%x_centroid": 0.0, | ||
| "patch_icpp(1)%y_centroid": 0.0, | ||
| "patch_icpp(1)%length_x": 10 * D, | ||
| "patch_icpp(1)%length_y": 10 * D, | ||
| # Specify the patch primitive variables | ||
| "patch_icpp(1)%vel(1)": v1, | ||
| "patch_icpp(1)%vel(2)": 0.0, | ||
| "patch_icpp(1)%pres": P, | ||
| "patch_icpp(1)%alpha_rho(1)": rho, | ||
| "patch_icpp(1)%alpha(1)": 1.0e00, | ||
| # Fluids Physical Parameters | ||
| "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00), # 2.50(Not 1.40) | ||
| "fluid_pp(1)%pi_inf": 0, | ||
| "fluid_pp(1)%Re(1)": 1.0 / mu, | ||
| # ibs wrap around domain | ||
| "periodic_ibs": "T", | ||
| } | ||
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| case_dict.update(ib_dict) | ||
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| print(json.dumps(case_dict)) | ||
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,150 @@ | ||||||
| import json | ||||||
| import math | ||||||
| import numpy as np | ||||||
|
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| gam_a = 1.4 | ||||||
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| # sphere diameter | ||||||
| D = 0.1 | ||||||
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| # sphere density | ||||||
| rho_s = 200 | ||||||
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| # domain length | ||||||
| L = 10 * D | ||||||
|
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| # mach number | ||||||
| M = 1.2 | ||||||
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| # reynolds number | ||||||
| Re = 400.0 | ||||||
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| # pressure | ||||||
| P = 101325 | ||||||
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| # density | ||||||
| rho = 1.0 | ||||||
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| # fluid velocity | ||||||
| v1 = M * np.sqrt(gam_a * P / rho) | ||||||
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| # dynamic viscosity | ||||||
| mu = rho * v1 * D / Re | ||||||
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| dt = 2.0e-06 | ||||||
| Nt = 2000 | ||||||
| t_save = Nt // 250 | ||||||
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| # to fully resolve requires 40-60 cells across sphere diameter | ||||||
| Nx = 127 | ||||||
| Ny = Nx | ||||||
| Nz = Ny | ||||||
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| # immersed boundary dictionary | ||||||
| ib_dict = {} | ||||||
| ib_dict.update( | ||||||
| { | ||||||
| f"patch_ib({1})%geometry": 8, | ||||||
| f"patch_ib({1})%x_centroid": 0.5 * L, | ||||||
| f"patch_ib({1})%y_centroid": 0.5 * L, | ||||||
| f"patch_ib({1})%z_centroid": 0.5 * L, | ||||||
| f"patch_ib({1})%radius": D / 2, | ||||||
| f"patch_ib({1})%slip": "F", | ||||||
| f"patch_ib({1})%moving_ibm": 0, | ||||||
| f"patch_ib({1})%mass": rho_s * 4.0 / 3.0 * np.pi * (D / 2.0) ** 3, | ||||||
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|
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| } | ||||||
| ) | ||||||
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| # Configuring case dictionary | ||||||
| case_dict = { | ||||||
| # Logistics | ||||||
| "run_time_info": "T", | ||||||
| # Computational Domain Parameters | ||||||
| # x direction | ||||||
| "x_domain%beg": -5.0 * D, | ||||||
| "x_domain%end": 5.0 * D, | ||||||
| # y direction | ||||||
| "y_domain%beg": -5.0 * D, | ||||||
| "y_domain%end": 5.0 * D, | ||||||
| # z direction | ||||||
| "z_domain%beg": -5.0 * D, | ||||||
| "z_domain%end": 5.0 * D, | ||||||
| "cyl_coord": "F", | ||||||
| "m": Nx, | ||||||
| "n": Ny, | ||||||
| "p": Nz, | ||||||
| "dt": dt, | ||||||
| "t_step_start": 0, | ||||||
| "t_step_stop": Nt, | ||||||
| "t_step_save": t_save, | ||||||
| # Simulation Algorithm Parameters | ||||||
| # Only one patch is necessary for one fluid | ||||||
| "num_patches": 1, | ||||||
| # Use the 5 equation model | ||||||
| "model_eqns": 2, | ||||||
| # 6 equations model does not need the K \div(u) term | ||||||
| "alt_soundspeed": "F", | ||||||
| # One fluids: air | ||||||
| "num_fluids": 1, | ||||||
| # time step | ||||||
| "mpp_lim": "F", | ||||||
| # Correct errors when computing speed of sound | ||||||
| "mixture_err": "T", | ||||||
| # Use TVD RK3 for time marching | ||||||
| "time_stepper": 3, | ||||||
| # Reconstruct the primitive variables to minimize spurious | ||||||
| # Use WENO5 | ||||||
| "weno_order": 5, | ||||||
| "weno_eps": 1.0e-14, | ||||||
| "weno_Re_flux": "T", | ||||||
| "weno_avg": "T", | ||||||
| "avg_state": 2, | ||||||
| "mapped_weno": "T", | ||||||
| "null_weights": "F", | ||||||
| "mp_weno": "T", | ||||||
| "riemann_solver": 2, | ||||||
| "wave_speeds": 1, | ||||||
| # periodic bc | ||||||
| "bc_x%beg": -1, | ||||||
| "bc_x%end": -1, | ||||||
| "bc_y%beg": -1, | ||||||
| "bc_y%end": -1, | ||||||
| "bc_z%beg": -1, | ||||||
| "bc_z%end": -1, | ||||||
| # Set IB to True and add 1 patch for every sphere | ||||||
| "ib": "T", | ||||||
| "num_ibs": 1, | ||||||
| "viscous": "T", | ||||||
| # Formatted Database Files Structure Parameters | ||||||
| "format": 1, | ||||||
| "precision": 2, | ||||||
| "prim_vars_wrt": "T", | ||||||
| "E_wrt": "T", | ||||||
| "parallel_io": "T", | ||||||
| # Patch: cube filled with air | ||||||
| "patch_icpp(1)%geometry": 9, | ||||||
| # Uniform properties, centroid is at the center of the domain | ||||||
| "patch_icpp(1)%x_centroid": 0.0, | ||||||
| "patch_icpp(1)%y_centroid": 0.0, | ||||||
| "patch_icpp(1)%z_centroid": 0.0, | ||||||
| "patch_icpp(1)%length_x": 10 * D, | ||||||
| "patch_icpp(1)%length_y": 10 * D, | ||||||
| "patch_icpp(1)%length_z": 10 * D, | ||||||
| # Specify the patch primitive variables | ||||||
| "patch_icpp(1)%vel(1)": v1, | ||||||
|
Contributor
There was a problem hiding this comment. Suggestion: The value assigned to the velocity entry is a NumPy scalar ( Severity Level: Major
|
||||||
| "patch_icpp(1)%vel(1)": v1, | |
| "patch_icpp(1)%vel(1)": float(v1), |
Steps of Reproduction ✅
1. Run the example script directly: execute `python
examples/3D_ibm_sphere_periodic/case.py`. The module's top-level code runs and builds
`case_dict` (file `examples/3D_ibm_sphere_periodic/case.py` lines 1-150).
2. During module execution the velocity is computed at
`examples/3D_ibm_sphere_periodic/case.py:29` where `v1 = M * np.sqrt(gam_a * P / rho)`
(NumPy returns a numpy scalar).
3. That numpy scalar `v1` is inserted into `case_dict` under the key
`"patch_icpp(1)%vel(1)"` at `examples/3D_ibm_sphere_periodic/case.py:134`.
4. The final statement `print(json.dumps(case_dict))` at
`examples/3D_ibm_sphere_periodic/case.py:150` calls `json.dumps`; JSON encoder encounters
the numpy scalar at the velocity key and raises TypeError (e.g., "Object of type float64
is not JSON serializable"), aborting the script.Prompt for AI Agent 🤖
This is a comment left during a code review.
**Path:** examples/3D_ibm_sphere_periodic/case.py
**Line:** 134:134
**Comment:**
*Type Error: The value assigned to the velocity entry is a NumPy scalar (`v1` is created via `np.sqrt`), which `json.dumps` cannot serialize and will raise a TypeError; casting it to a native Python float before inserting into the dictionary avoids this runtime failure.
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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