Volume filtered Euler-Lagrange framework for particle-laden flow explicit unclosed term computation #1043
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| import json | ||
| import math | ||
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| eps = 1e-6 | ||
| time_end = 1.0 | ||
| time_save = time_end / 100.0 | ||
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| import json | ||
| import math | ||
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| mu = 1.0e-4 | ||
| lambd = 1.0 | ||
| time_end = 15.0 | ||
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| import json | ||
| import math | ||
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| mu = 1.0e-3 | ||
| time_end = 1.0 | ||
| time_save = time_end / 100.0 | ||
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| 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 | ||||||||||||||||||||||||
| # domain length | ||||||||||||||||||||||||
| L = 10 * D | ||||||||||||||||||||||||
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| # mach number | ||||||||||||||||||||||||
| M = 0.8 | ||||||||||||||||||||||||
| # reynolds number | ||||||||||||||||||||||||
| Re = 1000.0 | ||||||||||||||||||||||||
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| # pressure | ||||||||||||||||||||||||
| P = 101325 | ||||||||||||||||||||||||
| # density | ||||||||||||||||||||||||
| rho = 1.225 | ||||||||||||||||||||||||
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| # fluid x velocity | ||||||||||||||||||||||||
| v1 = M * np.sqrt(gam_a * P / rho) | ||||||||||||||||||||||||
| # dynamic viscosity | ||||||||||||||||||||||||
| mu = rho * v1 * D / Re | ||||||||||||||||||||||||
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| dt = 1.0e-06 | ||||||||||||||||||||||||
| Nt = int(2 * L / v1 / dt) # roughly 2 flows through domain | ||||||||||||||||||||||||
| t_save = Nt // 5 | ||||||||||||||||||||||||
| t_step_start_stats = Nt // 2 | ||||||||||||||||||||||||
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| Nx = 127 # to accurately resolve = 399 | ||||||||||||||||||||||||
| Ny = Nx | ||||||||||||||||||||||||
| Nz = Ny | ||||||||||||||||||||||||
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| # load initial sphere locations | ||||||||||||||||||||||||
| sphere_loc = np.loadtxt("sphere_array_locations.txt") | ||||||||||||||||||||||||
| N_sphere = len(sphere_loc) | ||||||||||||||||||||||||
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Comment on lines
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Contributor
There was a problem hiding this comment. Handle single-row sphere files safely.
✅ Proposed fix-# load initial sphere locations
-sphere_loc = np.loadtxt("sphere_array_locations.txt")
-N_sphere = len(sphere_loc)
+# load initial sphere locations
+sphere_loc = np.atleast_2d(np.loadtxt("sphere_array_locations.txt"))
+N_sphere = sphere_loc.shape[0]📝 Committable suggestion
Suggested change
🤖 Prompt for AI Agents |
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| # immersed boundary dictionary | ||||||||||||||||||||||||
| ib_dict = {} | ||||||||||||||||||||||||
| for i in range(N_sphere): | ||||||||||||||||||||||||
| ib_dict.update( | ||||||||||||||||||||||||
| { | ||||||||||||||||||||||||
| f"patch_ib({i+1})%geometry": 8, | ||||||||||||||||||||||||
| f"patch_ib({i+1})%x_centroid": sphere_loc[i, 0], | ||||||||||||||||||||||||
| f"patch_ib({i+1})%y_centroid": sphere_loc[i, 1], | ||||||||||||||||||||||||
| f"patch_ib({i+1})%z_centroid": sphere_loc[i, 2], | ||||||||||||||||||||||||
| f"patch_ib({i+1})%radius": D / 2, | ||||||||||||||||||||||||
| f"patch_ib({i+1})%slip": "F", | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
| ) | ||||||||||||||||||||||||
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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, | ||||||||||||||||||||||||
| "t_step_start_stats": t_step_start_stats, | ||||||||||||||||||||||||
| # 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": N_sphere, | ||||||||||||||||||||||||
| "viscous": "T", | ||||||||||||||||||||||||
| # Formatted Database Files Structure Parameters | ||||||||||||||||||||||||
| "format": 1, | ||||||||||||||||||||||||
| "precision": 2, | ||||||||||||||||||||||||
| "prim_vars_wrt": "T", | ||||||||||||||||||||||||
| "E_wrt": "T", | ||||||||||||||||||||||||
| "q_filtered_wrt": "T", # write filtered data statistics | ||||||||||||||||||||||||
| "parallel_io": "T", | ||||||||||||||||||||||||
| # Patch: cube filled with air | ||||||||||||||||||||||||
| # Specify the cylindrical air tube grid geometry | ||||||||||||||||||||||||
| "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, | ||||||||||||||||||||||||
| "patch_icpp(1)%vel(2)": 0.0e00, | ||||||||||||||||||||||||
| "patch_icpp(1)%vel(3)": 0.0e00, | ||||||||||||||||||||||||
| "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) | ||||||||||||||||||||||||
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Contributor
There was a problem hiding this comment. Suggestion: The value assigned to Severity Level: Critical 🚨- ❌ Case JSON contains incorrect gamma value.
- ⚠️ Thermodynamic properties computed incorrectly.
- ⚠️ Simulation equation-of-state behavior altered.
Suggested change
Steps of Reproduction ✅1. Open `examples/3D_random_sphere_array/case.py` and note gamma variable at line 5
(`gam_a = 1.4`).
2. Run `python examples/3D_random_sphere_array/case.py` to print the case JSON (print at
line 164).
3. Inspect printed JSON field `fluid_pp(1)%gamma` populated from line 140; it will be `1.0
/ (gam_a - 1.0)` → 2.5 for gam_a=1.4.
4. Confirm that the produced value differs from the physical specific-heat ratio
(gam_a=1.4) by inspecting lines 5 and 140. This shows the script sets 2.5 into
`fluid_pp(1)%gamma` rather than 1.4.Prompt for AI Agent 🤖This is a comment left during a code review.
**Path:** examples/3D_random_sphere_array/case.py
**Line:** 140:140
**Comment:**
*Logic Error: The value assigned to `"fluid_pp(1)%gamma"` is `1.0 / (gam_a - 1.0)` which equals 1/(gamma-1) (e.g. 2.5 for gamma=1.4); if the field expects the physical ratio of specific heats it should be `gam_a` instead — the current assignment likely mixes up gamma with (gamma-1) and is a logic error.
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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| "fluid_pp(1)%pi_inf": 0, | ||||||||||||||||||||||||
| "fluid_pp(1)%Re(1)": 1.0 / mu, | ||||||||||||||||||||||||
| # force flow to desired bulk quantities | ||||||||||||||||||||||||
| "periodic_forcing": "T", | ||||||||||||||||||||||||
| "u_inf_ref": v1, | ||||||||||||||||||||||||
| "rho_inf_ref": rho, | ||||||||||||||||||||||||
| "P_inf_ref": P, | ||||||||||||||||||||||||
| "mom_f_idx": 1, | ||||||||||||||||||||||||
| "forcing_window": 1, | ||||||||||||||||||||||||
| "forcing_dt": 1.0 / (0.5 * dt), | ||||||||||||||||||||||||
|
Contributor
There was a problem hiding this comment. Suggestion: Severity Level: Critical 🚨- ❌ Forcing timestep misconfigured in case JSON.
- ⚠️ Periodic forcing frequency will be incorrect.
- ⚠️ Simulation bulk forcing behavior altered.
Suggested change
Steps of Reproduction ✅1. Inspect dt definition at line 27 (`dt = 1.0e-06`) in
`examples/3D_random_sphere_array/case.py`.
2. Run script: `python examples/3D_random_sphere_array/case.py` to print case JSON (print
at line 164).
3. In produced JSON, observe `case_dict["forcing_dt"]` printed from line 150 with value
`1.0 / (0.5 * dt)` → for dt=1e-6 this equals 2_000_000.0, not the likely intended 5e-07.
4. Confirm mismatch between intended "half timestep" and the reciprocal value by
inspecting line 150 and dt at line 27.Prompt for AI Agent 🤖This is a comment left during a code review.
**Path:** examples/3D_random_sphere_array/case.py
**Line:** 150:150
**Comment:**
*Logic Error: `forcing_dt` is computed as the reciprocal of `0.5 * dt` (i.e. 2/dt) which yields an extremely large value for small `dt`; it's almost certainly intended to be half the timestep (`0.5 * dt`) rather than its inverse.
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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| "fluid_volume_fraction": 1.0 - 0.1, # 1 - particle volume fraction | ||||||||||||||||||||||||
| # ibs wrap around domain | ||||||||||||||||||||||||
| "periodic_ibs": "T", | ||||||||||||||||||||||||
| # compute unclosed terms in volume filtered momentum equation | ||||||||||||||||||||||||
| "volume_filter_momentum_eqn": "T", | ||||||||||||||||||||||||
| "filter_width": 3.0 * D / 2 * np.sqrt(2 / (9 * np.pi)), | ||||||||||||||||||||||||
| "compute_particle_drag": "T", | ||||||||||||||||||||||||
| # do not store a levelset field for every ib (only works for spheres) | ||||||||||||||||||||||||
| "store_levelset": "F", | ||||||||||||||||||||||||
| # MPI domain decomposition into slabs instead of blocks | ||||||||||||||||||||||||
| "slab_domain_decomposition": "T", | ||||||||||||||||||||||||
| } | ||||||||||||||||||||||||
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| case_dict.update(ib_dict) | ||||||||||||||||||||||||
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| print(json.dumps(case_dict)) | ||||||||||||||||||||||||
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Comment on lines
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Contributor
There was a problem hiding this comment. Prevent JSON serialization errors from NumPy scalars.
✅ Proposed fix-case_dict.update(ib_dict)
-
-print(json.dumps(case_dict))
+case_dict.update(ib_dict)
+
+def _json_default(obj):
+ if isinstance(obj, np.generic):
+ return obj.item()
+ raise TypeError(f"Object of type {type(obj).__name__} is not JSON serializable")
+
+print(json.dumps(case_dict, default=_json_default))📝 Committable suggestion
Suggested change
🤖 Prompt for AI Agents |
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Suggestion: np.loadtxt returns a 1-D array for a single-row file which makes subsequent indexing like
sphere_loc[i, 0]crash; convert the result to a 2-D array and compute the number of spheres fromshape[0]so single-row and multi-row inputs both work. [possible bug]Severity Level: Critical 🚨
Steps of Reproduction ✅
Prompt for AI Agent 🤖