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Periodic Immersed Boundary Wrapping for Circular and Spherical Geometries #1117

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8906810
periodic ib wrapping for spheres
conraddelgado Jan 28, 2026
837b18b
periodic ib wrap for circle geometry + tests
conraddelgado Jan 28, 2026
3441ef4
Merge branch 'MFlowCode:master' into master
conraddelgado Jan 28, 2026
6338eea
formatting
conraddelgado Jan 28, 2026
1aa4b08
Merge branch 'master' of github.com:conraddelgado/periodic_ibs
conraddelgado Jan 28, 2026
8571caf
regenerate test data, gpu update
conraddelgado Jan 30, 2026
85903b3
formatting
conraddelgado Jan 30, 2026
067a337
r2 on GPU
conraddelgado Jan 30, 2026
19341ab
Merge branch 'master' into master
sbryngelson Feb 2, 2026
f6b7d1e
refactor periodic centroid projection into a single subroutine
conraddelgado Feb 2, 2026
6c3975a
Merge branch 'master' of github.com:conraddelgado/periodic_ibs
conraddelgado Feb 2, 2026
4ab107d
moved domain_glb to global_parameters
conraddelgado Feb 2, 2026
d371d40
Merge branch 'master' into master
conraddelgado Feb 3, 2026
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141 changes: 141 additions & 0 deletions examples/2D_ibm_circle_periodic/case.py
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Original file line number Diff line number Diff line change
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import json
import math
import numpy as np

gam_a = 1.4

# sphere diameter
D = 0.1

# circle density
rho_c = 200

# domain length
L = 10 * D

# mach number
M = 1.2

# reynolds number
Re = 400.0

# pressure
P = 101325

# density
rho = 1.0

# fluid velocity
v1 = M * np.sqrt(gam_a * P / rho)

# dynamic viscosity
mu = rho * v1 * D / Re

dt = 1.0e-06
Nt = 5000
t_save = 20

# to fully resolve requires 40-60 cells across circle diameter
Nx = 511
Ny = Nx
Nz = 0

# 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,
}
)

# 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",
}

case_dict.update(ib_dict)

print(json.dumps(case_dict))
150 changes: 150 additions & 0 deletions examples/3D_ibm_sphere_periodic/case.py
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Original file line number Diff line number Diff line change
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import json
import math
import numpy as np

gam_a = 1.4

# sphere diameter
D = 0.1

# sphere density
rho_s = 200

# domain length
L = 10 * D

# mach number
M = 1.2

# reynolds number
Re = 400.0

# pressure
P = 101325

# density
rho = 1.0

# fluid velocity
v1 = M * np.sqrt(gam_a * P / rho)

# dynamic viscosity
mu = rho * v1 * D / Re

dt = 2.0e-06
Nt = 2000
t_save = Nt // 250

# to fully resolve requires 40-60 cells across sphere diameter
Nx = 127
Ny = Nx
Nz = Ny

# 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,
}
)

# 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,
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Suggestion: 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. [type error]

Severity Level: Major ⚠️ 
- ❌ Example script fails to output JSON configuration.
- ❌ Running example terminated with TypeError traceback.
- ⚠️ Prevents straightforward reproduction of periodic-IB example.
- ⚠️ Does not alter core solver algorithms or binaries.
Suggested change
"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.

"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)
"fluid_pp(1)%pi_inf": 0,
"fluid_pp(1)%Re(1)": 1.0 / mu,
# ibs wrap around domain
"periodic_ibs": "T",
}

case_dict.update(ib_dict)

print(json.dumps(case_dict))
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