Functions
	n_to_d_nm (n)

Variables
	MODULE_ROOT = Path(__file__).resolve().parent.parent.parent

	REPO_ROOT = MODULE_ROOT.parent

float	Omega = 1.18e-29

float	b_111 = 2.482e-10

dict	SOLVER_CONFIG

	I_SIM

	V_SIM

int	i_mobile = 10

dict	OVERRIDES

	saved = sys.stdout, sys.stderr

	stdout

	stderr

	sim

	inp = sim.input_data

bool	placed = False

	results

	d = inp.derived

	G = d['G']

	dose = results['dose']

	idx_01 = np.argmin(np.abs(dose - 0.1))

	actual_dose = dose[idx_01]

	t_01 = results['t'][idx_01]

	y = results['y'][:, idx_01]

	c_i = np.maximum(y[0:I_SIM], 0.0)

	c_v = np.maximum(y[I_SIM:2*I_SIM], 0.0)

	ci1 = c_i[0]

	cv1 = c_v[0]

float	s2m = 1.0 / d['Omega']

	rr = sim.reaction_rates

	re = sim.rate_equations

	cn = c_i[n-1]

	K_g = rr.K_SIA_grow[n-1]

	K_s = rr.K_SIA_shrink[n-1]

	G_em = rr.G_SIA[n-1]

	k2 = rr.k2_SIA[n-1]

	v_net = K_g * ci1 - K_s * cv1

	growth_flux = K_g * ci1 * cn

	shrink_flux = K_s * cv1 * cn

int	ratio = growth_flux / max(shrink_flux, 1e-300) if shrink_flux > 0 else float('inf')

	Pr_1 = re.Pr_SIA[0]

	sink_loss = rr.k2_SIA[0] * ci1

	growth_loss = ci1 * np.dot(rr.K_SIA_grow, c_i)

	recom_loss = rr.K_iv * ci1 * cv1

	K_3D = rr.K_3D_cav_pref

	m13 = np.arange(1, V_SIM+1)**(1./3.)

	cav_loss = ci1 * K_3D * np.dot(m13, c_v)

	total_loss = sink_loss + growth_loss + recom_loss + cav_loss

	v_growth = np.array([rr.K_SIA_grow[n-1]ci1 - rr.K_SIA_shrink[n-1]cv1 for n in range(1, I_SIM+1)])

	sorted_idx = np.argsort(c_i)[::-1]

int	n = sorted_idx[rank] + 1

Detailed Description

Growth rate diagnostic — examines WHY the SIA peak doesn't move.

At ~0.1 dpa, extracts the SIA distribution and computes:
  - Net growth rate v(n) = K_grow(n)*c_1 - K_shrink(n)*c_v1  [size increments per second]
  - Production contribution at each n
  - Sink loss at each n
  - Monomer SIA and vacancy concentrations

This tells us whether loops are growing (v > 0) or shrinking (v < 0) at each size.

Function Documentation

◆ n_to_d_nm()

growth_diagnostic.n_to_d_nm ( n )

Definition at line 42 of file growth_diagnostic.py.

Variable Documentation

◆ actual_dose

growth_diagnostic.actual_dose = dose[idx_01]

Definition at line 116 of file growth_diagnostic.py.

◆ b_111

float growth_diagnostic.b_111 = 2.482e-10

Definition at line 40 of file growth_diagnostic.py.

◆ c_i

growth_diagnostic.c_i = np.maximum(y[0:I_SIM], 0.0)

Definition at line 120 of file growth_diagnostic.py.

◆ c_v

growth_diagnostic.c_v = np.maximum(y[I_SIM:2*I_SIM], 0.0)

Definition at line 121 of file growth_diagnostic.py.

◆ cav_loss

growth_diagnostic.cav_loss = ci1 * K_3D * np.dot(m13, c_v)

Definition at line 190 of file growth_diagnostic.py.

◆ ci1

growth_diagnostic.ci1 = c_i[0]

Definition at line 123 of file growth_diagnostic.py.

◆ cn

growth_diagnostic.cn = c_i[n-1]

Definition at line 151 of file growth_diagnostic.py.

◆ cv1

growth_diagnostic.cv1 = c_v[0]

Definition at line 124 of file growth_diagnostic.py.

◆ d

growth_diagnostic.d = inp.derived

Definition at line 112 of file growth_diagnostic.py.

◆ dose

growth_diagnostic.dose = results['dose']

Definition at line 114 of file growth_diagnostic.py.

◆ G

growth_diagnostic.G = d['G']

Definition at line 113 of file growth_diagnostic.py.

◆ G_em

growth_diagnostic.G_em = rr.G_SIA[n-1]

Definition at line 154 of file growth_diagnostic.py.

◆ growth_flux

growth_diagnostic.growth_flux = K_g * ci1 * cn

Definition at line 159 of file growth_diagnostic.py.

◆ growth_loss

growth_diagnostic.growth_loss = ci1 * np.dot(rr.K_SIA_grow, c_i)

Definition at line 180 of file growth_diagnostic.py.

◆ i_mobile

int growth_diagnostic.i_mobile = 10

Definition at line 60 of file growth_diagnostic.py.

◆ I_SIM

growth_diagnostic.I_SIM

Definition at line 59 of file growth_diagnostic.py.

◆ idx_01

growth_diagnostic.idx_01 = np.argmin(np.abs(dose - 0.1))

Definition at line 115 of file growth_diagnostic.py.

◆ inp

growth_diagnostic.inp = sim.input_data

Definition at line 80 of file growth_diagnostic.py.

◆ k2

growth_diagnostic.k2 = rr.k2_SIA[n-1]

Definition at line 155 of file growth_diagnostic.py.

◆ K_3D

growth_diagnostic.K_3D = rr.K_3D_cav_pref

Definition at line 188 of file growth_diagnostic.py.

◆ K_g

growth_diagnostic.K_g = rr.K_SIA_grow[n-1]

Definition at line 152 of file growth_diagnostic.py.

◆ K_s

growth_diagnostic.K_s = rr.K_SIA_shrink[n-1]

Definition at line 153 of file growth_diagnostic.py.

◆ m13

growth_diagnostic.m13 = np.arange(1, V_SIM+1)**(1./3.)

Definition at line 189 of file growth_diagnostic.py.

◆ MODULE_ROOT

growth_diagnostic.MODULE_ROOT = Path(__file__).resolve().parent.parent.parent

Definition at line 18 of file growth_diagnostic.py.

◆ n

int growth_diagnostic.n = sorted_idx[rank] + 1

Definition at line 222 of file growth_diagnostic.py.

◆ Omega

float growth_diagnostic.Omega = 1.18e-29

Definition at line 39 of file growth_diagnostic.py.

◆ OVERRIDES

dict growth_diagnostic.OVERRIDES

Initial value:

=  {
    'eta': 0.3, 'f_cl_i': 0.3, 'f_cl_v': 0.25,
    'E_m_1D': 0.4, 'i_mobile': i_mobile, 'L_hat': 71.8,
    'c_C': 1.94e-4, 'E_b_C_SIA': 0.65,
    'rho_d': 1e13, 'Z_i': 1.05, 'Z_ii': 1.2,
    'shape_function': 'linear',
}

Definition at line 62 of file growth_diagnostic.py.

◆ placed

bool growth_diagnostic.placed = False

Definition at line 82 of file growth_diagnostic.py.

◆ Pr_1

growth_diagnostic.Pr_1 = re.Pr_SIA[0]

Definition at line 172 of file growth_diagnostic.py.

◆ ratio

int growth_diagnostic.ratio = growth_flux / max(shrink_flux, 1e-300) if shrink_flux > 0 else float('inf')

Definition at line 161 of file growth_diagnostic.py.

◆ re

growth_diagnostic.re = sim.rate_equations

Definition at line 135 of file growth_diagnostic.py.

◆ recom_loss

growth_diagnostic.recom_loss = rr.K_iv * ci1 * cv1

Definition at line 184 of file growth_diagnostic.py.

◆ REPO_ROOT

growth_diagnostic.REPO_ROOT = MODULE_ROOT.parent

Definition at line 19 of file growth_diagnostic.py.

◆ results

growth_diagnostic.results

Initial value:

=  sim.run_adaptive(
        solver_config=SOLVER_CONFIG, save_output=False,
        progress_callback=None, boundary_threshold=0.1,
        max_doublings=0, points_per_segment=10,
    )

Definition at line 99 of file growth_diagnostic.py.

◆ rr

growth_diagnostic.rr = sim.reaction_rates

Definition at line 134 of file growth_diagnostic.py.

◆ s2m

float growth_diagnostic.s2m = 1.0 / d['Omega']

Definition at line 126 of file growth_diagnostic.py.

◆ saved

growth_diagnostic.saved = sys.stdout, sys.stderr

Definition at line 71 of file growth_diagnostic.py.

◆ shrink_flux

growth_diagnostic.shrink_flux = K_s * cv1 * cn

Definition at line 160 of file growth_diagnostic.py.

◆ sim

growth_diagnostic.sim

Initial value:

=  RadClusterSimulation(
        I=I_SIM, V=V_SIM,
        solver_mode='active_window', physics_option='full_CD_fission',
        C_floor=1e-25, he_kinetics='quasi_steady_state',
        i_mobile=i_mobile, v_mobile=5,
    )

Definition at line 74 of file growth_diagnostic.py.

◆ sink_loss

growth_diagnostic.sink_loss = rr.k2_SIA[0] * ci1

Definition at line 176 of file growth_diagnostic.py.

◆ SOLVER_CONFIG

dict growth_diagnostic.SOLVER_CONFIG

Initial value:

=  {
    't_span':   (1e-6, 1e5),
    'n_points': 100,
    'log_time': True,
    'rtol':     1e-5,
    'atol':     1e-20,
    'solver_method': {
        'linsol': 'gmres',
        'window_width': 50,
        'concentration_threshold': 1e-18, 'window_pad': 10,
    }
}

Definition at line 46 of file growth_diagnostic.py.

◆ sorted_idx

growth_diagnostic.sorted_idx = np.argsort(c_i)[::-1]

Definition at line 220 of file growth_diagnostic.py.

◆ stderr

growth_diagnostic.stderr

Definition at line 72 of file growth_diagnostic.py.

◆ stdout

growth_diagnostic.stdout

Definition at line 72 of file growth_diagnostic.py.

◆ t_01

growth_diagnostic.t_01 = results['t'][idx_01]

Definition at line 117 of file growth_diagnostic.py.

◆ total_loss

growth_diagnostic.total_loss = sink_loss + growth_loss + recom_loss + cav_loss

Definition at line 193 of file growth_diagnostic.py.

◆ v_growth

growth_diagnostic.v_growth = np.array([rr.K_SIA_grow[n-1]*ci1 - rr.K_SIA_shrink[n-1]*cv1 for n in range(1, I_SIM+1)])

Definition at line 206 of file growth_diagnostic.py.

◆ v_net

growth_diagnostic.v_net = K_g * ci1 - K_s * cv1

Definition at line 157 of file growth_diagnostic.py.

◆ V_SIM

growth_diagnostic.V_SIM

Definition at line 59 of file growth_diagnostic.py.

◆ y

growth_diagnostic.y = results['y'][:, idx_01]

Definition at line 119 of file growth_diagnostic.py.

Functions

Variables

Detailed Description

Function Documentation

◆ n_to_d_nm()

Variable Documentation

◆ actual_dose

◆ b_111

◆ c_i

◆ c_v

◆ cav_loss

◆ ci1

◆ cn

◆ cv1

◆ d

◆ dose

◆ G

◆ G_em

◆ growth_flux

◆ growth_loss

◆ i_mobile

◆ I_SIM

◆ idx_01

◆ inp

◆ k2

◆ K_3D

◆ K_g

◆ K_s

◆ m13

◆ MODULE_ROOT

◆ n

◆ Omega

◆ OVERRIDES

◆ placed

◆ Pr_1

◆ ratio

◆ re

◆ recom_loss

◆ REPO_ROOT

◆ results

◆ rr

◆ s2m

◆ saved

◆ shrink_flux

◆ sim

◆ sink_loss

◆ SOLVER_CONFIG

◆ sorted_idx

◆ stderr

◆ stdout

◆ t_01

◆ total_loss

◆ v_growth

◆ v_net

◆ V_SIM

◆ y