multizone-v02/source/rod.py

"""Conservative planar extensible rod. L=EA=1; chi=EI/(EA L^2).

Rod: linear angle FE, midpoint axial elimination. Chain: Ye et al. (2026)
cell rotations, first cell clamped; kr=chi*n. Independent implementations
share ONLY the reduced local energy density. No contact or dynamics.
SPDX-License-Identifier: Apache-2.0
"""
from dataclasses import dataclass, asdict
import numpy as np
from scipy.linalg import solve, eigh
from scipy.optimize import root

@dataclass
class Controls:
    chi: float = .001
    fx: float = 0.
    fy: float = 0.
    moment: float = 0.
    h: float = 0.
    delta: float = .1
    k1: float = 0.
    k2: float = 0.
    k3: float = 0.
    curvatures: tuple | None = None

class Rod:
    def __init__(self, n=48, kind="rod"):
        self.n, self.kind, self.ds = n, kind, 1/n
        if kind == "rod":
            self.d = n
            A = np.zeros((n,n+1)); B = A.copy()
            for i in range(n):
                A[i,i:i+2] = .5
                B[i,i:i+2] = [-n,n]
            self.A,self.B = A[:,1:],B[:,1:]
            self.mass = (A[:,1:].T@A[:,1:])/n
        elif kind == "chain":
            self.d = n-1
            self.A = np.eye(n)[:,1:]
            self.B = np.diff(np.eye(n),axis=0)[:,1:]*n
            self.mass = np.eye(n-1)/n
        else: raise ValueError(kind)
        self.s = (np.arange(n)+.5)/n

    def terms(self, z, c):
        angle=self.A@z
        ks=np.asarray(c.curvatures if c.curvatures is not None else [c.k1,c.k2,c.k3])
        intrinsic=ks[np.minimum((np.arange(self.B.shape[0])+.5)*len(ks)/self.B.shape[0],len(ks)-1).astype(int)]
        curvature=self.B@z-intrinsic
        a=c.fx+2*c.h
        f=a*np.cos(angle)+c.fy*np.sin(angle)
        fp=-a*np.sin(angle)+c.fy*np.cos(angle)
        g=4*c.h*c.delta
        density=-f-.5*f*f+g*np.cos(angle)
        energy=self.ds*(.5*c.chi*(curvature@curvature)+density.sum())-c.moment*z[-1]
        local_g=-(1+f)*fp-g*np.sin(angle)
        local_h=(1+f)*f-fp*fp-g*np.cos(angle)
        grad=self.ds*(c.chi*self.B.T@curvature+self.A.T@local_g)
        grad[-1]-=c.moment
        tangent=self.ds*(c.chi*self.B.T@self.B+self.A.T@(local_h[:,None]*self.A))
        return energy,grad,tangent

    def solve(self,c,seed=None):
        z=np.zeros(self.d) if seed is None else np.array(seed,dtype=float).copy()
        it=0; trace=[]; fallback_nfev=0
        for it in range(60):
            _,r,K=self.terms(z,c)
            trace.append(dict(iteration=it,residual_inf=float(np.max(np.abs(r)))))
            if np.max(np.abs(r))<1e-10: break
            try: dz=solve(K,-r,assume_a='sym')
            except Exception: break
            old=np.linalg.norm(r)
            step=1.
            for _ in range(16):
                trial=z+step*dz
                if np.linalg.norm(self.terms(trial,c)[1])<old: break
                step*=.5
            else: break
            z=trial
            trace[-1]['accepted_step_scale']=step
        residual=float(np.max(np.abs(self.terms(z,c)[1])))
        if residual>1e-9:
            sol=root(lambda v:self.terms(v,c)[1],z,jac=lambda v:self.terms(v,c)[2],tol=1e-10)
            z=sol.x; fallback_nfev=sol.nfev
        energy,r,K=self.terms(z,c)
        residual=float(np.max(np.abs(r)))
        angle=self.A@z
        stretch=1+(c.fx+2*c.h)*np.cos(angle)+c.fy*np.sin(angle)
        admissible=bool(np.min(stretch)>(2*c.delta if c.h!=0 else 0))
        good=bool(residual<1e-9 and admissible and np.all(np.isfinite(z)))
        eig=float(eigh(K,self.mass,subset_by_index=[0,0],eigvals_only=True)[0]/c.chi) if good else None
        stability='unknown' if eig is None else ('stable' if eig>1e-4 else 'unstable' if eig< -1e-4 else 'critical')
        segments=self.ds*stretch[:,None]*np.column_stack([np.cos(angle),np.sin(angle)])
        xy=np.vstack([np.zeros(2),np.cumsum(segments,axis=0)])
        # Output resampled on reference coordinate, not current arc length.
        center=np.column_stack([np.interp(np.linspace(0,1,65),np.linspace(0,1,self.n+1),xy[:,j]) for j in range(2)])
        return dict(z=z,centerline=center,angle=angle,strain=stretch-1,energy=float(energy),residual=residual,
                    iterations=it+1,accepted=good,lambda_min_over_chi=eig,stability=stability,
                    tip=center[-1],min_stretch=float(stretch.min()),solver_trace=trace,fallback_nfev=fallback_nfev)

    def mode_seed(self,amplitude):
        s=np.arange(1,self.d+1)/self.n
        return amplitude*np.sin(np.pi*s/2)

def serial(result):
    return {k:(v.tolist() if isinstance(v,np.ndarray) else v) for k,v in result.items()}