From 86126d9267e434f59dbe24e49a382c3d3e2d8ac0 Mon Sep 17 00:00:00 2001
From: romain veltz <romain.veltz@inria.fr>
Date: Sun, 5 Jan 2025 10:27:33 +0100
Subject: [PATCH] build_jacobian -> generate_jacobian

---
 src/periodicorbit/PeriodicOrbitCollocation.jl | 5 +++--
 src/periodicorbit/codim2/codim2.jl            | 6 +++---
 test/lorenz84.jl                              | 2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/periodicorbit/PeriodicOrbitCollocation.jl b/src/periodicorbit/PeriodicOrbitCollocation.jl
index 287a0558..b02f6f90 100644
--- a/src/periodicorbit/PeriodicOrbitCollocation.jl
+++ b/src/periodicorbit/PeriodicOrbitCollocation.jl
@@ -620,6 +620,7 @@ Compute the jacobian of the problem defining the periodic orbits by orthogonal c
         mul!(pj, uc[:, rg], L) # pj ≈ (L * uj')'
         # put the jacobian of the vector field
         for l in 1:m
+            _rgX = rgNx .+ (l-1)*n
             if _transpose == false
                 J0 .= jacobian(VF, pj[:,l], pars)
             else
@@ -986,7 +987,7 @@ function newton(probPO::PeriodicOrbitOCollProblem,
     _newton_pocoll(probPO, orbitguess, options; defOp = defOp, kwargs...)
 end
 
-function build_jacobian(coll::PeriodicOrbitOCollProblem, 
+function generate_jacobian(coll::PeriodicOrbitOCollProblem, 
                         orbitguess, 
                         par; 
                         δ = convert(eltype(orbitguess), 1e-8))
@@ -1038,7 +1039,7 @@ function continuation(coll::PeriodicOrbitOCollProblem,
                     plot_solution = nothing,
                     kwargs...)
 
-    jacPO = build_jacobian(coll, orbitguess, getparams(coll); δ)
+    jacPO = generate_jacobian(coll, orbitguess, getparams(coll); δ)
     _Jcoll = analytical_jacobian(coll, orbitguess, getparams(coll))
     if linear_algo isa COPBLS
         linear_algo = COPBLS(coll)
diff --git a/src/periodicorbit/codim2/codim2.jl b/src/periodicorbit/codim2/codim2.jl
index 17596c1c..6e9fd252 100644
--- a/src/periodicorbit/codim2/codim2.jl
+++ b/src/periodicorbit/codim2/codim2.jl
@@ -276,7 +276,7 @@ function _continuation(gh::Bautin, br::AbstractResult{Tkind, Tprob},
     _recordsol = modify_po_record(probPO, kwargs, getparams(probPO), getlens(probPO))
     _plotsol = modify_po_plot(probPO, kwargs)
 
-    jac = build_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
+    jac = generate_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
     pbwrap = _wrap(probPO, jac, orbitguess, getparams(probPO), getlens(probPO), _plotsol, _recordsol)
 
     # we have to change the Bordered linearsolver to cope with our type FloquetWrapper
@@ -394,7 +394,7 @@ function _continuation(hh::HopfHopf, br::AbstractResult{Tkind, Tprob},
     _recordsol = modify_po_record(probPO, _kwargs, getparams(probPO), getlens(probPO))
     _plotsol = modify_po_plot(probPO, _kwargs)
 
-    jac = build_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
+    jac = generate_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
     pbwrap = _wrap(probPO, jac, orbitguess, getparams(probPO), getlens(probPO), _plotsol, _recordsol)
 
     # we have to change the Bordered linearsolver to cope with our type FloquetWrapper
@@ -524,7 +524,7 @@ function _continuation(zh::ZeroHopf, br::AbstractResult{Tkind, Tprob},
     _recordsol = modify_po_record(probPO, kwargs, getparams(probPO), getlens(probPO))
     _plotsol = modify_po_plot(probPO, kwargs)
 
-    jac = build_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
+    jac = generate_jacobian(probPO, orbitguess, getparams(probPO); δ = getdelta(prob_vf))
     pbwrap = _wrap(probPO, jac, orbitguess, getparams(probPO), getlens(probPO), _plotsol, _recordsol)
 
     # we have to change the Bordered linearsolver to cope with our type FloquetWrapper
diff --git a/test/lorenz84.jl b/test/lorenz84.jl
index 95d5d3e1..b4987bff 100644
--- a/test/lorenz84.jl
+++ b/test/lorenz84.jl
@@ -221,7 +221,7 @@ for _jac in (:autodiff, :minaug, :finiteDifferences, :MinAugMatrixBased)
     @test bpbt_2.nfsupp.H0002 ≈ [-0.34426541029040103, 0.7403628764888541, 0.5020796040084594, 0.7211107457956355] rtol = 1e-3 rtol = 1e-3
     @test bpbt_2.nfsupp.H1001 ≈ [0.8609019479520158, 0.3666091456682787, 0.09272126477464948, -1.1252591151814477] rtol = 1e-3
     @test bpbt_2.nfsupp.H2000 ≈ [-1.1430891994241816, 0.5090981254844374, 0.4300904962638521, -0.4240003230561569] rtol = 1e-3
- # test branch switching from BT points
+    # test branch switching from BT points
     hp_codim2_2 = continuation(sn_codim2, 1, ContinuationPar(opts_br, ds = -0.001, dsmax = 0.02, dsmin = 1e-4, n_inversion = 6, detect_bifurcation = 1, p_max = 15.) ;
         normC = norminf,
         detect_codim2_bifurcation = 2,