CW-structures and Morse functions: a reference request The following is probably well known, but I wasn't able to locate a reference in the literature.


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*Let $f$ be a Morse function on a smooth compact manifold $M$ without boundary and let $\rho$ be a Riemannian metric on $M$. As explained in Milnor's Morse theory and many other sources, starting from $f$ and $\rho$ we can construct a CW-complex $M'$ homotopy equivalent to $M$. However, it seems natural to ask whether $f$ gives a CW-structure on $M$ itself, say, such that the corresponding cellular chain complex is isomorphic to the cellular chain complex of $M'$. Is there a reference for that (preferably, one that contains detailed proofs)?

*For a generic choice of the couple $(\rho,f)$ one can construct a chain complex (which I believe is called the Morse complex and) which computes the homology of $M$. What is the standard reference for that? This is implicitly done in Milnor's h-cobordism book, chapter 7. Is it true that the Morse complex is isomorphic to the cellular chain complex of $M'$ from question 1?
upd: the original version of the posting contained some very wrong claims and had to be rewritten.
upd1: restored part of question 2 from the original posting. I deleted it thinking it would be trivial, but it seems that it isn't.
 A: For 2, I'm going to make the simplifying assumption that $f$ is "weakly self-indexing", i.e. that if $c_1$ and $c_2$ are critical points with $ind(c_1)\geq ind(c_2)$ then $f(c_1)\geq f(c_2)$. This means that the cells are attached in the "right" order. 
I claim that in this case the Morse homology complex of a Morse-Smale pair $(\rho,f)$ is isomorphic - not just quasi-isomorphic! - to the cellular homology complex of the handle decomposition. (As Ryan indicates, the latter involves $\rho$ too.)
The isomorphism sends a critical point of index $k$ to the $k$-cell given by its descending manifold. Each matrix entry in the Morse differential counts (with signs) gradient flow-lines from an index $k$ to an index $k-1$ critical point, or equivalently intersections between descending and ascending manifolds. The corresponding matrix entry in the cellular differential is the degree of the map $S^{k-1}\to S^{k-1}$ obtained from the attaching map by collapsing the $(k-2)$-skeleton to get a wedge sum of spheres, then projecting to one summand. But you can "see" the latter map by watching the downward gradient flow of points on the attaching sphere for some large fixed time; most points end up in the $(k-2)$-skeleton; the ones that don't are the ones which (approximately) flow towards an index $k-1$ critical point. This makes it a good exercise to equate matrix entries over $\mathbb{Z}/2$, and a more painful exercise to do it over $\mathbb{Z}$.
A: You may also be interested in a preprint by Cohen, Jones, and Segal, Morse Theory and Classifying Spaces which uses a Morse function to construct a category out of the critical points and the flow lines.  The classifying space of this category is homeomorphic to the original manifold (under certain conditions on the Morse function).  The preprint can be found on the "papers" section of Ralph Cohen's homepage.
A: Historically first reference (as I know) positively answering on your question 1 is the appendix by F. Laudenbach in the paper:
Bismut, Jean-Michel; Zhang, Weiping
An extension of a theorem by Cheeger and Müller. (French summary)
With an appendix by François Laudenbach.
Astérisque No. 205 (1992),
A: Seeing that algori is asking for a reference, I'd like to offer Liviu Nicolaescu's "Invitation to Morse Theory" as a superb modern treatment of the subject. I am fairly certain the result you are looking for is in there.
A: I have not read it (It is on my ever-growing todo list), but the paper
Qin, Lizhen(1-WYNS)
On moduli spaces and CW structures arising from Morse theory on Hilbert manifolds.
J. Topol. Anal. 2 (2010), no. 4, 469–526.
58E05 (37D15 57R19)

should contain the proofs of what you want. From the Mathscinet review of D. Hurtubise

This paper contains precise statements and careful proofs of several
  essential results that are fundamental to the moduli space approach to
  Morse theory. Most of the results in this paper have appeared and/or
  been used in other papers, but this is the first self-contained
  reference that provides clear and complete proofs of all of the
  following: (1) the smooth structures on the compactified spaces that
  arise from the gradient flow of a Morse-Smale function, (2)
  orientation formulas for the strata of the compactified spaces, and
  (3) the CW structure determined by the unstable manifolds of a
  Morse-Smale function. The results are proved for a Morse function on a
  complete Hilbert manifold that satisfies the Palais-Smale Condition
  (C) and has finite index at each critical point (the CF case).

Of course this also proves the CW structure in the finite dimensional case. 
A: The result you are looking for is Theorem 4.18 in "An Introduction to Morse Theory" by Yukio Matsumoto, published by AMS in 2002 (translated from Japanese). The connections between Morse functions, handle structures, and CW complex structures are all explained here.  Mapping cylinders play a key role in the proof of the theorem, which is similar in spirit to what Ryan outlined in his answer.  This chapter of the book also covers the connection to chain complexes, the Morse inequalities, and Poincaré duality. It looks like a nice exposition, though I haven't tried reading it closely.
A: I'm confused about your 2nd question.  Milnor's Morse theory does use a Riemann metric -- he's using the gradient flow.  To define the gradient he needs an inner product on the tangent spaces.  Without the gradient flow you don't have the cellular attaching maps. 
Regarding your 1st question, there's something that's much better than a CW-structure.  A Morse function gives a handle decomposition of the manifold.  This can be used to talk about the smooth structure.  A CW-decomposition is relatively degenerate in comparison.  The handle decomposition is described in Milnor's h-cobordism notes. 
Taking your 1st question more seriously, you run into technical problems.  The gradient flows do not give you a CW-decomposition of the manifold -- for example consider Milnor's Morse Theory example of a torus with height function.  The Morse function and its gradient flows gives you a genuine 1-skeleton (figure-8).  But the attaching map for the 2-cell (to the figure-8) is not a continuous function if you use the gradient flow -- all points except for two go to the global minimum for the height function.  This shows you the kind of problems you encounter if you want to produce a genuine CW-decomposition of the manifold. 
So if you're not going to use solely the gradient flows to define the attaching maps for the proposed CW-decomposition, what do you allow?  All smooth manifolds admit CW-decompositions so if you allow sufficient tweaking you can of course fix this construction but if you allow "too much" tweaking, the CW-decomposition won't be an invariant of the Morse function. 
edit: Here is a way to tweak the process.  The gradient flow does give you a genuine 1-skeleton.  So take a regular neighbourhood of the 1-skeleton, and perturb the original vector field in this regular neighbourhood to point in towards the 1-skeleton.  This makes the 2-cell attaching maps continuous (terminating in a finite amount of time).  Then take a regular neighbourhood of the 2-skeleton, and perturb the vector field to point in towards the 2-skeleton.  Again, you get flow lines terminating in finite-time so you get genuine 2-cell attaching maps.  The problem with this is you're getting a CW-decomposition but it depends on more than the Morse function as you need to choose smooth regular neighbourhoods of the skeleta. 
