The Vedanta Sutras, commentary by Sankaracharya (SBE34), tr. by George Thibaut  at sacred-texts.com
12. In both cases also (in the cases of the adrishta inhering either in the atoms or the soul) action (of the atoms) is not (possible); hence absence of that (viz. creation and pralaya).
The Sûtrakâra now proceeds to refute the doctrine of atoms being the cause of the world.--This doctrine arises in the following manner. We see that all ordinary substances which consist of parts as, for instance, pieces of cloth originate from the substances connected with them by the relation of inherence, as for instance threads, conjunction co-operating (with the parts to form the whole). We thence draw the general conclusion that whatever consists of parts has originated from those substances with which it is connected by the relation of inherence, conjunction cooperating. That thing now at which the distinction of whole and parts stops and which marks the limit of division into minuter parts is the atom.--This whole world, with its mountains, oceans, and so on, is composed of parts; because it is composed of parts it has a beginning and an end 1; an effect may not be assumed without a cause; therefore the atoms are the cause of the world. Such is Kanâda's doctrine.--As we observe four elementary substances consisting of parts, viz. earth, water, fire, and air (wind), we have to assume four different kinds of atoms. These atoms marking the limit of subdivision into minuter parts cannot
be divided themselves; hence when the elements are destroyed they can be divided down to atoms only; this state of atomic division of the elements constitutes the pralaya (the periodical destruction of the world). After that when the time for creation comes, motion (karman) springs up in the aerial atoms. This motion which is due to the unseen principle 1 joins the atom in which it resides to another atom; thus binary compounds, &c. are produced, and finally the element of air. In a like manner are produced fire, water, earth, the body with its organs. Thus the whole world originates from atoms. From the qualities inhering in the atoms the qualities belonging to the binary compounds are produced, just as the qualities of the cloth result from the qualities of the threads.--Such, in short, is the teaching of the followers of Kanâda.
This doctrine we controvert in the following manner.--It must be admitted that the atoms when they are in a state of isolation require action (motion) to bring about their conjunction; for we observe that the conjunction of threads and the like is effected by action. Action again, which is itself an effect, requires some operative cause by which it is brought about; for unless some such cause exists, no original motion can take place in the atoms. If, then, some operative cause is assumed, we may, in the first place, assume some cause analogous to seen causes, such as endeavour or impact. But in that case original motion could not occur at all in the atoms, since causes of that kind are, at the time, impossible. For in the pralaya state endeavour, which is a quality of the soul, cannot take place because no body exists then. For the quality of the soul called endeavour originates when the soul is connected with the internal organ which abides in the body. The same reason precludes the assumption of other seen causes such as impact and the like. For they all are possible only after the creation of the world has taken place, and cannot therefore be the
causes of the original action (by which the world is produced).--If, in the second place, the unseen principle is assumed as the cause of the original motion of the atoms, we ask: Is this unseen principle to be considered as inhering in the soul or in the atom? In both cases it cannot be the cause of motion in the atoms, because it is non-intelligent. For, as we have shown above in our examination of the Sânkhya system, a non-intelligent thing which is not directed by an intelligent principle cannot of itself either act or be the cause of action, and the soul cannot be the guiding principle of the adrishta because at the time of pralaya its intelligence has not yet arisen 1. If, on the other hand, the unseen principle is supposed to inhere in the soul, it cannot be the cause of motion in the atoms, because there exists no connexion of it with the latter. If you say that the soul in which the unseen principle inheres is connected with the atoms, then there would result, from the continuity of connexion 2, continuity of action, as there is no other restricting principle.--Hence, there being no definite cause of action, original action cannot take place in the atoms; there being no action, conjunction of the atoms which depends on action cannot take place; there being no conjunction, all the effects depending on it, viz. the formation of binary atomic compounds, &c., cannot originate.
How, moreover, is the conjunction of one atom with another to be imagined? Is it to be total interpenetration of the two or partial conjunction? If the former, then no increase of bulk could take place, and consequently atomic size only would exist; moreover, it would be contrary to what is observed, as we see that conjunction takes place between substances having parts (pradesa). If the latter, it would follow that the atoms are composed of parts.--Let then the atoms be imagined to consist of parts.--If so, imagined things being unreal, the conjunction also of the atoms would be unreal and thus could not be the noninherent
cause of real things. And without non-inherent causes effected substances such as binary compounds, &c. could not originate. And just as at the time of the first creation motion of the atoms leading to their conjunction could not take place, there being no cause of such motion; thus at the time of a general pralaya also no action could take place leading to their separation, since for that occurrence also no definite seen cause could be alleged. Nor could the unseen principle be adduced as the cause, since its purport is to effect enjoyment (of reward and punishment on the part of the soul), not to bring about the pralaya. There being then no possibility of action to effect either the conjunction or the separation of the atoms, neither conjunction nor separation would actually take place, and hence neither creation nor pralaya of the world.--For these reasons the doctrine of the atoms being the cause of the world must be rejected.
386:1 Like other things, let us say a piece of cloth, which consists of parts.
387:1 Or, more particularly, to the conjunction of the atoms with the souls to which merit and demerit belong.--Adrishtâpeksham adrishtavatkshetragñasamyogâpeksham iti yâvat. Ãn. Gi.
388:1 According to the Vaiseshikas intelligence is not essential to the soul, but a mere adventitious quality arising only when the soul is joined to an internal organ.
388:2 The soul being all-pervading.