It's been a while since I watched Master and Commander, but the movies is very much historically accurate -- the only quibble I have with it, which is very minor, is that they exaggerate the size (particularly the height) of interior spaces somewhat, though I can see why they do that. (It wouldn't make for good camera angles to shoot with 5' deck heads.)

Before a British ship would go into battle, there was a more or less consistent set of preparatory steps that would be taken:

• make a "clean sweep" fore and aft of the gundecks. This would include breaking down the partitions that created an admiral's and/or captain's cabin, as well as the wardroom space and officers' cabins below, and striking furniture and ornaments down into the hold. This would create a space where there were no extra bulkheads or other partitions to be broken up and cause splinter damage in battle, as well as facilitating movement fore and aft.

• Send any women or small children below, to a remote part of the hold

• Strike below any animals or other baggage in the foc'sle, and dismantle the manger or chicken coops

• Rig chains to the ship's yards, so they would be less likely to crash to the deck if standing rigging was cut through.

• Rig netting above the decks, to catch blocks or other parts of rigging that could be shot away

• Place tubs of slow-match near groups of guns, either to fire them with or to use as a backup if a flintlock firing mechanism failed

• Fill racks of shot, and fill powder charges for each gun

• Draw and reload the guns, if there was time, to ensure that a fresh powder charge would fire quickly (in case the one in the guns had gotten damp or otherwise degraded). Count off the tools for firing the gun (rammer, swab, match/lock, quoins, fire bucket)

• Issue small arms to the men (including sharpening swords/tomahawks/pikes/other sharp things if there were time)

• Wet the decks and sprinkle sand on them, to help with footing when blood was spilled. Fill fire buckets.

• Depending on the tactical situation, most ships brailed up their sails somewhat to reduce the area that could be shot at, and to offer them a quick burst of extra speed (by dropping a sail) if they needed it in battle

• Officers would dress in their best uniforms, to be seen by the men in their division and as a mark of respect for the enemy. Men would usually strip off their jackets and shirts, and tie bandannas around their ears to help mitigate the sound of the guns.

• If there was time, most captains attempted to feed their men some sort of hot meal, even if it were just burgoo or a pudding, before the battle. Some would issue extra rum, while others thought it made the men clumsy in battle. (The ration amount was half a pint per day.)

• Some captains that were particularly religious or evangelical would have a prayer service before the battle.

It's worth keeping in mind that engagements developed slowly in the Age of Sail -- on the morning of Trafalgar, Nelson's ships proceeded toward the Allied line at the pace of a slow walk. Nelson ordered preparations for battle to begin at 6 a.m., and the Allied fleet fired the first shots at noon.

Sharpening swords was important: a potentially key element of naval warfare in the Age of Sail - especially in small ship actions like those depicted in Master and Commander - was boarding actions. Taking an enemy ship as a prize was far more valuable than sinking it, and could prove extremely lucrative for the victorious crew. In many cases, the sheer destruction caused by close-range broadside fire could be enough to force a ship to strike its colours, but often boarding actions were necessary, or alternatively it could be necessary to repel boarders. During the Battle of Trafalgar, for example, HMS Victory had to repel boarders from the French warship Redoutable.

Salt water and steel don't often mix well, especially when trying to keep a sharp edge on a blade, and blades themselves blunt naturally over time. The last thing you need when fighting off boarders or storming the enemy decks is a blunted sword or one rusted and corroded in its scabbard. It was therefore good practice to sharpen a sword as close as practically possible to when you might need it.

Rodger, N.A.M., The Command of the Ocean