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I think I do not have problem with hardware. Sometimes the WiFi connection simply disconnects, apparently. So this is not necessarily the same as this case, I might not need to reload any modules.

But how to just restart wlan0? I tried restart network-manager, but this seems to leave wlan0 alone.

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You just need to restart Network Manager:

sudo service network-manager restart
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it works for me after my wifi get stuck. – Felipe Micaroni Lalli Mar 28 '15 at 14:12

Try this:

ifconfig wlan0 down
ifconfig wlan0 up
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You could try killing the power to your device. Assuming you are unable/unwilling to physically disconnect the device, you should run (as root): iwconfig wlan0 txpower off. I would then wait 10-15 seconds to make sure whatever hardware issue has caused the problem has been stopped, then: iwconfig wlan0 txpower auto.

Or, you can simply run rfkill and block/unblock your device. . (as root) rfkill block wifi, followed by rfkill unblock wifi. This second option should be faster, since you only need to wait 2-3 seconds between commands, as opposed to 10-15 seconds. In fact, on my machine, I don't need to wait at all, although I suspect this depends on your WiFi hardware.

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These don't need root, in case you are scripting:

nmcli networking off 
nmcli networking on

For more do: man nmcli

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