I'm really confused about bus standards like ide,ata,sata,pci etc.
You should separate PCI from ATA, SATA and IDE.
ATA, SATA and IDE are not a bus like PCI.
My first question is how hdd microcontroller clock frequency is determined?
That's a decision based on what is cost effective versus what level of performance is required.
And according to above article why there is a word like "sata drive"? I mean if "ata" or "sata" etc. are just bus interfaces between the cpu and device controllers why "ata","sata" or "pci" words become a prefix for peripheral devices?
SATA and ATA are interfaces, not "bus interfaces".
It is used as an adjective to designate the type of interface that the peripheral has and what is required on the host computer side.
If you have a "SATA drive" and have no free SATA ports on your PC's motherboard, then you cannot connect it. If there are other unused interfaces (such as a PCI slot or IDE port or USB port), then you could use the appropriate adapter (with added cost and maybe a performance penalty).
i understood that two seperate communications occur when we want to read sectors from hdd, first is between "cpu - device controller" and second is "device controller - hdd".So how these seperate communications work each other?
The device controller is in the middle of both of these operations.
The modern disk controller that is embedded in a SATA disk drive has its own CPU (aka microcontroller), RAM and flash, and executes its own firmware to perform its functions.
BTW you have the data flow 100% backwards. For a read sector from the disk, the first transfer is 'hdd -> device controller', and then the second transfer is 'device controller -> host'.
Also "data transfer" is a more accurate description of the operation than "communications".
Finally if "ata" or "sata" are interfaces that just stand for "cpu&memory(dma)-device controller" communication gateway, why this interface is slower than the front side bus(fsb)?
A peripheral interface is generally slower than a processor bus simply because of length and construction. The Front Side Bus is only a few centimeters in length, and fully contained on the motherboard. The circuit designer has excellent control of the anticipated electrical noise the bus will have to reject. A peripheral interface is almost always for an off-board device using a flexible cable. There are numerous cost versus performance tradeoffs that factor into the design of such interfaces.
BTW that is not a good definition for an interface.
A "communication gateway" is altogether another animal.
i mean if i speak for dma transfer, after disk controller reads one sector from hdd it must transfer this sector to memory right?
A peripheral interface as fast as a FSB over a 0.25 meter flexible cable could be 1000 times more expensive. The cost versus benefit ratio is poor because only one phase of a multi-phase data transfer is being improved.
So why these slow bus interfaces are used for communication between the memory and device controllers?
Cost.
To confuse you even more, these peripheral interfaces do not connect directly to "memory" (as you have written several times). Usually the host side of such an interface would connect to a local system bus, so that either the CPU (using PIO) or the DMA controller can access the interface's data register.
Maybe this is too much detail for you, but then perhaps it is this lack of detail and oversimplification that contributes to confusion.