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is there any book or guide for Cyclon 3 standart configuration onto PCB?
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The data sheet has all the required details for configuration. However, most of your questions relate to "How do I design a board?". Here's an overview;
1) Define what your board needs to do.
2) Find parts that can implement the requirements in (1).
3) Create tables of voltages and currents for all of the devices in (2).
4) FPGA power; there's no current requirements listed in the data sheet, so you have to use the Early Power Estimator to get a preliminary estimate of your power requirements.
5) Design a power tree and clocking tree for all the devices.
6) Create a schematic and add the devices and power supplies. If the devices operate at different logic levels, then make sure to either add level translation devices, or use FPGA I/O banks with appropriate VCCIO voltages.
7) Create a design for your FPGA to improve the power estimate in (4). Use PowerPlay to determine the current required on its power supplies. Confirm the current from your power supplies is sufficient (allow some margin for design changes increasing the current).
8) Decide how your FPGA will be configured (passive serial, active serial, etc). The choice may depend on the requirements in (1). For example, PCI/PCIe devices have to configure at power-on very quickly, and active serial may not meet that requirement.
9) Iterate and confirm all the requirements are met.
10) Start a PCB design and layout the board. Depending on the space available on your PCB, you may have to revisit some earlier design decisions.
Before you start on this procedure, review reference designs. Look at their documentation, and you'll see examples of this design flow - you won't necessarily see all steps in their documentation - however you will see the results of those steps, eg., tables of power supply voltages and currents, power trees, clock trees etc. Use those references as the starting point for your own design.
Cheers,
Dave