SDC for ALTCLKCTRL

You definitely have to manually constrain this. You need to find the output of the altclkctrl in the node finder, and then do:

create_generated_clock -name pin1 -source [get_ports pin1] {altclkctrl|dout}

create_generated_clock -name pin2 -source [get_ports pin2] {altclkctrl|dout} -add

create_generated_clock -name pll_clk_1 -source [get_pins altpll...clkout1] {altclkctrl|dout} -add

create_generated_clock -name pll_clk_2 -source [get_pins altpll...clkout2] {altclkctrl|dout} -add

The last item is the name of the altclkctrl. The -source for the pins is just the name of the top-level port, while the -source for the PLL can be found when you run Report Clocks and is the Target column for the PLL generated clock. For the -name option, naturally name then whatever you want.

Then you'll need something like:

set_clock_groups -exclusive -group {pin1}

-group {pin2}

-group {pll_clk_1}

-group {pll_clk_2}

Naturally, add other clocks to this command as appropriate.