Navy officials said Monday that the fire ravaging the amphibious assault ship Bonhomme Richard for a second day has reached temperatures as high as 1,000 degrees, and it is still burning in various portions of the ship.Smoke and fumes continued to affect the skyline and air throughout San Diego.Rear Adm. Philip Sobeck, the commander of Expeditionary Strike Group 3, said Monday that the fire is in the superstructure of the ship and its upper decks and that the ship’s forward mast has collapsed.“There’s obviously burn damage all the way through the skin of the ship, and we are assessing that as we kind of go through each compartment,” he said. “Right now the priority is to get the fire out so that we can take a complete assessment.”