This appears to be one of the storylines in the Void Trilogy by Peter F. Hamilton. The series as a whole is SF, but that particular storyline is set inside the Void, where the laws of physics are somewhat different and the story resembles a fantasy story.
The main city is named Makkathran, which isn't similar to your memory, but the city is the capital of Querencia, which is, and the city is indeed made of a living crystal.
From a fan-wiki's description of the Void, we see what you remember about a sort of willpower-based 'magic', which is really psychic ability:
The primary feature of the Void is that it inhibits and eventually prohibits the use of advanced technology, particularly electronics (or even electricity), thus rendering the society on the planet to be similar to 18th century Europe, i.e. the most advanced technology are semi-automatic firearms.
On the other hand, the Void responds to the thoughts of its inhabitants, giving them pyschic powers, including perception at a distance (farsight), communication at a distance (longtalk) and telekinesis (the third hand). Inhabitants have these abilities at varying strengths, i.e. some people are stronger than other with each ability.
An entry on the city itself includes what you remember of the main character learning to 'talk' to the city:
As Edeard's powers grow, and he becomes more familiar with the city, he discovers that the city appears to have some form of awareness of its inhabitants and can respond to Edeard's requests to reshape stairs, or even walk through walls or sink through floors.