Chaos Hammer says, "You unleash chaotic power to smite your enemies. The power takes the form of a multicolored explosion of leaping, ricocheting energy. Only lawful and neutral (not chaotic) creatures are harmed by the spell.
The spell deals 1d8 points of damage per two caster levels (maximum 5d8) to lawful creatures (or 1d6 points of damage per caster level, maximum 10d6, to lawful outsiders) and slows them for 1d6 rounds (see the slow spell). A successful Will save reduces the damage by half and negates the slow effect.
The spell deals only half damage against creatures who are neither lawful nor chaotic, and they are not slowed. Such a creature can reduce the damage by half again (down to one-quarter) with a successful Will save."
So, I'm guessing it doesn't affect a CN aligned PC.
School evocation [chaotic]; Level cleric 4
Casting Time 1 standard action
Components V, S
Range medium (100 ft. + 10 ft./level)
Area 20-ft.-radius burst
Duration instantaneous (1d6 rounds); see text
Saving Throw Will partial; see text; Spell Resistance yes
You unleash chaotic power to smite your enemies. The power takes the form of a multicolored explosion of leaping, ricocheting energy. Only lawful and neutral (not chaotic) creatures are harmed by the spell.
The spell deals 1d8 points of damage per two caster levels (maximum 5d8) to lawful creatures (or 1d6 points of damage per caster level, maximum 10d6, to lawful outsiders) and slows them for 1d6 rounds (see the slow spell). A successful Will save reduces the damage by half and negates the slow effect.
The spell deals only half damage against creatures who are neither lawful nor chaotic, and they are not slowed. Such a creature can reduce the damage by half again (down to one-quarter) with a successful Will save.
Emphasis mine.
When the spell talks about neutral creatures, it's referring ONLY to the law/chaos axis. This is clarified by the "(not chaotic)" bit in the first paragraph. Then, when describing what happens to creatures that are neutral along the law/chaos axis, it specifically uses the phrase "neither lawful nor chaotic" instead of "neutral" to further clarify/avoid confusion.
So no, a Chaotic Neutral creature is in no way affected by the Chaos Hammer spell.