|MadSci Network: Physics|
Atoms have a magnetic dipole moment due to the motion of the electrons around the nucleus, so yes, they and molecules they comprise will have magnetic fields. As far as a magnetic field being due to the polarity of a molecule, the polarity you're speaking of is electric polarity, meaning the molecule, while being on the whole neutral, has a positive charge at one end and a net negative charge at the other end. As with any charge, if these charges are set in motion, they will create magnetic fields.
It is possible to contain atoms in an optical/magnetic trap using lasers and magnetic fields, but there will always be some loss. For more information on these traps, see this page
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