Not exactly sure what can cause the problem.

Please search the mailing list, there was some time ago a patch for symmetso.

From your description of the problem (optimized/non-optimized structure) it could be a symmetry problem, i.e. during optimization (hexagonal case ???) the symmetry of the positions in the struct file was slightly broken (rounding errors, something like 0.3333333334 or similar ...)

Otherwise you have to send me your struct file.

1. Is it ok to initialize the job using initso with unrelaxed structure but 
after initialization, replace it by relaxed
     structure file and run the job?

No, at least not in general as symmetso may/may not reduce symmetry depending on the direction of magnetism.

2. For spin polarized calculations, spin-orbit may reduce the symmetry 
depending on the choice of magnetization
     direction. According to user guide, initso picks up correct symmetry for 
such cases. But if the system does not
     have any symmetry to begin with, then is it ok to initialize the structure 
treating as non-magnetic case?

Yes, if you are already in P1 you are save and a further reduction of symmetry is obviously not possible. Symmetso will not do anything.

However, x kgen -so (or for P1: x kgen -fbz) is still necessary, as for a non-so case, kgen will by default add inversion symmetry to P1, which it should not do for a spin-polarized case.

Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
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