/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:63: FutureWarning: Please use atoms.calc = calc
  atoms.set_calculator(KIM(model))
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:69: FutureWarning: Please use len(self) or, if your atoms are distributed, self.get_global_number_of_atoms.
  nAtoms = atoms.get_number_of_atoms()
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:81: FutureWarning: Please use atoms.calc = calc
  superAtoms.set_calculator(KIM(self.model))
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:89: FutureWarning: Please use len(self) or, if your atoms are distributed, self.get_global_number_of_atoms.
  nAtoms = atoms.get_number_of_atoms()
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:95: FutureWarning: Please use atoms.calc = calc
  initial.set_calculator(KIM(self.model))
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:113: FutureWarning: Please use atoms.calc = calc
  final.set_calculator(KIM(self.model))
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:131: FutureWarning: Please use atoms.calc = calc
  image.set_calculator(KIM(self.model))
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:132: FutureWarning: Please import NEB from ase.mep, not ase.neb.
  neb = NEB(images)
/scratch.global/bwaters/jobs/1929eae6-59ef-40fc-b6b4-e8d7048b09e5-007/TE_823106475257_001-and-MO_786012902615_001-1752096832/staged_job_files/repository/te/VacancyFormationMigration_fcc_Pd__TE_823106475257_001/../../td/VacancyFormationMigration__TD_554849987965_001/runner:174: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
  res = np.linalg.lstsq(A, ydata)

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