Fix issues in parallel
Merge pull request #68 from TuckermanGroup/output

Fix output issues in parallel
Add preliminary tasks for minimization
Merge pull request #61 from TuckermanGroup/prelim_min

Add preliminary tasks for minimization
Add forgotten prototype
New NPT integrator for classical MD
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several fixes for parallel running of classical MD
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fix the degree of freedom for classical MD

revert to the old PINY code