Loop restructuring #7
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… commit is 1-reac only
… code duplication
…e of jac in dydotdy, then apply the transpose when scaling
…lling the scalar interface
… be true --- has_logft is explicitly set to 0, 1, or 2.
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Replaces most array-syntax/implicit loops with explicit loops. This should make the transition to the OpenACC/OpenMP versions a little less painful.
Also splits some diagnostic and computation loops and pre-computes in some cases where it might be advantageous.