[nonlinear] Fix occurrence of uninitialized variables in Newton

Closes #655

See merge request !1499

The problem was that `newtonConverged` was executed before
`newtonUpdate`, the place where the variables are initialized.
Change the while loop logic such that `newtonConverged` is called
at the end of each loop cycle, particularly after `newtonUpdate`.

[rans][iofields] Clean-up

See merge request !1500

* remove deprecated functions
* remove debug output

fixup /Adapt vtk_staggered test to RANS changes

See merge request !1498

Freeflow/rans problem redevelopment

Closes #574

See merge request !1391

[sequential 2p2c flash] fix flash

See merge request !1301

Beatrix Becker authored 6 years ago and Bernd Flemisch committed 6 years ago

[sequential 2p2c flash] revert change in Rachford-Rice equation (both quantities are mass-based), add literature, change references

Beatrix Becker authored 6 years ago and Bernd Flemisch committed 6 years ago

[sequential 2p2c flash] fix flash: correct equilibrium constants, correct calculation of phase mass fraction, general 2-phase check

Kilian Weishaupt authored 6 years ago and Ned Coltman committed 6 years ago

* ni models did not inherit from their non-ni base models,
  thus the wrong local residual and fluxvars were used (navierstokes)

Feature/improve flux over surface

See merge request !1495

* treat fluxes over boundaries properly (Neumann fluxes
  were not considered before)

* simplify volume flux calculation: just use v * A

[staggered][localresidual] Eval boundaries directly in flux calculation

See merge request !1493

Feature/rans outputplots

See merge request !1486

[cpgrid] Fix loadBalance for cpgrids

See merge request !1488

[md][newtonsolver] Pass sub solution vector to priVarSwitch.updateBoundary()

See merge request !1487

* error was not detected because updateBoundary only does something for box
* md test (stokesdarcy 1p2c2p2c) uses tpfa