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Changes to the NH fix enabling Cauchy stress control (Cauhchystat) due to Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys,

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144, 184107 (2016).
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Ronald E. Miller
2018-09-04 15:28:57 -04:00
parent 990f733d22
commit f120b18db8
15 changed files with 94843 additions and 1 deletions
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doc/src/fix_nh.txt
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@ -54,6 +54,9 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
{scaleyz} value = {yes} or {no} = scale yz with lz
{scalexz} value = {yes} or {no} = scale xz with lz
{flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed
{cauchystat} cauchystat values = alpha continue
alpha = strength of Cauchystat control parameter
continue = {yes} or {no} = whether of not to continue from a previous run
{fixedpoint} values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units)
{update} value = {dipole} or {dipole/dlm}
@ -606,6 +609,39 @@ can only be used if the 2nd dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
{tri}, {yz}, {xz}, and {xy}.
Without the {cauchystat} keyword, the barostat algorithm
controls the Second-Piola Kirchhoff stress, which is a stress measure
referred to the undeformed (initial) simulation box. If the box
deforms substantially during the equilibration, the difference between
the set values and the final true (Cauchy) stresses can be
considerable.
The {cauchystat} keyword modifies the barostat as per Miller et
al. (Miller)_"#nh-Miller" so that the Cauchy stress is controlled.
{alpha} is the non-dimensional parameter, typically set to 0.001 or
0.01 that determines how aggresively the algorithm drives the system
towards the set Cauchy stresses. Larger values of {alpha} will modify
the system more quickly, but can lead to instabilities. Smaller
values will lead to longer convergence time. Since {alpha} also
influences how much the stress fluctuations deviate from the
equilibrium fluctuations, it should be set as small as possible.
A {continue} value of {yes} indicates that the fix is subsequent to a
previous run with the Cauchystat fix, and the intention is to continue
from the converged stress state at the end of the previous run. This
may be required, for example, when implementing a multi-step loading/unloading
sequence over several fixes.
Setting {alpha} to zero is not permitted. To "turn off" the
Cauchystat control and thus restore the equilibrium stress
fluctuations, two subsequent fixes should be used. In the first, the
Cauchystat is used and the simulation box equilibrates to the correct
shape for the desired stresses. In the second, the {fix} statement is
identical except that the {cauchystat} keyword is removed (along with
related {alpha} and {continue} values). This restores the original
Parrinello-Rahman algorithm, but now with the correct simulation box
shape from the first fix.
These fixes can be used with dynamic groups as defined by the
"group"_group.html command. Likewise they can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
@ -623,6 +659,7 @@ over time or the atom count becomes very small.
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
cauchystat = no,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.
@ -644,3 +681,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006).
:link(nh-Dullweber)
[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
5840 (1997).
:link(nh-Miller)
[(Miller)] Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys,
144, 184107 (2016).