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creating clean fix npt/cauchy package and docs

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Ronald E. Miller
2018-11-29 19:55:31 -05:00
parent d0235dd018
commit 4d06e11cfd
4 changed files with 68 additions and 43 deletions
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doc/src/fix_nh.txt
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@ -11,6 +11,7 @@ fix nvt/intel command :h3
fix nvt/kk command :h3
fix nvt/omp command :h3
fix npt command :h3
fix npt/cauchy command :h3
fix npt/intel command :h3
fix npt/kk command :h3
fix npt/omp command :h3
@ -25,7 +26,7 @@ fix ID group-ID style_name keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt} or {npt} or {nph} :l
one or more keyword/value pairs may be appended :l
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint} or {update}
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint} or {update} or {alpha} or {continue}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
@ -58,7 +59,12 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
x,y,z = perform barostat dilation/contraction around this point (distance units)
{update} value = {dipole} or {dipole/dlm}
dipole = update dipole orientation (only for sphere variants)
dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) :pre
dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants)
{alpha} value = alpha
alpha = strength of Cauchystat control parameter. This keyword is only recognized by npt/cauchy and requires the USER-CAUCHY package.
{continue} value = {yes} or {no} = continue Cauchystat run using previously converged parameters. This keyword is only recognized by npt/cauchy and requires the USER-CAUCHY package.
:pre
:ule
[Examples:]
@ -102,9 +108,9 @@ integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman.
:line
The thermostat parameters for fix styles {nvt} and {npt} is specified
The thermostat parameters for fix styles {nvt} and {npt} are specified
using the {temp} keyword. Other thermostat-related keywords are
{tchain}, {tloop} and {drag}, which are discussed below.
{tchain}, {tloop}, and {drag}, which are discussed below.
The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
@ -136,7 +142,7 @@ they represent are varied together during a constant-pressure
simulation.
Other barostat-related keywords are {pchain}, {mtk}, {ploop},
{nreset}, {drag}, and {dilate}, which are discussed below.
{nreset}, {drag}, {dilate}, {alpha} and {continue}, which are discussed below.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
@ -286,6 +292,16 @@ length {dt}/{tloop}. This corresponds to using a first-order
Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop}
does the same thing for the barostat thermostat.
:line
By default, 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. There are two ways to
deal with this: the {nreset} keyword and the {npt/cauchy} fix style
provided by the USER-CAUCHY package.
The keyword {nreset} controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
@ -296,6 +312,33 @@ specified values of the external stress tensor. A value of {nstep}
means that every {nstep} timesteps, the reference dimensions are set
to those of the current simulation domain.
Installing the USER-CAUCHY package enables the {npt/cauchy} fix, which
implements the Cauchystat as per Miller et al. (Miller)_"#nh-Miller"
to directly control the Cauchy stress. For this fix style, {alpha} is a
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.
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
{npt/cauchy} fix is used and the simulation box equilibrates to the correct
shape for the desired stresses. In the second, the regular {npt} fix is
used, and it will restore the original
Parrinello-Rahman algorithm, but now with the correct simulation box
shape determined in the first fix.
A {continue} value of {yes} is used for the {npt/cauchy} fix to signal that
the fix is subsequent to a previous Cauchystat run, 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.
The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
not the corresponding tilt factors are scaled with the associated box
dimensions when barostatting triclinic periodic cells. The default
@ -329,6 +372,8 @@ far. In all cases, the particle trajectories are unaffected by the
chosen value, except for a time-dependent constant translation of
positions.
:line
If the {update} keyword is used with the {dipole} value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
@ -623,6 +668,7 @@ 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,
alpha = 0.001, continue = no,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.
@ -644,3 +690,7 @@ 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).