ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

correct fix npt/cauchy docs

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-08-20 11:29:30 -04:00
parent ba00626764
commit fc9f0dbcbc
1 changed files with 11 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
doc/src/fix_npt_cauchy.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *npt/cauchy*
* one or more keyword/value pairs may be appended
* 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*
.. parsed-literal::
@ -45,9 +45,8 @@ Syntax
*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 Cauchy stress control parameter
continue = *yes* or *no* = whether of not to continue from a previous run
*alpha* value = strength of Cauchy stress control parameter
*continue* value = *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)
@ -56,7 +55,7 @@ Examples
.. code-block:: LAMMPS
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 alpha 0.001
Description
"""""""""""
@ -573,14 +572,7 @@ can only be used if the second 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 unmodified (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
The *alpha* keyword modifies the barostat as per Miller et
al. (Miller)_"#nc-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 aggressively the algorithm drives the system
@ -598,13 +590,12 @@ 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 flag 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.
fluctuations, two subsequent fixes should be used. In the first, fix
npt/cauchy is used and the simulation box equilibrates to the
correct shape for the desired stresses. In the second,
:doc:`fix npt <fix_nh>` is used instead which uses the
original Parrinello-Rahman algorithm, but now with the corrected
simulation box shape from using fix npt/cauchy.
This fix can be used with dynamic groups as defined by the
:doc:`group <group>` command. Likewise it can be used with groups to