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cross ref fix deform and new fix nvt/uef

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This commit is contained in:
Steve Plimpton
2017-10-18 15:26:15 -06:00
parent 6dd55e49cb
commit f709a723cd
2 changed files with 21 additions and 11 deletions
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13
doc/src/fix_deform.txt
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@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics
run. Orthogonal simulation boxes have 3 adjustable parameters run. Orthogonal simulation boxes have 3 adjustable parameters
(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously by this command. This fix adjusted independently and simultaneously by this command.
can be used to perform non-equilibrium MD (NEMD) simulations of a
continuously strained system. See the "fix This fix can be used to perform non-equilibrium MD (NEMD) simulations
of a continuously strained system. See the "fix
nvt/sllod"_fix_nvt_sllod.html and "compute nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details. temp/deform"_compute_temp_deform.html commands for more details. Note
that simulation of a continuously extended (extensional flow) system
can be modeled using the "USER-UEF
package"_Section_packages.html#USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be For the {x}, {y}, {z} parameters, the associated dimension cannot be
shrink-wrapped. For the {xy}, {yz}, {xz} parameters, the associated shrink-wrapped. For the {xy}, {yz}, {xz} parameters, the associated

19
doc/src/fix_nh_uef.txt
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@ -36,18 +36,23 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr
[Description:] [Description:]
This fix is used to simulate non-equilibrium molecular dynamics (NEMD) This fix can be used to simulate non-equilibrium molecular dynamics
under diagonal flow fields, including uniaxial and biaxial flow. (NEMD) under diagonal flow fields, including uniaxial and biaxial
Simulations under extensional flow may be carried out for an flow. Simulations under continuous extensional flow may be carried
indefinite amount of time. It is an implementation of the boundary out for an indefinite amount of time. It is an implementation of the
conditions from "(Dobson)"_#Dobson, and also uses numerical lattice boundary conditions from "(Dobson)"_#Dobson, and also uses numerical
reduction as was proposed by "(Hunt)"_#Hunt. The lattice reduction lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice
algorithm is from "(Semaev)"_Semaev. The fix is intended for reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for
simulations of homogeneous flows, and integrates the SLLOD equations simulations of homogeneous flows, and integrates the SLLOD equations
of motion, originally proposed by Hoover and Ladd (see "(Evans and of motion, originally proposed by Hoover and Ladd (see "(Evans and
Morriss)"_#Sllod). Additional detail about this implementation can be Morriss)"_#Sllod). Additional detail about this implementation can be
found in "(Nicholson and Rutledge)"_#Nicholson. found in "(Nicholson and Rutledge)"_#Nicholson.
Note that NEMD simulations of a continuously strained system can be
performed using the "fix deform"_fix_deform.html, "fix
nvt/sllod"_fix_nvt_sllod.html, and "compute
temp/deform"_compute_temp_deform.html commands.
The applied flow field is set by the {eps} keyword. The values The applied flow field is set by the {eps} keyword. The values
{edot_x} and {edot_y} correspond to the strain rates in the xx and yy {edot_x} and {edot_y} correspond to the strain rates in the xx and yy
directions. It is implicitly assumed that the flow field is directions. It is implicitly assumed that the flow field is