forked from lijiext/lammps
Merge pull request #698 from lammps/doc-update
small updates to recently added docs and rename of an example dir
This commit is contained in:
Steve Plimpton
GitHub
commit
6dd55e49cb
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@ -2777,8 +2777,8 @@ USER-UEF package :link(USER-UEF),h4
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[Contents:]
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A fix style for the integration of the equations of motion under
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extensional flow with proper boundary conditions, as well
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as several supporting compute styles and an output option.
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extensional flow with proper boundary conditions, as well as several
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supporting compute styles and an output option.
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[Author:] David Nicholson (MIT).
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@ -2807,9 +2807,9 @@ USER-VTK package :link(USER-VTK),h4
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[Contents:]
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A "dump vtk"_dump_vtk.html command which outputs
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snapshot info in the "VTK format"_vtk, enabling visualization by
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"Paraview"_paraview or other visuzlization packages.
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A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
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"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
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other visuzlization packages.
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:link(vtk,http://www.vtk.org)
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:link(paraview,http://www.paraview.org)
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@ -20,10 +20,11 @@ style_name = {nvt/uef} or {npt/uef} :l
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one or more keyword/value pairs may be appended :l
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keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
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{ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
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This keyword sets the external dimensions used to calculate the scalar pressure
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sets the external dimensions used to calculate the scalar pressure
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{strain} values = e_x e_y = initial strain
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Use of this keyword is usually not necessary, but may be needed to resume a run with a data file.
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The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords are documented in the "fix npt"_fix_nh.html command. :pre
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usually not needed, but may be needed to resume a run with a data file.
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{iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
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documented by the "fix npt"_fix_nh.html command :pre
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:ule
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[Examples:]
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@ -35,84 +36,92 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr
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[Description:]
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This fix is used to simulate non-equilibrium molecular dynamics (NEMD)
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under diagonal flow fields, including uniaxial and biaxial flow.
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Simulations under extensional flow may be carried out for an
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indefinite amount of time. It is an implementation of the boundary
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conditions from "(Dobson)"_#Dobson, and also uses numerical lattice reduction
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as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from
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"(Semaev)"_Semaev. The fix is intended for simulations of
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homogeneous flows, and integrates the SLLOD equations of motion,
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originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod).
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Additional detail about this implementation can be found in
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"(Nicholson and Rutledge)"_#Nicholson.
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under diagonal flow fields, including uniaxial and biaxial flow.
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Simulations under extensional flow may be carried out for an
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indefinite amount of time. It is an implementation of the boundary
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conditions from "(Dobson)"_#Dobson, and also uses numerical lattice
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reduction as was proposed by "(Hunt)"_#Hunt. The lattice reduction
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algorithm is from "(Semaev)"_Semaev. The fix is intended for
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simulations of homogeneous flows, and integrates the SLLOD equations
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of motion, originally proposed by Hoover and Ladd (see "(Evans and
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Morriss)"_#Sllod). Additional detail about this implementation can be
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found in "(Nicholson and Rutledge)"_#Nicholson.
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The applied flow field is set by the {eps} keyword. The values {edot_x}
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and {edot_y} correspond to the strain rates in the xx and yy directions.
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It is implicitly assumed that the flow field is traceless, and therefore
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the strain rate in the zz direction is eqal to -({edot_x} + {edot_y}).
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The applied flow field is set by the {eps} keyword. The values
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{edot_x} and {edot_y} correspond to the strain rates in the xx and yy
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directions. It is implicitly assumed that the flow field is
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traceless, and therefore the strain rate in the zz direction is eqal
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to -({edot_x} + {edot_y}).
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NOTE: Due to an instability in the SLLOD equations under extension,
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NOTE: Due to an instability in the SLLOD equations under extension,
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"fix momentum"_fix_momentum.html should be used to regularly reset the
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linear momentum.
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linear momentum.
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The boundary conditions require a simulation box that does not have a
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consistent alignment relative to the applied flow field. Since LAMMPS
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utilizes an upper-triangular simulation box, it is not possible to express
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the evolving simulation box in the same coordinate system as the flow field.
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This fix keeps track of two coordinate systems: the flow frame, and the
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upper triangular LAMMPS frame. The coordinate systems are related to
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each other through the QR decomposition, as is illustrated in the image below.
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The boundary conditions require a simulation box that does not have a
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consistent alignment relative to the applied flow field. Since LAMMPS
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utilizes an upper-triangular simulation box, it is not possible to
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express the evolving simulation box in the same coordinate system as
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the flow field. This fix keeps track of two coordinate systems: the
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flow frame, and the upper triangular LAMMPS frame. The coordinate
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systems are related to each other through the QR decomposition, as is
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illustrated in the image below.
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:c,image(JPG/uef_frames.jpg)
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During most molecular dynamics operations, the system is represented in the
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LAMMPS frame. Only when the positions and velocities are updated is the system
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rotated to the flow frame, and it is rotated back to the LAMMPS frame
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immediately afterwards. For this reason, all vector-valued quantities
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(except for the tensors from "compute_pressure/uef"_compute_pressure_uef.html
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and "compute_temp/uef"_compute_temp_uef.html) will
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be computed in the LAMMPS frame. Rotationally invariant scalar quantities like
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the temperature and hydrostatic pressure are frame-invariant and will be
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computed correctly. Additionally, the system is in the LAMMPS frame during all of the
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output steps, and therefore trajectory files made using the dump command
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will be in the LAMMPS frame unless the "dump_cfg/uef"_dump_cfg_uef.html command is used.
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During most molecular dynamics operations, the system is represented
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in the LAMMPS frame. Only when the positions and velocities are
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updated is the system rotated to the flow frame, and it is rotated
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back to the LAMMPS frame immediately afterwards. For this reason, all
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vector-valued quantities (except for the tensors from
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"compute_pressure/uef"_compute_pressure_uef.html and
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"compute_temp/uef"_compute_temp_uef.html) will be computed in the
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LAMMPS frame. Rotationally invariant scalar quantities like the
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temperature and hydrostatic pressure are frame-invariant and will be
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computed correctly. Additionally, the system is in the LAMMPS frame
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during all of the output steps, and therefore trajectory files made
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using the dump command will be in the LAMMPS frame unless the
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"dump_cfg/uef"_dump_cfg_uef.html command is used.
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:line
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Temperature control is achieved with the default Nose-Hoover style
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thermostat documented in "fix npt"_fix_nh.html. When this fix is active,
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only the peculiar velocity of each atom is stored, defined as the velocity
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relative to the streaming velocity. This is in contrast to
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"fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and
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removes the contribution from the streaming velocity in order to compute
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the temperature.
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Temperature control is achieved with the default Nose-Hoover style
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thermostat documented in "fix npt"_fix_nh.html. When this fix is
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active, only the peculiar velocity of each atom is stored, defined as
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the velocity relative to the streaming velocity. This is in contrast
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to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
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velocity, and removes the contribution from the streaming velocity in
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order to compute the temperature.
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Pressure control is achieved using the default Nose-Hoover barostat documented
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in "fix npt"_fix_nh.html. There are two ways to control the pressure using this
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fix. The first method involves using the {ext} keyword along with the {iso} pressure
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style. With this method, the pressure is controlled by scaling the simulation box
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isotropically to achieve the average pressure only in the directions specified by {ext}.
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For example, if the {ext} value is set to {xy}, the average pressure (Pxx+Pyy)/2
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will be controlled.
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Pressure control is achieved using the default Nose-Hoover barostat
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documented in "fix npt"_fix_nh.html. There are two ways to control the
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pressure using this fix. The first method involves using the {ext}
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keyword along with the {iso} pressure style. With this method, the
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pressure is controlled by scaling the simulation box isotropically to
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achieve the average pressure only in the directions specified by
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{ext}. For example, if the {ext} value is set to {xy}, the average
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pressure (Pxx+Pyy)/2 will be controlled.
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This example command will control the total hydrostatic pressure under uniaxial tension:
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This example command will control the total hydrostatic pressure under
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uniaxial tension:
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fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
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This example command will control the average stress in compression directions, which would
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typically correspond to free surfaces under drawing with uniaxial tension:
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This example command will control the average stress in compression
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directions, which would typically correspond to free surfaces under
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drawing with uniaxial tension:
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fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
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The second method for pressure control involves setting the normal stresses using
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the {x}, {y} , and/or {z} keywords. When using this method, the same pressure must be
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specified via {Pstart} and {Pstop} for all dimensions controlled. Any choice of
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pressure conditions that would cause LAMMPS to compute a deviatoric stress are not
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permissible and will result in an error. Additionally, all dimensions with
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controlled stress must have the same applied strain rate. The {ext} keyword must be
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set to the default value ({xyz}) when using this method.
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The second method for pressure control involves setting the normal
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stresses using the {x}, {y} , and/or {z} keywords. When using this
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method, the same pressure must be specified via {Pstart} and {Pstop}
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for all dimensions controlled. Any choice of pressure conditions that
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would cause LAMMPS to compute a deviatoric stress are not permissible
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and will result in an error. Additionally, all dimensions with
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controlled stress must have the same applied strain rate. The {ext}
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keyword must be set to the default value ({xyz}) when using this
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method.
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For example, the following commands will work:
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@ -127,8 +136,9 @@ fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
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:line
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These fix computes a temperature and pressure each timestep. To do
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this, it creates its own computes of style "temp/uef" and "pressure/uef",
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as if one of these two sets of commands had been issued:
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this, it creates its own computes of style "temp/uef" and
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"pressure/uef", as if one of these two sets of commands had been
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issued:
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compute fix-ID_temp group-ID temp/uef
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compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
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@ -137,61 +147,62 @@ compute fix-ID_temp all temp/uef
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compute fix-ID_press all pressure/uef fix-ID_temp :pre
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See the "compute temp/uef"_compute_temp_uef.html and "compute
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pressure/uef"_compute_pressure_uef.html commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
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+ underscore + "press".
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pressure/uef"_compute_pressure_uef.html commands for details. Note
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that the IDs of the new computes are the fix-ID + underscore + "temp"
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or fix_ID + underscore + "press".
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[Restart, fix_modify, output, run start/stop, minimize info:]
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The fix writes the state of all the thermostat and barostat
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variables, as well as the cumulative strain applied, to
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"binary restart files"_restart.html. See the
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"read_restart"_read_restart.html command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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The fix writes the state of all the thermostat and barostat variables,
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as well as the cumulative strain applied, to "binary restart
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files"_restart.html. See the "read_restart"_read_restart.html command
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for info on how to re-specify a fix in an input script that reads a
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restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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NOTE: It is not necessary to set the {strain} keyword when resuming
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a run from a restart file. Only for resuming from data files,
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which do not contain the cumulative applied strain, will
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this keyword be necessary.
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NOTE: It is not necessary to set the {strain} keyword when resuming a
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run from a restart file. Only for resuming from data files, which do
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not contain the cumulative applied strain, will this keyword be
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necessary.
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This fix can be used with the "fix_modify"_fix_modify.html
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{temp} and {press} options. The temperature and pressure computes
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used must be of type {temp/uef} and {pressure/uef}.
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This fix can be used with the "fix_modify"_fix_modify.html {temp} and
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{press} options. The temperature and pressure computes used must be of
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type {temp/uef} and {pressure/uef}.
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This fix computes the same global scalar and vecor quantities
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as "fix npt"_fix_nh.html.
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This fix computes the same global scalar and vecor quantities as "fix
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npt"_fix_nh.html.
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The fix is not invoked during "energy
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minimization"_minimize.html.
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The fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:]
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This fix is part of the USER-UEF package. It is only enabled if
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LAMMPS was built with that package. See the
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"Making LAMMPS"_Section_start.html#start_3 section for more info.
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This fix is part of the USER-UEF package. It is only enabled if LAMMPS
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was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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Due to requirements of the boundary conditions, when the {strain} keyword
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is set to zero (or unset), the initial simulation box must be cubic and
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have style triclinic. If the box is initially of type ortho, use
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"change_box"_change_box.html before invoking the fix.
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Due to requirements of the boundary conditions, when the {strain}
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keyword is set to zero (or unset), the initial simulation box must be
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cubic and have style triclinic. If the box is initially of type ortho,
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use "change_box"_change_box.html before invoking the fix.
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NOTE: When resuming from restart files, you may need to use "box tilt large"_box.html
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since lammps has internal criteria from lattice reduction that are not
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the same as the criteria in the numerical lattice reduction algorithm.
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NOTE: When resuming from restart files, you may need to use "box tilt
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large"_box.html since lammps has internal criteria from lattice
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reduction that are not the same as the criteria in the numerical
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lattice reduction algorithm.
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[Related commands:]
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"fix nvt"_fix_nh.html,
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"fix nvt/sllod"_fix_nvt_sllod.html,
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"compute temp/uef"_compute_temp_uef.html,
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"compute pressure/uef"_compute_pressure_uef.html,
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"dump cfg/uef"_dump_cfg_uef.html
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"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
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temp/uef"_compute_temp_uef.html, "compute
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pressure/uef"_compute_pressure_uef.html, "dump
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cfg/uef"_dump_cfg_uef.html
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[Default:]
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The default keyword values specific to this fix are exy = xyz, strain = 0 0.
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The remaining defaults are the same as for {fix npt}_fix_nh.html except tchain = 1.
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The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html.
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The default keyword values specific to this fix are exy = xyz, strain
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= 0 0. The remaining defaults are the same as for {fix
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npt}_fix_nh.html except tchain = 1. The reason for this change is
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given in "fix nvt/sllod"_fix_nvt_sllod.html.
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:line
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@ -208,4 +219,5 @@ The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html.
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[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
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:link(Nicholson)
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[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
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[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
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244903 (2016).
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@ -19,24 +19,23 @@ a = anchor point of bias potential :ul
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fix bias all rhok 16 0 0 4.0 16.0
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fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
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# output U_bias rho_k_RE rho_k_IM |rho_k|
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# output of 4 values from fix rhok: U_bias rho_k_RE rho_k_IM |rho_k|
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thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
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[Description:]
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The fix applies an force to atoms given by the potential
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The fix applies a force to atoms given by the potential
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:c,image(Eqs/fix_rhok.jpg)
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as described in "(Pedersen)"_#Pedersen.
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as described in "(Pedersen)"_#Pedersen.
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This field, that bias configurations with long-range order,
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can be used to study crystal-liquid interfaces
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and determine melting temperatures "(Pedersen)"_#Pedersen.
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This field, which biases configurations with long-range order, can be
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used to study crystal-liquid interfaces and determine melting
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temperatures "(Pedersen)"_#Pedersen.
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An example of using the interface pinning method
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is located in the folder
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{examples/USER/pinning} of the source code to LAMMPS.
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An example of using the interface pinning method is located in the
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{examples/USER/misc/rhok} directory.
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[Restrictions:]
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@ -47,7 +47,7 @@ fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
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fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
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fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310
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fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
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fix rhok, Ulf Pedersen (Roskilde U), ulf AT urp.dk, 25 Sep 2017
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fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017
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fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
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fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
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fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015
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