Merge pull request #698 from lammps/doc-update

small updates to recently added docs and rename of an example dir

doc/src/Section_packages.txt

@@ -2777,8 +2777,8 @@ USER-UEF package :link(USER-UEF),h4
 [Contents:]
 
 A fix style for the integration of the equations of motion under
-extensional flow with proper boundary conditions, as well 
-as several supporting compute styles and an output option.
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
 
 [Author:] David Nicholson (MIT).
 
@@ -2807,9 +2807,9 @@ USER-VTK package :link(USER-VTK),h4
 
 [Contents:]
 
-A "dump vtk"_dump_vtk.html command which outputs
-snapshot info in the "VTK format"_vtk, enabling visualization by
-"Paraview"_paraview or other visuzlization packages.
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+other visuzlization packages.
 
 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)

doc/src/fix_nh_uef.txt

@@ -20,10 +20,11 @@ style_name = {nvt/uef} or {npt/uef} :l
 one or more keyword/value pairs may be appended :l
 keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
   {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
-    This keyword sets the external dimensions used to calculate the scalar pressure
+    sets the external dimensions used to calculate the scalar pressure
   {strain} values = e_x e_y = initial strain
-    Use of this keyword is usually not necessary, but may be needed to resume a run with a data file. 
-  The {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, and {mtk} keywords  are documented in the "fix npt"_fix_nh.html command. :pre
+    usually not needed, but may be needed to resume a run with a data file.
+  {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
+    documented by the "fix npt"_fix_nh.html command :pre
 :ule
 
 [Examples:]
@@ -35,84 +36,92 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr
 
 [Description:]
 
-
 This fix is used to simulate non-equilibrium molecular dynamics (NEMD)
-under diagonal flow fields, including uniaxial and biaxial flow. 
-Simulations under extensional flow may be carried out for an 
-indefinite amount of time. It is an implementation of the boundary 
-conditions from "(Dobson)"_#Dobson, and also uses numerical lattice reduction
-as was proposed by "(Hunt)"_#Hunt. The lattice reduction algorithm is from 
-"(Semaev)"_Semaev. The fix is intended for simulations of 
-homogeneous flows, and integrates the SLLOD equations of motion, 
-originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod).
-Additional detail about this implementation can be found in 
-"(Nicholson and Rutledge)"_#Nicholson.
-
-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 directions.
-It is implicitly assumed that the flow field is traceless, and therefore
-the strain rate in the zz direction is eqal to -({edot_x} + {edot_y}).
-
-NOTE: Due to an instability in the SLLOD equations under extension, 
+under diagonal flow fields, including uniaxial and biaxial flow.
+Simulations under extensional flow may be carried out for an
+indefinite amount of time. It is an implementation of the boundary
+conditions from "(Dobson)"_#Dobson, and also uses numerical lattice
+reduction as was proposed by "(Hunt)"_#Hunt. The lattice reduction
+algorithm is from "(Semaev)"_Semaev. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see "(Evans and
+Morriss)"_#Sllod).  Additional detail about this implementation can be
+found in "(Nicholson and Rutledge)"_#Nicholson.
+
+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
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -({edot_x} + {edot_y}).
+
+NOTE: Due to an instability in the SLLOD equations under extension,
 "fix momentum"_fix_momentum.html should be used to regularly reset the
-linear momentum. 
+linear momentum.
 
-The boundary conditions require a simulation box that does not have a 
-consistent alignment relative to the applied flow field. Since LAMMPS 
-utilizes an upper-triangular simulation box, it is not possible to express 
-the evolving simulation box in the same coordinate system as the flow field. 
-This fix keeps track of two coordinate systems: the flow frame, and the 
-upper triangular LAMMPS frame. The coordinate systems are related to 
-each other through the QR decomposition, as is illustrated in the image below.
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
 
 :c,image(JPG/uef_frames.jpg)
 
-During most molecular dynamics operations, the system is represented in the 
-LAMMPS frame. Only when the positions and velocities are updated is the system
-rotated to the flow frame, and it is rotated back to the LAMMPS frame 
-immediately afterwards. For this reason, all vector-valued quantities 
-(except for the tensors from "compute_pressure/uef"_compute_pressure_uef.html 
-and "compute_temp/uef"_compute_temp_uef.html) will 
-be computed in the LAMMPS frame. Rotationally invariant scalar quantities like 
-the temperature and hydrostatic pressure are frame-invariant and will be 
-computed correctly. Additionally, the system is in the LAMMPS frame during all of the 
-output steps, and therefore trajectory files made using the dump command 
-will be in the LAMMPS frame unless the "dump_cfg/uef"_dump_cfg_uef.html command is used.
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+"compute_pressure/uef"_compute_pressure_uef.html and
+"compute_temp/uef"_compute_temp_uef.html) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+"dump_cfg/uef"_dump_cfg_uef.html command is used.
 
 :line
 
-Temperature control is achieved with the default Nose-Hoover style 
-thermostat documented in "fix npt"_fix_nh.html. When this fix is active,
-only the peculiar velocity of each atom is stored, defined as the velocity
-relative to the streaming velocity. This is in contrast to 
-"fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame velocity, and 
-removes the contribution from the streaming velocity in order to compute 
-the temperature.
-
-Pressure control is achieved using the default Nose-Hoover barostat documented
-in "fix npt"_fix_nh.html. There are two ways to control the pressure using this 
-fix. The first method involves using the {ext} keyword along with the {iso} pressure 
-style. With this method, the pressure is controlled by scaling the simulation box 
-isotropically to achieve the average pressure only in the directions specified by {ext}.
-For example, if the {ext} value is set to  {xy}, the average pressure (Pxx+Pyy)/2 
-will be controlled.
-
-This example command will control the total hydrostatic pressure under uniaxial tension:
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in "fix npt"_fix_nh.html. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in "fix npt"_fix_nh.html. There are two ways to control the
+pressure using this fix. The first method involves using the {ext}
+keyword along with the {iso} pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+{ext}.  For example, if the {ext} value is set to {xy}, the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
 
 fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
 
-This example command will control the average stress in compression directions, which would 
-typically correspond to free surfaces under drawing with uniaxial tension:
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
 
 fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
 
-The second method for pressure control involves setting the normal stresses using 
-the {x}, {y} , and/or {z} keywords. When using this method, the same pressure must be 
-specified via {Pstart} and {Pstop} for all dimensions controlled. Any choice of
-pressure conditions that would cause LAMMPS to compute a deviatoric stress are not
-permissible and will result in an error. Additionally, all dimensions with 
-controlled stress must have the same applied strain rate. The {ext} keyword must be 
-set to the default value ({xyz}) when using this method.
+The second method for pressure control involves setting the normal
+stresses using the {x}, {y} , and/or {z} keywords. When using this
+method, the same pressure must be specified via {Pstart} and {Pstop}
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The {ext}
+keyword must be set to the default value ({xyz}) when using this
+method.
 
 For example, the following commands will work:
 
@@ -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
 :line
 
 These fix computes a temperature and pressure each timestep.  To do
-this, it creates its own computes of style "temp/uef" and "pressure/uef",
-as if one of these two sets of commands had been issued:
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
 
 compute fix-ID_temp group-ID temp/uef
 compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
@@ -137,61 +147,62 @@ compute fix-ID_temp all temp/uef
 compute fix-ID_press all pressure/uef fix-ID_temp :pre
 
 See the "compute temp/uef"_compute_temp_uef.html and "compute
-pressure/uef"_compute_pressure_uef.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  
+pressure/uef"_compute_pressure_uef.html commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID + underscore + "press".
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-The fix writes the state of all the thermostat and barostat
-variables, as well as the cumulative strain applied, to 
-"binary restart files"_restart.html.  See the
-"read_restart"_read_restart.html command for info on how to re-specify
-a fix in an input script that reads a restart file, so that the
-operation of the fix continues in an uninterrupted fashion.
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to "binary restart
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
 
-NOTE: It is not necessary to set the {strain} keyword when resuming
-a run from a restart file. Only for resuming from data files, 
-which do not contain the cumulative applied strain, will 
-this keyword be necessary.
+NOTE: It is not necessary to set the {strain} keyword when resuming a
+run from a restart file. Only for resuming from data files, which do
+not contain the cumulative applied strain, will this keyword be
+necessary.
 
-This fix can be used with the "fix_modify"_fix_modify.html 
-{temp} and {press} options. The temperature and pressure computes
-used must be of type {temp/uef} and {pressure/uef}. 
+This fix can be used with the "fix_modify"_fix_modify.html {temp} and
+{press} options. The temperature and pressure computes used must be of
+type {temp/uef} and {pressure/uef}.
 
-This fix computes the same global scalar and vecor quantities 
-as "fix npt"_fix_nh.html.
+This fix computes the same global scalar and vecor quantities as "fix
+npt"_fix_nh.html.
 
-The fix is not invoked during "energy
-minimization"_minimize.html.
+The fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
 
-This fix is part of the USER-UEF package. It is only enabled if 
-LAMMPS was built with that package. See the 
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
-Due to requirements of the boundary conditions, when the {strain} keyword
-is set to zero (or unset), the initial simulation box must be cubic and
-have style triclinic. If the box is initially of type ortho, use 
-"change_box"_change_box.html before invoking the fix.
+Due to requirements of the boundary conditions, when the {strain}
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use "change_box"_change_box.html before invoking the fix.
 
-NOTE: When resuming from restart files, you may need to use "box tilt large"_box.html
-since lammps has internal criteria from lattice reduction that are not
-the same as the criteria in the numerical lattice reduction algorithm.
+NOTE: When resuming from restart files, you may need to use "box tilt
+large"_box.html since lammps has internal criteria from lattice
+reduction that are not the same as the criteria in the numerical
+lattice reduction algorithm.
 
 [Related commands:]
-"fix nvt"_fix_nh.html, 
-"fix nvt/sllod"_fix_nvt_sllod.html,
-"compute temp/uef"_compute_temp_uef.html,
-"compute pressure/uef"_compute_pressure_uef.html,
-"dump cfg/uef"_dump_cfg_uef.html
+
+"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
+temp/uef"_compute_temp_uef.html, "compute
+pressure/uef"_compute_pressure_uef.html, "dump
+cfg/uef"_dump_cfg_uef.html
 
 [Default:]
 
-The default keyword values specific to this fix are exy = xyz, strain = 0 0.
-The remaining defaults are the same as for {fix npt}_fix_nh.html except tchain = 1.
-The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html.
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for {fix
+npt}_fix_nh.html except tchain = 1.  The reason for this change is
+given in "fix nvt/sllod"_fix_nvt_sllod.html.
 
 :line
 
@@ -208,4 +219,5 @@ The reason for this change is given in "fix nvt/sllod"_fix_nvt_sllod.html.
 [(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
 
 :link(Nicholson)
-[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
+[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).

doc/src/fix_rhok.txt

@@ -19,24 +19,23 @@ a = anchor point of bias potential :ul
 
 fix bias all rhok 16 0 0 4.0 16.0
 fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
-# output                             U_bias rho_k_RE  rho_k_IM  |rho_k|
+# output of 4 values from fix rhok: U_bias rho_k_RE  rho_k_IM  |rho_k|
 thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
 
 [Description:]
 
-The fix applies an force to atoms given by the potential
+The fix applies a force to atoms given by the potential
 
 :c,image(Eqs/fix_rhok.jpg)
 
-as described in "(Pedersen)"_#Pedersen. 
+as described in "(Pedersen)"_#Pedersen.
 
-This field, that bias configurations with long-range order, 
-can be used to study crystal-liquid interfaces
-and determine melting temperatures "(Pedersen)"_#Pedersen.
+This field, which biases configurations with long-range order, can be
+used to study crystal-liquid interfaces and determine melting
+temperatures "(Pedersen)"_#Pedersen.
 
-An example of using the interface pinning method 
-is located in the folder 
-{examples/USER/pinning} of the source code to LAMMPS.
+An example of using the interface pinning method is located in the
+{examples/USER/misc/rhok} directory.
 
 [Restrictions:]
 

src/USER-MISC/README

@@ -47,7 +47,7 @@ fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
 fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
 fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310
 fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
-fix rhok, Ulf Pedersen (Roskilde U), ulf AT urp.dk, 25 Sep 2017
+fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017
 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
 fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
 fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015