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Math replacements and cosmetic edits to documentation

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This commit is contained in:
Karl Hammond
2022-09-01 01:01:46 -05:00
parent f54e7b1e18
commit c03ef56965
16 changed files with 298 additions and 283 deletions
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2
doc/src/accel_styles.rst
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@ -6,7 +6,7 @@ page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues. produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS, These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if OPENMP, and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` page for more info. LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script You can specify the accelerated styles explicitly in your input script

32
doc/src/dump.rst
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@ -55,13 +55,13 @@ dump command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump ID group-ID style N file args dump ID group-ID style N file args
* ID = user-assigned name for the dump * ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped * group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* * style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* N = dump every this many timesteps * N = dump every this many timesteps
* file = name of file to write dump info to * file = name of file to write dump info to
* args = list of arguments for a particular style * args = list of arguments for a particular style
@ -69,10 +69,10 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*atom* args = none *atom* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* args = none *atom/gz* args = none
*atom/zstd* args = none *atom/zstd* args = none
*atom/mpiio* args = none *atom/mpiio* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*cfg* args = same as *custom* args, see below *cfg* args = same as *custom* args, see below
*cfg/gz* args = same as *custom* args, see below *cfg/gz* args = same as *custom* args, see below
*cfg/zstd* args = same as *custom* args, see below *cfg/zstd* args = same as *custom* args, see below
@ -223,7 +223,7 @@ page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
are identical in command syntax to the corresponding styles without are identical in command syntax to the corresponding styles without
"gz", however, they generate compressed files using the zlib "gz," however, they generate compressed files using the zlib
library. Thus the filename suffix ".gz" is mandatory. This is an library. Thus the filename suffix ".gz" is mandatory. This is an
alternative approach to writing compressed files via a pipe, as done alternative approach to writing compressed files via a pipe, as done
by the regular dump styles, which may be required on clusters where by the regular dump styles, which may be required on clusters where
@ -287,13 +287,13 @@ where xlo,xhi are the maximum extents of the simulation box in the
:math:`x`-dimension, and similarly for :math:`y` and :math:`z`. The :math:`x`-dimension, and similarly for :math:`y` and :math:`z`. The
"xx yy zz" terms are six characters that encode the style of boundary for each "xx yy zz" terms are six characters that encode the style of boundary for each
of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of
the six characters is either p (periodic), f (fixed), s (shrink wrap), the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
or m (shrink wrapped with a minimum value). See the or *m* (shrink wrapped with a minimum value). See the
:doc:`boundary <boundary>` command for details. :doc:`boundary <boundary>` command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output, bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (*xy*, *xz*, *yz*) of the triclinic box, along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
formatted as follows: formatted as follows:
.. parsed-literal:: .. parsed-literal::
@ -332,8 +332,8 @@ added for each atom via dump_modify.
Style *custom* allows you to specify a list of atom attributes to be Style *custom* allows you to specify a list of atom attributes to be
written to the dump file for each atom. Possible attributes are written to the dump file for each atom. Possible attributes are
listed above and will appear in the order specified. You cannot listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation - specify a quantity that is not defined for a particular simulation---such as
such as *q* for atom style *bond*, since that atom style does not *q* for atom style *bond*, since that atom style does not
assign charges. Dumps occur at the very end of a timestep, so atom assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during attributes will include effects due to fixes that are applied during
the timestep. An explanation of the possible dump custom attributes the timestep. An explanation of the possible dump custom attributes
@ -566,7 +566,7 @@ files. You can use the ".bin" or ".lammpsbin" suffix described below in an
MPI-IO dump file; again this file will be written in parallel and have the MPI-IO dump file; again this file will be written in parallel and have the
same binary format as if it were written without MPI-IO. same binary format as if it were written without MPI-IO.
If the filename ends with ".bin" or ".lammpsbin", the dump file (or files, if If the filename ends with ".bin" or ".lammpsbin," the dump file (or files, if
"\*" or "%" is also used) is written in binary format. A binary dump file "\*" or "%" is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically will be about the same size as a text version, but will typically
write out much faster. Of course, when post-processing, you will need write out much faster. Of course, when post-processing, you will need
@ -575,7 +575,7 @@ write your own code to read the binary file. The format of the binary file can
be understood by looking at the :file:`tools/binary2txt.cpp` file. This option be understood by looking at the :file:`tools/binary2txt.cpp` file. This option
is only available for the *atom* and *custom* styles. is only available for the *atom* and *custom* styles.
If the filename ends with ".gz", the dump file (or files, if "\*" or "%" If the filename ends with ".gz," the dump file (or files, if "\*" or "%"
is also used) is written in gzipped format. A gzipped dump file will be about is also used) is written in gzipped format. A gzipped dump file will be about
:math:`3\times` smaller than the text version, but will also take longer :math:`3\times` smaller than the text version, but will also take longer
to write. This option is not available for the *dcd* and *xtc* styles. to write. This option is not available for the *dcd* and *xtc* styles.
@ -683,8 +683,8 @@ of atom velocity and force and atomic charge.
There are several options for outputting atom coordinates. The *x*, There are several options for outputting atom coordinates. The *x*,
*y*, and *z* attributes write atom coordinates "unscaled," in the *y*, and *z* attributes write atom coordinates "unscaled," in the
appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`, appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
:math:`\sigma`, etc.). Use *xs*, *ys*, *zs* if you want the coordinates :math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the coordinates
"scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation "scaled" to the box size so that each value is 0.0 to 1.0. If the simulation
box is triclinic (tilted), then all atom coords will still be between 0.0 and box is triclinic (tilted), then all atom coords will still be between 0.0 and
1.0. The actual unscaled :math:`(x,y,z)` coordinate is 1.0. The actual unscaled :math:`(x,y,z)` coordinate is
:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
@ -727,7 +727,7 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
finite-size aspherical particles that have an angular momentum. Only finite-size aspherical particles that have an angular momentum. Only
the *ellipsoid* atom style defines this quantity. the *ellipsoid* atom style defines this quantity.
The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
can sustain a rotational torque due to interactions with other can sustain a rotational torque due to interactions with other
particles. particles.
@ -766,8 +766,8 @@ If *f_ID* is used as a attribute, then the per-atom vector calculated
by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
range from 1 to :math:`M`, which will print the :math:`i`\ th column of the range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
per-atom array with :math:`M` columns calculated by the fix. See the per-atom array with :math:`M` columns calculated by the fix. See the
discussion above for how :math:`i` can be specified with a wildcard asterisk to discussion above for how :math:`i` can be specified with a wildcard asterisk
effectively specify multiple values. to effectively specify multiple values.
The *v_name* attribute allows per-atom vectors calculated by a The *v_name* attribute allows per-atom vectors calculated by a
:doc:`variable <variable>` to be output. The name in the attribute :doc:`variable <variable>` to be output. The name in the attribute

13
doc/src/dump_adios.rst
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@ -10,10 +10,9 @@ dump custom/adios command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump ID group-ID atom/adios N file.bp dump ID group-ID atom/adios N file.bp
dump ID group-ID custom/adios N file.bp args dump ID group-ID custom/adios N file.bp args
* ID = user-assigned name for the dump * ID = user-assigned name for the dump
@ -21,7 +20,7 @@ Syntax
* adios = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page) * adios = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps * N = dump every this many timesteps
* file.bp = name of file/stream to write to * file.bp = name of file/stream to write to
* args = same options as in :doc:`\ *dump custom*\ <dump>` command * args = same options as in :doc:`dump custom <dump>` command
Examples Examples
"""""""" """"""""
@ -35,10 +34,10 @@ Examples
Description Description
""""""""""" """""""""""
Dump a snapshot of atom coordinates every N timesteps in the `ADIOS Dump a snapshot of atom coordinates every :math:`N` timesteps in the `ADIOS
<adios_>`_ based "BP" file format, or using different I/O solutions in <adios_>`_-based "BP" file format, or using different I/O solutions in
ADIOS, to a stream that can be read on-line by another program. ADIOS, to a stream that can be read on-line by another program.
ADIOS-BP files are binary, portable and self-describing. ADIOS-BP files are binary, portable, and self-describing.
.. _adios: https://github.com/ornladios/ADIOS2 .. _adios: https://github.com/ornladios/ADIOS2
@ -67,7 +66,7 @@ create a new file at each individual dump.
Restrictions Restrictions
"""""""""""" """"""""""""
The number of atoms per snapshot CAN change with the adios style. The number of atoms per snapshot **can** change with the adios style.
When using the ADIOS tool 'bpls' to list the content of a .bp file, When using the ADIOS tool 'bpls' to list the content of a .bp file,
bpls will print *__* for the size of the output table indicating that bpls will print *__* for the size of the output table indicating that
its size is changing every step. its size is changing every step.

10
doc/src/dump_cfg_uef.rst
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@ -6,7 +6,7 @@ dump cfg/uef command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump ID group-ID cfg/uef N file mass type xs ys zs args dump ID group-ID cfg/uef N file mass type xs ys zs args
@ -32,9 +32,8 @@ Description
This command is used to dump atomic coordinates in the This command is used to dump atomic coordinates in the
reference frame of the applied flow field when reference frame of the applied flow field when
:doc:`fix nvt/uef <fix_nh_uef>` or :doc:`fix nvt/uef <fix_nh_uef>` or :doc:`fix npt/uef <fix_nh_uef>` is used.
:doc:`fix npt/uef <fix_nh_uef>` or is used. Only the atomic Only the atomic coordinates and frame-invariant scalar quantities
coordinates and frame-invariant scalar quantities
will be in the flow frame. If velocities are selected will be in the flow frame. If velocities are selected
as output, for example, they will not be in the same as output, for example, they will not be in the same
reference frame as the atomic positions. reference frame as the atomic positions.
@ -43,7 +42,8 @@ Restrictions
"""""""""""" """"""""""""
This fix is part of the UEF package. It is only enabled if LAMMPS This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info. was built with that package. See the :doc:`Build package <Build_package>`
page for more info.
This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>` This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
or :doc:`fix npt/uef <fix_nh_uef>` is active. or :doc:`fix npt/uef <fix_nh_uef>` is active.

105
doc/src/dump_image.rst
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@ -12,7 +12,7 @@ dump movie command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump ID group-ID style N file color diameter keyword value ... dump ID group-ID style N file color diameter keyword value ...
@ -28,7 +28,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*atom* = yes/no = do or do not draw atoms *atom* = *yes* or *no* = do or do not draw atoms
*adiam* size = numeric value for atom diameter (distance units) *adiam* size = numeric value for atom diameter (distance units)
*bond* values = color width = color and width of bonds *bond* values = color width = color and width of bonds
color = *atom* or *type* or *none* color = *atom* or *type* or *none*
@ -68,21 +68,20 @@ Syntax
*box* values = yes/no diam = draw outline of simulation box *box* values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length diam = diameter of box lines as fraction of shortest box length
*axes* values = yes/no length diam = draw xyz axes *axes* values = axes length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length diam = diameter of axes lines as fraction of shortest box length
*subbox* values = yes/no diam = draw outline of processor sub-domains *subbox* values = lines diam = draw outline of processor sub-domains
yes/no = do or do not draw sub-domain lines lines = *yes* or *no* = do or do not draw sub-domain lines
diam = diameter of sub-domain lines as fraction of shortest box length diam = diameter of sub-domain lines as fraction of shortest box length
*shiny* value = sfactor = shinyness of spheres and cylinders *shiny* value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0 sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
*ssao* value = yes/no seed dfactor = SSAO depth shading *ssao* value = shading seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off shading = *yes* or *no* = turn depth shading on/off
seed = random # seed (positive integer) seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0 dfactor = strength of shading from 0.0 to 1.0
.. _dump_modify_image: .. _dump_modify_image:
dump_modify options for dump image/movie dump_modify options for dump image/movie
@ -162,7 +161,7 @@ Examples
Description Description
""""""""""" """""""""""
Dump a high-quality rendered image of the atom configuration every N Dump a high-quality rendered image of the atom configuration every :math:`N`
timesteps and save the images either as a sequence of JPEG or PNG or timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as PPM files, or as a single movie file. The options for this command as
well as the :doc:`dump_modify <dump_modify>` command control what is well as the :doc:`dump_modify <dump_modify>` command control what is
@ -179,7 +178,7 @@ has been run, using the :doc:`rerun <rerun>` command to read snapshots
from an existing dump file, and using these dump commands in the rerun from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie. script to generate the images/movie.
Here are two sample images, rendered as 1024x1024 JPEG files. Here are two sample images, rendered as :math:`1024\times 1024` JPEG files.
.. |dump1| image:: img/dump1.jpg .. |dump1| image:: img/dump1.jpg
:width: 48% :width: 48%
@ -197,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The
alter what atoms are included in the image. alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the *image* dump style. If the suffix is ".jpg" or created with the *image* dump style. If the suffix is ".jpg" or
".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the ".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
suffix is ".png", then a `PNG format <png_format_>`_ is created, else suffix is ".png," then a `PNG format <png_format_>`_ is created, else
a `PPM (aka NETPBM) format <ppm_format_>`_ file is created. a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
The JPEG and PNG files are binary; PPM has a text mode header followed The JPEG and PNG files are binary; PPM has a text mode header followed
by binary data. JPEG images have lossy compression, PNG has lossless by binary data. JPEG images have lossy compression, PNG has lossless
@ -232,22 +231,22 @@ details.
---------- ----------
Dumps are performed on timesteps that are a multiple of N (including Dumps are performed on timesteps that are a multiple of :math:`N` (including
timestep 0) and on the last timestep of a minimization if the timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked, performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be if the current timestep is not a multiple of :math:`N`. This behavior can be
changed via the :doc:`dump_modify first <dump_modify>` command, which changed via the :doc:`dump_modify first <dump_modify>` command, which
can be useful if the dump command is invoked after a minimization can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by ended on an arbitrary timestep. :math:`N` can be changed between runs by
using the :doc:`dump_modify every <dump_modify>` command. using the :doc:`dump_modify every <dump_modify>` command.
Dump *image* filenames must contain a wildcard character "\*", so that Dump *image* filenames must contain a wildcard character "\*" so that
one image file per snapshot is written. The "\*" character is replaced one image file per snapshot is written. The "\*" character is replaced
with the timestep value. For example, tmp.dump.\*.jpg becomes with the timestep value. For example, tmp.dump.\*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the :doc:`dump_modify pad <dump_modify>` command can be used to that the :doc:`dump_modify pad <dump_modify>` command can be used to
insure all timestep numbers are the same length (e.g. 00010), which insure all timestep numbers are the same length (e.g., 00010), which
can make it easier to convert a series of images into a movie in the can make it easier to convert a series of images into a movie in the
correct ordering. correct ordering.
@ -262,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined
for the :doc:`dump custom <dump>` command, including *type* and for the :doc:`dump custom <dump>` command, including *type* and
*element*\ . This includes per-atom quantities calculated by a *element*\ . This includes per-atom quantities calculated by a
:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`, :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
which are prefixed by "c\_", "f\_", or "v\_" respectively. Note that the which are prefixed by "c\_," "f\_," or "v\_," respectively. Note that the
*diameter* setting can be overridden with a numeric value applied to *diameter* setting can be overridden with a numeric value applied to
all atoms by the optional *adiam* keyword. all atoms by the optional *adiam* keyword.
@ -277,7 +276,7 @@ to colors is as follows:
* type 5 = aqua * type 5 = aqua
* type 6 = cyan * type 6 = cyan
and repeats itself for types > 6. This mapping can be changed by the and repeats itself for types :math:`> 6`. This mapping can be changed by the
"dump_modify acolor" command, as described below. "dump_modify acolor" command, as described below.
If *type* is specified for the *diameter* setting then the diameter of If *type* is specified for the *diameter* setting then the diameter of
@ -298,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
If other atom attributes are used for the *color* or *diameter* If other atom attributes are used for the *color* or *diameter*
settings, they are interpreted in the following way. settings, they are interpreted in the following way.
If "vx", for example, is used as the *color* setting, then the color If "vx," for example, is used as the *color* setting, then the color
of the atom will depend on the x-component of its velocity. The of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the dump_modify command, as a "color map," which can be specified via the dump_modify command, as
described below. The basic idea is that the atom-attribute will be described below. The basic idea is that the atom-attribute will be
within a range of values, and every value within the range is mapped within a range of values, and every value within the range is mapped
to a specific color. Depending on how the color map is defined, that to a specific color. Depending on how the color map is defined, that
mapping can take place via interpolation so that a value of -3.2 is mapping can take place via interpolation so that a value of -3.2 is
halfway between "red" and "blue", or discretely so that the value of halfway between "red" and "blue," or discretely so that the value of
-3.2 is "orange". -3.2 is "orange".
If "vx", for example, is used as the *diameter* setting, then the atom If "vx," for example, is used as the *diameter* setting, then the atom
will be rendered using the x-component of its velocity as the will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by drawn. Note that finite-size spherical particles, as defined by
@ -773,10 +772,11 @@ the number 5.0 would be used. But for a fractional map, the number
The *delta* setting must be specified for all styles, but is only used The *delta* setting must be specified for all styles, but is only used
for the sequential style; otherwise the value is ignored. It for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to consecutive colors to. For example, if the range is from :math:`-10.0` to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to :math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
the range. The first will be from -10.0 <= color1 < -9.0, then second assigned to the range. The first will be from
from -9.0 <= color2 < -8.0, etc. :math:`-10.0 \le \text{color1} < -9.0`, then second from
:math:`-9.0 \le color2 < -8.0`, etc.
The *N* setting is how many entries follow. The format of the entries The *N* setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or depends on whether the color map style is continuous, discrete or
@ -793,13 +793,13 @@ as absolute numbers or as fractions (0.0 to 1.0) of the range,
depending on the "a" or "f" in the style setting for the color map. depending on the "a" or "f" in the style setting for the color map.
Here is how the entries are used to determine the color of an Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. X will fall individual atom, given the value :math:`X` of its atom attribute.
between 2 of the entry values. The color of the atom is linearly :math:`X` will fall between 2 of the entry values. The color of the atom is
interpolated (in each of the RGB values) between the 2 colors linearly interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if X = -5.0 and the 2 associated with those entries. For example, if :math:`X = -5.0` and the two
surrounding entries are "red" at -10.0 and "blue" at 0.0, then the surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
atom's color will be halfway between "red" and "blue", which happens then the atom's color will be halfway between "red" and "blue," which happens
to be "purple". to be "purple."
For discrete color maps, each entry has a *lo* and *hi* value and a For discrete color maps, each entry has a *lo* and *hi* value and a
*color*\ . The *lo* and *hi* settings are either numbers within the *color*\ . The *lo* and *hi* settings are either numbers within the
@ -864,20 +864,20 @@ The *bcolor* keyword can be used with the dump image command, with its
*bond* keyword, when its color setting is *type*, to set the color *bond* keyword, when its color setting is *type*, to set the color
that bonds of each type will be drawn in the image. that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Nbondtypes = the The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
number of bond types. A wildcard asterisk can be used in place of or is the number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of bond in conjunction with the *type* argument to specify a range of bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
the number of bond types, then an asterisk with no numeric values is the number of bond types, then an asterisk with no numerical values
means all types from 1 to N. A leading asterisk means all types from means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). (inclusive).
The specified *color* can be a single color which is any of the 140 The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the pre-defined colors (see below) or a color name defined by the
dump_modify color option. Or it can be two or more colors separated dump_modify color option. Or it can be two or more colors separated
by a "/" character, e.g. red/green/blue. In the former case, that by a "/" character (e.g., red/green/blue). In the former case, that
color is assigned to all the specified bond types. In the latter color is assigned to all the specified bond types. In the latter
case, the list of colors are assigned in a round-robin fashion to each case, the list of colors are assigned in a round-robin fashion to each
of the specified bond types. of the specified bond types.
@ -885,13 +885,13 @@ of the specified bond types.
---------- ----------
The *bdiam* keyword can be used with the dump image command, with its The *bdiam* keyword can be used with the dump image command, with its
*bond* keyword, when its diam setting is *type*, to set the diameter *bond* keyword, when its *diam* setting is *type*, to set the diameter
that bonds of each type will be drawn in the image. The specified that bonds of each type will be drawn in the image. The specified
*type* should be an integer from 1 to Nbondtypes. As with the *type* should be an integer from 1 to Nbondtypes. As with the
*bcolor* keyword, a wildcard asterisk can be used as part of the *bcolor* keyword, a wildcard asterisk can be used as part of the
*type* argument to specify a range of bond types. The specified *type* argument to specify a range of bond types. The specified
*diam* is the size in whatever distance :doc:`units <units>` you are *diam* is the size in whatever distance :doc:`units <units>` you are
using, e.g. Angstroms. using (e.g., Angstroms).
---------- ----------
@ -922,7 +922,7 @@ dump_modify color option.
---------- ----------
The *color* keyword allows definition of a new color name, in addition The *color* keyword allows definition of a new color name, in addition
to the 140-predefined colors (see below), and associates 3 to the 140-predefined colors (see below), and associates three
red/green/blue RGB values with that color name. The color name can red/green/blue RGB values with that color name. The color name can
then be used with any other dump_modify keyword that takes a color then be used with any other dump_modify keyword that takes a color
name as a value. The RGB values should each be floating point values name as a value. The RGB values should each be floating point values
@ -959,15 +959,15 @@ PNG library.
To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase, machine where LAMMPS is being run. Typically its name is lowercase
i.e. ffmpeg. (i.e., "ffmpeg").
See the :doc:`Build settings <Build_settings>` page for details. See the :doc:`Build settings <Build_settings>` page for details.
Note that since FFmpeg is run as an external program via a pipe, Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about LAMMPS has limited control over its execution and no knowledge about
errors and warnings printed by it. Those warnings and error messages errors and warnings printed by it. Those warnings and error messages
will be printed to the screen only. Due to the way image data is will be printed to the screen only. Due to the way image data are
communicated to FFmpeg, it will often print the message communicated to FFmpeg, it will often print the message
.. parsed-literal:: .. parsed-literal::
@ -976,7 +976,7 @@ communicated to FFmpeg, it will often print the message
which can be safely ignored. Other warnings which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation. and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1 One known issue is that certain movie file formats (e.g., MPEG level 1
and 2 format streams) have video bandwidth limits that can be crossed and 2 format streams) have video bandwidth limits that can be crossed
when rendering too large of image sizes. Typical warnings look like when rendering too large of image sizes. Typical warnings look like
this: this:
@ -987,10 +987,9 @@ this:
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018 [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018 [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
In this case it is recommended to either reduce the size of the image In this case it is recommended either to reduce the size of the image
or encode in a different format that is also supported by your copy of or to encode in a different format that is also supported by your copy of
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv, FFmpeg and which does not have this limitation (e.g., .avi, .mkv, mp4).
mp4).
Related commands Related commands
"""""""""""""""" """"""""""""""""

13
doc/src/dump_vtk.rst
View File

@ -6,13 +6,13 @@ dump vtk command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump ID group-ID vtk N file args dump ID group-ID vtk N file args
* ID = user-assigned name for the dump * ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped * group-ID = ID of the group of atoms to be dumped
* vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page) * vtk = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps * N = dump every this many timesteps
* file = name of file to write dump info to * file = name of file to write dump info to
* args = same as arguments for :doc:`dump_style custom <dump>` * args = same as arguments for :doc:`dump_style custom <dump>`
@ -28,17 +28,18 @@ Examples
Description Description
""""""""""" """""""""""
Dump a snapshot of atom quantities to one or more files every N Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it, timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
e.g. `ParaView <http://www.paraview.org>`_. The timesteps on which dump such as `ParaView <http://www.paraview.org>`_. The time steps on which dump
output is written can also be controlled by a variable; see the output is written can also be controlled by a variable; see the
:doc:`dump_modify every <dump_modify>` command for details. :doc:`dump_modify every <dump_modify>` command for details.
This dump style is similar to :doc:`dump_style custom <dump>` but uses This dump style is similar to :doc:`dump_style custom <dump>` but uses
the VTK library to write data to VTK simple legacy or XML format the VTK library to write data to VTK simple legacy or XML format,
depending on the filename extension specified for the dump file. This depending on the filename extension specified for the dump file. This
can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*, can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
respectively, for XML format; see the `VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed respectively, for XML format; see the
`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
description of these formats. Since this naming convention conflicts description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), the with the way binary output is usually specified (see below), the
:doc:`dump_modify binary <dump_modify>` command allows setting of a :doc:`dump_modify binary <dump_modify>` command allows setting of a

31
doc/src/fix_accelerate_cos.rst
View File

@ -6,8 +6,7 @@ fix accelerate/cos command
Syntax Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
fix ID group-ID accelerate value fix ID group-ID accelerate value
@ -19,7 +18,6 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix 1 all accelerate/cos 0.02e-5 fix 1 all accelerate/cos 0.02e-5
@ -34,8 +32,8 @@ The acceleration is a periodic function along the z-direction:
a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right) a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length where :math:`A` is the acceleration amplitude, :math:`l_z` is the
of the simulation box. :math:`z`-length of the simulation box.
At steady state, the acceleration generates a velocity profile: At steady state, the acceleration generates a velocity profile:
.. math:: .. math::
@ -49,17 +47,18 @@ shear viscosity :math:`\eta` by:
V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2} V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
and it can be obtained from ensemble average of the velocity profile: and it can be obtained from ensemble average of the velocity profile:
.. math:: .. math::
V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}} V = \frac{\sum\limits_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum\limits_i m_{i}},
where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass, where :math:`m_i`, :math:`v_{i,x}`, and :math:`z_i` are the mass,
x-component velocity and z coordinate of a particle. :math:`x`-component velocity, and :math:`z`-coordinate of a particle,
respectively.
The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`, The velocity amplitude :math:`V` can be calculated with
:doc:`compute viscosity/cos <compute_viscosity_cos>`,
which enables viscosity calculation with periodic perturbation method, which enables viscosity calculation with periodic perturbation method,
as described by :ref:`Hess<Hess2>`. as described by :ref:`Hess<Hess2>`.
Because the applied acceleration drives the system away from equilibration, Because the applied acceleration drives the system away from equilibration,
@ -79,15 +78,17 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. No information about this fix is written to binary restart files.
None of the fix_modify options are relevant to this fix. None of the fix_modify options are relevant to this fix.
No global or per-atom quantities are stored by this fix for access by various output commands. No global or per-atom quantities are stored by this fix for access by various
No parameter of this fix can be used with the start/stop keywords of the run command. output commands. No parameter of this fix can be used with the start/stop
keywords of the run command.
This fix is not invoked during energy minimization. This fix is not invoked during energy minimization.
Restrictions Restrictions
"""""""""""" """"""""""""
This command is only available when LAMMPS was built with the MISC package. This command is only available when LAMMPS was built with the MISC package.
Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations. Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used
in 2d simulations.
Related commands Related commands
"""""""""""""""" """"""""""""""""
@ -96,10 +97,10 @@ Related commands
Default Default
""""""" """""""
none none
---------- ----------
.. _Hess2: .. _Hess2:
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217. **(Hess)** Hess, B. Journal of Chemical Physics 2002, 116 (1), 209--217.

13
doc/src/fix_acks2_reaxff.rst
View File

@ -9,7 +9,7 @@ Accelerator Variants: *acks2/reaxff/kk*
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
@ -37,10 +37,10 @@ Examples
Description Description
""""""""""" """""""""""
Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge Perform the atom-condensed Kohn--Sham DFT to second order (ACKS2) charge
equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`. equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
ACKS2 impedes unphysical long-range charge transfer sometimes seen with ACKS2 impedes unphysical long-range charge transfer sometimes seen with
QEq (e.g. for dissociation of molecules), at increased computational QEq (e.g., for dissociation of molecules), at increased computational
cost. It is typically used in conjunction with the ReaxFF force field cost. It is typically used in conjunction with the ReaxFF force field
model as implemented in the :doc:`pair_style reaxff <pair_reaxff>` model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it command, but it can be used with any potential in LAMMPS, so long as it
@ -71,7 +71,8 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
bond cutoff distance. Note that these 4 quantities are also in the bond cutoff distance. Note that these 4 quantities are also in the
ReaxFF potential file, except that eta is defined here as twice the eta ReaxFF potential file, except that eta is defined here as twice the eta
value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge. of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and
electronic charge.
The optional *maxiter* keyword allows changing the max number The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200. of iterations in the linear solver. The default value is 200.
@ -110,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms. periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`.
This fix may be used in combination with :doc:`fix efield <fix_efield>` This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration, and will apply the external electric field during charge equilibration,
@ -132,7 +133,7 @@ maxiter 200
.. _O'Hearn: .. _O'Hearn:
**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020). **(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
.. _Verstraelen: .. _Verstraelen:

139
doc/src/fix_adapt.rst
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@ -6,7 +6,7 @@ fix adapt command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID adapt N attribute args ... keyword value ... fix ID group-ID adapt N attribute args ... keyword value ...
@ -19,22 +19,22 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*pair* args = pstyle pparam I J v_name *pair* args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam v_name = variable with name that calculates value of pparam
*bond* args = bstyle bparam I v_name *bond* args = bstyle bparam I v_name
bstyle = bond style name, e.g. harmonic bstyle = bond style name (e.g., harmonic)
bparam = parameter to adapt over time bparam = parameter to adapt over time
I = type bond to set parameter for I = type bond to set parameter for
v_name = variable with name that calculates value of bparam v_name = variable with name that calculates value of bparam
*angle* args = astyle aparam I v_name *angle* args = astyle aparam I v_name
astyle = angle style name, e.g. harmonic astyle = angle style name (e.g., harmonic)
aparam = parameter to adapt over time aparam = parameter to adapt over time
I = type angle to set parameter for I = type angle to set parameter for
v_name = variable with name that calculates value of aparam v_name = variable with name that calculates value of aparam
*kspace* arg = v_name *kspace* arg = v_name
v_name = variable with name that calculates scale factor on K-space terms v_name = variable with name that calculates scale factor on :math:`k`-space terms
*atom* args = atomparam v_name *atom* args = atomparam v_name
atomparam = *charge* or *diameter* or *diameter/disc* = parameter to adapt over time atomparam = *charge* or *diameter* or *diameter/disc* = parameter to adapt over time
v_name = variable with name that calculates value of atomparam v_name = variable with name that calculates value of atomparam
@ -70,22 +70,22 @@ Examples
Description Description
""""""""""" """""""""""
Change or adapt one or more specific simulation attributes or settings Change or adapt one or more specific simulation attributes or settings over
over time as a simulation runs. Pair potential and K-space and atom time as a simulation runs. Pair potential and :math:`k`-space and atom
attributes which can be varied by this fix are discussed below. Many attributes which can be varied by this fix are discussed below. Many other
other fixes can also be used to time-vary simulation parameters, fixes can also be used to time-vary simulation parameters (e.g., the
e.g. the "fix deform" command will change the simulation box :doc:`fix deform <fix_deform>` command will change the simulation box
size/shape and the "fix move" command will change atom positions and size/shape and the :doc:`fix move <fix_move>` command will change atom
velocities in a prescribed manner. Also note that many commands allow positions and velocities in a prescribed manner). Also note that many commands
variables as arguments for specific parameters, if described in that allow variables as arguments for specific parameters, if described in that
manner on their doc pages. An equal-style variable can calculate a manner on their doc pages. An equal-style variable can calculate a
time-dependent quantity, so this is another way to vary a simulation time-dependent quantity, so this is another way to vary a simulation parameter
parameter over time. over time.
If *N* is specified as 0, the specified attributes are only changed If :math:`N` is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If *N* > 0, then changes associated variables are not time-dependent. If :math:`N > 0`, then changes
are made every *N* steps during the simulation, presumably with a are made every :math:`N` steps during the simulation, presumably with a
variable that is time-dependent. variable that is time-dependent.
Depending on the value of the *reset* keyword, attributes changed by Depending on the value of the *reset* keyword, attributes changed by
@ -98,9 +98,9 @@ If the *scale* keyword is set to *no*, which is the default, then
the value of the altered parameter will be whatever the variable the value of the altered parameter will be whatever the variable
generates. If the *scale* keyword is set to *yes*, then the value generates. If the *scale* keyword is set to *yes*, then the value
of the altered parameter will be the initial value of that parameter of the altered parameter will be the initial value of that parameter
multiplied by whatever the variable generates. I.e. the variable is multiplied by whatever the variable generates (i.e., the variable is
now a "scale factor" applied in (presumably) a time-varying fashion to now a "scale factor" applied in (presumably) a time-varying fashion to
the parameter. the parameter).
Note that whether scale is *no* or *yes*, internally, the parameters Note that whether scale is *no* or *yes*, internally, the parameters
themselves are actually altered by this fix. Make sure you use the themselves are actually altered by this fix. Make sure you use the
@ -120,9 +120,9 @@ The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. If there are multiple *pstyle* should be a sub-style name. If there are multiple
sub-styles using the same pair style, then *pstyle* should be specified sub-styles using the same pair style, then *pstyle* should be specified
as "style:N" where N is which instance of the pair style you wish to as "style:N", where :math:`N` is which instance of the pair style you wish to
adapt, e.g. the first, second, etc. For example, *pstyle* could be adapt (e.g., the first or second). For example, *pstyle* could be
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2." The
*pparam* argument is the name of the parameter to change. This is the *pparam* argument is the name of the parameter to change. This is the
current list of pair styles and parameters that can be varied by this current list of pair styles and parameters that can be varied by this
fix. See the doc pages for individual pair styles and their energy fix. See the doc pages for individual pair styles and their energy
@ -216,45 +216,46 @@ formulas for the meaning of these parameters:
to this list. All it typically takes is adding an extract() method to to this list. All it typically takes is adding an extract() method to
the pair\_\*.cpp file associated with the potential. the pair\_\*.cpp file associated with the potential.
Some parameters are global settings for the pair style, e.g. the Some parameters are global settings for the pair style (e.g., the
viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`. viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`).
Other parameters apply to atom type pairs within the pair style, Other parameters apply to atom type pairs within the pair style (e.g., the
e.g. the prefactor "a" for :doc:`pair_style soft <pair_soft>`. prefactor :math:`a` for :doc:`pair_style soft <pair_soft>`).
Note that for many of the potentials, the parameter that can be varied Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale" potential (e.g., the lj/cut epsilon). The parameters listed as "scale"
are exactly that, since the energy expression for the are exactly that, since the energy expression for the
:doc:`coul/cut <pair_coul>` potential (for example) has no labeled :doc:`coul/cut <pair_coul>` potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the potentials, multiple parameters need to be altered. For example, the
:doc:`Buckingham potential <pair_buck>` needs both the A and C terms :doc:`Buckingham potential <pair_buck>` needs both the :math:`A` and
altered together. To scale the Buckingham potential, you should thus :math:`C` terms altered together. To scale the Buckingham potential, you
list the pair style twice, once for A and once for C. should thus list the pair style twice, once for :math:`A` and once for
:math:`C`.
If a type pair parameter is specified, the *I* and *J* settings should If a type pair parameter is specified, the :math:`I` and :math:`J` settings
be specified to indicate which type pairs to apply it to. If a global should be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the *I* and *J* settings still need to be parameter is specified, the :math:`I` and :math:`J` settings still need to be
specified, but are ignored. specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
specified in one of two ways. Explicit numeric values can be used for can be specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. I <= J is required. LAMMPS sets each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values. the coefficients for the symmetric :math:`J,I` interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
the number of atom types, then an asterisk with no numeric values is the number of atom types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if (inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where J < I, they are ignored. asterisks imply type pairs where :math:`J < I`, they are ignored.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
<pair_hybrid>` is being used, then the *pstyle* will be a sub-style <pair_hybrid>` is being used, then the *pstyle* will be a sub-style
name. You must specify I,J arguments that correspond to type pair name. You must specify :math:`I,J` arguments that correspond to type pair
values defined (via the :doc:`pair_coeff <pair_coeff>` command) for values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
that sub-style. that sub-style.
@ -289,12 +290,11 @@ given bond type is adapted.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with
the bond type argument to set the coefficients for multiple bond the bond type argument to set the coefficients for multiple bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
the number of bond types, then an asterisk with no numeric values is the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n (inclusive).
(inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work hybrid/overlay as bond styles. The bond styles that currently work
@ -325,12 +325,11 @@ given angle type is adapted.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with
the angle type argument to set the coefficients for multiple angle the angle type argument to set the coefficients for multiple angle
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
the number of angle types, then an asterisk with no numeric values is the number of angle types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n (inclusive).
(inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work hybrid/overlay as angle styles. The angle styles that currently work
@ -348,7 +347,7 @@ this fix uses to reset theta0 needs to generate values in radians.
---------- ----------
The *kspace* keyword used the specified variable as a scale factor on The *kspace* keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is the energy, forces, virial calculated by whatever :math:`k`-space solver is
defined by the :doc:`kspace_style <kspace_style>` command. If the defined by the :doc:`kspace_style <kspace_style>` command. If the
variable has a value of 1.0, then the solver is unaltered. variable has a value of 1.0, then the solver is unaltered.
@ -373,17 +372,17 @@ with equal-style variables. The new value is assigned to the
corresponding attribute for all atoms in the fix group. corresponding attribute for all atoms in the fix group.
If the atom parameter is *diameter* and per-atom density and per-atom If the atom parameter is *diameter* and per-atom density and per-atom
mass are defined for particles (e.g. :doc:`atom_style granular mass are defined for particles (e.g., :doc:`atom_style granular
<atom_style>`), then the mass of each particle is, by default, also <atom_style>`), then the mass of each particle is, by default, also
changed when the diameter changes. The mass is set from the particle changed when the diameter changes. The mass is set from the particle
volume for 3d systems (density is assumed to stay constant). For 2d, volume for 3d systems (density is assumed to stay constant). For 2d,
the default is for LAMMPS to model particles with a radius attribute the default is for LAMMPS to model particles with a radius attribute
as spheres. However, if the atom parameter is *diameter/disc*, then the as spheres. However, if the atom parameter is *diameter/disc*, then the
mass is set from the particle area (the density is assumed to be in mass is set from the particle area (the density is assumed to be in
mass/distance^2 units). The mass of the particle may also be kept constant mass/distance\ :math:`^2` units). The mass of the particle may also be kept
if the *mass* keyword is set to *no*. This can be useful to account for constant if the *mass* keyword is set to *no*. This can be useful to account
diameter changes that do not involve mass changes, e.g., thermal expansion. for diameter changes that do not involve mass changes (e.g., thermal
expansion).
For example, these commands would shrink the diameter of all granular For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion particles in the "center" group from 1.0 to 0.1 in a linear fashion
@ -405,11 +404,11 @@ their original values at the end of the last restarted run.
Note that all the parameters changed by this fix are written into a Note that all the parameters changed by this fix are written into a
restart file in their current changed state. A new restarted restart file in their current changed state. A new restarted
simulation does not know their original time=0 values, unless the simulation does not know the original time=0 values, unless the
input script explicitly resets the parameters (after the restart file input script explicitly resets the parameters (after the restart file
is read), to their original values. is read) to the original values.
Also note, that the time-dependent variable(s) used in the restart Also note that the time-dependent variable(s) used in the restart
script should typically be written as a function of time elapsed since script should typically be written as a function of time elapsed since
the original simulation began. the original simulation began.
@ -430,8 +429,8 @@ the one used in the original script.
In a restarted run, if the *reset* keyword is set to *yes*, and the In a restarted run, if the *reset* keyword is set to *yes*, and the
run ends in this script (as opposed to just writing more restart run ends in this script (as opposed to just writing more restart
files, parameters will be restored to the values they were at the files), parameters will be restored to the values they were at the
beginning of the run command in the restart script. Which as beginning of the run command in the restart script, which as
explained above, may or may not be the original values of the explained above, may or may not be the original values of the
parameters. Again, an exception is if the *atom* keyword is being parameters. Again, an exception is if the *atom* keyword is being
used with *reset yes* (in all the runs). In that case, the original used with *reset yes* (in all the runs). In that case, the original

67
doc/src/fix_adapt_fep.rst
View File

@ -6,7 +6,7 @@ fix adapt/fep command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID adapt/fep N attribute args ... keyword value ... fix ID group-ID adapt/fep N attribute args ... keyword value ...
@ -19,7 +19,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*pair* args = pstyle pparam I J v_name *pair* args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam v_name = variable with name that calculates value of pparam
@ -66,12 +66,12 @@ Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. over time as a simulation runs.
This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command
with two differences, with two differences:
* It is possible to modify the charges of chosen atom types only, * It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system. instead of scaling all the charges in the system.
* There is a new option *after* for better compatibility with "fix * There is a new option *after* for better compatibility with
ave/time". :doc:`fix ave/time <fix_ave_time>`.
This version is suited for free energy calculations using This version is suited for free energy calculations using
:doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`. :doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`.
@ -92,8 +92,8 @@ If the *scale* keyword is set to *no*, then the value the parameter is
set to will be whatever the variable generates. If the *scale* set to will be whatever the variable generates. If the *scale*
keyword is set to *yes*, then the value of the altered parameter will keyword is set to *yes*, then the value of the altered parameter will
be the initial value of that parameter multiplied by whatever the be the initial value of that parameter multiplied by whatever the
variable generates. I.e. the variable is now a "scale factor" applied variable generates (i.e., the variable is now a "scale factor" applied
in (presumably) a time-varying fashion to the parameter. Internally, in (presumably) a time-varying fashion to the parameter). Internally,
the parameters themselves are actually altered; make sure you use the the parameters themselves are actually altered; make sure you use the
*reset yes* option if you want the parameters to be restored to their *reset yes* option if you want the parameters to be restored to their
initial values after the run. initial values after the run.
@ -115,7 +115,7 @@ overrides the parameters.
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
a sub-style name. For example, *pstyle* could be specified as "soft" a sub-style name. For example, *pstyle* could be specified as "soft"
or "lubricate". The *pparam* argument is the name of the parameter to or "lubricate." The *pparam* argument is the name of the parameter to
change. This is the current list of pair styles and parameters that change. This is the current list of pair styles and parameters that
can be varied by this fix. See the doc pages for individual pair can be varied by this fix. See the doc pages for individual pair
styles and their energy formulas for the meaning of these parameters: styles and their energy formulas for the meaning of these parameters:
@ -188,7 +188,7 @@ styles and their energy formulas for the meaning of these parameters:
Note that for many of the potentials, the parameter that can be varied Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale" potential (e.g., the lj/cut epsilon). The parameters listed as "scale"
are exactly that, since the energy expression for the are exactly that, since the energy expression for the
:doc:`coul/cut <pair_coul>` potential (for example) has no labeled :doc:`coul/cut <pair_coul>` potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some prefactor in its formula. To apply an effective prefactor to some
@ -204,23 +204,23 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. I <= J is required. LAMMPS sets each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values. the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is
number of atom types, then an asterisk with no numeric values means the number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if (inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where J < I, they are ignored. asterisks imply type pairs where :math:`J < I`, they are ignored.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is
be a sub-style name. You must specify I,J arguments that correspond being used, then the *pstyle* will be a sub-style name. You must specify
to type pair values defined (via the :doc:`pair_coeff <pair_coeff>` :math:`I,J` arguments that correspond to type pair values defined (via the
command) for that sub-style. :doc:`pair_coeff <pair_coeff>` command) for that sub-style.
The *v_name* argument for keyword *pair* is the name of an The *v_name* argument for keyword *pair* is the name of an
:doc:`equal-style variable <variable>` which will be evaluated each time :doc:`equal-style variable <variable>` which will be evaluated each time
@ -232,8 +232,7 @@ simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the consecutive runs in a continuous fashion. For the latter, see the
*start* and *stop* keywords of the :doc:`run <run>` command and the *start* and *stop* keywords of the :doc:`run <run>` command and the
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for *elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
details.
For example, these commands would change the prefactor coefficient of For example, these commands would change the prefactor coefficient of
the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
@ -247,7 +246,7 @@ linear fashion over the course of a simulation:
---------- ----------
The *kspace* keyword used the specified variable as a scale factor on The *kspace* keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is the energy, forces, virial calculated by whatever :math:`k`-space solver is
defined by the :doc:`kspace_style <kspace_style>` command. If the defined by the :doc:`kspace_style <kspace_style>` command. If the
variable has a value of 1.0, then the solver is unaltered. variable has a value of 1.0, then the solver is unaltered.
@ -263,8 +262,8 @@ current list of atom parameters that can be varied by this fix:
* charge = charge on particle * charge = charge on particle
* diameter = diameter of particle * diameter = diameter of particle
The *I* argument indicates which atom types are affected. A wild-card The :math:`I` argument indicates which atom types are affected. A wild-card
asterisk can be used in place of or in conjunction with the I argument asterisk can be used in place of or in conjunction with the :math:`I` argument
to set the coefficients for multiple atom types. to set the coefficients for multiple atom types.
The *v_name* argument of the *atom* keyword is the name of an The *v_name* argument of the *atom* keyword is the name of an
@ -276,9 +275,9 @@ variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group. for all atoms in the fix group.
If the atom parameter is *diameter* and per-atom density and per-atom If the atom parameter is *diameter* and per-atom density and per-atom
mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also mass are defined for particles (e.g., :doc:`atom_style granular <atom_style>`),
changed when the diameter changes (density is assumed to stay then the mass of each particle is also changed when the diameter changes
constant). (density is assumed to stay constant).
For example, these commands would shrink the diameter of all granular For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion particles in the "center" group from 1.0 to 0.1 in a linear fashion
@ -297,11 +296,14 @@ parameters on the outermost rRESPA level.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options No information about this fix is written to
:doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`. by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""
@ -310,7 +312,8 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>` :doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`,
:doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
Default Default
""""""" """""""

62
doc/src/fix_addforce.rst
View File

@ -6,7 +6,7 @@ fix addforce command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID addforce fx fy fz keyword value ... fix ID group-ID addforce fx fy fz keyword value ...
@ -24,7 +24,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*every* value = Nevery *every* value = Nevery
Nevery = add force every this many timesteps Nevery = add force every this many time steps
*region* value = region-ID *region* value = region-ID
region-ID = ID of region atoms must be in to have added force region-ID = ID of region atoms must be in to have added force
*energy* value = v_name *energy* value = v_name
@ -42,31 +42,31 @@ Examples
Description Description
""""""""""" """""""""""
Add fx,fy,fz to the corresponding component of force for each atom in Add :math:`(f_x,f_y,f_z)` to the corresponding component of the force for each
the group. This command can be used to give an additional push to atom in the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel. a channel.
Any of the 3 quantities defining the force components can be specified Any of the three quantities defining the force components, namely :math:`f_x`,
as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*, :math:`f_y`, and :math:`f_z`, can be specified as an equal-style or atom-style
*fy*, *fz*\ . If the value is a variable, it should be specified as :doc:`variable <variable>`. If the value is a variable, it should be specified
v_name, where name is the variable name. In this case, the variable as v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value(s) used to determine will be evaluated each time step, and its value(s) will be used to determine
the force component. the force component(s).
Equal-style variables can specify formulas with various mathematical Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command functions and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed keywords for the simulation box parameters, time step, and elapsed time.
time. Thus it is easy to specify a time-dependent force field. Thus, it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force coordinates. Thus, it is easy to specify a spatially-dependent force
field with optional time-dependence as well. field with optional time-dependence as well.
If the *every* keyword is used, the *Nevery* setting determines how If the *every* keyword is used, the *Nevery* setting determines how
often the forces are applied. The default value is 1, for every often the forces are applied. The default value is 1, for every
timestep. time step.
If the *region* keyword is used, the atom must also be in the If the *region* keyword is used, the atom must also be in the
specified geometric :doc:`region <region>` in order to have force added specified geometric :doc:`region <region>` in order to have force added
@ -83,10 +83,14 @@ potential energy to formulate a self-consistent minimization problem
(see below). (see below).
The *energy* keyword is not allowed if the added force is a constant The *energy* keyword is not allowed if the added force is a constant
vector F = (fx,fy,fz), with all components defined as numeric vector :math:`\vec F = (f_x,f_y,f_z)`, with all components defined as numeric
constants and not as variables. This is because LAMMPS can compute constants and not as variables. This is because LAMMPS can compute
the energy for each atom directly as E = -x dot F = -(x\*fx + y\*fy + the energy for each atom directly as
z\*fz), so that -Grad(E) = F.
.. math::
E = -\vec x \cdot \vec F = -(x f_x + y f_y + z f_z),
so that :math:`-\vec\nabla E = \vec F`.
The *energy* keyword is optional if the added force is defined with The *energy* keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the one or more variables, and if you are performing dynamics via the
@ -98,16 +102,16 @@ one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the name of an the "minimize" command. The keyword specifies the name of an
atom-style :doc:`variable <variable>` which is used to compute the atom-style :doc:`variable <variable>` which is used to compute the
energy of each atom as function of its position. Like variables used energy of each atom as function of its position. Like variables used
for *fx*, *fy*, *fz*, the energy variable is specified as v_name, for :math:`f_x`, :math:`f_y`, :math:`f_z`, the energy variable is specified as
where name is the variable name. v_name, where name is the variable name.
Note that when the *energy* keyword is used during an energy Note that when the *energy* keyword is used during an energy
minimization, you must insure that the formula defined for the minimization, you must insure that the formula defined for the
atom-style :doc:`variable <variable>` is consistent with the force atom-style :doc:`variable <variable>` is consistent with the force
variable formulas, i.e. that -Grad(E) = F. For example, if the force variable formulas (i.e., that :math:`-\vec\nabla E = \vec F`).
were a spring-like F = kx, then the energy formula should be E = For example, if the force were a spring-like, :math:`\vec F = -k\vec x`, then
-0.5kx\^2. If you don't do this correctly, the minimization will not the energy formula should be :math:`E = \frac12 kx^2`. If you do not do this
converge properly. correctly, the minimization will not converge properly.
---------- ----------
@ -128,8 +132,8 @@ the global potential energy of the system as part of
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
energy is a fictitious quantity but is needed so that the energy is a fictitious quantity but is needed so that the
:doc:`minimize <minimize>` command can include the forces added by :doc:`minimize <minimize>` command can include the forces added by
this fix in a consistent manner. I.e. there is a decrease in this fix in a consistent manner (i.e., there is a decrease in
potential energy when atoms move in the direction of the added force. potential energy when atoms move in the direction of the added force).
The :doc:`fix_modify <fix_modify>` *virial* option is supported by The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to this fix to add the contribution due to the added forces on atoms to
@ -144,12 +148,12 @@ fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the <run_style>` integrator the fix is adding its forces. Default is the
outermost level. outermost level.
This fix computes a global scalar and a global 3-vector of forces, This fix computes a global scalar and a global three-vector of forces,
which can be accessed by various :doc:`output commands which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above. <Howto_output>`. The scalar is the potential energy discussed above.
The vector is the total force on the group of atoms before the forces The vector is the total force on the group of atoms before the forces
on individual atoms are changed by the fix. The scalar and vector on individual atoms are changed by the fix. The scalar and vector
values calculated by this fix are "extensive". values calculated by this fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. the :doc:`run <run>` command.
@ -157,7 +161,7 @@ the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization, The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as use with a minimizer, since the minimizer increments the time step as
the iteration count during the minimization. the iteration count during the minimization.
.. note:: .. note::

21
doc/src/fix_addtorque.rst
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@ -6,7 +6,7 @@ fix addtorque command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID addtorque Tx Ty Tz fix ID group-ID addtorque Tx Ty Tz
@ -30,13 +30,13 @@ Add a set of forces to each atom in
the group such that: the group such that:
* the components of the total torque applied on the group (around its * the components of the total torque applied on the group (around its
center of mass) are Tx,Ty,Tz center of mass) are :math:`T_x`, :math:`T_y`, and :math:`T_z`
* the group would move as a rigid body in the absence of other * the group would move as a rigid body in the absence of other
forces. forces.
This command can be used to drive a group of atoms into rotation. This command can be used to drive a group of atoms into rotation.
Any of the 3 quantities defining the torque components can be specified Any of the three quantities defining the torque components can be specified
as an equal-style :doc:`variable <variable>`, namely *Tx*, as an equal-style :doc:`variable <variable>`, namely *Tx*,
*Ty*, *Tz*\ . If the value is a variable, it should be specified as *Ty*, *Tz*\ . If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable v_name, where name is the variable name. In this case, the variable
@ -53,7 +53,8 @@ time. Thus it is easy to specify a time-dependent torque.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. No information about this fix is written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential "energy" inferred by the added torques this fix to add the potential "energy" inferred by the added torques
@ -62,8 +63,8 @@ to the global potential energy of the system as part of
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
is a fictitious quantity but is needed so that the :doc:`minimize is a fictitious quantity but is needed so that the :doc:`minimize
<minimize>` command can include the forces added by this fix in a <minimize>` command can include the forces added by this fix in a
consistent manner. I.e. there is a decrease in potential energy when consistent manner (i.e., there is a decrease in potential energy when
atoms move in the direction of the added forces. atoms move in the direction of the added forces).
The :doc:`fix_modify <fix_modify>` *respa* option is supported by The :doc:`fix_modify <fix_modify>` *respa* option is supported by
this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>` this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
@ -74,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`. The scalar
is the potential energy discussed above. The vector is the total is the potential energy discussed above. The vector is the total
torque on the group of atoms before the forces on individual atoms are torque on the group of atoms before the forces on individual atoms are
changed by the fix. The scalar and vector values calculated by this changed by the fix. The scalar and vector values calculated by this
fix are "extensive". fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. the :doc:`run <run>` command.
@ -99,9 +100,9 @@ invoked by the :doc:`minimize <minimize>` command.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the EXTRA-FIX package. It is only enabled if This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was
LAMMPS was built with that package. See the :doc:`Build package built with that package. See the :doc:`Build package <Build_package>` page for
<Build_package>` page for more info. more info.
Related commands Related commands
"""""""""""""""" """"""""""""""""

10
doc/src/fix_amoeba_bitorsion.rst
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@ -6,7 +6,7 @@ fix amoeba/bitorsion command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID ameoba/bitorsion filename fix ID group-ID ameoba/bitorsion filename
@ -55,8 +55,8 @@ should have a line like this in its header section:
N bitorsions N bitorsions
where N is the number of bitorsion 5-body interactions. It should where :math:`N` is the number of bitorsion 5-body interactions. It should
also have a section in the body of the data file like this with N also have a section in the body of the data file like this with :math:`N`
lines: lines:
.. parsed-literal:: .. parsed-literal::
@ -68,7 +68,7 @@ lines:
[...] [...]
N 3 314 315 317 318 330 N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the bitorsion The first column is an index from 1 to :math:`N` to enumerate the bitorsion
5-atom tuples; it is ignored by LAMMPS. The second column is the 5-atom tuples; it is ignored by LAMMPS. The second column is the
*type* of the interaction; it is an index into the bitorsion force *type* of the interaction; it is an index into the bitorsion force
field file. The remaining 5 columns are the atom IDs of the atoms in field file. The remaining 5 columns are the atom IDs of the atoms in
@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential :doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is energy discussed above. The scalar value calculated by this fix is
"extensive". "extensive."
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. the :doc:`run <run>` command.

38
doc/src/fix_amoeba_pitorsion.rst
View File

@ -6,7 +6,7 @@ fix amoeba/pitorsion command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID ameoba/pitorsion fix ID group-ID ameoba/pitorsion
@ -29,14 +29,16 @@ Description
This command enables 6-body pitorsion interactions to be added to This command enables 6-body pitorsion interactions to be added to
simulations which use the AMOEBA and HIPPO force fields. It matches simulations which use the AMOEBA and HIPPO force fields. It matches
how the Tinker MD code computes its pitorsion interactions for the how the Tinker MD code computes its pitorsion interactions for the
AMOEBA and HIPPO force fields. See the :doc:`Howto amoeba AMOEBA and HIPPO force fields. See the :doc:`Howto amoeba <Howto_amoeba>`
<Howto_amoeba>` doc page for more information about the implementation doc page for more information about the implementation of AMOEBA and HIPPO in
of AMOEBA and HIPPO in LAMMPS. LAMMPS.
Pitorsion interactions add additional potential energy contributions Pitorsion interactions add additional potential energy contributions
to 6-tuples of atoms IJKLMN which have a bond between atoms K and L, to 6-tuples of atoms :math:`IJKLMN` that have a bond between atoms
where both K and L are additionally bonded to exactly two other atoms. :math:`K` and :math:`L`, where both :math:`K` and :math:`L` are additionally
Namely K is also bonded to I and J. And L is also bonded to M and N. bonded to exactly two other atoms. Namely, :math:`K` is also bonded to
:math:`I` and :math:`J`, and :math:`L` is also bonded to :math:`M` and
:math:`N`.
The examples/amoeba directory has a sample input script and data file The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/pitorsion for ubiquitin, which illustrates use of the fix amoeba/pitorsion
@ -47,7 +49,7 @@ file that contains a listing of pitorsion interactions.
The data file read by the :doc:`read_data <read_data>` command must The data file read by the :doc:`read_data <read_data>` command must
contain the topology of all the pitorsion interactions, similar to the contain the topology of all the pitorsion interactions, similar to the
topology data for bonds, angles, dihedrals, etc. Specifically it topology data for bonds, angles, dihedrals, etc. Specifically, it
should have two lines like these in its header section: should have two lines like these in its header section:
.. parsed-literal:: .. parsed-literal::
@ -55,9 +57,9 @@ should have two lines like these in its header section:
M pitorsion types M pitorsion types
N pitorsions N pitorsions
where N is the number of pitorsion 5-body interactions and M is the where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
number of pitorsion types. It should also have two sections in the body the number of pitorsion types. It should also have two sections in the body
of the data file like these with M and N lines each: of the data file like these with :math:`M` and :math:`N` lines each:
.. parsed-literal:: .. parsed-literal::
@ -77,11 +79,11 @@ of the data file like these with M and N lines each:
[...] [...]
N 3 314 315 317 318 330 N 3 314 315 317 318 330
For PiTorsion Coeffs, the first column is an index from 1 to M to For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
enumerate the pitorsion types. The second column is the single enumerate the pitorsion types. The second column is the single
prefactor coefficient needed for each type. prefactor coefficient needed for each type.
For PiTorsions, the first column is an index from 1 to N to enumerate For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
column is the "type" of the interaction; it is an index into the column is the "type" of the interaction; it is an index into the
PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
@ -90,8 +92,8 @@ atoms in the two 4-atom dihedrals that overlap to create the pitorsion
Note that the *pitorsion types* and *pitorsions* and *PiTorsion Note that the *pitorsion types* and *pitorsions* and *PiTorsion
Coeffs* and *PiTorsions* keywords for the header and body sections of Coeffs* and *PiTorsions* keywords for the header and body sections of
the data file match those specified in the :doc:`read_data the data file match those specified in the :doc:`read_data <read_data>`
<read_data>` command following the data file name. command following the data file name.
The data file should be generated by using the The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
@ -136,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential :doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is energy discussed above. The scalar value calculated by this fix is
"extensive". "extensive."
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. the :doc:`run <run>` command.
@ -161,8 +163,8 @@ Restrictions
"""""""""""" """"""""""""
To function as expected this fix command must be issued *before* a To function as expected this fix command must be issued *before* a
:doc:`read_data <read_data>` command but *after* a :doc:`read_restart :doc:`read_data <read_data>` command but *after* a
<read_restart>` command. :doc:`read_restart <read_restart>` command.
This fix can only be used if LAMMPS was built with the AMOEBA package. This fix can only be used if LAMMPS was built with the AMOEBA package.
See the :doc:`Build package <Build_package>` page for more info. See the :doc:`Build package <Build_package>` page for more info.

17
doc/src/fix_append_atoms.rst
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@ -6,7 +6,7 @@ fix append/atoms command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID append/atoms face ... keyword value ... fix ID group-ID append/atoms face ... keyword value ...
@ -66,7 +66,7 @@ specific basis atoms as they are created. See the
defined for the unit cell of the lattice. By default, all created defined for the unit cell of the lattice. By default, all created
atoms are assigned type = 1 unless this keyword specifies differently. atoms are assigned type = 1 unless this keyword specifies differently.
The *size* keyword defines the size in z of the chunk of material to The *size* keyword defines the size in :math:`z` of the chunk of material to
be added. be added.
The *random* keyword will give the atoms random displacements around The *random* keyword will give the atoms random displacements around
@ -79,7 +79,8 @@ measured from zhi and is set with the *extent* argument.
The *units* keyword determines the meaning of the distance units used The *units* keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used. to define a wall position, but only when a numeric constant is used.
A *box* value selects standard distance units as defined by the A *box* value selects standard distance units as defined by the
:doc:`units <units>` command, e.g. Angstroms for units = real or metal. :doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
for units = real or metal.
A *lattice* value means the distance units are in lattice spacings. A *lattice* value means the distance units are in lattice spacings.
The :doc:`lattice <lattice>` command must have been previously used to The :doc:`lattice <lattice>` command must have been previously used to
define the lattice spacings. define the lattice spacings.
@ -89,17 +90,21 @@ define the lattice spacings.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`. by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix style is part of the SHOCK package. It is only enabled if This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
The boundary on which atoms are added with append/atoms must be The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other shrink/minimum. The opposite boundary may be any boundary type other

6
doc/utils/sphinx-config/LAMMPSLexer.py
View File

@ -6,7 +6,7 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"clear", "comm_modify", "comm_style", "clear", "comm_modify", "comm_style",
"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms", "compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension", "delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
"fix_modify", "group2ndx", "hyper", "if", "improper_coeff", "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
"improper_style", "include", "info", "jump", "kim", "improper_style", "include", "info", "jump", "kim",
"kspace_modify", "kspace_style", "label", "lattice", "kspace_modify", "kspace_style", "label", "lattice",
@ -16,8 +16,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"partition", "prd", "print", "processors", "python", "quit", "read_data", "partition", "prd", "print", "processors", "python", "quit", "read_data",
"read_dump", "read_restart", "replicate", "rerun", "reset_ids", "read_dump", "read_restart", "replicate", "rerun", "reset_ids",
"reset_timestep", "restart", "run", "run_style", "server", "set", "shell", "reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then",
"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep", "thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep",
"units", "velocity", "write_coeff", "units", "velocity", "write_coeff",
"write_data", "write_restart") "write_data", "write_restart")