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more doc reformatting

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Axel Kohlmeyer
2024-08-14 01:34:42 -04:00
parent 5a55ca39bc
commit 308ecaef1c
4 changed files with 118 additions and 119 deletions
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7
doc/src/fix_bocs.rst
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@ -122,6 +122,10 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the BOCS package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
As this is computing a (modified) pressure, group-ID should be *all*\ . As this is computing a (modified) pressure, group-ID should be *all*\ .
The pressure correction has only been tested for use with an isotropic The pressure correction has only been tested for use with an isotropic
@ -135,9 +139,6 @@ the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1). example, the ID of the fix bocs command is 1).
This fix is part of the BOCS package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Further information Further information
""""""""""""""""""" """""""""""""""""""

18
doc/src/fix_box_relax.rst
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@ -159,10 +159,7 @@ these 4 keywords:
.. parsed-literal:: .. parsed-literal::
x Ptarget x Ptarget y Ptarget z Ptarget couple xyz
y Ptarget
z Ptarget
couple xyz
The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled
independently using the *Pxx*, *Pyy*, and *Pzz* components of the independently using the *Pxx*, *Pyy*, and *Pzz* components of the
@ -172,10 +169,7 @@ keywords:
.. parsed-literal:: .. parsed-literal::
x Ptarget x Ptarget y Ptarget z Ptarget couple none
y Ptarget
z Ptarget
couple none
The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions
are controlled independently using their individual stress components are controlled independently using their individual stress components
@ -185,13 +179,7 @@ these 7 keywords:
.. parsed-literal:: .. parsed-literal::
x Ptarget x Ptarget y Ptarget z Ptarget xy 0.0 yz 0.0 xz 0.0 couple none
y Ptarget
z Ptarget
xy 0.0
yz 0.0
xz 0.0
couple none
---------- ----------

178
doc/src/fix_colvars.rst
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@ -46,25 +46,26 @@ Description
""""""""""" """""""""""
This fix interfaces LAMMPS to the collective variables `Colvars This fix interfaces LAMMPS to the collective variables `Colvars
<https://colvars.github.io>`_ library, which allows to accelerate sampling of <https://colvars.github.io>`_ library, which allows to accelerate
rare events and the computation of free energy surfaces and potentials of sampling of rare events and the computation of freeenergy surfaces and
mean force (PMFs) for any set of collective variables using a variety of potentials of mean force (PMFs) for any set of collective variables
sampling methods (e.g. umbrella-sampling, metadynamics, ABF...). using a variety of sampling methods (e.g. umbrella-sampling,
metadynamics, ABF...).
This documentation describes only the "fix colvars" command itself in This documentation describes only the "fix colvars" command itself in a
a LAMMPS script. The Colvars library is fully documented in the included LAMMPS script. The Colvars library is fully documented in the included
`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or in the webpage `PDF manual <PDF/colvars-refman-lammps.pdf>`_ or in the webpage
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html `https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_. <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.
The Colvars library is developed at `https://github.com/Colvars/colvars The Colvars library is developed at `https://github.com/Colvars/colvars
<https://github.com/colvars/colvars>`_ A detailed discussion of its <https://github.com/colvars/colvars>`_. A detailed discussion of its
implementation is in :ref:`(Fiorin) <Fiorin>`; additional citations for implementation is in :ref:`(Fiorin) <Fiorin>`; additional citations for
specific features are printed at runtime if these features are used. specific features are printed at runtime if these features are used.
There are example scripts on the `Colvars website <https://colvars.github.io>`_ There are example scripts on the `Colvars website
as well as in the ``examples/PACKAGES/colvars`` directory in the LAMMPS <https://colvars.github.io>`_ as well as in the
source tree. ``examples/PACKAGES/colvars`` directory in the LAMMPS source tree.
---------- ----------
@ -75,42 +76,44 @@ units that are specific to each engine. In LAMMPS, the units used by
Colvars are consistent with those specified by the :doc:`units <units>` Colvars are consistent with those specified by the :doc:`units <units>`
command. command.
.. versionadded:: Colvars_2023-06-04 The special value "*none*" .. versionadded:: Colvars_2023-06-04
(lowercase) initializes an empty Colvars module, which
allows loading configuration dynamically using The special value "*none*" (lowercase) initializes an empty Colvars
module, which allows loading configuration dynamically using
:doc:`fix_modify <fix_modify>` (see below). :doc:`fix_modify <fix_modify>` (see below).
The *group-ID* entry is ignored. "fix colvars" will always apply to The *group-ID* entry is ignored. "fix colvars" will always apply to the
the entire system, but specific atoms will be selected based on entire system, but specific atoms will be selected based on selection
selection keywords in the Colvars configuration file or files. There is keywords in the Colvars configuration file or files. There is no need
no need to define multiple "fix colvars" instances and it is not to define multiple "fix colvars" instances and it is not allowed.
allowed.
The "output" keyword allows to specify the prefix of output files generated The "output" keyword allows to specify the prefix of output files
by Colvars, for example "*output*.colvars.traj" or "output.pmf". Supplying generated by Colvars, for example "*output*.colvars.traj" or
an empty string suppresses any file output from Colvars to file, except for "output.pmf". Supplying an empty string suppresses any file output from
data saved into the LAMMPS :doc:`binary restart <restart>` files. Colvars to file, except for data saved into the LAMMPS :doc:`binary
restart <restart>` files.
The "input" keyword allows to specify an optional state file that contains The "input" keyword allows to specify an optional state file that
the restart information needed to continue a previous simulation state. contains the restart information needed to continue a previous
However, because "fix colvars" records its state in LAMMPS :doc:`binary simulation state. However, because "fix colvars" records its state in
restart <restart>` files, this is usually not needed when using the LAMMPS :doc:`binary restart <restart>` files, this is usually not needed
:doc:`read_restart <read_restart>` command. when using the :doc:`read_restart <read_restart>` command.
The *unwrap* keyword controls whether wrapped or unwrapped coordinates are The *unwrap* keyword controls whether wrapped or unwrapped coordinates
passed to the Colvars library for calculation of the collective variables and are passed to the Colvars library for calculation of the collective
the resulting forces. The default is *yes*, i.e. the image flags are used to variables and the resulting forces. The default is *yes*, i.e. the
reconstruct the absolute atom positions. Setting this to *no* will use the image flags are used to reconstruct the absolute atom positions.
current local coordinates that are wrapped back into the simulation cell at Setting this to *no* will use the current local coordinates that are
each re-neighboring step instead. For information about when and how this wrapped back into the simulation cell at each re-neighboring step
affects results, please see instead. For information about when and how this affects results,
please see
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping `https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_. <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.
The *tstat* keyword can be either "NULL" or the label of a thermostatting The *tstat* keyword can be either "NULL" or the label of a
fix that thermostats all atoms in the fix colvars group. This will be thermostatting fix that thermostats all atoms in the fix colvars
used to provide the colvars module with the current thermostat target group. This will be used to provide the colvars module with the current
temperature. thermostat target temperature.
The *seed* keyword contains the seed for the random number generator The *seed* keyword contains the seed for the random number generator
that will be used in the colvars module. that will be used in the colvars module.
@ -119,36 +122,38 @@ that will be used in the colvars module.
Restarting Restarting
"""""""""" """"""""""
This fix writes the current state of the Colvars module into :doc:`binary This fix writes the current state of the Colvars module into
restart files <restart>`. This is in addition to the text-mode :doc:`binary restart files <restart>`. This is in addition to the
".colvars.state" state file that is written by the Colvars module itself. text-mode ".colvars.state" state file that is written by the Colvars
The information contained in both files is identical, and the binary LAMMPS module itself. The information contained in both files is identical,
restart file is also used by fix colvars when :doc:`read_restart and the binary LAMMPS restart file is also used by fix colvars when
<read_restart>` is called in a LAMMPS script. In that case, there is :doc:`read_restart <read_restart>` is called in a LAMMPS script. In
typically no need to specify the *input* keyword. that case, there is typically no need to specify the *input* keyword.
As long as LAMMPS binary restarts will be used to continue a simulation, it As long as LAMMPS binary restarts will be used to continue a simulation,
is safe to delete the ".colvars.state" files to save space. However, when a it is safe to delete the ".colvars.state" files to save space. However,
LAMMPS simulation is restarted using :doc:`read_data <read_data>`, the when a LAMMPS simulation is restarted using :doc:`read_data
Colvars state file must be available and loaded via the "input" keyword or <read_data>`, the Colvars state file must be available and loaded via
via a "fix_modify Colvars load" command (see below). the "input" keyword or via a "fix_modify Colvars load" command (see
below).
When restarting, the fix and the Colvars module should be created and When restarting, the fix and the Colvars module should be created and
configured using either the original configuration file(s). configured using the original configuration file(s).
Output Output
"""""" """"""
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 energy due to all :doc:`output commands <Howto_output>`. The scalar is the energy due to
external potentials defined in the Colvars configuration. The scalar value all external potentials defined in the Colvars configuration. The
calculated by this fix is "extensive". scalar value calculated by this fix is "extensive".
Aside from the state information in a ".colvars.state" file, other Aside from the state information in a ".colvars.state" file, other
`output files <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_output>`_ `output files
are produced by Colvars depending on the type of simulation. <https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_output>`_
For this reason, the "output" keyword is required for fix colvars. are produced by Colvars depending on the type of simulation. For this
reason, the "output" keyword is required for fix colvars.
Controlling Colvars via `fix_modify` Controlling Colvars via `fix_modify`
@ -156,18 +161,18 @@ Controlling Colvars via `fix_modify`
.. versionadded:: Colvars_2023-06-04 .. versionadded:: Colvars_2023-06-04
The :doc:`fix_modify <fix_modify>` command may be used on "fix colvars" in The :doc:`fix_modify <fix_modify>` command may be used on "fix colvars"
either one of two ways: in either one of two ways:
(1) Provide updated values for the fix parameters, such as *output*, *input*, (1) Provide updated values for the fix parameters, such as *output*,
*unwrap*, *tstat* and *seed*. Additionally, the :doc:`fix_modify *input*, *unwrap*, *tstat* and *seed*. Additionally, the
<fix_modify>` *energy* keyword is supported by this fix to add the energy :doc:`fix_modify <fix_modify>` *energy* keyword is supported by this fix
change from the biasing force added by Colvars to the global potential to add the energy change from the biasing force added by Colvars to the
energy of the system as part of :doc:`thermodynamic output <thermo_style>` global potential energy of the system as part of :doc:`thermodynamic
(the default is :doc:`fix_modify energy no <fix_modify>`). output <thermo_style>` (the default is :doc:`fix_modify energy no
For example, in a multi-step LAMMPS script involving multiple thermostats <fix_modify>`). For example, in a multi-step LAMMPS script involving
(e.g. fix nvt followed by fix npt), Colvars can read a new thermostat's multiple thermostats (e.g. fix nvt followed by fix npt), Colvars can
target temperature like this: read a new thermostat's target temperature like this:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -186,10 +191,11 @@ either one of two ways:
LAMMPS variables referenced by their string representation LAMMPS variables referenced by their string representation
"${variable}" will be expanded immediately. Note also that this "${variable}" will be expanded immediately. Note also that this
variable expansion *will also happen within quotes*, similar to what the variable expansion *will also happen within quotes*, similar to what
:doc:`mdi <mdi>` command provides. This feature makes it possible to use the :doc:`mdi <mdi>` command provides. This feature makes it
the values of certain LAMMPS variables in Colvars configuration strings. possible to use the values of certain LAMMPS variables in Colvars
For example, to synchronize the LAMMPS and Colvars dump frequencies: configuration strings. For example, to synchronize the LAMMPS and
Colvars dump frequencies:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -199,27 +205,27 @@ either one of two ways:
.. note:: .. note::
Although it is possible to use :doc:`fix_modify <fix_modify>` at any time, Although it is possible to use :doc:`fix_modify <fix_modify>` at any
its results will only reflect the state of the Colvars module at the end time, its results will only reflect the state of the Colvars module
of the most recent "run" or "minimize" command. Any new configuration at the end of the most recent "run" or "minimize" command. Any new
added via "fix_modify Colvars configfile" or "fix_modify Colvars config" configuration added via "fix_modify Colvars configfile" or
will only be loaded when the simulation resumes. Configuration files or "fix_modify Colvars config" will only be loaded when the simulation
strings will be parsed in the same sequence as they were provided in the resumes. Configuration files or strings will be parsed in the same
LAMMPS script. sequence as they were provided in the LAMMPS script.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is provided by the COLVARS package and is only available if LAMMPS This fix is provided by the COLVARS package and is only available if
was built with that package (default in most builds). Some of the features LAMMPS was built with that package (default in most builds). Some of
also require code available from the LEPTON package. See the :doc:`Build the features also require code available from the LEPTON package. See
package <Build_package>` page for more info. the :doc:`Build package <Build_package>` page for more info.
There can only be one Colvars instance defined at a time. Since the There can only be one Colvars instance defined at a time. Since the
interface communicates only the minimum required amount of information, and interface communicates only the minimum required amount of information,
the Colvars module itself can handle an arbitrary number of collective and the Colvars module itself can handle an arbitrary number of
variables, this is not a limitation of functionality. collective variables, this is not a limitation of functionality.
Related commands Related commands

32
doc/src/fix_damping_cundall.rst
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@ -85,9 +85,12 @@ using an :doc:`atom-style variable <variable>`.
This non-viscous damping presents the following advantages: This non-viscous damping presents the following advantages:
1. damping is independent of velocity, equally damping regions with distinct natural frequencies, #. damping is independent of velocity, equally damping regions with
2. damping affects acceleration and vanishes for steady uniform motion of the particles, distinct natural frequencies,
3. damping parameter :math:`\gamma` is dimensionless and does not require scaling. #. damping affects acceleration and vanishes for steady uniform motion
of the particles,
#. damping parameter :math:`\gamma` is dimensionless and does not
require scaling.
---------- ----------
@ -95,27 +98,28 @@ Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are <restart>`. No global or per-atom quantities are stored by this fix for
relevant to this fix. No global or per-atom quantities are stored by access by various :doc:`output commands <Howto_output>`. No parameter
this fix for access by various :doc:`output commands <Howto_output>`. of this fix can be used with the *start/stop* keywords of the :doc:`run
No parameter of this fix can be used with the *start/stop* keywords of <run>` command.
the :doc:`run <run>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this 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>` fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is modifying forces/torques. Default is the outermost level. integrator the fix is modifying forces/torques. Default is the outermost
level.
The forces/torques due to this fix are imposed during an energy minimization, The forces/torques due to this fix are imposed during an energy
invoked by the :doc:`minimize <minimize>` command. This fix should only minimization, invoked by the :doc:`minimize <minimize>` command. This
be used with damped dynamics minimizers that allow for fix should only be used with damped dynamics minimizers that allow for
non-conservative forces. See the :doc:`min_style <min_style>` command non-conservative forces. See the :doc:`min_style <min_style>` command
for details. for details.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the GRANULAR package. It is only enabled if This fix is part of the GRANULAR package. It is only enabled if LAMMPS
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 fix requires that atoms store torque and a radius as defined by the This fix requires that atoms store torque and a radius as defined by the
:doc:`atom_style sphere <atom_style>` command. :doc:`atom_style sphere <atom_style>` command.