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Steve Plimpton
2022-06-24 17:01:46 -06:00
parent 302287e4d0 ae18e1e01c
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29
doc/src/Developer_plugins.rst
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@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional
GNU makefiles. Some examples that can be used as a template are in the
``examples/plugins`` folder. The CMake script code has some small
adjustments to allow building the plugins for running unit tests with
them. Another example that converts the KIM package into a plugin can be
found in the ``examples/kim/plugin`` folder. No changes to the sources
of the KIM package themselves are needed; only the plugin interface and
loader code needs to be added. This example only supports building with
CMake, but is probably a more typical example. To compile you need to
run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
them.
Another example that converts the KIM package into a plugin can be found
in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the
``examples/PACKAGES/pace/plugin`` folder that will create a plugin from
the ML-PACE package. In this case the bulk of the code is in a static
external library that is being downloaded and compiled first and then
combined with the pair style wrapper and the plugin loader. This
example also contains a NSIS script that can be used to create an
Installer package for Windows (the mutual licensing terms of the
external library and LAMMPS conflict when distributing binaries, so the
ML-PACE package cannot be linked statically, but the LAMMPS headers
required to build the plugin are also available under a less restrictive
license). This will automatically set the required environment variable
and launching a (compatible) LAMMPS binary will load and register the
plugin and the ML-PACE package can then be used as it was linked into
LAMMPS.

4
doc/src/Howto_structured_data.rst
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@ -184,7 +184,7 @@ frame.
.. code-block:: python
import re, yaml
import yaml
import pandas as pd
try:
@ -193,7 +193,7 @@ frame.
from yaml import SafeLoader as Loader
with open("ave.yaml") as f:
ave = yaml.load(docs, Loader=Loader)
ave = yaml.load(f, Loader=Loader)
keys = ave['keywords']
df = {}

2
doc/src/Packages_details.rst
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@ -676,7 +676,7 @@ advection-diffusion-reaction systems. The equations of motion of these
DPD extensions are integrated through a modified velocity-Verlet (MVV)
algorithm.
**Author:** Zhen Li (Division of Applied Mathematics, Brown University)
**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University)
**Supporting info:**

3
doc/src/Speed_measure.rst
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@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
use the :doc:`timer sync <timer>` command to obtain synchronized timings.

17
doc/src/Tools.rst
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@ -95,7 +95,7 @@ Miscellaneous tools
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity <singularity_tool>`
* :ref:`singularity/apptainer <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -1007,14 +1007,15 @@ Ivanov, at University of Iceland (ali5 at hi.is).
.. _singularity_tool:
singularity tool
----------------------------------------
singularity/apptainer tool
--------------------------
The singularity sub-directory contains container definitions files
that can be used to build container images for building and testing
LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
container software. Contributions for additional variants are welcome.
For more details please see the README.md file in that folder.
The singularity sub-directory contains container definitions files that
can be used to build container images for building and testing LAMMPS on
specific OS variants using the `Apptainer <https://apptainer.org>`_ or
`Singularity <https://sylabs.io>`_ container software. Contributions for
additional variants are welcome. For more details please see the
README.md file in that folder.
----------

61
doc/src/compute_ave_sphere_atom.rst
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@ -35,16 +35,24 @@ Examples
Description
"""""""""""
Define a computation that calculates the local density and temperature
for each atom and neighbors inside a spherical cutoff.
Define a computation that calculates the local mass density and
temperature for each atom based on its neighbors inside a spherical
cutoff. If an atom has M neighbors, then its local mass density is
calculated as the sum of its mass and its M neighbor masses, divided
by the volume of the cutoff sphere (or circle in 2d). The local
temperature of the atom is calculated as the temperature of the
collection of M+1 atoms, after subtracting the center-of-mass velocity
of the M+1 atoms from each of the M+1 atom's velocities. This is
effectively the thermal velocity of the neighborhood of the central
atom, similar to :doc:`compute temp/com <compute_temp_com>`.
The optional keyword *cutoff* defines the distance cutoff
used when searching for neighbors. The default value is the cutoff
specified by the pair style. If no pair style is defined, then a cutoff
must be defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is defined),
the *comm_modify cutoff* option must also be set to match that of the
*cutoff* keyword.
The optional keyword *cutoff* defines the distance cutoff used when
searching for neighbors. The default value is the cutoff specified by
the pair style. If no pair style is defined, then a cutoff must be
defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is
defined), the *comm_modify cutoff* option must also be set to match
that of the *cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
@ -55,16 +63,16 @@ too frequently.
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
:doc:`rerun <rerun>` command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
interactions between atoms in the same bond, angle, or dihedral.
This is the default setting for the :doc:`special_bonds
<special_bonds>` command, and means those pairwise interactions do
not appear in the neighbor list. Because this compute uses the
neighbor list, it also means those pairs will not be included in
the order parameter. This difficulty can be circumvented by
writing a dump file, and using the :doc:`rerun <rerun>` command to
compute the order parameter for snapshots in the dump file. The
rerun script can use a :doc:`special_bonds <special_bonds>` command
that includes all pairs in the neighbor list.
----------
@ -77,17 +85,20 @@ too frequently.
Output info
"""""""""""
This compute calculates a per-atom array with two columns: density and temperature.
This compute calculates a per-atom array with two columns: mass
density in density :doc:`units <units>` and temperature in temperature
:doc:`units <units>`.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
from a compute as input. See the :doc:`Howto output <Howto_output>`
doc page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
@ -97,5 +108,5 @@ Related commands
Default
"""""""
The option defaults are *cutoff* = pair style cutoff
The option defaults are *cutoff* = pair style cutoff.

10
doc/src/fix_mdi_aimd.rst
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@ -12,7 +12,6 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* mdi/aimd = style name of this fix command
* optional keyword = *plugin*
Examples
""""""""
@ -20,7 +19,6 @@ Examples
.. code-block:: LAMMPS
fix 1 all mdi/aimd
fix 1 all mdi/aimd plugin
Description
"""""""""""
@ -53,14 +51,6 @@ same time as LAMMPS, or as a plugin library. See the :doc:`mdi plugin
Again, the examples/mdi/README file explains how to launch both driver
and engine codes so that engine is used in plugin mode.
To use this fix with a plugin engine, you must specify the
*plugin* keyword as the last argument, as illustrated above.
.. note::
As of April 2022, the *plugin* keyword is needed. In a future
version of the MDI library it will no longer be necessary.
----------
This fix performs the timestepping portion of an AIMD simulation.

4
doc/src/kspace_style.rst
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@ -129,8 +129,8 @@ Examples
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace style msm 1.0e-4
kspace style scafacos fmm 1.0e-4
kspace_style msm 1.0e-4
kspace_style scafacos fmm 1.0e-4
kspace_style none
Used in input scripts:

91
doc/src/pair_e3b.rst
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@ -50,6 +50,12 @@ Examples
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
pair_coeff * * e3b preset 2011
Used in example input script:
.. parsed-literal::
examples/PACKAGES/e3b/in.e3b-tip4p2005
Description
"""""""""""
@ -68,21 +74,27 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r
0 & r>R_f\\
\end{cases}
This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*.
The three body interactions are split into three types: A, B, and C.
Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
See :ref:`(Kumar 2008) <Kumar>` for more details.
This potential was developed as a water model that includes the
three-body cooperativity of hydrogen bonding explicitly. To use it in
this way, it must be applied in conjunction with a conventional two-body
water model, through pair style :doc:`hybrid/overlay <pair_hybrid>`. The
three body interactions are split into three types: A, B, and C. Type A
corresponds to anti-cooperative double hydrogen bond donor interactions.
Type B corresponds to the cooperative interaction of molecules that both
donate and accept a hydrogen bond. Type C corresponds to
anti-cooperative double hydrogen bond acceptor interactions. The
three-body interactions are smoothly cutoff by the switching function
s(r) between Rs and Rc3. The two-body interactions are designed to
correct for the effective many-body interactions implicitly included in
the conventional two-body potential. The two-body interactions are cut
off sharply at Rc2, because K3 is typically significantly smaller than
K2. See :ref:`(Kumar 2008) <Kumar>` for more details.
Only a single *pair_coeff* command is used with the *e3b* style.
The first two arguments must be \* \*.
The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command.
The hydrogen atom type is inferred by the ordering of the atoms.
Only a single :doc:`pair_coeff <pair_coeff>` command is used with the
*e3b* style and the first two arguments must be \* \*. The oxygen atom
type for the pair style is passed as the only argument to the
*pair_style* command, not in the *pair_coeff* command. The hydrogen
atom type is inferred from the ordering of the atoms.
.. note::
@ -90,26 +102,41 @@ The hydrogen atom type is inferred by the ordering of the atoms.
Each water molecule must have consecutive IDs with the oxygen first.
This pair style does not test that this criteria is met.
The *pair_coeff* command must have at least one keyword/value pair, as described above.
The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) <Tainter2011>` or :ref:`(Tainter 2015) <Tainter2015>`.
To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above.
The *preset 2011* option should be used with the :doc:`TIP4P water model <Howto_tip4p>`.
The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model <Howto_tip4p>`.
If the *preset* keyword is used, no other keyword is needed.
Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ .
Note that the other keywords must come after *preset* in the pair_style command.
The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, *Rs*, and *bondL*\ .
The keyword *bondL* specifies the intramolecular OH bond length of the water model being used.
This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
The *pair_coeff* command must have at least one keyword/value pair, as
described above. The *preset* keyword sets the potential parameters to
the values used in :ref:`(Tainter 2011) <Tainter2011>` or
:ref:`(Tainter 2015) <Tainter2015>`. To use the water models defined in
those references, the *e3b* style should always be used in conjunction
with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*,
as demonstrated in the second example above. The *preset 2011* option
should be used with the :doc:`TIP4P water model <Howto_tip4p>`. The
*preset 2015* option should be used with the :doc:`TIP4P/2005 water
model <Howto_tip4p>`. If the *preset* keyword is used, no other keyword
is needed. Changes to the preset parameters can be made by specifying
the *preset* keyword followed by the specific parameter to change, like
*Ea*\ . Note that the other keywords must come after *preset* in the
pair_style command. The *e3b* style can also be used to implement any
three-body potential of the same form by specifying all the keywords
except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*,
*Rs*, and *bondL*\ . The keyword *bondL* specifies the intramolecular
OH bond length of the water model being used. This is needed to include
H atoms that are within the cutoff even when the attached oxygen atom is
not.
This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument.
If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
If the neigh setting is too large, the pair style will use more memory than necessary.
This pair style allocates arrays sized according to the number of
pairwise interactions within Rc3. To do this it needs an estimate for
the number of water molecules within Rc3 of an oxygen atom. This
estimate defaults to 10 and can be changed using the *neigh* keyword,
which takes an integer as an argument. If the neigh setting is too
small, the simulation will fail with the error "neigh is too small". If
the neigh setting is too large, the pair style will use more memory than
necessary.
This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
This pair style tallies a breakdown of the total E3B potential energy
into sub-categories, which can be accessed via the :doc:`compute pair
<compute_pair>` command as a vector of values of length 4. The 4 values
correspond to the terms in the first equation above: the E2 term, the Ea
term, the Eb term, and the Ec term.
See the examples/PACKAGES/e3b directory for a complete example script.

4
doc/src/pair_sw_angle_table.rst
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@ -23,9 +23,9 @@ Examples
Used in example input script:
.. parsed-literal::
.. parsed-literal::
examples/PACKAGES/manybody_table/in.spce_sw
examples/PACKAGES/manybody_table/in.spce_sw
Description

6
doc/src/pair_threebody_table.rst
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@ -27,10 +27,10 @@ Examples
Used in example input scripts:
.. parsed-literal::
.. parsed-literal::
examples/PACKAGES/manybody_table/in.spce
examples/PACKAGES/manybody_table/in.spce2
examples/PACKAGES/manybody_table/in.spce
examples/PACKAGES/manybody_table/in.spce2
Description
"""""""""""

4
doc/src/read_data.rst
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@ -56,7 +56,7 @@ Examples
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent
read_data data.water add merge group solvent
Description
"""""""""""
@ -622,6 +622,8 @@ of analysis.
- atom-ID molecule-ID atom-type x y z
* - charge
- atom-ID atom-type q x y z
* - dielectric
- atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature
* - dipole
- atom-ID atom-type q x y z mux muy muz
* - dpd

102
doc/src/read_restart.rst
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@ -11,7 +11,6 @@ Syntax
read_restart file flag
* file = name of binary restart file to read in
* flag = remap (optional)
Examples
""""""""
@ -19,44 +18,40 @@ Examples
.. code-block:: LAMMPS
read_restart save.10000
read_restart save.10000 remap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
Description
"""""""""""
Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simulation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
information is stored (and not stored) in a restart file is given below.
Basically this operation will re-create the simulation box with all its
atoms and their attributes as well as some related global settings, at
the point in time it was written to the restart file by a previous
simulation. The simulation box will be partitioned into a regular 3d
grid of rectangular bricks, one per processor, based on the number of
processors in the current simulation and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
.. note::
Normally, restart files are written by the
:doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
so that all atoms in the restart file are inside the simulation box.
If this is not the case, the read_restart command will print an error
that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional *remap* flag can be appended to the read_restart command.
This should avoid the error, by explicitly remapping each atom back
into the simulation box, updating image flags for the atom
appropriately.
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
those produced by the original run had it continued on.
The binary restart file format was not designed with backward, forward,
or cross-platform compatibility in mind, so the files are only expected
to be read correctly by the same LAMMPS executable on the same platform.
Changes to the architecture, compilation settings, or LAMMPS version can
render a restart file unreadable or it may read the data incorrectly.
If you want a more portable format, you can use the data file format as
created by the :doc:`write_data <write_data>` command. Binary restart
files can also be converted into a data file from the command line by
the LAMMPS executable that wrote them using the :ref:`-restart2data
<restart2data>` command line flag.
Several things can prevent exact restarts due to round-off effects, in
which case the trajectories in the 2 runs will slowly diverge. These
include running on a different number of processors or changing
@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
these cases.
Certain fixes will not restart exactly, though they should provide
statistically similar results. These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
statistically similar results. These include :doc:`fix shake
<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
machines. In this case, you can use the :doc:`-restart command-line
switch <Run_options>` to convert a restart file to a data file.
Similar to how restart files are written (see the
:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
commands), the restart filename can contain two wild-card characters.
If a "\*" appears in the filename, the directory is searched for all
filenames that match the pattern where "\*" is replaced with a timestep
value. The file with the largest timestep value is read in. Thus,
this effectively means, read the latest restart file. It's useful if
you want your script to continue a run from where it left off. See
the :doc:`run <run>` command and its "upto" option for how to specify
the run command so it does not need to be changed either.
Similar to how restart files are written (see the :doc:`write_restart
<write_restart>` and :doc:`restart <restart>` commands), the restart
filename can contain two wild-card characters. If a "\*" appears in the
filename, the directory is searched for all filenames that match the
pattern where "\*" is replaced with a timestep value. The file with the
largest timestep value is read in. Thus, this effectively means, read
the latest restart file. It's useful if you want your script to
continue a run from where it left off. See the :doc:`run <run>` command
and its "upto" option for how to specify the run command so it does not
need to be changed either.
If a "%" character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The :doc:`restart <restart>` and
@ -222,17 +219,17 @@ its calculations in a consistent manner.
.. note::
There are a handful of commands which can be used before or
between runs which may require a system initialization. Examples
include the "balance", "displace_atoms", "delete_atoms", "set" (some
options), and "velocity" (some options) commands. This is because
they can migrate atoms to new processors. Thus they will also discard
unused "state" information from fixes. You will know the discard has
There are a handful of commands which can be used before or between
runs which may require a system initialization. Examples include the
"balance", "displace_atoms", "delete_atoms", "set" (some options),
and "velocity" (some options) commands. This is because they can
migrate atoms to new processors. Thus they will also discard unused
"state" information from fixes. You will know the discard has
occurred because a list of discarded fixes will be printed to the
screen and log file, as explained above. This means that if you wish
to retain that info in a restarted run, you must re-specify the
relevant fixes and computes (which create fixes) before those commands
are used.
relevant fixes and computes (which create fixes) before those
commands are used.
Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
use a fix to store "state" information that persists from timestep to
@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or
deleted in various ways, which can affect how their info is stored in
a restart file.
If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command,
their info will be written to a restart file as if they are turned on.
This means they will need to be turned off again in a new run after
the restart file is read.
If bonds (angles, etc) have been turned off by the :doc:`fix shake
<fix_shake>` or :doc:`delete_bonds <delete_bonds>` command, their info
will be written to a restart file as if they are turned on. This means
they will need to be turned off again in a new run after the restart
file is read.
Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
system. No information about these bonds is written to the restart
file.
Bonds that have been broken by the :doc:`fix bond/break
<fix_bond_break>` command have disappeared from the system. No
information about these bonds is written to the restart file.
----------