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Merge branch 'lammps:develop' into mliappy_unified

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This commit is contained in:
Steven Anaya
2022-09-15 03:01:03 -06:00
committed by GitHub
parent 3d7a31a59f 83224f631d
commit e89899955b
483 changed files with 7320 additions and 4810 deletions
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1
cmake/CMakeLists.txt
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@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)

7
cmake/Modules/Packages/MDI.cmake
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@ -6,13 +6,10 @@ else()
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.10.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "1c203b7fd462d9934834f643f09f3c06" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)

13
cmake/presets/clang.cmake
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@ -3,6 +3,13 @@
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()
set(FC_STD_VERSION "-std=f2003")
endif()
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

2
doc/src/Bibliography.rst
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@ -1373,7 +1373,7 @@ Bibliography
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
**(Ziegler)**
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
**(Zimmerman2004)**
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

1
doc/src/Commands_all.rst
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@ -61,6 +61,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`

9
doc/src/Developer_utils.rst
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@ -175,6 +175,12 @@ and parsing files or arguments.
.. doxygenfunction:: is_double
:project: progguide
.. doxygenfunction:: is_id
:project: progguide
.. doxygenfunction:: is_type
:project: progguide
Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^
@ -205,6 +211,9 @@ Argument processing
.. doxygenfunction:: expand_args
:project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions
^^^^^^^^^^^^^^^^^^^^^

40
doc/src/Errors_messages.rst
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@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom
types.
*Invalid label2type() function syntax in variable formula*
The first argument must be a label map kind (atom, bond, angle,
dihedral, or improper) and the second argument must be a valid type
label that has been assigned to a numeric type.
*Invalid use of library file() function*
This function is called through the library interface. This
error should not occur. Contact the developers if it does.
@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script*
Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually
orthogonal.
@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Must not have multiple fixes change box parameter ...*
Self-explanatory.
*Must read Angle Type Labels before Angles*
An Angle Type Labels section of a data file must come before the Angles section.
*Must read Atom Type Labels before Atoms*
An Atom Type Labels section of a data file must come before the Atoms section.
*Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section.
@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
The Atoms section of a data file must come before a Velocities
section.
*Must read Bond Type Labels before Bonds*
A Bond Type Labels section of a data file must come before the Bonds section.
*Must read Dihedral Type Labels before Dihedrals*
An Dihedral Type Labels section of a data file must come before the Dihedrals section.
*Must read Improper Type Labels before Impropers*
An Improper Type Labels section of a data file must come before the Impropers section.
*Must re-specify non-restarted pair style (xxx) after read_restart*
For pair styles, that do not store their settings in a restart file,
it must be defined with a new 'pair_style' command after read_restart.
@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple*
Self-explanatory.
*The %s type label %s is already in use for type %s*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type label string %s for %s type %s is invalid*
See the labelmap command documentation for valid type labels.
*Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package

1
doc/src/Howto.rst
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@ -34,6 +34,7 @@ Settings howto
:maxdepth: 1
Howto_2d
Howto_type_labels
Howto_triclinic
Howto_thermostat
Howto_barostat

126
doc/src/Howto_type_labels.rst Normal file
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@ -0,0 +1,126 @@
Type labels
===========
.. versionadded:: TBD
Each atom in LAMMPS has an associated numeric atom type. Similarly,
each bond, angle, dihedral, and improper is assigned a bond type,
angle type, and so on. The primary use of these types is to map
potential (force field) parameters to the interactions of the atom,
bond, angle, dihedral, and improper.
By default, type values are entered as integers from 1 to Ntypes
wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
number of types is locked in when creating the simulation box, and
potential parameters for each type must be provided even if not used
by any interactions.
A collection of type labels for all type-kinds (atom types, bond types,
etc.) is stored as a "label map" which is simply a list of numeric types
and their associated type labels. Within a type-kind, each type label
must be unique. It can be assigned to only one numeric type. To read
and write type labels to data files for a given type-kind, *all*
associated numeric types need have a type label assigned. Partial
maps can be saved with the :doc:`labelmap write <labelmap>` command
and read back with the :doc:`include <include>` command.
Valid type labels can contain most ASCII characters, but cannot start
with a number, a '#', or a '*'. Also, labels must not contain whitespace
characters. When using the :doc:`labelmap command <labelmap>` in the
LAMMPS input, if certain characters appear in the type label, such as
the single (') or double (") quote or the '#' character, the label
must be put in either double, single, or triple (""") quotes. Triple
quotes allow for the most generic type label strings, but they require
to have a leading and trailing blank space. When defining type labels
the blanks will be ignored. Example:
.. code-block:: LAMMPS
labelmap angle 1 """ C1'-C2"-C3# """
This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
There are two ways to define label maps. One is via the :doc:`labelmap
<labelmap>` command. The other is via the :doc:`read_data <read_data>`
command. A data file can have sections such as *Atom Type Labels*, *Bond
Type Labels*, etc., which assign type labels to numeric types. The
label map can be written out to data files by the :doc:`write_data
<write_data>` command. This map is also written to and read from
restart files, by the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands.
----------
Use of type labels in LAMMPS input or output
""""""""""""""""""""""""""""""""""""""""""""
Many LAMMPS input script commands that take a numeric type as an
argument can use the associated type label instead. If a type label
is not defined for a particular numeric type, only its numeric type
can be used.
This example assigns labels to the atom types, and then uses the type
labels to redefine the pair coefficients.
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 # numeric types
labelmap atom 1 C 2 H
pair_coeff C H 1.0 1.0 # type labels
Adding support for type labels to various commands is an ongoing
project. If an input script command (or a section in a file read by a
command) allows substituting a type label for a numeric type argument,
it will be explicitly mentioned in that command's documentation page.
As a temporary measure, input script commands can take advantage of
variables and how they can be expanded during processing of the input.
The variables can use functions that will translate type label strings
to their respective number as defined in the current label map. See the
:doc:`variable <variable>` command for details.
For example, here is how the pair_coeff command could be used with
type labels if it did not yet support them, either with an explicit
variable command or an implicit variable used in the pair_coeff
command.
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
variable atom1 equal label2type(atom,C)
variable atom2 equal label2type(atom,H)
pair_coeff ${atom1} ${atom2} 1.0 1.0
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
----------
Commands that can use label types
"""""""""""""""""""""""""""""""""
Any workflow that involves reading multiple data files, molecule
templates or a combination of the two can be streamlined by using type
labels instead of numeric types, because types are automatically synced
between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.

6
doc/src/Packages_details.rst
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@ -276,7 +276,7 @@ the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
molecular liquids", J. Chem. Phys. 143, 243148 (2015).
**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
Pennsylvania State University)
@ -932,6 +932,10 @@ EXTRA-MOLECULE package
Additional bond, angle, dihedral, and improper styles that are less commonly used.
**Install:**
To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
**Supporting info:**
* src/EXTRA-MOLECULE: filenames -> commands

2
doc/src/Run_options.rst
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@ -495,7 +495,7 @@ run:
write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
Note that the specified restartfile and dumpfile names may contain
wild-card characters ("\*","%") as explained on the
wild-card characters ("\*" or "%") as explained on the
:doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
pages. The use of "%" means that a parallel restart file and/or
parallel dump file can be read and/or written. Note that a filename

2
doc/src/Speed_intel.rst
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@ -536,6 +536,6 @@ supported.
References
""""""""""
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

50
doc/src/angle_coeff.rst
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@ -10,7 +10,7 @@ Syntax
angle_coeff N args
* N = angle type (see asterisk form below)
* N = numeric angle type (see asterisk form below), or type label
* args = coefficients for one or more angle types
Examples
@ -22,6 +22,9 @@ Examples
angle_coeff * 5.0
angle_coeff 2*10 5.0
labelmap angle 1 hydroxyl
angle_coeff hydroxyl 300.0 107.0
Description
"""""""""""
@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple angle types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = 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 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
for the same angle type. For example, these commands set the coeffs
for all angle types, then overwrite the coeffs for just angle type 2:
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple angle types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of angle types,
then an asterisk with no numeric values 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 :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can
override a previous setting for the same angle type. For example,
these commands set the coeffs for all angle types, then overwrite the
coeffs for just angle type 2:
.. code-block:: LAMMPS
@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
angle_coeff 2 50.0 107.0
A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Angle Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
command in an input script, except that wild-card asterisks should not
be used since coefficients for all :math:`N` types must be listed in the
file. For example, under the "Angle Coeffs" section of a data file, the
line that corresponds to the first example above would be listed as
.. parsed-literal::
@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
The :doc:`angle_style class2 <angle_class2>` is an exception to this
rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its
doc page for details.
allow specification of the cross-term coefficients. See its doc page
for details.
----------
The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc
page.
compact form on the :ref:`Commands angle <angle>` doc page.
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated

30
doc/src/bond_coeff.rst
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@ -10,7 +10,7 @@ Syntax
bond_coeff N args
* N = bond type (see asterisk form below)
* N = numeric bond type (see asterisk form below), or type label
* args = coefficients for one or more bond types
Examples
@ -21,7 +21,10 @@ Examples
bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0
bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
labelmap bond 5 carbonyl
bond_coeff carbonyl 80.0 1.2
Description
"""""""""""
@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
:math:`N` can be specified in one of several ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple bond types. This takes the form "\*" or "\*n"
or "n\*" or "m\*n". If :math:`N` is the number of bond types, then an
asterisk with no numeric values 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 (inclusive). A middle asterisk
means all types from m to n (inclusive).
asterisk means all types from n to :math:`N` (inclusive). A middle
asterisk means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs
@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Bond Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
.. parsed-literal::

1
doc/src/commands_list.rst
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@ -56,6 +56,7 @@ Commands
kspace_modify
kspace_style
label
labelmap
lattice
log
mass

2
doc/src/compute_angmom_chunk.rst
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@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
mass-velocity-distance :doc:`units <units>`.
Restrictions

2
doc/src/compute_born_matrix.rst
View File

@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
the :doc:`Howto output <Howto_output>` doc page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "extensive."
The array values calculated by this compute are all "extensive".
Restrictions
""""""""""""

2
doc/src/compute_com.rst
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@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The vector values are "intensive." The vector values will be in
The vector values are "intensive". The vector values will be in
distance :doc:`units <units>`.
Restrictions

2
doc/src/compute_com_chunk.rst
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@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
distance :doc:`units <units>`.
Restrictions

2
doc/src/compute_dipole.rst
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@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
dipole vector. See the :doc:`Howto output <Howto_output>` page for
an overview of LAMMPS output options.
The computed values are "intensive." The array values will be in
The computed values are "intensive". The array values will be in
dipole units (i.e., charge :doc:`units <units>` times distance
:doc:`units <units>`).

2
doc/src/compute_dipole_chunk.rst
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@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
array values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
dipole units (i.e., charge :doc:`units <units>` times distance
:doc:`units <units>`).

2
doc/src/compute_erotate_asphere.rst
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@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_erotate_rigid.rst
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@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that
uses a global scalar value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_erotate_sphere.rst
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@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

4
doc/src/compute_event_displace.rst
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@ -40,7 +40,7 @@ further than the threshold distance.
If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false positives."
local atom displacements and may generate "false positives".
Output info
"""""""""""
@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive." The
The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.
Restrictions

2
doc/src/compute_fep.rst
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@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
scalar or vector from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
The values calculated by this compute are "extensive."
The values calculated by this compute are "extensive".
Restrictions
""""""""""""

2
doc/src/compute_group_group.rst
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@ -140,7 +140,7 @@ vector values from a compute as input. See the
options.
Both the scalar and vector values calculated by this compute are
"extensive." The scalar value will be in energy :doc:`units <units>`.
"extensive". The scalar value will be in energy :doc:`units <units>`.
The vector values will be in force :doc:`units <units>`.
Restrictions

2
doc/src/compute_gyration.rst
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@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output <Howto_output
options.
The scalar and vector values calculated by this compute are
"intensive." The scalar and vector values will be in distance and
"intensive". The scalar and vector values will be in distance and
distance\ :math:`^2` :doc:`units <units>`, respectively.
Restrictions

2
doc/src/compute_gyration_shape.rst
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@ -78,7 +78,7 @@ vector values from a compute as input. See the
options.
The vector values calculated by this compute are
"intensive." The first five vector values will be in
"intensive". The first five vector values will be in
distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
Restrictions

2
doc/src/compute_gyration_shape_chunk.rst
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@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The array calculated by this compute is
"intensive." The first five columns will be in
"intensive". The first five columns will be in
distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
Restrictions

14
doc/src/compute_heat_flux.rst
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@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` documentation for an overview of
LAMMPS output options.
The vector values calculated by this compute are "extensive," meaning
The vector values calculated by this compute are "extensive", meaning
they scale with the number of atoms in the simulation. They can be
divided by the appropriate volume to get a flux, which would then be
an "intensive" value, meaning independent of the number of atoms in
the simulation. Note that if the compute is "all," then the
appropriate volume to divide by is the simulation box volume.
However, if a sub-group is used, it should be the volume containing
those atoms.
divided by the appropriate volume to get a flux, which would then be an
"intensive" value, meaning independent of the number of atoms in the
simulation. Note that if the compute group is "all", then the
appropriate volume to divide by is the simulation box volume. However,
if a group with a subset of atoms is used, it should be the volume
containing those atoms.
The vector values will be in energy\*velocity :doc:`units <units>`. Once
divided by a volume the units will be that of flux, namely

2
doc/src/compute_hma.rst
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@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
capacity). The elements of the vector can be accessed by indices 1--n by any
command that uses global vector values as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
The vector values calculated by this compute are "extensive." The
The vector values calculated by this compute are "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_inertia_chunk.rst
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@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
mass\*distance\ :math:`^2` :doc:`units <units>`.
Restrictions

2
doc/src/compute_ke.rst
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@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_ke_rigid.rst
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@ -48,7 +48,7 @@ global scalar value from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_momentum.rst
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@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The vector value calculated by this compute is "extensive." The vector
The vector value calculated by this compute is "extensive". The vector
value will be in mass\*velocity :doc:`units <units>`.
Restrictions

2
doc/src/compute_msd.rst
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@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The vector values are "intensive." The vector values will be in
The vector values are "intensive". The vector values will be in
distance\ :math:`^2` :doc:`units <units>`.
Restrictions

2
doc/src/compute_msd_chunk.rst
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@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from
a compute as input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
distance\ :math:`^2` :doc:`units <units>`.
Restrictions

2
doc/src/compute_msd_nongauss.rst
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@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The vector values are "intensive." The first vector value will be in
The vector values are "intensive". The first vector value will be in
distance\ :math:`^2` :doc:`units <units>`, the second is in
distance\ :math:`^4` units, and the third is dimensionless.

2
doc/src/compute_omega_chunk.rst
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@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array
values from a compute as input. See the :doc:`Howto output <Howto_output>`
page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
velocity/distance :doc:`units <units>`.
Restrictions

4
doc/src/compute_pe.rst
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@ -27,7 +27,7 @@ Description
"""""""""""
Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all." See the
entire system of atoms. The specified group must be "all". See the
:doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
energies. These per-atom values could be summed for a group of atoms
via the :doc:`compute reduce <compute_reduce>` command.
@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive." The
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy :doc:`units <units>`.
Restrictions

2
doc/src/compute_plasticity_atom.rst
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@ -73,5 +73,5 @@ none
.. _Mitchell:
**(Mitchell)** Mitchell, "A non-local, ordinary-state-based
viscoelasticity model for peridynamics," Sandia National Lab Report,
viscoelasticity model for peridynamics", Sandia National Lab Report,
8064:1-28 (2011).

6
doc/src/compute_pressure.rst
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@ -29,7 +29,7 @@ Description
"""""""""""
Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all." See the
of atoms. The specified group must be "all". See the
:doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the :doc:`compute reduce <compute_reduce>` command.
@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script:
compute thermo_press all pressure thermo_temp
where thermo_temp is the ID of a similarly defined compute of style
"temp." See the :doc:`thermo_style <thermo_style>` command for more details.
"temp". See the :doc:`thermo_style <thermo_style>` command for more details.
----------
@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows:
:math:`p_{xz},` :math:`p_{yz}.`
The scalar and vector values calculated by this compute are
"intensive." The scalar and vector values will be in pressure
"intensive". The scalar and vector values will be in pressure
:doc:`units <units>`.
Restrictions

2
doc/src/compute_property_chunk.rst
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@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as
input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
The vector or array values are "intensive." The values will be
The vector or array values are "intensive". The values will be
unitless or in the units discussed above.
Restrictions

2
doc/src/compute_property_local.rst
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@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types. The number
of bond types is defined in the data file read by the
:doc:`read_data <read_data>` command.
The attributes that start with "a," "d," and "i" refer to similar values
The attributes that start with "a", "d", and "i" refer to similar values
for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
:doc:`impropers <improper_style>`.

2
doc/src/compute_rdf.rst
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@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See
the :doc:`Howto output <Howto_output>` page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive."
The array values calculated by this compute are all "intensive".
The first column of array values will be in distance
:doc:`units <units>`. The :math:`g(r)` columns of array values are normalized

12
doc/src/compute_reduce.rst
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@ -128,7 +128,7 @@ inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
If a value begins with "c\_," a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
:doc:`compute <compute>` page for details. If no bracketed integer
@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how :math:`I` can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "f\_," a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual :doc:`fix <fix>` page for
details. Note that some fixes only produce their values on certain
@ -152,7 +152,7 @@ is used. Users can also write code for their own fix style and
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "v\_," a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. It must be an
:doc:`atom-style variable <variable>`. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of
inputs specified.
As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
produced by this compute are all "extensive," meaning their value
produced by this compute are all "extensive", meaning their value
scales linearly with the number of atoms involved. If normalized
values are desired, this compute can be accessed by the
:doc:`thermo_style custom <thermo_style>` command with
@ -218,9 +218,9 @@ compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are
"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on
"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
per-atom or local vectors, in which case the calculated values are
"extensive."
"extensive".
The scalar or vector values will be in whatever :doc:`units <units>` the
quantities being reduced are in.

2
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@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script.
Imagine a collection of polymer chains or small molecules with
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
to a group called "phobic."
to a group called "phobic".
These commands will assign a unique cluster ID to all HP atoms within
a specified distance of each other. A cluster will contain all HP

2
doc/src/compute_stress_profile.rst
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@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
compute p all stress/cartesian x 0.1
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
The values calculated by this compute are "intensive." The stress
The values calculated by this compute are "intensive". The stress
values will be in pressure :doc:`units <units>`. The number density
values are in inverse volume :doc:`units <units>`.

2
doc/src/compute_tally.rst
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@ -182,7 +182,7 @@ Output info
from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are
"extensive."
"extensive".
Restrictions
""""""""""""

2
doc/src/compute_temp.rst
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@ -91,7 +91,7 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The

4
doc/src/compute_temp_asphere.rst
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@ -134,8 +134,8 @@ vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_body.rst
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@ -117,8 +117,8 @@ vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_chunk.rst
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@ -242,8 +242,8 @@ can be accessed by any command that uses global array values from a
compute as input. Again, see the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive." The array values are "intensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`. The array values

4
doc/src/compute_temp_com.rst
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@ -87,8 +87,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_cs.rst
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@ -101,8 +101,8 @@ vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

2
doc/src/compute_temp_deform.rst
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@ -134,7 +134,7 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.

4
doc/src/compute_temp_deform_eff.rst
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@ -53,8 +53,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_drude.rst
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@ -67,8 +67,8 @@ vector values from a compute as input. See the
options.
Both the scalar value and the first two values of the vector
calculated by this compute are "intensive." The other four vector values
are "extensive."
calculated by this compute are "intensive". The other four vector values
are "extensive".
Restrictions
""""""""""""

4
doc/src/compute_temp_eff.rst
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@ -88,9 +88,9 @@ thermostatting.
Output info
"""""""""""
The scalar value calculated by this compute is "intensive," meaning it
The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive," meaning they scale with the number of atoms in
values are "extensive", meaning they scale with the number of atoms in
the simulation.
Restrictions

4
doc/src/compute_temp_partial.rst
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@ -94,8 +94,8 @@ vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_profile.rst
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@ -183,8 +183,8 @@ vector or array values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive." The array values are "intensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`. The first column

4
doc/src/compute_temp_ramp.rst
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@ -106,8 +106,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_region.rst
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@ -99,8 +99,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_region_eff.rst
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@ -46,8 +46,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_rotate.rst
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@ -86,8 +86,8 @@ vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

4
doc/src/compute_temp_sphere.rst
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@ -122,8 +122,8 @@ vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive." The
vector values are "extensive."
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.

2
doc/src/compute_ti.rst
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@ -125,7 +125,7 @@ value can be used by any command that uses a global scalar value from
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive."
The scalar value calculated by this compute is "extensive".
The scalar value will be in energy :doc:`units <units>`.

2
doc/src/compute_torque_chunk.rst
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@ -83,7 +83,7 @@ array values from a compute as input.
See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
force-distance :doc:`units <units>`.
Restrictions

2
doc/src/compute_vacf.rst
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@ -66,7 +66,7 @@ accessed by indices 1--4 by any command that uses global vector values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
The vector values are "intensive." The vector values will be in
The vector values are "intensive". The vector values will be in
velocity\ :math:`^2` :doc:`units <units>`.
Restrictions

2
doc/src/compute_vcm_chunk.rst
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@ -69,7 +69,7 @@ each chunk. These values can be accessed by any command that uses global array
values from a compute as input. See the :doc:`Howto output <Howto_output>`
page for an overview of LAMMPS output options.
The array values are "intensive." The array values will be in
The array values are "intensive". The array values will be in
velocity :doc:`units <units>`.
Restrictions

6
doc/src/compute_viscosity_cos.rst
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@ -134,9 +134,9 @@ These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive." The
first six elements of vector values are "extensive,"
and the seventh element of vector values is "intensive."
The scalar value calculated by this compute is "intensive". The
first six elements of vector values are "extensive",
and the seventh element of vector values is "intensive".
The scalar value will be in temperature :doc:`units <units>`.
The first six elements of vector values will be in energy :doc:`units <units>`.

2
doc/src/compute_voronoi_atom.rst
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@ -198,7 +198,7 @@ Voronoi volume, the second is the neighbor count, as described above
(read above for the output data in case the *occupation* keyword is
specified). 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>` page for an overview of LAMMPS output
options. If the *peratom* keyword is set to "no," the per-atom array
options. If the *peratom* keyword is set to "no", the per-atom array
is still created, but it is not accessible.
If the *edge_histo* keyword is used, then this compute generates a

2
doc/src/compute_xrd.rst
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@ -219,7 +219,7 @@ The array can be accessed by any command that uses global values from
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive."
All array values calculated by this compute are "intensive".
Restrictions
""""""""""""

4
doc/src/create_atoms.rst
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@ -95,7 +95,7 @@ typically created via the :doc:`create_box <create_box>` command.
Before using this command, a lattice must also be defined using the
:doc:`lattice <lattice>` command, unless you specify the *single* style
with units = box or the *random* style. For the remainder of this doc
page, a created atom or molecule is referred to as a "particle."
page, a created atom or molecule is referred to as a "particle".
If created particles are individual atoms, they are assigned the
specified atom *type*, though this can be altered via the *basis*
@ -352,7 +352,7 @@ As an example, these commands can be used in a 2d simulation, to
create a sinusoidal surface. Note that the surface is "rough" due to
individual lattice points being "above" or "below" the mathematical
expression for the sinusoidal curve. If a finer lattice were used,
the sinusoid would appear to be "smoother." Also note the use of the
the sinusoid would appear to be "smoother". Also note the use of the
"xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords, which
converts lattice spacings to distance.

37
doc/src/dihedral_coeff.rst
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@ -10,7 +10,7 @@ Syntax
dihedral_coeff N args
* N = dihedral type (see asterisk form below)
* N = numeric dihedral type (see asterisk form below) or alphanumeric type label
* args = coefficients for one or more dihedral types
Examples
@ -22,26 +22,35 @@ Examples
dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2* 80.0 1 3 0.5
labelmap dihedral 1 backbone
dihedral_coeff backbone 80.0 1 3
Description
"""""""""""
Specify the dihedral force field coefficients for one or more dihedral types.
The number and meaning of the coefficients depends on the dihedral style.
Dihedral coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
Specify the dihedral force field coefficients for one or more dihedral
types. The number and meaning of the coefficients depends on the
dihedral style. Dihedral coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple dihedral types. This takes the
form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of dihedral
types, then an asterisk with no numeric values 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 m to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be
an alphanumeric type label, which is a string defined by the
:doc:`labelmap <labelmap>` command or in a corresponding section of a
data file read by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple dihedral types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of dihedral types,
then an asterisk with no numeric values 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 :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using a dihedral_coeff command can override a previous setting
for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2:
for all dihedral types, then overwrite the coeffs for just dihedral type
2:
.. code-block:: LAMMPS

233
doc/src/dump.rst
View File

@ -224,30 +224,29 @@ page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
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
alternative approach to writing compressed files via a pipe, as done
by the regular dump styles, which may be required on clusters where
the interface to the high-speed network disallows using the fork()
library call (which is needed for a pipe). For the remainder of this
page, you should thus consider the *atom* and *atom/gz* styles
(etc.) to be inter-changeable, with the exception of the required
filename suffix.
alternative approach to writing compressed files via a pipe, as done by
the regular dump styles, which may be required on clusters where the
interface to the high-speed network disallows using the fork() library
call (which is needed for a pipe). For the remainder of this page, you
should thus consider the *atom* and *atom/gz* styles (etc.) to be
inter-changeable, with the exception of the required filename suffix.
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and
*xyz/zstd* styles are identical to the gz styles, but use the Zstd
compression library instead and require the ".zst" suffix. See the
:doc:`dump_modify <dump_modify>` page for details on how to control
the compression level in both variants.
:doc:`dump_modify <dump_modify>` page for details on how to control the
compression level in both variants.
As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
*xyz/mpiio* styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
"mpiio," except the single dump file they produce is written in
parallel via the MPI-IO library. For the remainder of this page,
you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
*xyz/mpiio* styles are identical in command syntax and in the format of
the dump files they create, to the corresponding styles without "mpiio",
except the single dump file they produce is written in parallel via the
MPI-IO library. For the remainder of this page, you should thus
consider the *atom* and *atom/mpiio* styles (etc.) to be
inter-changeable. The one exception is how the filename is specified
for the MPI-IO styles, as explained below.
.. warning::
@ -434,7 +433,7 @@ Below is an example for a YAML format dump created by the following commands.
dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
The tags "time," "units," and "thermo" are optional and enabled by the
The tags "time", "units", and "thermo" are optional and enabled by the
dump_modify command. The list under the "box" tag has three lines for
orthogonal boxes and four lines for triclinic boxes, where the first three are
the box boundaries and the fourth the three tilt factors (:math:`xy`,
@ -553,15 +552,14 @@ package installed, viz.,
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a dump filename which contains ".mpiio." Note that it
does not have to end in ".mpiio," just contain those characters.
Unlike MPI-IO restart files, which must be both written and read using
MPI-IO, the dump files produced by these MPI-IO styles are identical
in format to the files produced by their non-MPI-IO style
counterparts. This means you can write a dump file using MPI-IO and
use the :doc:`read_dump <read_dump>` command or perform other
post-processing, just as if the dump file was not written using
MPI-IO.
Second, use a dump filename which contains ".mpiio". Note that it does
not have to end in ".mpiio", just contain those characters. Unlike
MPI-IO restart files, which must be both written and read using MPI-IO,
the dump files produced by these MPI-IO styles are identical in format
to the files produced by their non-MPI-IO style counterparts. This
means you can write a dump file using MPI-IO and use the :doc:`read_dump
<read_dump>` command or perform other post-processing, just as if the
dump file was not written using MPI-IO.
.. warning::
@ -570,37 +568,40 @@ MPI-IO.
Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple
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
same binary format as if it were written without MPI-IO.
above in the filename since that specifies generation of multiple 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 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
"\*" 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
write out much faster. Of course, when post-processing, you will need
to convert it back to text format (see the :ref:`binary2txt tool <binary>`) or
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
is only available for the *atom* and *custom* styles.
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 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 to convert it back to text format (see the :ref:`binary2txt
tool <binary>`) or 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 is only available for
the *atom* and *custom* styles.
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
: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.
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 :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.
----------
Note that in the discussion which follows, for styles which can
reference values from a compute or fix or custom atom property, like
the *custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*"
or "m\*n." If :math:`N` is the number of columns in the array, then an
asterisk with no numeric values means all column indices from 1 to :math:`N`.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from m to :math:`N` (inclusive). A middle
asterisk means all indices from m to n (inclusive).
reference values from a compute or fix or custom atom property, like the
*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i`
can be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the number of columns in the array, then an
asterisk with no numeric values means all column indices from 1 to
:math:`N`. A leading asterisk means all indices from 1 to n
(inclusive). A trailing asterisk means all indices from m to :math:`N`
(inclusive). A middle asterisk means all indices from m to n
(inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. For example, these two dump commands are
@ -679,37 +680,38 @@ The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
*Id* is the atom ID. *Mol* is the molecule ID, included in the data
file for molecular systems. *Proc* is the ID of the processor (0 to
:math:`N_\text{procs}-1`) that currently owns the atom.
*Procp1* is the proc ID+1, which can be convenient in place of a *type*
attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization
program. *Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
typically the chemical name of an element, which you must assign to each type
via the :doc:`dump_modify element <dump_modify>` command. More generally, it
can be any string you wish to associated with an atom type. *Mass* is the atom
mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
of atom velocity and force and atomic charge.
:math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the
proc ID+1, which can be convenient in place of a *type* attribute (1 to
:math:`N_\text{types}`) for coloring atoms in a visualization program.
*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
typically the chemical name of an element, which you must assign to each
type via the :doc:`dump_modify element <dump_modify>` command. More
generally, it can be any string you wish to associated with an atom
type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
*fy*, *fz*, and *q* are components of atom velocity and force and atomic
charge.
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}`,
: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
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
:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
vectors of the simulation box edges, as discussed on the
:doc:`Howto triclinic <Howto_triclinic>` page.
: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 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 :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are
the non-orthogonal vectors of the simulation box edges, as discussed on
the :doc:`Howto triclinic <Howto_triclinic>` page.
Use *xu*, *yu*, and *zu* if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
passed through a periodic boundary one or more times, the value is
printed for what the coordinate would be if it had not been wrapped
back into the periodic box. Note that using *xu*, *yu*, and *zu* means
that the coordinate values may be far outside the box bounds printed
with the snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using
*xu*, *yu*, and *zu*, except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding coordinate increased or decreased by 1.0.
image flags for each atom. Unwrapped means that if the atom has passed
through a periodic boundary one or more times, the value is printed for
what the coordinate would be if it had not been wrapped back into the
periodic box. Note that using *xu*, *yu*, and *zu* means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using *xu*, *yu*,
and *zu*, except that the unwrapped coordinates are scaled by the box
size. Atoms that have passed through a periodic boundary will have the
corresponding coordinate increased or decreased by 1.0.
The image flags can be printed directly using the *ix*, *iy*, and *iz*
attributes. For periodic dimensions, they specify which image of the
@ -721,8 +723,8 @@ periodic boundaries during the simulation.
The *mux*, *muy*, and *muz* attributes are specific to dipolar systems
defined with an atom style of *dipole*\ . They give the orientation of
the atom's point dipole moment. The *mu* attribute gives the
magnitude of the atom's dipole moment.
the atom's point dipole moment. The *mu* attribute gives the magnitude
of the atom's dipole moment.
The *radius* and *diameter* attributes are specific to spherical
particles that have a finite size, such as those defined with an atom
@ -736,17 +738,17 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
finite-size aspherical particles that have an angular momentum. Only
the *ellipsoid* atom style defines this quantity.
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
can sustain a rotational torque due to interactions with other
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles
that can sustain a rotational torque due to interactions with other
particles.
The *c_ID* and *c_ID[I]* attributes allow per-atom vectors or arrays
calculated by a :doc:`compute <compute>` to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
:doc:`compute <compute>` command for details. There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.
been defined previously in the input script. See the :doc:`compute
<compute>` command for details. There are computes for calculating the
per-atom energy, stress, centro-symmetry parameter, and coordination
number of individual atoms.
Note that computes which calculate global or local quantities, as
opposed to per-atom quantities, cannot be output in a dump custom
@ -754,39 +756,39 @@ command. Instead, global quantities can be output by the
:doc:`thermo_style custom <thermo_style>` command, and local quantities
can be output by the dump local command.
If *c_ID* is used as a attribute, then the per-atom vector calculated
by the compute is printed. If *c_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
per-atom array with :math:`M` columns calculated by the compute. See the
discussion above for how :math:`i` can be specified with a wildcard asterisk to
effectively specify multiple values.
If *c_ID* is used as a attribute, then the per-atom vector calculated by
the compute is printed. If *c_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 per-atom array with :math:`M` columns calculated by the compute.
See the discussion above for how :math:`i` can be specified with a
wildcard asterisk to effectively specify multiple values.
The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom
quantities calculated by a :doc:`fix <fix>` to be output. The ID in
the attribute should be replaced by the actual ID of the fix that has
been defined previously in the input script. The :doc:`fix ave/atom
quantities calculated by a :doc:`fix <fix>` to be output. The ID in the
attribute should be replaced by the actual ID of the fix that has been
defined previously in the input script. The :doc:`fix ave/atom
<fix_ave_atom>` command is one that calculates per-atom quantities.
Since it can time-average per-atom quantities produced by any
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
:doc:`variable <variable>`, this allows those time-averaged results to
be written to a dump file.
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style :doc:`variable
<variable>`, this allows those time-averaged results to be written to a
dump file.
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
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
discussion above for how :math:`i` can be specified with a wildcard asterisk
to effectively specify multiple values.
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
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 discussion above for how :math:`i` can be specified with a wildcard
asterisk to effectively specify multiple values.
The *v_name* attribute allows per-atom vectors calculated by a
:doc:`variable <variable>` to be output. The name in the attribute
should be replaced by the actual name of the variable that has been
defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
defined previously in the input script. Only an atom-style variable can
be referenced, since it is the only style that generates per-atom
values. Variables of style *atom* can reference individual atom
attributes, per-atom attributes, thermodynamic keywords, or invoke
other computes, fixes, or variables when they are evaluated, so this
is a very general means of creating quantities to output to a dump file.
attributes, per-atom attributes, thermodynamic keywords, or invoke other
computes, fixes, or variables when they are evaluated, so this is a very
general means of creating quantities to output to a dump file.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been
@ -794,10 +796,11 @@ added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is in the
range from 1 to :math:`M`, where :math:`M` is the number of columns in the
custom array). See the discussion above for how :math:`i` can be specified with
a wildcard asterisk to effectively specify multiple values.
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
in the range from 1 to :math:`M`, where :math:`M` is the number of
columns in the custom array). See the discussion above for how :math:`i`
can be specified with a wildcard asterisk to effectively specify
multiple values.
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

55
doc/src/dump_image.rst
View File

@ -196,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The
alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the *image* dump style. If the suffix is ".jpg" or
".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
suffix is ".png," then a `PNG format <png_format_>`_ is created, else
".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
suffix is ".png", then a `PNG format <png_format_>`_ is created, else
a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
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
@ -261,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined
for the :doc:`dump custom <dump>` command, including *type* and
*element*\ . This includes per-atom quantities calculated by a
: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
all atoms by the optional *adiam* keyword.
@ -297,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
If other atom attributes are used for the *color* or *diameter*
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
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
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
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".
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
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
@ -792,14 +792,14 @@ increasing values. Note that numeric values can be specified either
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.
Here is how the entries are used to determine the color of an
individual atom, given the value :math:`X` of its atom attribute.
:math:`X` will fall between 2 of the entry values. The color of the atom is
linearly interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if :math:`X = -5.0` and the two
surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
then the atom's color will be halfway between "red" and "blue," which happens
to be "purple."
Here is how the entries are used to determine the color of an individual
atom, given the value :math:`X` of its atom attribute. :math:`X` will
fall between 2 of the entry values. The color of the atom is linearly
interpolated (in each of the RGB values) between the 2 colors associated
with those entries. For example, if :math:`X = -5.0` and the two
surrounding entries are "red" at :math:`-10.0` and "blue" at
:math:`0.0`, then the atom's color will be halfway between "red" and
"blue", which happens to be "purple".
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
@ -807,19 +807,18 @@ range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
and *hi* settings of the last entry must be *min* and *max*\ . Other
entries can have any *lo* and *hi* values and the sub-ranges of
different values can overlap. Note that numeric *lo* and *hi* values
can be specified either 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.
can be specified either 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.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. The entries
are scanned from first to last. The first time that *lo* <= X <=
*hi*, X is assigned the color associated with that entry. You can
think of the last entry as assigning a default color (since it will
always be matched by X), and the earlier entries as colors that
override the default. Also note that no interpolation of a color RGB
is done. All atoms will be drawn with one of the colors in the list
of entries.
Here is how the entries are used to determine the color of an individual
atom, given the value X of its atom attribute. The entries are scanned
from first to last. The first time that *lo* <= X <= *hi*, X is
assigned the color associated with that entry. You can think of the
last entry as assigning a default color (since it will always be matched
by X), and the earlier entries as colors that override the default.
Also note that no interpolation of a color RGB is done. All atoms will
be drawn with one of the colors in the list of entries.
For sequential color maps, each entry has only a *color*\ . Here is how
the entries are used to determine the color of an individual atom,
@ -867,7 +866,7 @@ that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
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
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
is the number of bond types, then an asterisk with no numerical values
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 m to :math:`N`

57
doc/src/dump_modify.rst
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@ -176,6 +176,31 @@ extra buffering.
----------
.. versionadded:: 4May2022
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names. Using the *scale* or *image* keyword will also
reset all header keywords to their default values.
----------
The *delay* keyword applies to all dump styles. No snapshots will be
output until the specified *Dstep* timestep or later. Specifying
*Dstep* < 0 is the same as turning off the delay setting. This is a
@ -365,7 +390,7 @@ always occur if the current timestep is a multiple of $N$, the
frequency specified in the :doc:`dump <dump>` command or
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
It will also always occur if the current simulation time is a multiple
of *Delta*, the time interval specified in the doc:`dump_modify
of *Delta*, the time interval specified in the :doc:`dump_modify
every/time <dump_modify>` command.
But if this is not the case, a dump snapshot will only be written if
@ -373,7 +398,7 @@ the setting of this keyword is *yes*\ . If it is *no*, which is the
default, then it will not be written.
Note that if the argument to the :doc:`dump_modify every
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
<dump_modify>` :doc:`dump_modify every/time <dump_modify>` commands is
a variable and not a numeric value, then specifying *first yes* is the
only way to write a dump snapshot on the first timestep after the dump
command is invoked.
@ -388,30 +413,6 @@ performed with dump style *xtc*\ .
----------
.. versionadded:: 4May2022
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names.
----------
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
@ -498,6 +499,8 @@ boundary twice and is really two box lengths to the left of its
current coordinate. Note that for dump style *custom* these various
values can be printed in the dump file by using the appropriate atom
attributes in the dump command itself.
Using this keyword will reset all custom header names set with
*dump_modify colname* to their respective default values.
----------
@ -671,6 +674,8 @@ value of *yes* means atom coords are written in normalized units from
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of *no* means they are written in absolute distance units
(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
Using this keyword will reset all custom header names set with
*dump_modify colname* to their respective default values.
----------

56
doc/src/fix_adapt.rst
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@ -122,7 +122,7 @@ The *pstyle* argument is the name of the pair style. If
sub-styles using the same pair style, then *pstyle* should be specified
as "style:N", where :math:`N` is which instance of the pair style you wish to
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
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
@ -245,7 +245,7 @@ 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
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
is the number of atom types, then an asterisk with no numeric values
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 m to :math:`N`
@ -260,17 +260,17 @@ values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
that sub-style.
The *v_name* argument for keyword *pair* is the name of an
:doc:`equal-style variable <variable>` which will be evaluated each
time this fix is invoked to set the parameter to a new value. It
should be specified as v_name, where name is the variable name.
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify parameters that change as a function
of time or span consecutive runs in a continuous fashion. For the
latter, see the *start* and *stop* keywords of the :doc:`run <run>`
command and the *elaplong* keyword of :doc:`thermo_style custom
<thermo_style>` for details.
:doc:`equal-style variable <variable>` which will be evaluated each time
this fix is invoked to set the parameter to a new value. It should be
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions, and
include :doc:`thermo_style <thermo_style>` command keywords for the
simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
*start* and *stop* keywords of the :doc:`run <run>` command and the
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
details.
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
@ -288,13 +288,14 @@ a bond coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now a bond coefficient for a
given bond type is adapted.
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
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of bond types, then an asterisk with no numeric values
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 m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive).
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 types.
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
the number of bond types, then an asterisk with no numeric values 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 m to
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
@ -323,13 +324,14 @@ an angle coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now an angle coefficient for a
given angle type is adapted.
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
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of angle types, then an asterisk with no numeric values
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 m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive).
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 types.
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
the number of angle types, then an asterisk with no numeric values 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 m to
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work

4
doc/src/fix_adapt_fep.rst
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@ -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
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
can be varied by this fix. See the doc pages for individual pair
styles and their energy formulas for the meaning of these parameters:
@ -209,7 +209,7 @@ 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
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
the number of atom types, then an asterisk with no numeric values 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 m to :math:`N`

2
doc/src/fix_addforce.rst
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@ -153,7 +153,7 @@ which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above.
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
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
the :doc:`run <run>` command.

2
doc/src/fix_addtorque.rst
View File

@ -75,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`. The scalar
is the potential energy discussed above. The vector is the total
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
fix are "extensive."
fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

2
doc/src/fix_amoeba_bitorsion.rst
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@ -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
:doc:`output commands <Howto_output>`. The scalar is the potential
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
the :doc:`run <run>` command.

2
doc/src/fix_amoeba_pitorsion.rst
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@ -138,7 +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
:doc:`output commands <Howto_output>`. The scalar is the potential
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
the :doc:`run <run>` command.

2
doc/src/fix_atc.rst
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@ -135,7 +135,7 @@ fix are listed below.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the energy
discussed in the previous paragraph. The scalar value is "extensive."
discussed in the previous paragraph. The scalar value is "extensive".
No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not

2
doc/src/fix_atom_swap.rst
View File

@ -167,7 +167,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive."
The vector values calculated by this fix are "extensive".
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

8
doc/src/fix_ave_atom.rst
View File

@ -70,7 +70,7 @@ per-atom vectors.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
@ -127,7 +127,7 @@ specifying an input value from that compute.
:doc:`compute property/atom <compute_property_atom>`
command via its *xu*, *yu*, and *zu* attributes.
If a value begins with "c\_," a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index :math:`I` is appended, the
@ -137,7 +137,7 @@ used. Users can also write code for their own compute styles and
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "f\_," a fix ID must follow which has been previously
If a value begins with "f\_", a fix ID must follow which has been previously
defined in the input script. If no bracketed term is appended, the per-atom
vector calculated by the fix is used. If a bracketed term containing an index
:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
@ -148,7 +148,7 @@ and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "v\_," a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script as an
:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
thermodynamic keywords or invoke other computes, fixes, or variables

36
doc/src/fix_ave_chunk.rst
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@ -288,7 +288,7 @@ together as one set of atoms to calculate their temperature. The
compute allows the center-of-mass velocity of each chunk to be
subtracted before calculating the temperature; this fix does not.
If a value begins with "c\_," a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -297,7 +297,7 @@ their own compute styles and :doc:`add them to LAMMPS <Modify>`.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f\_," a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -308,7 +308,7 @@ their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v\_," a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. Variables of style
*atom* can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
@ -348,7 +348,7 @@ at each sampling step.
If the *norm* setting is *none*, a similar computation as for the
*sample* setting is done, except the individual "average sample
values" are "summed sample values." A summed sample value is simply
values" are "summed sample values". A summed sample value is simply
the chunk value summed over atoms in the sample, without dividing by
the number of atoms in the sample. The output value for the chunk on
the :math:`N_\text{freq}` timesteps is the average of the
@ -494,21 +494,21 @@ relevant to this fix.
This fix computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. The values can only be
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
is when averaging is performed. The global array has # of rows = the number
of chunks :math:`N_\text{chunk}`, as calculated by the specified
:doc:`compute chunk/atom <compute_chunk_atom>` command. The # of columns is
:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
depending on whether the optional
columns for OrigID and CoordN are used, as explained above. Following
the optional columns, the next column contains the count of atoms in
the chunk, and the remaining columns are the Nvalue quantities. When
the array is accessed with a row :math:`I` that exceeds the current number of
chunks, than a 0.0 is returned by the fix instead of an error, since
the number of chunks can vary as a simulation runs depending on how
that value is computed by the compute chunk/atom command.
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since
that is when averaging is performed. The global array has # of rows =
the number of chunks :math:`N_\text{chunk}`, as calculated by the
specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The #
of columns is :math:`M+1+N_\text{values}`, where :math:`M \in
\{1,\dotsc,4\}`, depending on whether the optional columns for OrigID
and CoordN are used, as explained above. Following the optional
columns, the next column contains the count of atoms in the chunk, and
the remaining columns are the Nvalue quantities. When the array is
accessed with a row :math:`I` that exceeds the current number of chunks,
than a 0.0 is returned by the fix instead of an error, since the number
of chunks can vary as a simulation runs depending on how that value is
computed by the compute chunk/atom command.
The array values calculated by this fix are treated as "intensive,"
The array values calculated by this fix are treated as "intensive",
since they are typically already normalized by the count of atoms in
each chunk.

6
doc/src/fix_ave_correlate.rst
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@ -189,7 +189,7 @@ Also, if the *ave* keyword is set to *one* which is the default, then
----------
If a value begins with "c\_," a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the :math:`I^\text{th}` element of the global
@ -206,7 +206,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_," a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the :math:`I^\text{th}` element of the global
@ -219,7 +219,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
result. Users can also write code for their own fix styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "v\_," a variable name must follow which has been
If a value begins with "v\_", a variable name must follow which has been
previously defined in the input script. Only equal-style or vector-style
variables can be referenced; the latter requires a bracketed term to specify
the :math:`I^\text{th}` element of the vector calculated by the variable.

6
doc/src/fix_ave_histo.rst
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@ -193,7 +193,7 @@ inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then
specifying an input value from that compute.
If a value begins with "c\_," a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -215,7 +215,7 @@ these commands which give the IDs of these computes. Users can also
write code for their own compute styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_," a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@ -232,7 +232,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
result. Users can also write code for their own fix styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "v\_," a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. If *mode* = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires

6
doc/src/fix_ave_time.rst
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@ -358,11 +358,11 @@ of rows = length of the input vectors and # of columns = number of
inputs.
If the fix produces a scalar or vector, then the scalar and each
element of the vector can be either "intensive" or "extensive,"
element of the vector can be either "intensive" or "extensive",
depending on whether the values contributing to the scalar or vector
element are "intensive" or "extensive." If the fix produces an array,
element are "intensive" or "extensive". If the fix produces an array,
then all elements in the array must be the same, either "intensive" or
"extensive." If a compute or fix provides the value being time
"extensive". If a compute or fix provides the value being time
averaged, then the compute or fix determines whether the value is
intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.

4
doc/src/fix_balance.rst
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@ -361,7 +361,7 @@ The "SQUARES" section lists the node IDs of the four vertices in a
rectangle for each processor (1 to 4).
For a 3d problem, the syntax is similar but with eight vertices listed for
each processor instead of four, and "SQUARES" replaced by "CUBES."
each processor instead of four, and "SQUARES" replaced by "CUBES".
----------
@ -387,7 +387,7 @@ number of particles (or total weight) per processor.
These quantities can be accessed by various
:doc:`output commands <Howto_output>`. The scalar and vector values calculated
by this fix are "intensive."
by this fix are "intensive".
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

68
doc/src/fix_latte.rst
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@ -8,18 +8,27 @@ Syntax
.. parsed-literal::
fix ID group-ID latte peID
fix ID group-ID latte keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* latte = style name of this fix command
* peID = NULL or ID of compute used to calculate per-atom energy
* zero or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *coulomb* or *exclude*
*coulomb* value = peID
peID = ID of compute used to calculate per-atom energy
*exclude* value = fixID
fixID = ID of fix which potentially excludes atoms before calling LATTE
Examples
""""""""
.. code-block:: LAMMPS
fix dftb all latte NULL
fix dftb all latte
fix dftb all exclude GCMC
Description
"""""""""""
@ -48,10 +57,41 @@ found in examples/latte.
A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
The *peID* argument is not yet supported by fix latte, so it must be
specified as NULL. Eventually it will be used to enable LAMMPS to
calculate a Coulomb potential as an alternative to LATTE performing
the calculation.
Currently, LAMMPS must be run in serial or as a single MPI task, to
use this fix. This is because the version of the LATTE library LAMMPS
uses does not support MPI. On the LAMMPS size, this is typically not
a bottleneck, since LATTE will be doing 99% or more of the work to
compute quantum-accurate forces. On the LATTE side, the LATTE library
does support threaded parallelism via OpenMP. You must build the
LATTE library with OpenMP support, then set the OMP_NUM_THREADS
environment variable before performing a LAMMPS + LATTE simulation to
tell LATTE how many threads to invoke.
.. note::
NEB calculations can be done using this fix using multiple
replicas and running LAMMPS in parallel. However, each replica must
be run on a single MPI task. For details, see the :doc:`neb <neb>`
command page and the :doc:`-partition command-line switch <Run_options>`
----------
The *coulomb* argument is not yet supported by fix latte (as of Sept
2022). Eventually it will be used to enable LAMMPS to calculate a
Coulomb potential as an alternative to LATTE performing the
calculation.
The *exclude* argument allows this fix to work in tandem with another
fix which may decide to delete one or more atoms of molecules. The
specified fixID is the ID of the other fix.
The one current example of such a fix is the :doc:`fix gcmc
<fix_gcmc>` command which performs Monte Carlo insertions and
deletions. If a trial deletion is performed, then LAMMPS needs to
only pass LATTE the atoms which remain. Fix gcmc does not actually
remove any atoms until after the new energy is computed (in this case
by LATTE), and a Monte Carlo accept/reject decision is made for the
trial deletion.
----------
@ -153,18 +193,8 @@ use this fix.
LATTE does not currently compute per-atom energy or per-atom virial
contributions. So they will not show up as part of the calculations
performed by the :doc:`compute pe/atom <compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>` commands.
Currently, LAMMPS must be run in serial or as a single MPI task, to
use this fix. This is typically not a bottleneck, since LATTE will be
doing 99% or more of the work to compute quantum-accurate forces.
.. note::
NEB calculations can be done using this fix using multiple
replicas and running LAMMPS in parallel. However, each replica must
be run on a single MPI task. For details, see the :doc:`neb <neb>`
command page and the :doc:`-partition command-line switch <Run_options>`
performed by the :doc:`compute pe/atom <compute_pe_atom>` or
:doc:`compute stress/atom <compute_stress_atom>` commands.
Related commands
""""""""""""""""

2
doc/src/group.rst
View File

@ -318,7 +318,7 @@ Restrictions
""""""""""""
There can be no more than 32 groups defined at one time, including
"all."
"all".
The parent group of a dynamic group cannot itself be a dynamic group.

41
doc/src/improper_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
improper_coeff N args
* N = improper type (see asterisk form below)
* N = numeric improper type (see asterisk form below), or type label
* args = coefficients for one or more improper types
Examples
@ -22,27 +22,34 @@ Examples
improper_coeff * 80.2 -1 2
improper_coeff *4 80.2 -1 2
labelmap improper 1 benzene
improper_coeff benzene 300.0 0.0
Description
"""""""""""
Specify the improper force field coefficients for one or more improper
types. The number and meaning of the coefficients depends on the
improper style. Improper coefficients can also be set in the data
file read by the :doc:`read_data <read_data>` command or in a restart
file.
improper style. Improper coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple improper types. This takes
the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of improper
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 (inclusive). A
trailing asterisk means all types from n to N (inclusive). A middle
asterisk means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple improper types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` = the number of improper types,
then an asterisk with no numeric values 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 :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an improper_coeff command can override a previous
setting for the same improper type. For example, these commands set
the coeffs for all improper types, then overwrite the coeffs for just
setting for the same improper type. For example, these commands set the
coeffs for all improper types, then overwrite the coeffs for just
improper type 2:
.. code-block:: LAMMPS
@ -53,9 +60,9 @@ improper type 2:
A line in a data file that specifies improper coefficients uses the
exact same format as the arguments of the improper_coeff command in an
input script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Improper Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Improper Coeffs" section of a data file, the line
that corresponds to the first example above would be listed as
.. parsed-literal::

2
doc/src/kim_commands.rst
View File

@ -981,7 +981,7 @@ In the last example, "new-property.edn" and
"/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files
that contain user-defined (local) property definitions.
A KIM property instance takes the form of a "map," i.e. a set of key-value
A KIM property instance takes the form of a "map", i.e. a set of key-value
pairs akin to Perl's hash, Python's dictionary, or Java's Hashtable. It
consists of a set of property key names, each of which is referred to here by
the *key_name* argument, that are defined as part of the relevant KIM Property

100
doc/src/labelmap.rst Normal file
View File

@ -0,0 +1,100 @@
.. index:: labelmap
labelmap command
==================
Syntax
""""""
.. code-block:: LAMMPS
labelmap option args
* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
.. parsed-literal::
*clear* = no args
*write* arg = filename
*atom* or *bond* or *angle* or *dihedral* or *improper*
args = list of one or more numeric-type/type-label pairs
Examples
""""""""
.. code-block:: LAMMPS
labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
labelmap atom $(label2type(atom,carbon)) C # change type label from 'carbon' to 'C'
labelmap clear
labelmap write mymap.include
Description
"""""""""""
.. versionadded:: TBD
Define alphanumeric type labels to associate with one or more numeric
atom, bond, angle, dihedral or improper types. A collection of type
labels for all atom types, bond types, etc. is stored as a label map.
The label map can also be defined by the :doc:`read_data <read_data>`
command when it reads these sections in a data file: Atom Type Labels,
Bond Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for a general discussion of how type
labels can be used.
Valid type labels can contain any alphanumeric character, but must not
start with a number, a '#', or a '*' character. They can contain other
standard ASCII characters such as angular or square brackets '<' and '>'
or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
'+' and equals '=' signs and more. They must not contain blanks or any
other whitespace. Note that type labels must be put in single or double
quotation marks if they contain the '#' character or if they contain a
double (") or single quotation mark ('). If the label contains both
a single and a double quotation mark, then triple quotation (""") must
be used. When enclosing a type label with quotation marks, the
LAMMPS input parser may require adding leading or trailing blanks
around the type label so it can identify the enclosing quotation
marks. Those blanks will be removed when defining the label.
A *labelmap* command can only modify the label map for one type-kind
(atom types, bond types, etc). Any number of numeric-type/type-label
pairs may follow. If a type label already exists for the same numeric
type, it will be overwritten. Type labels must be unique; assigning the
same type label to multiple numeric types within the same type-kind is
not allowed. When reading and writing data files, it is required that
there is a label defined for *every* numeric type within a given
type-kind in order to write out the type label section for that
type-kind.
The *clear* option resets the label map and thus discards all previous
settings.
The *write* option takes a filename as argument and writes the current
label mappings to a file as a sequence of *labelmap* commands, so the
file can be copied into a new LAMMPS input file or read in using the
:doc:`include <include>` command.
----------
Restrictions
""""""""""""
This command must come after the simulation box is defined by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.
Label maps are currently not supported when using the KOKKOS package.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`write_data <write_data>`,
:doc:`molecule <molecule>`, :doc:`fix bond/react <fix_bond_react>`
Default
"""""""
none

21
doc/src/mass.rst
View File

@ -10,7 +10,7 @@ Syntax
mass I value
* I = atom type (see asterisk form below)
* I = atom type (see asterisk form below), or type label
* value = mass
Examples
@ -22,6 +22,9 @@ Examples
mass * 62.5
mass 2* 62.5
labelmap atom 1 C
mass C 12.01
Description
"""""""""""
@ -30,12 +33,16 @@ values can also be set in the :doc:`read_data <read_data>` data file
using the "Masses" keyword. See the :doc:`units <units>` command for
what mass units to use.
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or a wild-card
asterisk can be used to set the mass for multiple atom types. This
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = 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
The I index can be specified in one of several ways. An explicit
numeric value can be used, as in the first example above. Or I can be
a type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command, and which converts
internally to a numeric type. Or a wild-card asterisk can be used to
set the mass for multiple atom types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n", where m and n are numbers. If N = 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
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).

100
doc/src/molecule.rst
View File

@ -70,8 +70,9 @@ and underscores.
A single template can contain multiple molecules, listed one per file.
Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template
contains multiple molecules. The :doc:`atom_style template <atom_style>` command allows multiple-molecule templates
to define a system with more than one templated molecule.
contains multiple molecules. The :doc:`atom_style template
<atom_style>` command allows multiple-molecule templates to define a
system with more than one templated molecule.
Each filename can be followed by optional keywords which are applied
only to the molecule in the file as used in this template. This is to
@ -88,6 +89,12 @@ molecule file. E.g. if *toff* = 2, and the file uses atom types
individual values will be ignored if the molecule template does not
use that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** on lines using type labels, as the type
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *scale* keyword scales the size of the molecule. This can be
useful for modeling polydisperse granular rigid bodies. The scale
factor is applied to each of these properties in the molecule file, if
@ -118,14 +125,18 @@ The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
A molecule file has a header and a body. The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only white-space after comment is deleted), it is
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
blank between any valid content and the comment. If the line is blank
(i.e. contains only white-space after comments are deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it does not contain a header
keyword, the line begins the body of the file.
value(s) is/are read from the line. A line that is *not* blank and does
*not* contains a header keyword begins the body of the file.
The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
@ -173,31 +184,43 @@ These are the allowed section keywords for the body of the file.
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
atom/bond/angle/etc type can be specified either as a number (numeric
type) or as an alphanumeric type label. The latter is only allowed if
type labels have been defined, either by the :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
When using type labels, any values specified as *offset* are ignored.
If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
:doc:`special_bonds <special_bonds>` command for more details. One
reason to list the special bond info explicitly is for the
:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the
bonds between nuclear cores and Drude electrons in a different manner.
interactions between bonded atoms. See the :doc:`special_bonds
<special_bonds>` command for more details. One reason to list the
special bond info explicitly is for the :doc:`thermalized Drude
oscillator model <Howto_drude>` which treats the bonds between nuclear
cores and Drude electrons in a different manner.
.. note::
Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords
and Types sections are required. To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
Whether a section is required depends on how the molecule template
is used by other LAMMPS commands. For example, to add a molecule
via the :doc:`fix deposit <fix_deposit>` command, the Coords and
Types sections are required. To add a rigid body via the :doc:`fix
pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the :doc:`fix pour <fix_pour>`
command can be used to add "molecules" which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
of 1.0. See the doc pages for LAMMPS commands that use molecule
templates for more details.
specified, each particle in the molecule will have a default
diameter of 1.0. See the doc pages for LAMMPS commands that use
molecule templates for more details.
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
@ -222,7 +245,7 @@ order.
* one line per atom
* line syntax: ID type
* type = atom type of atom
* type = atom type of atom (1-Natomtype, or type label)
----------
@ -289,7 +312,7 @@ included, the default mass for each atom is derived from its volume
* one line per bond
* line syntax: ID type atom1 atom2
* type = bond type (1-Nbondtype)
* type = bond type (1-Nbondtype, or type label)
* atom1,atom2 = IDs of atoms in bond
The IDs for the two atoms in each bond should be values
@ -301,7 +324,7 @@ from 1 to Natoms, where Natoms = # of atoms in the molecule.
* one line per angle
* line syntax: ID type atom1 atom2 atom3
* type = angle type (1-Nangletype)
* type = angle type (1-Nangletype, or type label)
* atom1,atom2,atom3 = IDs of atoms in angle
The IDs for the three atoms in each angle should be values from 1 to
@ -315,7 +338,7 @@ which the angle is computed) is the atom2 in the list.
* one line per dihedral
* line syntax: ID type atom1 atom2 atom3 atom4
* type = dihedral type (1-Ndihedraltype)
* type = dihedral type (1-Ndihedraltype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
The IDs for the four atoms in each dihedral should be values from 1 to
@ -328,7 +351,7 @@ ordered linearly within the dihedral.
* one line per improper
* line syntax: ID type atom1 atom2 atom3 atom4
* type = improper type (1-Nimpropertype)
* type = improper type (1-Nimpropertype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in improper
The IDs for the four atoms in each improper should be values from 1 to
@ -447,11 +470,15 @@ This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.
The a,b,c values are bond types for all bonds in the SHAKE cluster that
this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes)
or bond type labels as defined by the :doc:`labelmap <labelmap>` command
or a "Bond Type Labels" section of a data file.
The number of values that must appear is determined by the shake flag
for the atom (see the Shake Flags section above). All atoms in a
particular cluster should list their a,b,c values identically.
If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.
@ -459,8 +486,9 @@ If flag = 0, no a,b,c values are listed on the line, just the
If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
the second non-central atom (value c in the Shake Atoms section), and c
= the angle type (1 to Nangletypes, or angle type label) of the angle
between the 3 atoms.
If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.
@ -473,9 +501,9 @@ and the second non-central atom (value c in the Shake Atoms section).
If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the third non-central
atom (value d in the Shake Atoms section).
the second non-central atom (value c in the Shake Atoms section), and c
= bondtype of the bond between the central atom and the third
non-central atom (value d in the Shake Atoms section).
See the :doc:`fix shake <fix_shake>` page for a further description
of SHAKE clusters.

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