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import updates to the manual from the progguide branch

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Axel Kohlmeyer 2020-06-14 11:25:02 -04:00
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2
doc/src/Build_basics.rst
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@ -225,7 +225,7 @@ A few example command lines are:
For compiling with the Clang/LLVM compilers a CMake preset is provided that
can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the
`-C ../cmake/presets/intel.cmake` should switch the
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By

10
doc/src/Build_development.rst
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@ -126,7 +126,7 @@ in the next section.
.. note::
This unit test framework is new and still under development.
The unit test framework is new and still under development.
The coverage is only minimal and will be expanded over time.
Tests styles of the same kind of style (e.g. pair styles or
bond styles) are performed with the same executable using
@ -237,12 +237,12 @@ and working.
performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different
summation orders.
- When compiling with aggressive compiler optimization, some tests
- When compiling with (aggressive) compiler optimization, some tests
are likely to fail. It is recommended to inspect the individual
tests in detail to decide whether the specific error for a specific
tests in detail to decide, whether the specific error for a specific
property is acceptable (it often is), or this may be an indication
of mis-compiled code (or undesired large of precision due to
reordering of operations).
of mis-compiled code (or an undesired large loss of precision due
to significant reordering of operations and thus less error cancellation).
Collect and visualize code coverage metrics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

88
doc/src/Build_link.rst
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@ -1,12 +1,12 @@
Link LAMMPS as a library to another code
========================================
LAMMPS is designed as a library of C++ objects and can thus be
LAMMPS is designed as a library of C++ objects that can be
integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the :doc:`Howto
library <Howto_library>` doc page for a description of the interface
and how to extend it for your needs.
library <Howto_library>` page for a description of the interface
and how to use it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in a file
@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
----------
**Link with LAMMPS as a static library**\ :
Link with LAMMPS as a static library
------------------------------------
The calling application can link to LAMMPS as a static library with
compilation and link commands as in the examples shown below. These
are examples for a code written in C in the file *caller.c*.
are examples for a code written in C in the file ``caller.c``.
The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required
executable code from the library is copied into the calling executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
This assumes that LAMMPS has been compiled in the folder
``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
need to include all flags, libraries, and paths for the coupled
executable, that are also required to link the LAMMPS executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
When using CMake, additional libraries with sources in the lib folder
are built, but not included in ``liblammps.a`` and (currently) not
installed with "make install" and not included in the *pkgconfig*
installed with ``make install`` and not included in the ``pkgconfig``
configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is
therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared
library instead.
.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=static serial". And you also
@ -110,10 +111,10 @@ change to:
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since the
LAMMPS library is C++ code. You can display the currently applied
settings for building LAMMPS for the "serial" machine target by using
the command:
Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
written your code in C, since LAMMPS itself is C++ code. You can display the
currently applied settings for building LAMMPS for the "serial" machine target
by using the command:
.. code-block:: bash
@ -123,25 +124,24 @@ Which should output something like:
.. code-block:: bash
# Compiler:
# Compiler:
CXX=g++
# Linker:
# Linker:
LD=g++
# Compilation:
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
# Linking:
# Linking:
LDFLAGS=-g -O
# Libraries:
# Libraries:
LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the
equivalent and replace "serial" with the corresponding *machine* name
equivalent and replace "serial" with the corresponding "machine" name
of the makefile.
----------
**Link with LAMMPS as a shared library**\ :
Link with LAMMPS as a shared library
------------------------------------
When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
@ -151,7 +151,8 @@ linking the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library with
the POEMS package installed becomes:
*CMake build*\ :
CMake build
^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the CMake
build process are the same as for the static library.
@ -161,10 +162,11 @@ build process are the same as for the static library.
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shared serial" becomes:
traditional make build using ``make mode=shared serial`` becomes:
.. code-block:: bash
@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface from a shared library through the `ctypes python module <ctypes_>`_.
See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _ctypes: https://docs.python.org/3/library/ctypes.html

19
doc/src/Build_settings.rst
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@ -169,12 +169,12 @@ ARRAY mode.
.. _size:
Size of LAMMPS data types
Size of LAMMPS integer types
------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
LAMMPS has a few integer data types which can be defined as either
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
The default setting of "smallbig" is almost always adequate.
**CMake variable**\ :
@ -420,8 +420,8 @@ Exception handling when using LAMMPS as a library
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course the calling code has to be set up to
*catch* exceptions from within LAMMPS.
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions thrown from within LAMMPS.
**CMake variable**\ :
@ -434,3 +434,10 @@ e.g. to Python. Of course the calling code has to be set up to
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
.. note::
When LAMMPS is running in parallel, it is not always possible to
cleanly recover from an exception since not all parallel ranks may
throw an exception and thus other MPI ranks may get stuck waiting for
messages from the ones with errors.

6
doc/src/Commands_input.rst
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@ -31,9 +31,9 @@ does something different than this sequence:
run 100
In the first case, the specified timestep (0.5 fs) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
timestep is used for the 2nd one.
simulations of 100 timesteps each. In the second case, the default
timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
timestep is used for the second one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms

2
doc/src/Commands_pair.rst
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@ -78,7 +78,7 @@ OPT.
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>`

2
doc/src/Developer/developer.tex
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@ -142,7 +142,7 @@ follows:
minimize.
\item The Special class walks the bond topology of a molecular system
to find 1st, 2nd, 3rd neighbors of each atom. It is invoked by
to find first, second, third neighbors of each atom. It is invoked by
several commands, like read\_data, read\_restart, and replicate.
\item The Atom class stores all per-atom arrays. More precisely, they

18
doc/src/Errors_debug.rst
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@ -23,7 +23,7 @@ We use it to show how to identify the origin of a segmentation fault.
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ double comx = 0.0;
inum = list->inum;
ilist = list->ilist;
@@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
@ -31,7 +31,7 @@ We use it to show how to identify the origin of a segmentation fault.
}
}
- }
+ comx += atom->rmass[i]*x[i][0]; /* BUG */
+ }
+ printf("comx = %g\n",comx);
@ -42,7 +42,7 @@ After recompiling LAMMPS and running the input you should get something like thi
.. code-block:
$ ./lmp -in in.melt
$ ./lmp -in in.melt
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
@ -98,11 +98,11 @@ drop back to the GDB prompt.
Unit style : lj
Current step : 0
Time step : 0.005
Program received signal SIGSEGV, Segmentation fault.
0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
139 comx += atom->rmass[i]*x[i][0]; /* BUG */
(gdb)
(gdb)
Now typing the command "where" will show the stack of functions starting from
the current function back to "main()".
@ -119,7 +119,7 @@ the current function back to "main()".
#4 0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
#5 0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
#6 0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
(gdb)
(gdb)
You can also print the value of variables and see if there is anything
unexpected. Segmentation faults, for example, commonly happen when a
@ -189,12 +189,12 @@ the console are not mixed.
.. code-block::
$ valgrind ./lmp -in in.melt
$ valgrind ./lmp -in in.melt
==1933642== Memcheck, a memory error detector
==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==1933642== Command: ./lmp -in in.melt
==1933642==
==1933642==
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
@ -228,7 +228,7 @@ the console are not mixed.
==1933642== by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
==1933642== by 0x409339: main (main.cpp:65)
==1933642== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==1933642==
==1933642==
As you can see, the stack trace information is similar to that obtained
from GDB. In addition you get a more specific hint about what cause the

22
doc/src/Errors_messages.rst
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@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are defined.
*Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
the atoms are too far apart to make a valid bond.
*Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor.
The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are too far apart to make a valid bond.
*Bond atoms %d %d missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond atoms missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
template does not qualify.
*Cannot use fix box/relax on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two
When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
also keyword tri or xy, this is wrong.
*Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
When specifying scaling on a tilt factor component, the 2nd of the two
When specifying scaling on a tilt factor component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
This would be changing the same box dimension twice.
*Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two
When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory.
*Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix pour rigid and not molecule*
Self-explanatory.
@ -7192,7 +7192,7 @@ keyword to allow for additional bonds to be formed
does not exist.
*Replacing a fix, but new style != old style*
A fix ID can be used a 2nd time, but only if the style matches the
A fix ID can be used a second time, but only if the style matches the
previous fix. In this case it is assumed you with to reset a fix's
parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to.

8
doc/src/Errors_warnings.rst
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@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Self-explanatory.
*Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor.
The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
*Bond atoms missing at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -486,7 +486,7 @@ This will most likely cause errors in kinetic fluctuations.
a new style.
*No Kspace calculation with verlet/split*
The 2nd partition performs a kspace calculation so the kspace_style
The second partition performs a kspace calculation so the kspace_style
command must be used.
*No automatic unit conversion to XTC file format conventions possible for units lj*

2
doc/src/Examples.rst
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@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site.

2
doc/src/Howto_chunk.rst
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@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered
chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment

32
doc/src/Howto_cmake.rst
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@ -114,19 +114,19 @@ summary screen will look like this:
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.25.2")
-- Found Git: /usr/bin/git (found version "2.25.2")
-- Running check for auto-generated files from make-based build system
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Looking for C++ include omp.h
-- Looking for C++ include omp.h - found
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Performing Test COMPILER_SUPPORTS-ffast-math
-- Performing Test COMPILER_SUPPORTS-ffast-math - Success
-- Performing Test COMPILER_SUPPORTS-march=native
@ -143,7 +143,7 @@ summary screen will look like this:
* JPEG
* PNG
* ZLIB
-- <<< Build configuration >>>
Build type: RelWithDebInfo
Install path: /home/akohlmey/.local
@ -157,7 +157,7 @@ summary screen will look like this:
Options: -ffast-math;-march=native
-- <<< Linker flags: >>>
-- Executable name: lmp
-- Static library flags:
-- Static library flags:
-- <<< MPI flags >>>
-- MPI includes: /usr/include/mpich-x86_64
-- MPI libraries: /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
@ -291,7 +291,7 @@ Some common CMake variables
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``CMAKE_INSTALL_PREFIX``
@ -313,13 +313,13 @@ Some common CMake variables
- Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
* - ``CXX_COMPILER_LAUNCHER``
- tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
Some common LAMMPS specific variables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``BUILD_MPI``
@ -438,7 +438,7 @@ the target name to the command. Example: ``cmake --build . --target all`` or
* - ``clean``
- remove all generated files
Choosing generators
-------------------

2
doc/src/Howto_coreshell.rst
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@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle). The
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the *group-ID* (2nd argument) of the compute. The
into account by the *group-ID* (second argument) of the compute. The
groups can be defined using the :doc:`group *type*\ <group>` command.
Note that to perform thermostatting using this definition of
temperature, the :doc:`fix modify temp <fix_modify>` command should be

2
doc/src/Howto_multiple.rst
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@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
the fourth simulation, and so forth, until all 8 were completed.

2
doc/src/Howto_restart.rst
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@ -28,7 +28,7 @@ scripts are based on. If that script had the line
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
This script could be used to read the first restart file and re-run the
last 50 timesteps:
.. code-block:: LAMMPS

6
doc/src/Howto_triclinic.rst
View File

@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` doc page for further details.
One exception to this rule is if the 1st dimension in the tilt
One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this

2
doc/src/Intro_nonfeatures.rst
View File

@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
describes a variety of 3rd party tools for this task. Furthermore,
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems.

3
doc/src/Manual.rst
View File

@ -32,11 +32,12 @@ a brief description of the basic code structure of LAMMPS.
----------
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
every LAMMPS command.
.. _lws: https://lammps.sandia.gov
.. _user_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3

177
doc/src/Manual_build.rst
View File

@ -1,60 +1,62 @@
Building the LAMMPS manual
**************************
Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
Depending on how you obtained LAMMPS and whether you have built the
manual yourself, this directory has a number of sub-directories and
files. Here is a list with descriptions:
.. code-block:: bash
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
docenv # virtualenv for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
README # brief info about the documentation
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
docenv # virtualenv folder for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
doxygen # doxygen configuration and output
.gitignore # list of files and folders to be ignored by git
doxygen-warn.log # logfile with warnings from running doxygen
github-development-workflow.md # notes on the LAMMPS development workflow
include-file-conventions.md # notes on LAMMPS' include file conventions
If you downloaded LAMMPS as a tarball from the web site, the html folder
and the PDF files should be included.
If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one
of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should download a html_www
site. Just type ``make fetch``. This should download a html_www
directory and Manual_www.pdf/Developer_www.pdf files. Note that if
new LAMMPS features have been added more recently than the date of
your LAMMPS version, the fetched documentation will include those
changes (but your source code will not, unless you update your local
repository).
b. You can build the HTML or PDF files yourself, by typing "make html"
or "make pdf". This requires various tools including Sphinx, git,
and the MathJax javascript library, which the build process will attempt
to download automatically into a virtual environment in the folder
doc/docenv and the folder mathjax, respectively, if not already available.
This download is required only once, unless you type "make clean-all".
After that, viewing and processing of the documentation can be done
without internet access. To generate the PDF version of the manual,
the PDFLaTeX software and several LaTeX packages are required as well.
However, those cannot be installed automatically at the moment.
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf``. This requires various tools and files. Some of them
have to be installed (more on that below). For the rest the build
process will attempt to download and install them into a python
virtual environment and local folders. This download is required
only once, unless you type ``make clean-all``. After that, viewing and
processing of the documentation can be done without internet access.
----------
The generation of all documentation is managed by the Makefile in
the doc directory.
The generation of all documentation is managed by the Makefile in the
doc directory. The following documentation related make commands are
available:
.. code-block:: bash
Documentation Build Options:
make html # generate HTML in html dir using Sphinx
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
# in doc dir via htmldoc and pdflatex
@ -62,8 +64,10 @@ the doc directory.
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
make anchor_check # check for duplicate anchor labels
make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
@ -74,29 +78,30 @@ the doc directory.
Installing prerequisites for HTML build
=======================================
To run the HTML documentation build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
To run the HTML documentation build toolchain, python 3, git, doxygen,
and virtualenv have to be installed locally. Here are instructions for
common setups:
Ubuntu
------
.. code-block:: bash
sudo apt-get install python-virtualenv
sudo apt-get install python-virtualenv git doxygen
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
------------------------------------------------------------------------------------
.. code-block:: bash
sudo yum install python3-virtualenv
sudo yum install python3-virtualenv git doxygen
Fedora (since version 22)
-------------------------
.. code-block:: bash
sudo dnf install python3-virtualenv
sudo dnf install python3-virtualenv git doxygen
MacOS X
-------
@ -120,22 +125,92 @@ Once Python 3 is installed, open a Terminal and type
This will install virtualenv from the Python Package Index.
----------
Installing prerequisites for PDF build
======================================
Installing prerequisites for epub build
=======================================
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with support for PDFLaTeX and a selection
of LaTeX styles/packages are required.
ePUB
----
Installing prerequisites for e-book reader builds
=================================================
Same as for HTML. This uses mostly the same tools and configuration
files as the HTML tree. In addition it uses LaTeX to convert embedded
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with a few add-on LaTeX packages
as well as the ``dvipng`` tool are required to convert embedded
math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file
(for e-book readers, like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
On the Kindle readers in particular, you also have support for
PDF files, so you could download and view the PDF version as an alternative.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
files, so you could download and view the PDF version as an alternative.
Instructions for Developers
===========================
When adding new styles or options to the LAMMPS code, corresponding
documentation is required and either existing files in the ``src``
folder need to be updated or new files added. These files are written
in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
Before contributing any documentation, please check that both the HTML
and the PDF format documentation can translate without errors. Please also
check the output to the console for any warnings or problems. There will
be multiple tests run automatically:
- A test for correctness of all anchor labels and their references
- A test that all LAMMPS packages (= folders with sources in
``lammps/src``) are documented and listed. A typical warning shows
the name of the folder with the suspected new package code and the
documentation files where they need to be listed:
.. parsed-literal::
Found 33 standard and 41 user packages
Standard package NEWPACKAGE missing in Packages_standard.rst
Standard package NEWPACKAGE missing in Packages_details.rst
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:
.. parsed-literal::
Parsed style names w/o suffixes from C++ tree in ../src:
Angle styles: 21 Atom styles: 24
Body styles: 3 Bond styles: 17
Command styles: 41 Compute styles: 143
Dihedral styles: 16 Dump styles: 26
Fix styles: 223 Improper styles: 13
Integrate styles: 4 Kspace styles: 15
Minimize styles: 9 Pair styles: 234
Reader styles: 4 Region styles: 8
Compute style entry newcomp is missing or incomplete in Commands_compute.rst
Compute style entry newcomp is missing or incomplete in compute.rst
Fix style entry newfix is missing or incomplete in Commands_fix.rst
Fix style entry newfix is missing or incomplete in fix.rst
Pair style entry new is missing or incomplete in Commands_pair.rst
Pair style entry new is missing or incomplete in pair_style.rst
Found 6 issue(s) with style lists
In addition, there is the option to run a spellcheck on the entire
manual with ``make spelling``. This requires `a library called enchant
<https://github.com/AbiWord/enchant>`_. To avoid printing out *false
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov

2
doc/src/Modify_fix.rst
View File

@ -27,7 +27,7 @@ derived class. See fix.h for details.
+---------------------------+--------------------------------------------------------------------------------------------+
| setup_pre_force | called before force computation in setup (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+
| setup | called immediately before the 1st timestep and after forces are computed (optional) |
| setup | called immediately before the first timestep and after forces are computed (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+
| min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+

18
doc/src/Modify_kspace.rst
View File

@ -10,12 +10,12 @@ Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
+---------------+----------------------------------------------+
| init | initialize the calculation before a run |
+---------------+----------------------------------------------+
| setup | computation before the 1st timestep of a run |
+---------------+----------------------------------------------+
| compute | every-timestep computation |
+---------------+----------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+----------------------------------------------+
+---------------+------------------------------------------------+
| init | initialize the calculation before a run |
+---------------+------------------------------------------------+
| setup | computation before the first timestep of a run |
+---------------+------------------------------------------------+
| compute | every-timestep computation |
+---------------+------------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+------------------------------------------------+

2
doc/src/Packages_details.rst
View File

@ -489,7 +489,7 @@ interactions. These include Ewald, particle-particle particle-mesh
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a
library provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` doc page for details on how to select
different FFT options for your LAMPMS build.

9
doc/src/Python_library.rst
View File

@ -254,12 +254,3 @@ following steps:
* You should now be able to invoke the new interface function from a
Python script.
----------
.. autoclass:: lammps.lammps
:members:
:no-undoc-members:
.. autoclass:: lammps.NeighList
:members:
:no-undoc-members:

2
doc/src/Python_test.rst
View File

@ -10,7 +10,7 @@ and type:
>>> lmp = lammps()
If you get no errors, you're ready to use LAMMPS from Python. If the
2nd command fails, the most common error to see is
second command fails, the most common error to see is
.. parsed-literal::

8
doc/src/Run_options.rst
View File

@ -324,17 +324,17 @@ physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using
the :doc:`run_style verlet/split <run_style>` command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
to insure that a specific Kspace processor (in the second partition) is
matched up with a specific set of processors in the first partition.
See the :doc:`Speed tips <Speed_tips>` doc page for more details.
If the keyword *nth* is used with a setting *N*\ , then it means every
Nth processor will be moved to the end of the ranking. This is useful
when using the :doc:`run_style verlet/split <run_style>` command with 2
partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd
processors will be in the first partition, the second set in the second
partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition
the first N procs in the first partition and one proc in the second partition
will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the

2
doc/src/angle_charmm.rst
View File

@ -37,7 +37,7 @@ The *charmm* angle style uses the potential
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
with an additional Urey_Bradley term based on the distance :math:`r` between
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`,
the first and third atoms in the angle. :math:`K`, :math:`\theta_0`,
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
type.

4
doc/src/angle_coeff.rst
View File

@ -31,7 +31,7 @@ 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 1st example above. Or a wild-card asterisk can be
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
@ -53,7 +53,7 @@ same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in
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 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

10
doc/src/angle_table.rst
View File

@ -75,7 +75,7 @@ parenthesized comments):
...
181 180.0 0.0 0.0
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -99,7 +99,7 @@ is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and
fplo and fphi, which are the second derivatives at the innermost and
outermost angle settings. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two
@ -110,9 +110,9 @@ equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix
set to 180.0.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
On each line, the first value is the index from 1 to N, the second value is
the angle value (in degrees), the third value is the energy (in energy
units), and the fourth is -dE/d(theta) (also in energy units). The third
term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term

4
doc/src/atc_control_momentum.rst
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@ -15,7 +15,7 @@ Syntax
fix_modify AtC control momentum glc_velocity
fix_modify AtC control momentum hoover
fix_modify AtC control momentum flux [faceset face_set_id, interpolate]
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
* control = name of the AtC sub-command
* physics_type = *thermal* or *momentum*
@ -52,7 +52,7 @@ the finite element temperature. *flux* is a similar mode, but rather
adds energy to the atoms based on conservation of energy.
*correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the
compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the
controller's matrix solver.

2
doc/src/atc_control_thermal.rst
View File

@ -56,7 +56,7 @@ adds energy to the atoms based on conservation of energy. *hoover* and
atoms.
*correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the
compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the
controller's matrix solver.

6
doc/src/atc_hardy_fields.rst
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@ -25,8 +25,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume
@ -37,7 +37,7 @@ Syntax
- eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
- vacancy_concentration : volume fraction of vacancy content
- type_concentration : volume fraction of a specific atom type
Examples
""""""""

4
doc/src/atc_hardy_gradients.rst
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@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume

2
doc/src/atc_hardy_kernel.rst
View File

@ -25,7 +25,7 @@ Syntax
- *quartic_bar* : <half_width>
- *quartic_cylinder* : <radius>
- *quartic_sphere* : <radius>
Examples

4
doc/src/atc_hardy_rates.rst
View File

@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume

2
doc/src/atc_remove_species.rst
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@ -38,7 +38,7 @@ Related AtC commands
- :doc:`fix_modify AtC add_species <atc_add_species>`
- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
Default
"""""""

2
doc/src/atc_set_reference_pe.rst
View File

@ -22,7 +22,7 @@ Examples
fix_modify AtC set reference_potential_energy
fix_modify AtC set reference_potential_energy -0.05
fix_modify AtC set reference_potential_energy myPEvalues
fix_modify AtC set reference_potential_energy myPEvalues
Description
"""""""""""

18
doc/src/atc_time_integration.rst
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@ -33,11 +33,11 @@ Command to select the thermal or momentum time integration.
Options for thermal time integration:
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, thermostats based on controlling power
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, thermostats based on controlling power
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal temperature
atomic velocity update with second order Verlet, mixed nodal temperature
update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
thermostats based on controlling discrete energy changes
@ -46,18 +46,18 @@ Options for thermal time integration:
Options for momentum time integration:
*verlet*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 2nd order Verlet, kinetostats based on controlling force
atomic velocity update with second order Verlet, nodal temperature update
with second order Verlet, kinetostats based on controlling force
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal momentum
update, 2nd order Verlet for continuum and exact 2nd order Verlet for
atomic velocity update with second order Verlet, mixed nodal momentum
update, second order Verlet for continuum and exact second order Verlet for
atomic contributions, kinetostats based on controlling discrete
momentum changes
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, kinetostats based on controlling power.
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, kinetostats based on controlling power.
---------

4
doc/src/bond_coeff.rst
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@ -32,7 +32,7 @@ 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 1st example above. Or a wild-card asterisk can be
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
@ -54,7 +54,7 @@ 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
corresponds to the 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

4
doc/src/bond_fene.rst
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@ -38,8 +38,8 @@ The *fene* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the

4
doc/src/bond_fene_expand.rst
View File

@ -32,12 +32,12 @@ The *fene/expand* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
term is attractive, the second Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
now extends to :math:`R_0 + \Delta` and the second term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

8
doc/src/bond_table.rst
View File

@ -74,7 +74,7 @@ parenthesized comments):
...
101 1.00 338.0000 -1352.0000
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -109,9 +109,9 @@ equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix
length is to the distance in the table with the lowest potential energy.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
On each line, the first value is the index from 1 to N, the second value is
the bond length r (in distance units), the third value is the energy (in
energy units), and the fourth is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the calculation is

4
doc/src/boundary.rst
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@ -76,9 +76,9 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y

2
doc/src/box.rst
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@ -38,7 +38,7 @@ skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` do
boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st
than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to
*small*\ , which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*

8
doc/src/compute_adf.rst
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@ -82,9 +82,9 @@ neighbor atom in each requested ADF.
is what is specified with the :doc:`neighbor <neighbor>` command.
The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 1st example
ways. An explicit numeric value can be used, as in the first example
above. Or a wild-card asterisk can be used to specify a range of atom
types as in the 2nd example above.
types as in the second example above.
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
@ -92,12 +92,12 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n
(inclusive).
If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the 1st example
If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example
above, this means that the ADF is computed where atoms of type *itypeN*
are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN*
are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN*
represent a range of values via
the wild-card asterisk, as in the 2nd example above, this means that the
the wild-card asterisk, as in the second example above, this means that the
ADF is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and the angle is formed by two neighbors,
one neighbor in the range of types represented by *jtypeN* and another neighbor

6
doc/src/compute_chunk_atom.rst
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@ -218,8 +218,8 @@ into ellipses.
The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the
numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
3rd dimension. For *bin/sphere*\ , the bin with smallest radii is chunk
x, y, or z), next rapidly in the second dimension, and most slowly in the
third dimension. For *bin/sphere*\ , the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For
*bin/cylinder*\ , the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction.
@ -614,7 +614,7 @@ Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are
scaled by the lattice spacing or reduced value of the *x* dimension.
Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
are scaled by the lattice spacing or reduced value of the 1st
are scaled by the lattice spacing or reduced value of the first
dimension perpendicular to the cylinder axis. E.g. y for an x-axis
cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.

2
doc/src/compute_coord_atom.rst
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@ -63,7 +63,7 @@ keywords are listed, a single coordination number is calculated, which
includes atoms of all types (same as the "\*" format, see below).
The *typeN* keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a
numeric value can be used, as in the second example above. Or a
wild-card asterisk can be used to specify a range of 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

2
doc/src/compute_displace_atom.rst
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@ -36,7 +36,7 @@ all effects due to atoms passing through periodic boundaries.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
dz\*dz).
The displacement of an atom is from its original position at the time

2
doc/src/compute_fep.rst
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@ -224,7 +224,7 @@ the pair\_\*.cpp file associated with the potential.
Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
each, as in the first example above. I <= J is required. LAMMPS sets
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 I,J arguments to set the coefficients for multiple pairs of

2
doc/src/compute_group_group.rst
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@ -64,7 +64,7 @@ If the *kspace* keyword is set to *yes*\ , which is not the default, and
if a :doc:`kspace_style <kspace_style>` is defined, then the interaction
energy will include a Kspace component which is the long-range
Coulombic energy between all the atoms in the first group and all the
atoms in the 2nd group. Likewise, the interaction force calculated by
atoms in the second group. Likewise, the interaction force calculated by
this compute will include the force on the compute group atoms due to
long-range Coulombic interactions with atoms in the specified group2.

2
doc/src/compute_msd.rst
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@ -38,7 +38,7 @@ parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <comp
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
and averaged over atoms in the group. The fourth element is the total
squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
averaged over atoms in the group.

2
doc/src/compute_msd_chunk.rst
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@ -36,7 +36,7 @@ they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
center-of-mass. The fourth component is the total squared displacement,
i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass. These
calculations include all effects due to atoms passing through periodic
boundaries.

4
doc/src/compute_msd_nongauss.rst
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@ -39,7 +39,7 @@ element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion parameter NGP =
group. The third component is the nonGaussian diffusion parameter NGP =
3\*drfourth/(5\*drsquared\*drsquared), i.e.
.. math::
@ -68,7 +68,7 @@ page for an overview of LAMMPS output options.
The vector values are "intensive". The first vector value will be in
distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
the 3rd is dimensionless.
the third is dimensionless.
Restrictions
""""""""""""

2
doc/src/compute_property_chunk.rst
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@ -63,7 +63,7 @@ chunkID. This means that the original chunk IDs (e.g. molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned
to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The *id* attribute will
then be 415 for the 3rd chunk.
then be 415 for the third chunk.
The *coordN* attributes can only be used if a *binning* style was used
in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced

6
doc/src/compute_rdf.rst
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@ -97,7 +97,7 @@ listed, then a separate histogram is generated for each
*itype*\ ,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 4th example
ways. An explicit numeric value can be used, as in the fourth example
above. Or a wild-card asterisk can be used to specify a range of 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
@ -106,11 +106,11 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n
(inclusive).
If both *itypeN* and *jtypeN* are single values, as in the 4th example
If both *itypeN* and *jtypeN* are single values, as in the fourth example
above, this means that a g(r) is computed where atoms of type *itypeN*
are the central atom, and atoms of type *jtypeN* are the distribution
atom. If either *itypeN* and *jtypeN* represent a range of values via
the wild-card asterisk, as in the 5th example above, this means that a
the wild-card asterisk, as in the fifth example above, this means that a
g(r) is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and atoms of any of the range of
types represented by *jtypeN* are the distribution atom.

2
doc/src/compute_temp_cs.rst
View File

@ -49,7 +49,7 @@ respective group IDs, which can be defined using the
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the *group-ID* (2nd
these groups, they are taken into account by the *group-ID* (second
argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where

2
doc/src/compute_ti.rst
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@ -76,7 +76,7 @@ with respect to *lambda*\ .
To perform this calculation, you provide one or more atom types as
*atype*\ . *Atype* can be specified in one of two ways. An explicit
numeric values can be used, as in the 1st example above. Or a
numeric values can be used, as in the first example above. Or a
wildcard asterisk can be used in place of or in conjunction with the
*atype* argument to select multiple atom types. This takes the form
"\*" or "\*n" or "n\*" or "m\*n". If N = the number of atom types, then

2
doc/src/compute_vacf.rst
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@ -33,7 +33,7 @@ A vector of four quantities is calculated by this compute. The first 3
elements of the vector are vx \* vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector
x-component of velocity for the atom. The fourth element of the vector
is the total VACF, i.e. (vx\*vx0 + vy\*vy0 + vz\*vz0), summed and
averaged over atoms in the group.

6
doc/src/dihedral_charmm.rst
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@ -73,7 +73,7 @@ or :doc:`read_restart <read_restart>` commands:
The weighting factor is required to correct for double counting
pairwise non-bonded Lennard-Jones interactions in cyclic systems or
when using the CHARMM dihedral style with non-CHARMM force fields.
With the CHARMM dihedral style, interactions between the 1st and 4th
With the CHARMM dihedral style, interactions between the first and fourth
atoms in a dihedral are skipped during the normal non-bonded force
computation and instead evaluated as part of the dihedral using
special epsilon and sigma values specified with the
@ -93,7 +93,7 @@ which applies to all 1-4 interactions in the system. For CHARMM force
fields, the special_bonds 1-4 interaction scaling factor should be set
to 0.0. Since the corresponding 1-4 non-bonded interactions are
computed with the dihedral. This means that if any of the weighting
factors defined as dihedral coefficients (4th coeff above) are
factors defined as dihedral coefficients (fourth coeff above) are
non-zero, then you must use a pair style with "lj/charmm" and set the
special_bonds 1-4 scaling factor to 0.0 (which is the
default). Otherwise 1-4 non-bonded interactions in dihedrals will be
@ -115,7 +115,7 @@ details.
Note that for AMBER force fields, which use pair styles with "lj/cut",
the special_bonds 1-4 scaling factor should be set to the AMBER
defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
defaults (1/2 and 5/6) and all the dihedral weighting factors (fourth
coeff above) must be set to 0.0. In this case, you can use any pair
style you wish, since the dihedral does not need any Lennard-Jones
parameter information and will not compute any 1-4 non-bonded

4
doc/src/dihedral_coeff.rst
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@ -31,7 +31,7 @@ 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 1st example above. Or a wild-card asterisk can be
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 "n\*" or "m\*n". If N = the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to N. A
@ -53,7 +53,7 @@ same format as the arguments of the dihedral_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 "Dihedral Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

16
doc/src/dihedral_table.rst
View File

@ -92,7 +92,7 @@ or blank lines.
...
30 180.0 -0.707106781187
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -102,10 +102,10 @@ any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value, the 3rd value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the
energy of the 4-atom configuration for the specified angle. The 4th
each line, the first value is the index from 1 to N, the second value is
the angle value, the third value is the energy (in energy units), and
the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
@ -147,9 +147,9 @@ choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated
the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or
indicated by the third column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
@ -157,7 +157,7 @@ degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.)
are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the

16
doc/src/dihedral_table_cut.rst
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@ -113,7 +113,7 @@ or blank lines.
...
30 180.0 -0.707106781187
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -123,10 +123,10 @@ any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value, the 3rd value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the
energy of the 4-atom configuration for the specified angle. The 4th
each line, the first value is the index from 1 to N, the second value is
the angle value, the third value is the energy (in energy units), and
the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
@ -168,9 +168,9 @@ choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated
the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or
indicated by the third column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
@ -178,7 +178,7 @@ degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.)
are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the

22
doc/src/dump_image.rst
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@ -134,17 +134,23 @@ 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 file is created, if the suffix is ".png",
then a PNG format is created, else a PPM (aka NETPBM) 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 compression; and PPM files are uncompressed but can
be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ".gz" suffix is used.
".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
compression, and PPM files are uncompressed but can be compressed with
gzip, if LAMMPS has been compiled with -DLAMMPS_GZIP and a ".gz" suffix
is used.
.. _jpeg_format: https://jpeg.org/jpeg/
.. _png_format: https://en.wikipedia.org/wiki/Portable_Network_Graphics
.. _ppm_format: https://en.wikipedia.org/wiki/Netpbm
Similarly, the format of the resulting movie is chosen with the
*movie* dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation.
and thus details have to be looked up in the `FFmpeg documentation
<http://ffmpeg.org/ffmpeg.html>`_.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the :doc:`dump_modify <dump_modify>` command.

6
doc/src/dump_modify.rst
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@ -306,7 +306,7 @@ must enclose in quotes if it is more than one field. The *int* and
*float* keywords take a single format argument and are applied to all
integer or floating-point quantities output. The setting for *M
string* also takes a single format argument which is used for the Mth
value output in each line, e.g. the 5th column is output in high
value output in each line, e.g. the fifth column is output in high
precision for "format 5 %20.15g".
.. note::
@ -419,7 +419,7 @@ be written, by processors 0,25,50,75. Each will collect information
from itself and the next 24 processors and write it to a dump file.
For the *fileper* keyword, the specified value of Np means write one
file for every Np processors. For example, if Np = 4, every 4th
file for every Np processors. For example, if Np = 4, every fourth
processor (0,4,8,12,etc) will collect information from itself and the
next 3 processors and write it to a dump file.
@ -790,7 +790,7 @@ for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
the range. The first will be from -10.0 <= color1 < -9.0, then 2nd
the range. The first will be from -10.0 <= color1 < -9.0, then second
from -9.0 <= color2 < -8.0, etc.
The *N* setting is how many entries follow. The format of the entries

2
doc/src/dynamical_matrix.rst
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@ -70,7 +70,7 @@ See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`,
:doc:`fix phonon <fix_phonon>`, :doc:`fix numdiff <fix_numdiff>`,
:doc:`compute hma <compute_hma>` uses an analytic formulation of the
Hessian provided by a pair_style's Pair::single_hessian() function,

2
doc/src/fix_adapt.rst
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@ -229,7 +229,7 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
each, as in the first example above. I <= J is required. LAMMPS sets
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

2
doc/src/fix_adapt_fep.rst
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@ -199,7 +199,7 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
each, as in the first example above. I <= J is required. LAMMPS sets
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

2
doc/src/fix_ave_chunk.rst
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@ -435,7 +435,7 @@ column is only used if the *compress* keyword was set to *yes* for the
the original chunk IDs (e.g. molecule IDs) will have been compressed
to remove chunk IDs with no atoms assigned to them. Thus a compressed
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
415. The OrigID column will list 415 for the 3rd chunk.
415. The OrigID column will list 415 for the third chunk.
The CoordN columns only appear if a *binning* style was used in the
:doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*\ ,

2
doc/src/fix_ave_correlate.rst
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@ -321,7 +321,7 @@ accessed on timesteps that are multiples of *Nfreq* since that is when
averaging is performed. The global array has # of rows = *Nrepeat*
and # of columns = Npair+2. The first column has the time delta (in
timesteps) between the pairs of input values used to calculate the
correlation, as described above. The 2nd column has the number of
correlation, as described above. The second column has the number of
samples contributing to the correlation average, as described above.
The remaining Npair columns are for I,J pairs of the N input values,
as determined by the *type* keyword, as described above.

6
doc/src/fix_ave_histo.rst
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@ -346,10 +346,10 @@ values:
* 4 = max value of all input values, including ones not histogrammed
The global array has # of rows = Nbins and # of columns = 3. The
first column has the bin coordinate, the 2nd column has the count of
values in that histogram bin, and the 3rd column has the bin count
first column has the bin coordinate, the second column has the count of
values in that histogram bin, and the third column has the bin count
divided by the total count (not including missing counts), so that the
values in the 3rd column sum to 1.0.
values in the third column sum to 1.0.
The vector and array values calculated by this fix are all treated as
intensive. If this is not the case, e.g. due to histogramming

12
doc/src/fix_bond_create.rst
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@ -154,13 +154,13 @@ of type *angletype*\ , with parameters assigned by the corresponding
.. note::
LAMMPS stores and maintains a data structure with a list of the
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
first, second, and third neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor
but may also induce \*many\* new 2nd and 3rd neighbors, depending on the
atoms. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new second and third neighbors, depending on the
molecular topology of your system. The "extra special per atom"
parameter must typically be set to allow for the new maximum total
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2
size (first + second + third neighbors) of this per-atom list. There are 2
ways to do this. See the :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` commands for details.
@ -172,12 +172,12 @@ of type *angletype*\ , with parameters assigned by the corresponding
considered for pairwise interactions, using the weighting rules set by
the :doc:`special_bonds <special_bonds>` command. Consider a new bond
created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the *atype* keyword is not used
becomes a second neighbor of I. Even if the *atype* keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
by the :doc:`special_bonds <special_bonds>` command. This is the case
even if the "angle yes" option was used with that command. The same
is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and
is true for third neighbors (1-4 interactions), the *dtype* keyword, and
the "dihedral yes" option used with the
:doc:`special_bonds <special_bonds>` command.

2
doc/src/fix_box_relax.rst
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@ -371,7 +371,7 @@ the meaning of the xy,xz,yz tilt factors.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic,
can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ .

2
doc/src/fix_cmap.rst
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@ -66,7 +66,7 @@ in the body of the data file like this with N lines:
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the CMAP terms;
it is ignored by LAMMPS. The 2nd column is the "type" of the
it is ignored by LAMMPS. The second column is the "type" of the
interaction; it is an index into the CMAP force field file. The
remaining 5 columns are the atom IDs of the atoms in the two 4-atom
dihedrals that overlap to create the CMAP 5-body interaction. Note

6
doc/src/fix_deform.rst
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@ -104,7 +104,7 @@ can be modeled using the :ref:`USER-UEF package <PKG-USER-UEF>` and its :doc:`fi
For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be
shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated
2nd dimension cannot be shrink-wrapped. Dimensions not varied by this
second dimension cannot be shrink-wrapped. Dimensions not varied by this
command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
@ -463,7 +463,7 @@ and the final tilt factor at the end of the simulation would be 0.0.
During each flip event, atoms are remapped into the new box in the
appropriate manner.
The one exception to this rule is if the 1st dimension in the tilt
The one exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
@ -601,7 +601,7 @@ Restrictions
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
You cannot apply xy, yz, or xz deformations to a second dimension (y in
xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
Related commands

6
doc/src/fix_eos_table.rst
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@ -66,7 +66,7 @@ parenthesized comments):
...
500 10.0 0.500
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -86,8 +86,8 @@ to match exactly what is in the tabulated file (with effectively no
preliminary interpolation), you should set Ntable = Nfile.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the internal temperature (in temperature units), the 3rd value is the
On each line, the first value is the index from 1 to N, the second value is
the internal temperature (in temperature units), the third value is the
internal energy (in energy units).
Note that the internal temperature and internal energy values must

6
doc/src/fix_eos_table_rx.rst
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@ -106,7 +106,7 @@ parenthesized comments):
...
500 10.0 0.500 ... 1.0000
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
@ -121,8 +121,8 @@ What LAMMPS does is a preliminary interpolation by creating splines
using the Nfile tabulated values as nodal points.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the internal temperature (in temperature units), the 3rd value until
On each line, the first value is the index from 1 to N, the second value is
the internal temperature (in temperature units), the third value until
the *m+3* value are the internal energies of the m species (in energy units).
Note that all internal temperature and internal energy values must

30
doc/src/fix_external.rst
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@ -109,20 +109,42 @@ etc.
To use this fix during energy minimization, the energy corresponding
to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly.
Correspondingly, the global virial needs to be updated to be use this
fix with variable cell calculations (e.g. :doc:`fix box/relax <fix_box_relax>`
or :doc:`fix npt <fix_nh>`).
This can be done from the external driver by calling this public
method of the FixExternal class:
This can be done from the external driver by calling these public
methods of the FixExternal class:
.. code-block:: c++
void set_energy(double eng);
void set_energy_global(double eng);
void set_virial_global(double *virial);
where eng is the potential energy. Eng is an extensive quantity,
where *eng* is the potential energy, and *virial* an array of the 6
stress tensor components. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in :doc:`energy units <units>`
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.
Additional public methods that the caller can use to update system
properties are:
.. code-block:: c++
void set_energy_peratom(double *eng);
void set_virial_peratom(double **virial);
void set_vector_length(int n);
void set_vector(int idx, double val);
These allow to set per-atom energy contributions, per-atom stress
contributions, the length and individual values of a global vector
of properties that the caller code may want to communicate to LAMMPS
(e.g. for use in :doc:`fix ave/time <fix_ave_time>` or in
:doc:`equal-style variables <variable>` or for
:doc:`custom thermo output <thermo_style>`.
----------
**Restart, fix_modify, output, run start/stop, minimize info:**

8
doc/src/fix_nh.rst
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@ -432,7 +432,7 @@ equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the
yield stress.
One exception to this rule is if the 1st dimension in the tilt factor
One exception to this rule is if the first dimension in the tilt factor
(x for xy) is non-periodic. In that case, the limits on the tilt
factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode,
@ -673,7 +673,7 @@ Restrictions
*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword
simulation domain is triclinic and the second dimension in the keyword
(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be
barostatted for 2D simulations. The :doc:`create_box <create_box>`,
:doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -687,7 +687,7 @@ is not allowed in the Nose/Hoover formulation.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic,
can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
@ -710,7 +710,7 @@ Default
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in second
dimension and not coupled to barostat, otherwise no.
----------

8
doc/src/fix_npt_cauchy.rst
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@ -354,7 +354,7 @@ equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the
yield stress.
One exception to this rule is if the 1st dimension in the tilt factor
One exception to this rule is if the first dimension in the tilt factor
(x for xy) is non-periodic. In that case, the limits on the tilt
factor are not enforced, since flipping the box in that dimension does
not change the atom positions due to non-periodicity. In this mode,
@ -555,7 +555,7 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>
*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword
simulation domain is triclinic and the second dimension in the keyword
(\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be
barostatted for 2D simulations. The :doc:`create_box <create_box>`,
:doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
@ -569,7 +569,7 @@ is not allowed in the Nose/Hoover formulation.
The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used
for 2D simulations. *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
can only be used if the 2nd dimension in the keyword is periodic,
can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
@ -626,7 +626,7 @@ Default
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
cauchystat = no,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
scaleyz = scalexz = scalexy = yes if periodic in second dimension and
not coupled to barostat, otherwise no.
----------

6
doc/src/fix_poems.rst
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@ -39,7 +39,7 @@ useful for treating a large biomolecule as a collection of connected,
coarse-grained particles.
The coupling, associated motion constraints, and time integration is
performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS) <poems_>`_ which computes the
performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the
constrained rigid-body motion of articulated (jointed) multibody
systems :ref:`(Anderson) <Anderson>`. POEMS was written and is distributed
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
@ -48,8 +48,6 @@ and other members of his group at Rensselaer Polytechnic Institute
copyright information on POEMS and other details, please refer to the
documents in the poems directory distributed with LAMMPS.
.. _poems: http://www.rpi.edu/~anderk5/lab
This fix updates the positions and velocities of the rigid atoms with
a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
@ -123,7 +121,7 @@ command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the POEMS package. It is only enabled if LAMMPS
This fix is part of the :ref:`POEMS <PKG-POEMS>` package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/fix_precession_spin.rst
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@ -158,7 +158,7 @@ atom_style "spin" was declared. See the :doc:`Build package <Build_package>` do
The *precession/spin* style can only be declared once. If more
than one precession type (for example combining an anisotropy and a Zeeman interactions)
has to be declared, they have to be chained in the same command
line (as shown in the examples above).
line (as shown in the examples above).
Related commands
""""""""""""""""

2
doc/src/fix_recenter.rst
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@ -116,7 +116,7 @@ Restrictions
""""""""""""
This fix should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM
shift in the system on the first timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost, especially in parallel. Instead, use the
:doc:`displace_atoms <displace_atoms>` command, which can be used to

2
doc/src/fix_restrain.rst
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@ -162,7 +162,7 @@ the restraint is
.. math::
E = 0 \qquad\quad\quad ,if\;r \ge r_0
with the following coefficients:
* :math:`K` (energy/distance\^2)

4
doc/src/fix_rigid.rst
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@ -248,7 +248,7 @@ differences may accumulate to produce divergent trajectories.
will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you
could displace the atoms in a body or add a large velocity to each atom
in a body to make it move in a desired direction before a 2nd run is
in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes
@ -727,7 +727,7 @@ In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the 2nd and 3rd options for a non-hybrid simulation
You could even use the second and third options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
and change the box dimensions, but not time integrate any particles.

2
doc/src/fix_rigid_meso.rst
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@ -108,7 +108,7 @@ internal energy and extrapolated velocity are also updated.
will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you
could displace the particles in a body or add a large velocity to each particle
in a body to make it move in a desired direction before a 2nd run is
in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes

10
doc/src/fix_rx.rst
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@ -18,7 +18,7 @@ Syntax
* file = filename containing the reaction kinetic equations and Arrhenius parameters
* localTemp = *none,lucy* = no local temperature averaging or local temperature defined through Lucy weighting function
* matrix = *sparse, dense* format for the stoichiometric matrix
* solver = *lammps_rk4,rkf45* = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method
* solver = *lammps_rk4,rkf45* = rk4 is an explicit fourth order Runge-Kutta method; rkf45 is an adaptive fourth-order Runge-Kutta-Fehlberg method
* minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
* maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
* relTol = relative tolerance for the rkf45 solver (rkf45 only)
@ -61,9 +61,9 @@ of *m* ordinary differential equations (ODEs) that describe the change
in concentration of a given species as a function of time are then
constructed based on the *n* reaction rate equations.
The ODE systems are solved over the full DPD timestep *dt* using either a 4th
The ODE systems are solved over the full DPD timestep *dt* using either a fourth
order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified
by the *lammps_rk4* keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method
by the *lammps_rk4* keyword, or a fourth order Runge-Kutta-Fehlberg (rkf45) method
with an adaptive step-size for *h*\ . The number of ODE steps per DPD timestep
for the rk4 method is optionally specified immediately after the rk4
keyword. The ODE step-size is set as *dt/num_steps*. Smaller
@ -76,7 +76,7 @@ can be specified by the user or estimated internally. It is recommended that the
specify *h0* since this will generally reduced the number of ODE integration steps
required. *h0* is defined as *dt / min_steps* if min_steps >= 1. If min_steps == 0,
*h0* is estimated such that an explicit Euler method would likely produce
an acceptable solution. This is generally overly conservative for the 4th-order
an acceptable solution. This is generally overly conservative for the fourth-order
method and users are advised to specify *h0* as some fraction of the DPD timestep.
For small DPD timesteps, only one step may be necessary depending upon the tolerances.
Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness
@ -172,7 +172,7 @@ parenthesized comments):
...
1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69
A section begins with a non-blank line whose 1st character is not a
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections.

6
doc/src/fix_saed_vtk.rst
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@ -45,7 +45,7 @@ Description
"""""""""""
Time average computed intensities from :doc:`compute saed <compute_saed>` and
write output to a file in the 3rd generation vtk image data format for
write output to a file in the third generation vtk image data format for
visualization directly in parallelized visualization software packages
like ParaView and VisIt. Note that if no time averaging is done, this
command can be used as a convenient way to simply output diffraction
@ -92,7 +92,7 @@ averaging is done; values are simply generated on timesteps
----------
The output for fix ave/time/saed is a file written with the 3rd generation
The output for fix ave/time/saed is a file written with the third generation
vtk image data formatting. The filename assigned by the *file* keyword is
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs.
@ -156,7 +156,7 @@ running or windowed average.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, the vector of saed intensity data is written to a new file using
the 3rd generation vtk format. The base of each file is assigned by
the third generation vtk format. The base of each file is assigned by
the *file* keyword and this string is appended with _N.vtk where N is
an index (0,1,2...) to account for situations with multiple diffraction
intensity outputs.

2
doc/src/fix_smd.rst
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@ -126,7 +126,7 @@ displacement).
The force is the total force on the group of atoms by the spring. In
the case of the *couple* style, it is the force on the fix group
(group-ID) or the negative of the force on the 2nd group (group-ID2).
(group-ID) or the negative of the force on the second group (group-ID2).
The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of

2
doc/src/fix_spring.rst
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@ -118,7 +118,7 @@ various :doc:`output commands <Howto_output>`. The first 3 quantities
in the vector are xyz components of the total force added to the group
of atoms by the spring. In the case of the *couple* style, it is the
force on the fix group (group-ID) or the negative of the force on the
2nd group (group-ID2). The 4th quantity in the vector is the
second group (group-ID2). The fourth quantity in the vector is the
magnitude of the force added by the spring, as a positive value if
(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention
can be useful when using the spring force to compute a potential of

4
doc/src/fix_tmd.rst
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@ -55,8 +55,8 @@ a .gz suffix). The format of the target file1 is as follows:
The first 3 lines may or may not be needed, depending on the format of
the atoms to follow. If image flags are included with the atoms, the
1st 3 lo/hi lines must appear in the file. If image flags are not
included, the 1st 3 lines should not appear. The 3 lines contain the
first 3 lo/hi lines must appear in the file. If image flags are not
included, the first 3 lines should not appear. The 3 lines contain the
simulation box dimensions for the atom coordinates, in the same format
as in a LAMMPS data file (see the :doc:`read_data <read_data>` command).

10
doc/src/group.rst
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@ -118,7 +118,7 @@ specified atom types, atom IDs, or molecule IDs into the group. These
3 styles can use arguments specified in one of two formats.
The first format is a list of values (types or IDs). For example, the
2nd command in the examples above puts all atoms of type 3 or 4 into
second command in the examples above puts all atoms of type 3 or 4 into
the group named *water*\ . Each entry in the list can be a
colon-separated sequence A:B or A:B:C, as in two of the examples
above. A "sequence" generates a sequence of values (types or IDs),
@ -131,9 +131,9 @@ uses an increment of 10 and would thus would add atoms IDs
The second format is a *logical* followed by one or two values (type
or ID). The 7 valid logicals are listed above. All the logicals
except <> take a single argument. The 3rd example above adds all
except <> take a single argument. The third example above adds all
atoms with IDs from 1 to 150 to the group named *sub*\ . The logical <>
means "between" and takes 2 arguments. The 4th example above adds all
means "between" and takes 2 arguments. The fourth example above adds all
atoms belonging to molecules with IDs from 50 to 250 (inclusive) to
the group named polyA.
@ -192,7 +192,7 @@ this operation is useful is if the *region* style has been used
previously to add atoms to a group that are within a geometric region.
If molecules straddle the region boundary, then atoms outside the
region that are part of molecules with atoms inside the region will
not be in the group. Using the group command a 2nd time with *include
not be in the group. Using the group command a second time with *include
molecule* will add those atoms that are outside the region to the
group.
@ -207,7 +207,7 @@ group.
atoms, and P is the number of processors.
The *subtract* style takes a list of two or more existing group names
as arguments. All atoms that belong to the 1st group, but not to any
as arguments. All atoms that belong to the first group, but not to any
of the other groups are added to the specified group.
The *union* style takes a list of one or more existing group names as

4
doc/src/improper_class2.rst
View File

@ -48,7 +48,7 @@ the :doc:`read_data <read_data>` command) are ordered I,J,K,L.
the plane of J,K,L, and the bond JK lies in both planes. Similarly for
:math:`\chi_{kjli}` and :math:`\chi_{ljik}`.
Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X
terms. Thus J (the 2nd atom in the quadruplet) is the atom of
terms. Thus J (the second atom in the quadruplet) is the atom of
symmetry in the 3 :math:`\chi` angles.
The subscripts on the various :math:`\theta`\ s refer to different
@ -56,7 +56,7 @@ combinations of 3 atoms (I,J,K,L) used to form a particular angle.
E.g. :math:`\theta_{ijl}` is the angle formed by atoms I,J,L with J
in the middle. :math:`\theta_1`, :math:`\theta_2`, :math:`\theta_3`
are the equilibrium positions of those angles. Again,
atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the
atom J (the second atom in the quadruplet) is the atom of symmetry in the
theta angles, since it is always the center atom.
Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L

4
doc/src/improper_coeff.rst
View File

@ -32,7 +32,7 @@ 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 1st example above. Or a wild-card asterisk can be
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
@ -55,7 +55,7 @@ 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 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

2
doc/src/improper_hybrid.rst
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@ -48,7 +48,7 @@ to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper
type will then be ignored.
An improper style of *none* can be specified as the 2nd argument to
An improper style of *none* can be specified as the second argument to
the improper_coeff command, if you desire to turn off certain improper
types.

2
doc/src/jump.rst
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@ -60,7 +60,7 @@ of SELF, e.g.
lmp_g++ -var fname in.script < in.script
The 2nd argument to the jump command is optional. If specified, it is
The second argument to the jump command is optional. If specified, it is
treated as a label and the new file is scanned (without executing
commands) until the label is found, and commands are executed from
that point forward. This can be used to loop over a portion of the

2
doc/src/kspace_style.rst
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@ -163,7 +163,7 @@ The *pppm/dipole/spin* style invokes a particle-particle particle-mesh solver
for magnetic dipole-dipole interactions between magnetic spins.
The *pppm/tip4p* style is identical to the *pppm* style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
adds a charge at the massless fourth site in each TIP4P water molecule.
It should be used with :doc:`pair styles <pair_style>` with a
*tip4p/long* in their style name.

4
doc/src/mass.rst
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@ -31,7 +31,7 @@ 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 1st example above. Or a wild-card
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
@ -44,7 +44,7 @@ A line in a :doc:`data file <read_data>` that follows the "Masses"
keyword specifies mass using the same format as the arguments of the
mass command in an input script, except that no wild-card asterisk can
be used. For example, under the "Masses" section of a data file, the
line that corresponds to the 1st example above would be listed as
line that corresponds to the first example above would be listed as
.. parsed-literal::

2
doc/src/message.rst
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@ -178,7 +178,7 @@ processing the rest of its input script after client/server
communication terminates.
If both codes cooperate in this manner, a new round of client/server
messaging can be initiated after termination by re-using a 2nd message
messaging can be initiated after termination by re-using a second message
command in your LAMMPS input script, followed by a new fix client or
server command, followed by another message quit command (if LAMMPS is
the client). As an example, this can be performed in a loop to use a

2
doc/src/minimize.rst
View File

@ -95,7 +95,7 @@ coordinates:
where the first term is the sum of all non-bonded :doc:`pairwise
interactions <pair_style>` including :doc:`long-range Coulombic
interactions <kspace_style>`, the 2nd through 5th terms are :doc:`bond
interactions <kspace_style>`, the second through fifth terms are :doc:`bond
<bond_style>`, :doc:`angle <angle_style>`, :doc:`dihedral
<dihedral_style>`, and :doc:`improper <improper_style>` interactions
respectively, and the last term is energy due to :doc:`fixes <fix>`

8
doc/src/molecule.rst
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@ -458,7 +458,7 @@ 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 2nd non-central atom (value c in the Shake Atoms section), and c =
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.
If flag = 2, only a is listed, where a = bondtype of the bond between
@ -467,13 +467,13 @@ the 2 atoms in the cluster.
If flag = 3, a,b 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), and b = bondtype of the bond between the central atom
and the 2nd non-central atom (value c in the Shake Atoms section).
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 2nd non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the 3rd non-central
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>` doc page for a further description

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