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Merge pull request #1214 from akohlmey/collected-small-changes 

Collected small changes and many spelling fixes for next release candidate
This commit is contained in:
Axel Kohlmeyer 2018-11-20 10:34:58 -05:00 committed by GitHub
parent 0d72c3769d 9f960baa4f
commit 421f97e444
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GPG Key ID: 4AEE18F83AFDEB23
262 changed files with 178891 additions and 738 deletions
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7
cmake/CMakeLists.txt
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@ -791,6 +791,13 @@ foreach(PKG ${DEFAULT_PACKAGES})
endif()
endforeach()
# packages that need defines set
foreach(PKG MPIIO)
if(PKG_${PKG})
add_definitions(-DLMP_${PKG})
endif()
endforeach()
# dedicated check for entire contents of accelerator packages
foreach(PKG ${ACCEL_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})

4
doc/github-development-workflow.md
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@ -107,7 +107,9 @@ Here are some items to check:
* new style docs should be added to the "overview" files in
`doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
and `doc/src/lammps.book`
* new files in packages should be added to `src/.gitignore`
* check whether manual cleanly translates with `make html` and `make pdf`
* check spelling of manual with `make spelling` in doc folder
* new source files in packages should be added to `src/.gitignore`
* removed or renamed files in packages should be added to `src/Purge.list`
* C++ source files should use C++ style include files for accessing
C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.

2
doc/src/Build_basics.txt
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@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
NOTE: You can also download a tarball of the documention for the
NOTE: You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
"download page"_http://lammps.sandia.gov/download.html.

8
doc/src/Build_extras.txt
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@ -732,7 +732,7 @@ can be shared across multiple MD packages and can be updated, for as
long as the shared PLUMED library is ABI-compatible. The third linkage
mode is "runtime" which allows to switch the PLUMED kernel at runtime
between different variants through setting the PLUMED_KERNEL environment
varible, which has to point to the location of the libplumedKernel.so
variable, which has to point to the location of the libplumedKernel.so
dynamical shared object, which is then loaded at runtime. This is
particularly convenient for doing PLUMED development and comparing
multiple PLUMED versions without having to recompile the hosting MD
@ -750,7 +750,7 @@ a global PLUMED installation or downloading it during building LAMMPS.
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
downloaded (the version of that is hardcoded to a vetted version of
downloaded (the version of that is hard-coded to a vetted version of
PLUMED, usually a recent stable release version) and built inside the
CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default),
CMake will try to detect an installed version of PLUMED and link to
@ -788,7 +788,7 @@ Note that 2 symbolic (soft) links, "includelink" and "liblink" are
created in lib/plumed to point into the location of the PLUMED build to
use and also a new file lib/plumed/Makefile.lammps is created with
settings suitable for LAMMPS to compile and link PLUMED in the desired
linkage mode. After this step is compleded, you can install the
linkage mode. After this step is completed, you can install the
USER-PLUMED package and compile LAMMPS in the usual manner:
make yes-user-plumed
@ -804,7 +804,7 @@ operating systems, using the static linkage is expected to be the most
portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings [and] do a reinstall if the
lib-plumed" with the desired settings [and] do a re-install if the
USER-PLUMED package with "make yes-user-plumed" to update the required
makefile settings with the changes in the lib/plumed folder.

2
doc/src/Build_settings.txt
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@ -139,7 +139,7 @@ adequate.
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
# default is LAMMMPS_SMALLBIG if not specified
# default is LAMMPS_SMALLBIG if not specified
[CMake and make info]:
The default "smallbig" setting allows for simulations with:

2
doc/src/Build_windows.txt
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@ -66,7 +66,7 @@ In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems
requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS github project.
them as an issue or pull request on the LAMMPS GitHub project.
Using a cross-compiler :h4,link(cross)

8
doc/src/Commands.txt
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@ -42,10 +42,10 @@ END_RST -->
"Input script structure"_Commands_structure.html
"Commands by category"_Commands_category.html :all(b)
"All commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"General commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"Bond, angle, dihedral, improper commands"_Commands_bond.html
"KSpace solvers"_Commands_kspace.html :all(b)

6
doc/src/Commands_all.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
All commands :h3
General commands :h3
An alphabetic list of all LAMMPS commands.
An alphabetic list of all general LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,

2
doc/src/Commands_bond.txt
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@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(ld,Manual.html)
:link(lc,Commands_all.html)
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

7
doc/src/Commands_category.txt
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@ -10,10 +10,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Commands by category :h3
This page lists most of the LAMMPS commands, grouped by category. The
"Commands all"_Commands_all.html doc page lists all commands
alphabetically. It also includes long lists of style options for
entries that appear in the following categories as a single command
(fix, compute, pair, etc).
"General commands"_Commands_all.html doc page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:

2
doc/src/Commands_compute.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

4
doc/src/Commands_fix.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
@ -235,4 +235,4 @@ OPT.
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/region/ees"_fix_wall_ees.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

2
doc/src/Commands_kspace.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

2
doc/src/Commands_pair.txt
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@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
"All commands"_Commands_all.html,
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,

2
doc/src/Commands_parse.txt
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@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
(4) The line is broken into "words" separated by white-space (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.

42
doc/src/Errors_messages.txt
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@ -421,9 +421,9 @@ This is an internal error. It should normally not occur. :dd
This is an internal error. It should normally not occur. :dd
{Bad real space Coulomb cutoff in fix tune/kspace} :dt
{Bad real space Coulombic cutoff in fix tune/kspace} :dt
Fix tune/kspace tried to find the optimal real space Coulomb cutoff using
Fix tune/kspace tried to find the optimal real space Coulombic cutoff using
the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd
{Balance command before simulation box is defined} :dt
@ -460,7 +460,7 @@ compute. :dd
{Big particle in fix srd cannot be point particle} :dt
Big particles must be extended spheriods or ellipsoids. :dd
Big particles must be extended spheroids or ellipsoids. :dd
{Bigint setting in lmptype.h is invalid} :dt
@ -780,7 +780,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd
Self-explanatory. :dd
{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt
{Cannot change box z boundary to non-periodic for a 2d simulation} :dt
Self-explanatory. :dd
@ -1288,7 +1288,7 @@ are defined. :dd
You cannot reset the timestep when a fix that keeps track of elapsed
time is in place. :dd
{Cannot run 2d simulation with nonperiodic Z dimension} :dt
{Cannot run 2d simulation with non-periodic Z dimension} :dt
Use the boundary command to make the z dimension periodic in order to
run a 2d simulation. :dd
@ -2116,29 +2116,29 @@ Self-explanatory. :dd
Fix setforce cannot be used in this manner. Use fix addforce
instead. :dd
{Cannot use nonperiodic boundares with fix ttm} :dt
{Cannot use non-periodic boundares with fix ttm} :dt
This fix requires a fully periodic simulation box. :dd
{Cannot use nonperiodic boundaries with Ewald} :dt
{Cannot use non-periodic boundaries with Ewald} :dt
For kspace style ewald, all 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with EwaldDisp} :dt
{Cannot use non-periodic boundaries with EwaldDisp} :dt
For kspace style ewald/disp, all 3 dimensions must have periodic
boundaries unless you use the kspace_modify command to define a 2d
slab with a non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with PPPM} :dt
{Cannot use non-periodic boundaries with PPPM} :dt
For kspace style pppm, all 3 dimensions must have periodic boundaries
unless you use the kspace_modify command to define a 2d slab with a
non-periodic z dimension. :dd
{Cannot use nonperiodic boundaries with PPPMDisp} :dt
{Cannot use non-periodic boundaries with PPPMDisp} :dt
For kspace style pppm/disp, all 3 dimensions must have periodic
boundaries unless you use the kspace_modify command to define a 2d
@ -3351,21 +3351,21 @@ probably due to errors in the Python code. :dd
The default minimum order is 2. This can be reset by the
kspace_modify minorder command. :dd
{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt
{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cut not supported in pair_style lj/long/coul/long} :dt
{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt
{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt
Must use long-range Coulombic interactions. :dd
{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt
{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt
If using a Kspace solver, all Coulomb cutoffs of long pair styles must
If using a Kspace solver, all Coulombic cutoffs of long pair styles must
be the same. :dd
{Coulombic cut not supported in pair_style lj/long/dipole/long} :dt
@ -5938,9 +5938,9 @@ map command will force an atom map to be created. :dd
Self-explanatory. :dd
{Input line quote not followed by whitespace} :dt
{Input line quote not followed by white-space} :dt
An end quote must be followed by whitespace. :dd
An end quote must be followed by white-space. :dd
{Insertion region extends outside simulation box} :dt
@ -7014,7 +7014,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd
{KSpace accuracy too large to estimate G vector} :dt
Reduce the accuracy request or specify gwald explicitly
Reduce the accuracy request or specify gewald explicitly
via the kspace_modify command. :dd
{KSpace accuracy too low} :dt
@ -8014,7 +8014,7 @@ Self-explanatory. :dd
{Package command after simulation box is defined} :dt
The package command cannot be used afer a read_data, read_restart, or
The package command cannot be used after a read_data, read_restart, or
create_box command. :dd
{Package gpu command without GPU package installed} :dt
@ -9198,7 +9198,7 @@ creates one large file for all processors. :dd
{Restart file byte ordering is not recognized} :dt
The file does not appear to be a LAMMPS restart file since it doesn't
contain a recognized byte-orderomg flag at the beginning. :dd
contain a recognized byte-ordering flag at the beginning. :dd
{Restart file byte ordering is swapped} :dt
@ -9410,7 +9410,7 @@ You may also want to boost the page size. :dd
{Small to big integers are not sized correctly} :dt
This error occurs whenthe sizes of smallint, imageint, tagint, bigint,
This error occurs when the sizes of smallint, imageint, tagint, bigint,
as defined in src/lmptype.h are not what is expected. Contact
the developers if this occurs. :dd

6
doc/src/Errors_warnings.txt
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@ -757,7 +757,7 @@ Self-explanatory. :dd
This may indicate the shell command did not operate as expected. :dd
{Should not allow rigid bodies to bounce off relecting walls} :dt
{Should not allow rigid bodies to bounce off reflecting walls} :dt
LAMMPS allows this, but their dynamics are not computed correctly. :dd
@ -850,10 +850,10 @@ Most FENE models need this setting for the special_bonds command. :dd
Most FENE models need this setting for the special_bonds command. :dd
{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt
{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt
This is likely not what you want to do. The exclusion settings will
eliminate neighbors in the neighbor list, which the manybody potential
eliminate neighbors in the neighbor list, which the many-body potential
needs to calculated its terms correctly. :dd
{Using compute temp/deform with inconsistent fix deform remap option} :dt

2
doc/src/Examples.txt
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@ -78,7 +78,7 @@ micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
nb3b: use of non-bonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel

2
doc/src/Howto.txt
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@ -45,7 +45,7 @@ General howto :h3
<!-- RST
.. toctree::
:name: general
:name: general_howto
:maxdepth: 1
Howto_restart

2
doc/src/Howto_barostat.txt
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@ -19,7 +19,7 @@ barostat attempts to equilibrate the system to the requested T and/or
P.
Barostatting in LAMMPS is performed by "fixes"_fix.html. Two
barosttating methods are currently available: Nose-Hoover (npt and
barostatting methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
"fix npt"_fix_nh.html

4
doc/src/Howto_chunk.txt
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@ -22,8 +22,8 @@ commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
Here, each of the 4 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
Here a brief overview for each of the 4 kinds of chunk-related commands
is provided. Then some examples are given of how to compute different
properties with chunk commands.
Compute chunk/atom command: :h4

4
doc/src/Howto_client_server.txt
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@ -64,7 +64,7 @@ client or server.
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
The server doc files give details of the message protocols
for data that is exchanged bewteen the client and server.
for data that is exchanged between the client and server.
These example directories illustrate how to use LAMMPS as either a
client or server code:
@ -87,7 +87,7 @@ DFT forces, thru a Python wrapper script on VASP.
Here is how to launch a client and server code together for any of the
4 modes of message exchange that the "message"_message.html command
and the CSlib support. Here LAMMPS is used as both the client and
server code. Another code could be subsitituted for either.
server code. Another code could be substituted for either.
The examples below show launching both codes from the same window (or
batch script), using the "&" character to launch the first code in the

6
doc/src/Howto_coreshell.txt
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@ -19,7 +19,7 @@ polarizable"_Howto_polarizable.html doc page for a discussion of all
the polarizable models available in LAMMPS.
Technically, shells are attached to the cores by a spring force f =
k*r where k is a parametrized spring constant and r is the distance
k*r where k is a parameterized spring constant and r is the distance
between the core and the shell. The charges of the core and the shell
add up to the ion charge, thus q(ion) = q(core) + q(shell). This
setup introduces the ion polarizability (alpha) given by
@ -111,7 +111,7 @@ the core and shell particles corresponds to the polarization,
hereby an instantaneous relaxation of the shells is approximated
and a fast core/shell spring frequency ensures a nearly constant
internal kinetic energy during the simulation.
Thermostats can alter this polarization behaviour, by scaling the
Thermostats can alter this polarization behavior, by scaling the
internal kinetic energy, meaning the shell will not react freely to
its electrostatic environment.
Therefore it is typically desirable to decouple the relative motion of
@ -165,7 +165,7 @@ fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification
If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small
momentum to the system, which is noticable over long trajectories.
momentum to the system, which is noticeable over long trajectories.
Therefore it is recommendable to use the "fix
momentum"_fix_momentum.html command in combination with "compute
temp/cs"_compute_temp_cs.html when equilibrating the system to

2
doc/src/Howto_dispersion.txt
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@ -74,7 +74,7 @@ command.
A reasonable approach that combines the upsides of both methods is to
make the first run using the {kspace_modify force/disp/real} and
{kspace_modify force/disp/kspace} commands, write down the PPPM
parameters from the outut, and specify these parameters using the
parameters from the output, and specify these parameters using the
second approach in subsequent runs (which have the same composition,
force field, and approximately the same volume).

2
doc/src/Howto_drude.txt
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@ -17,7 +17,7 @@ for a discussion of all the polarizable models available in LAMMPS.
The Drude model has a number of features aimed at its use in
molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
Thermostating of the additional degrees of freedom associated with the
Thermostatting of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
coordinates of the Drude particles with respect to their cores. This
makes the trajectory close to that of relaxed induced dipoles. :ulb,l

8
doc/src/Howto_drude2.txt
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@ -82,7 +82,7 @@ decouple the degrees of freedom associated with the Drude oscillators
from those of the normal atoms. Thermalizing the Drude dipoles at
temperatures comparable to the rest of the simulation leads to several
problems (kinetic energy transfer, very short timestep, etc.), which
can be remediate by the "cold Drude" technique ("Lamoureux and
can be remedied by the "cold Drude" technique ("Lamoureux and
Roux"_#Lamoureux2).
Two closely related models are used to represent polarization through
@ -213,7 +213,7 @@ of mass of the DC-DP pairs, with relaxation time 100 and with random
seed 12345. This fix applies also a Langevin thermostat at temperature
1. to the relative motion of the DPs around their DCs, with relaxation
time 20 and random seed 13977. Only the DCs and non-polarizable
atoms need to be in this fix's group. LAMMPS will thermostate the DPs
atoms need to be in this fix's group. LAMMPS will thermostat the DPs
together with their DC. For this, ghost atoms need to know their
velocities. Thus you need to add the following command:
@ -360,7 +360,7 @@ fix NPH all nph iso 1. 1. 500 :pre
It is also possible to use a Nose-Hoover instead of a Langevin
thermostat. This requires to use "{fix
drude/transform}"_fix_drude_transform.html just before and after the
time intergation fixes. The {fix drude/transform/direct} converts the
time integration fixes. The {fix drude/transform/direct} converts the
atomic masses, positions, velocities and forces into a reduced
representation, where the DCs transform into the centers of mass of
the DC-DP pairs and the DPs transform into their relative position
@ -396,7 +396,7 @@ global pressure and thus a global temperature whatever the fix group.
We do want the pressure to correspond to the whole system, but we want
the temperature to correspond to the fix group only. We must then use
the {fix_modify} command for this. In the end, the block of
instructions for thermostating and barostating will look like
instructions for thermostatting and barostatting will look like
compute TATOMS ATOMS temp
fix DIRECT all drude/transform/direct

2
doc/src/Howto_elastic.txt
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@ -30,7 +30,7 @@ examples/elastic directory described on the "Examples"_Examples.html
doc page.
Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
challenging, because it is necessary to run a simulation that performs
time averages of differential properties. One way to do this is to
measure the change in average stress tensor in an NVT simulations when
the cell volume undergoes a finite deformation. In order to balance

50
doc/src/Howto_github.txt
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@ -96,7 +96,7 @@ machine to a directory with the name you chose. If none is given, it will
default to "lammps". Typical names are "mylammps" or something similar.
You can use this local clone to make changes and
test them without interfering with the repository on Github.
test them without interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory
and use git pull:
@ -150,7 +150,7 @@ After the commit, the changes can be pushed to the same branch on GitHub:
$ git push :pre
Git will ask you for your user name and password on GitHub if you have
not configured anything. If your local branch is not present on Github yet,
not configured anything. If your local branch is not present on GitHub yet,
it will ask you to add it by running
$ git push --set-upstream origin github-tutorial-update :pre
@ -254,20 +254,53 @@ them, or if a developer has requested that something needs to be changed
before the feature can be accepted into the official LAMMPS version.
After each push, the automated checks are run again.
[Labels]
LAMMPS developers may add labels to your pull request to assign it to
categories (mostly for bookkeeping purposes), but a few of them are
important: needs_work, work_in_progress, test-for-regression, and
full-regression-test. The first two indicate, that your pull request
is not considered to be complete. With "needs_work" the burden is on
exclusively on you; while "work_in_progress" can also mean, that a
LAMMPS developer may want to add changes. Please watch the comments
to the pull requests. The two "test" labels are used to trigger
extended tests before the code is merged. This is sometimes done by
LAMMPS developers, if they suspect that there may be some subtle
side effects from your changes. It is not done by default, because
those tests are very time consuming.
[Reviews]
As of Summer 2018, a pull request needs at least 1 approving review
from a LAMMPS developer with write access to the repository.
In case your changes touch code that certain developers are associated
with, they are auto-requested by the GitHub software. Those associations
are set in the file
".github/CODEOWNERS"_https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS
Thus if you want to be automatically notified to review when anybody
changes files or packages, that you have contributed to LAMMPS, you can
add suitable patterns to that file, or a LAMMPS developer may add you.
Otherwise, you can also manually request reviews from specific developers,
or LAMMPS developers - in their assessment of your pull request - may
determine who else should be reviewing your contribution and add that person.
Through reviews, LAMMPS developers also may request specific changes from you.
If those are not addressed, your pull requests cannot be merged.
[Assignees]
There is an assignee label for pull requests. If the request has not
There is an assignee property for pull requests. If the request has not
been reviewed by any developer yet, it is not assigned to anyone. After
revision, a developer can choose to assign it to either a) you, b) a
LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
Case a) happens if changes are required on your part :ulb,l
Case b) means that at the moment, it is being tested and reviewed by a
LAMMPS developer with the expectation that some changes would be required.
After the review, the developer can choose to implement changes directly
or suggest them to you. :l
Case c) means that the pull request has been assigned to the lead
developer Steve Plimpton and means it is considered ready for merging. :ule,l
Case c) means that the pull request has been assigned to the developer
overseeing the merging of pull requests into the master branch. :ule,l
In this case, Axel assigned the tutorial to Steve:
@ -336,7 +369,7 @@ commit and push again:
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps :pre
This merge also shows up on the lammps Github page:
This merge also shows up on the lammps GitHub page:
:c,image(JPG/tutorial_reverse_pull_request7.png)
@ -381,3 +414,6 @@ Furthermore, the naming of the patches now follow the pattern
"patch_<Day><Month><Year>" to simplify comparisons between releases.
Finally, all patches and submissions are subject to automatic testing
and code checks to make sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file
"doc/github-development-workflow.md"_https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md

4
doc/src/Howto_manifold.txt
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@ -31,8 +31,8 @@ plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with norma
plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R
spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine
spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine
spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendritic spine
spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendritic spine
thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)

2
doc/src/Howto_nemd.txt
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@ -55,5 +55,5 @@ using the "fix flow/gauss"_fix_flow_gauss.html command.
:line
:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

6
doc/src/Howto_polarizable.txt
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@ -45,8 +45,8 @@ high symmetry around each site leads to stable trajectories of the
core-shell pairs. However, bonded atoms in molecules can be so close
that a core would interact too strongly or even capture the Drude
particle of a neighbor. The Drude dipole model is relatively more
complex in order to remediate this and other issues. Specifically, the
Drude model includes specific thermostating of the core-Drude pairs
complex in order to remedy this and other issues. Specifically, the
Drude model includes specific thermostatting of the core-Drude pairs
and short-range damping of the induced dipoles.
The three polarization methods can be implemented through a
@ -77,5 +77,5 @@ motion of the Drude particles with respect to their cores is kept
approaching the self-consistent regime. In both models the
temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostated separately as
relative core-Drude particle motion is thermostatted separately as
well.

8
doc/src/Howto_pylammps.txt
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@ -141,16 +141,16 @@ Python code if {L} was a lammps instance:
L.command("region box block 0 10 0 5 -0.5 0.5") :pre
With the PyLammps interface, any command can be split up into arbitrary parts
separated by whitespace, passed as individual arguments to a region method.
separated by white-space, passed as individual arguments to a region method.
L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre
Note that each parameter is set as Python literal floating-point number. In the
PyLammps interface, each command takes an arbitrary parameter list and transparently
merges it to a single command string, separating individual parameters by whitespace.
merges it to a single command string, separating individual parameters by white-space.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parametrization needed to be done
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre
@ -328,7 +328,7 @@ jupyter notebook :pre
IPyLammps Examples :h4
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch {jupyter notebook} inside this
sub-directory. To open these notebooks launch {jupyter notebook} inside this
directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.

2
doc/src/Howto_replica.txt
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@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Multi-replica simulations :h3
Several commands in LAMMPS run mutli-replica simulations, meaning
Several commands in LAMMPS run multi-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
simultaneously, with small amounts of data exchanged between replicas
periodically.

2
doc/src/Howto_spc.txt
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@ -30,7 +30,7 @@ r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
Angstrom cutoff for both LJ and Coulombic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.

4
doc/src/Howto_spherical.txt
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@ -35,7 +35,7 @@ There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
The sphere style defines particles that are spheriods and each
The sphere style defines particles that are spheroids and each
particle can have a unique diameter and mass (or density). These
particles store an angular velocity (omega) and can be acted upon by
torque. The "set" command can be used to modify the diameter and mass
@ -236,7 +236,7 @@ particles are point masses.
Also note that body particles cannot be modeled with the "fix
rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
as single particles, though they can store internal state, such as a
list of sub-particles. Individual body partices are typically treated
list of sub-particles. Individual body particles are typically treated
as rigid bodies, and their motion integrated with a command like "fix
nve/body"_fix_nve_body.html. Interactions between pairs of body
particles are computed via a command like "pair_style

2
doc/src/Howto_spins.txt
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@ -36,7 +36,7 @@ A Langevin thermostat can be applied to those magnetic spins using
"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
can be coupled to another Langevin thermostat applied to the atoms
using "fix langevin"_fix_langevin.html in order to simulate
thermostated spin-lattice system.
thermostatted spin-lattice system.
The magnetic Gilbert damping can also be applied using "fix
langevin/spin"_fix_langevin_spin.html. It allows to either dissipate

2
doc/src/Howto_thermostat.txt
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@ -96,5 +96,5 @@ temperature compute is used for default thermodynamic output.
:line
:link(Daivis-thermostat)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

2
doc/src/Howto_triclinic.txt
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@ -200,7 +200,7 @@ used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
"create_atoms"_create_atoms.html command.
A second use is to run Parinello-Rahman dynamics via the "fix
A second use is to run Parrinello-Rahman dynamics via the "fix
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analog for an "energy minimization"_minimize.html is

2
doc/src/Howto_viscosity.txt
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@ -140,5 +140,5 @@ with time at sufficiently long times.
:line
:link(Daivis-viscosity)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

2
doc/src/Install_git.txt
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@ -45,7 +45,7 @@ git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre
where "mylammps" is the name of the directory you wish to create on
your machine and "unstable" is one of the 3 branches listed above.
(Note that you actually download all 3 branches; you can switch
between them at any time using "git checkout <branchname>".)
between them at any time using "git checkout <branch name>".)
Once the command completes, your directory will contain the same files
as if you unpacked a current LAMMPS tarball, with two exceptions:

2
doc/src/Intro_authors.txt
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@ -48,7 +48,7 @@ Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
Mike Parks (Sandia), PERI package for Peridynamics
Roy Pollock (LLNL), Ewald and PPPM solvers
Christian Trott (Sandia), USER-CUDA and KOKKOS packages
Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
:line

4
doc/src/Intro_features.txt
View File

@ -68,7 +68,7 @@ commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
long-range interactions for charge, point-dipoles, and LJ dispersion: \
@ -114,7 +114,7 @@ Ensembles, constraints, and boundary conditions :h4,link(ensemble)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)

32
doc/src/Intro_nonfeatures.txt
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@ -13,15 +13,19 @@ LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of
functionality for setting up simulations and analyzing their output.
Specifically, LAMMPS does not:
Specifically, LAMMPS was not conceived and designed for:
run thru a GUI
build molecular systems
being run thru a GUI
build molecular systems, or building molecular topologies
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
perform sophisticated analysis of your MD simulation
visualize your MD simulation interactively
plot your output data :ul
Although over the years these limitations have been somewhat
reduced through features added to LAMMPS or external tools
that either interface with LAMMPS or extend LAMMPS.
Here are suggestions on how to perform these tasks:
GUI: LAMMPS can be built as a library and a Python wrapper that wraps
@ -29,7 +33,7 @@ the library interface is provided. Thus, GUI interfaces can be
written in Python (or C or C++ if desired) that run LAMMPS and
visualize or plot its output. Examples of this are provided in the
python directory and described on the "Python"_Python_head.html doc
page. :ulb,l
page. Also, there are several external wrappers or GUI front ends.:ulb,l
Builder: Several pre-processing tools are packaged with LAMMPS. Some
of them convert input files in formats produced by other MD codes such
@ -40,28 +44,36 @@ molecular builder that will generate complex molecular models. See
the "Tools"_Tools.html 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. :l
describes a variety of 3rd party tools for this task. Furthermore,
some LAMMPS internal commands to reconstruct topology, as well as
the option to insert molecule templates instead of atoms.:l
Force-field assignment: The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
or Accelerys force field files. :l
or BIOVIA (formerly Accelrys) force field files. :l
Simulation analyses: If you want to perform analyses on-the-fly as
Simulation analysis: If you want to perform analysis on-the-fly as
your simulation runs, see the "compute"_compute.html and
"fix"_fix.html doc pages, which list commands that can be used in a
LAMMPS input script. Also see the "Modify"_Modify.html doc page for
info on how to add your own analysis code or algorithms to LAMMPS.
For post-processing, LAMMPS output such as "dump file
snapshots"_dump.html can be converted into formats used by other MD or
post-processing codes. Some post-processing tools packaged with
post-processing codes. To some degree, that conversion can be done
directly inside of LAMMPS by interfacing to the VMD molfile plugins.
The "rerun"_rerun.html command also allows to do some post-processing
of existing trajectories, and through being able to read a variety
of file formats, this can also be used for analyzing trajectories
from other MD codes. Some post-processing tools packaged with
LAMMPS will do these conversions. Scripts provided in the
tools/python directory can extract and massage data in dump files to
make it easier to import into other programs. See the
"Tools"_Tools.html doc page for details on these various options. :l
Visualization: LAMMPS can produce JPG or PNG snapshot images
on-the-fly via its "dump image"_dump_image.html command. For
on-the-fly via its "dump image"_dump_image.html command and pass
them to an external program FFmpeg to generate movies from them. For
high-quality, interactive visualization there are many excellent and
free tools available. See the "Other Codes
page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for

4
doc/src/Modify_contribute.txt
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@ -33,11 +33,11 @@ how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
typical requirements. Once you have prepared everything, see the
"Howto github"_Howto_github.html doc page for instructions on how to
"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to
submit your changes or new files through a GitHub pull request. If you
prefer to submit patches or full files, you should first make certain,
that your code works correctly with the latest patch-level version of
LAMMPS and contains all bugfixes from it. Then create a gzipped tar
LAMMPS and contains all bug fixes from it. Then create a gzipped tar
file of all changed or added files or a corresponding patch file using
'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.

2
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@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Pair styles :h3
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
class. In LAMMPS, pairwise calculation include many-body potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.

4
doc/src/Modify_region.txt
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@ -20,6 +20,6 @@ Here is a brief description of methods you define in your new derived
class. See region.h for details.
inside: determine whether a point is in the region
surface_interior: determine if a point is within a cutoff distance inside of surc
surface_exterior: determine if a point is within a cutoff distance outside of surf
surface_interior: determine if a point is within a cutoff distance inside of surface
surface_exterior: determine if a point is within a cutoff distance outside of surface
shape_update : change region shape if set by time-dependent variable :tb(s=:)

6
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@ -494,7 +494,7 @@ MANYBODY package :link(PKG-MANYBODY),h4
[Contents:]
A variety of manybody and bond-order potentials. These include
A variety of many-body and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
[Supporting info:]
@ -518,7 +518,7 @@ MC package :link(PKG-MC),h4
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
(GCMC) in conjunction with dynamics.
[Supporting info:]
@ -1207,7 +1207,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
[Contents:]
The fix plumed command allows you to use the PLUMED free energy plugin
for molecular dynamics to analyse and bias your LAMMPS trajectory on
for molecular dynamics to analyze and bias your LAMMPS trajectory on
the fly. The PLUMED library is called from within the LAMMPS input
script by using the "fix plumed _fix_plumed.html command.

4
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@ -38,8 +38,8 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no

2
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@ -79,7 +79,7 @@ of Python and your machine to successfully build LAMMPS. See the
lib/python/README file for more info.
If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps overviewed in the "Python
must also follow the steps summarized in the "Python
run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared
library and insure that Python can find the python/lammps.py file and
the shared library.

2
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@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
The latter link is to AtomEye 3 which has the scriping
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
Note that for PyMol, you need to have built and installed the

2
doc/src/Run_windows.txt
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@ -41,7 +41,7 @@ path for the default location of this MPI package. After the
installation of the MPICH2 software, it needs to be integrated into
the system. For this you need to start a Command Prompt in
{Administrator Mode} (right click on the icon and select it). Change
into the MPICH2 installation directory, then into the subdirectory
into the MPICH2 installation directory, then into the sub-directory
[bin] and execute [smpd.exe -install]. Exit the command window.
Get a new, regular command prompt by going to Start->Run... ,

2
doc/src/Speed.txt
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@ -19,7 +19,7 @@ using code options that implement alternate algorithms that can
speed-up a simulation. The second is to use one of the several
accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi coprocessors.
Intel Xeon Phi co-processors.
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator

82
doc/src/Speed_intel.txt
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@ -14,11 +14,11 @@ Corporation. It provides two methods for accelerating simulations,
depending on the hardware you have. The first is acceleration on
Intel CPUs by running in single, mixed, or double precision with
vectorization. The second is acceleration on Intel Xeon Phi
coprocessors via offloading neighbor list and non-bonded force
co-processors via offloading neighbor list and non-bonded force
calculations to the Phi. The same C++ code is used in both cases.
When offloading to a coprocessor from a CPU, the same routine is run
When offloading to a co-processor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
LAMMPS to run on the CPU cores and co-processor cores simultaneously.
[Currently Available USER-INTEL Styles:]
@ -47,7 +47,7 @@ These are scalable in size; the results given are with 512K
particles (524K for Liquid Crystal). Most of the simulations are
standard LAMMPS benchmarks (indicated by the filename extension in
parenthesis) with modifications to the run length and to add a
warmup run (for use with offload benchmarks).
warm-up run (for use with offload benchmarks).
:c,image(JPG/user_intel.png)
@ -134,19 +134,19 @@ Do not use thread affinity (set KMP_AFFINITY=none) :l
The "newton off" setting may provide better scalability :l
:ule
For Intel Xeon Phi coprocessors (Offload):
For Intel Xeon Phi co-processors (Offload):
Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l
"-pk intel N omp 1" added to command-line where N is the number of
coprocessors per node. :l
co-processors per node. :l
:ule
:line
[Required hardware/software:]
In order to use offload to coprocessors, an Intel Xeon Phi
coprocessor and an Intel compiler are required. For this, the
In order to use offload to co-processors, an Intel Xeon Phi
co-processor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
@ -214,7 +214,7 @@ Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
Makefile.knl # Intel Compiler, Intel MPI, No Offload
Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload
Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre
Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload :pre
Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
it explicitly specifies that vectorization should be for Intel Xeon
@ -227,9 +227,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
However, if you do not have coprocessors on your system, building
Note that if you build with support for a Phi co-processor, the same
binary can be used on nodes with or without co-processors installed.
However, if you do not have co-processors on your system, building
without offload support will produce a smaller binary.
The general requirements for Makefiles with the USER-INTEL package
@ -272,7 +272,7 @@ Advanced performance tuning options are also described below to get
the best performance.
When running on a single node (including runs using offload to a
coprocessor), best performance is normally obtained by using 1 MPI
co-processor), best performance is normally obtained by using 1 MPI
task per physical core and additional OpenMP threads with SMT. For
Intel Xeon processors, 2 OpenMP threads should be used for SMT.
For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
@ -290,7 +290,7 @@ NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
threads to a core or group of cores so that memory access can be
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host (CPU) will be set by default on the host
{when using offload to a coprocessor}. In this case, it is unnecessary
{when using offload to a co-processor}. In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl,
I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
option to the "package intel"_package.html command or by disabling the
@ -310,15 +310,15 @@ editing the input script. This switch will automatically append
options for the USER-INTEL package. The default package command will
specify that USER-INTEL calculations are performed in mixed precision,
that the number of OpenMP threads is specified by the OMP_NUM_THREADS
environment variable, and that if coprocessors are present and the
binary was built with offload support, that 1 coprocessor per node
environment variable, and that if co-processors are present and the
binary was built with offload support, that 1 co-processor per node
will be used with automatic balancing of work between the CPU and the
coprocessor.
co-processor.
You can specify different options for the USER-INTEL package by using
the "-pk intel Nphi" "command-line switch"_Run_options.html with
keyword/value pairs as specified in the documentation. Here, Nphi = #
of Xeon Phi coprocessors/node (ignored without offload
of Xeon Phi co-processors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
override any OMP_NUM_THREADS setting and specify the number of OpenMP
threads, {mode} to set the floating-point precision mode, and {lrt} to
@ -332,7 +332,7 @@ Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision :pre
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre
[Or run with the USER-INTEL package by editing an input script:]
@ -364,7 +364,7 @@ intel"_package.html command that can improve performance when using
"PPPM"_kspace_style.html for long-range electrostatics on processors
with SMT. It generates an extra pthread for each MPI task. The thread
is dedicated to performing some of the PPPM calculations and MPI
communications. This feature requires setting the preprocessor flag
communications. This feature requires setting the pre-processor flag
-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but
it is set in all makefiles tuned for the USER-INTEL package. On Intel
@ -422,29 +422,29 @@ that MPI runs are performed in MCDRAM.
The default settings for offload should give good performance.
When using LAMMPS with offload to Intel coprocessors, best performance
When using LAMMPS with offload to Intel co-processors, best performance
will typically be achieved with concurrent calculations performed on
both the CPU and the coprocessor. This is achieved by offloading only
a fraction of the neighbor and pair computations to the coprocessor or
both the CPU and the co-processor. This is achieved by offloading only
a fraction of the neighbor and pair computations to the co-processor or
using "hybrid"_pair_hybrid.html pair styles where only one style uses
the "intel" suffix. For simulations with long-range electrostatics or
bond, angle, dihedral, improper calculations, computation and data
transfer to the coprocessor will run concurrently with computations
transfer to the co-processor will run concurrently with computations
and MPI communications for these calculations on the host CPU. This
is illustrated in the figure below for the rhodopsin protein benchmark
running on E5-2697v2 processors with a Intel Xeon Phi 7120p
coprocessor. In this plot, the vertical access is time and routines
co-processor. In this plot, the vertical access is time and routines
running at the same time are running concurrently on both the host and
the coprocessor.
the co-processor.
:c,image(JPG/offload_knc.png)
The fraction of the offloaded work is controlled by the {balance}
keyword in the "package intel"_package.html command. A balance of 0
runs all calculations on the CPU. A balance of 1 runs all
supported calculations on the coprocessor. A balance of 0.5 runs half
of the calculations on the coprocessor. Setting the balance to -1
(the default) will enable dynamic load balancing that continously
supported calculations on the co-processor. A balance of 0.5 runs half
of the calculations on the co-processor. Setting the balance to -1
(the default) will enable dynamic load balancing that continuously
adjusts the fraction of offloaded work throughout the simulation.
Because data transfer cannot be timed, this option typically produces
results within 5 to 10 percent of the optimal fixed balance.
@ -455,23 +455,23 @@ near-optimal setting that will carry over to additional runs.
The default for the "package intel"_package.html command is to have
all the MPI tasks on a given compute node use a single Xeon Phi
coprocessor. In general, running with a large number of MPI tasks on
co-processor. In general, running with a large number of MPI tasks on
each node will perform best with offload. Each MPI task will
automatically get affinity to a subset of the hardware threads
available on the coprocessor. For example, if your card has 61 cores,
available on the co-processor. For example, if your card has 61 cores,
with 60 cores available for offload and 4 hardware threads per core
(240 total threads), running with 24 MPI tasks per node will cause
each MPI task to use a subset of 10 threads on the coprocessor. Fine
each MPI task to use a subset of 10 threads on the co-processor. Fine
tuning of the number of threads to use per MPI task or the number of
threads to use per core can be accomplished with keyword settings of
the "package intel"_package.html command.
The USER-INTEL package has two modes for deciding which atoms will be
handled by the coprocessor. This choice is controlled with the {ghost}
handled by the co-processor. This choice is controlled with the {ghost}
keyword of the "package intel"_package.html command. When set to 0,
ghost atoms (atoms at the borders between MPI tasks) are not offloaded
to the card. This allows for overlap of MPI communication of forces
with computation on the coprocessor when the "newton"_newton.html
with computation on the co-processor when the "newton"_newton.html
setting is "on". The default is dependent on the style being used,
however, better performance may be achieved by setting this option
explicitly.
@ -482,21 +482,21 @@ cores. This is due to the fact that additional threads are generated
internally to handle the asynchronous offload tasks.
If pair computations are being offloaded to an Intel Xeon Phi
coprocessor, a diagnostic line is printed to the screen (not to the
co-processor, a diagnostic line is printed to the screen (not to the
log file), during the setup phase of a run, indicating that offload
mode is being used and indicating the number of coprocessor threads
mode is being used and indicating the number of co-processor threads
per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for "atom
sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
available co-processor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
switch"_Run_options.html is used to limit the coprocessor threads per
switch"_Run_options.html is used to limit the co-processor threads per
MPI task.
[Restrictions:]
When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
When offloading to a co-processor, "hybrid"_pair_hybrid.html styles
that require skip lists for neighbor builds cannot be offloaded.
Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel
accelerated style may be used with hybrid styles when offloading.
@ -510,7 +510,7 @@ supported.
[References:]
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l

42
doc/src/Speed_kokkos.txt
View File

@ -13,11 +13,11 @@ Kokkos is a templated C++ library that provides abstractions to allow
a single implementation of an application kernel (e.g. a pair style)
to run efficiently on different kinds of hardware, such as GPUs, Intel
Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
different backend languages such as CUDA, OpenMP, or Pthreads. The
different back end languages such as CUDA, OpenMP, or Pthreads. The
Kokkos library also provides data abstractions to adjust (at compile
time) the memory layout of data structures like 2d and 3d arrays to
optimize performance on different hardware. For more information on
Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part
of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
library was written primarily by Carter Edwards, Christian Trott, and
Dan Sunderland (all Sandia).
@ -106,9 +106,9 @@ modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described
below.
NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e.
NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP
backend (i.e. Makefile.kokkos_omp) because some of the overhead to make
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
the code thread-safe is removed.
NOTE: The default for the "package kokkos"_package.html command is to
@ -127,21 +127,21 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
If the "newton"_newton.html command is used in the input
script, it can also override the Newton flag defaults.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomics, which
don't require duplication. The use of atomics can be forced by compiling
with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
Kokkos-enabled pair_styles support data duplication. Alternatively, full
neighbor lists avoid the need for duplication or atomics but require
more compute operations per atom. When using the Kokkos Serial backend
or the OpenMP backend with a single thread, no duplication or atomics are
used. For CUDA and half neighbor lists, the KOKKOS package always uses
atomics.
For half neighbor lists and OpenMP, the KOKKOS package uses data
duplication (i.e. thread-private arrays) by default to avoid
thread-level write conflicts in the force arrays (and other data
structures as necessary). Data duplication is typically fastest for
small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomic operations
which do not require data duplication. The use of atomic operations can
be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS"
pre-processor flag. Most but not all Kokkos-enabled pair_styles support
data duplication. Alternatively, full neighbor lists avoid the need for
duplication or atomic operations but require more compute operations per
atom. When using the Kokkos Serial back end or the OpenMP back end with
a single thread, no duplication or atomic operations are used. For CUDA
and half neighbor lists, the KOKKOS package always uses atomic operations.
[Core and Thread Affinity:]
@ -193,7 +193,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. When running on KNL, this will
typically be best for pair-wise potentials. For manybody potentials,
typically be best for pair-wise potentials. For many-body potentials,
using "half" neighbor lists and setting the Newton flag to "on" may be
faster. It can also be faster to use non-threaded communication. Use
the "-pk kokkos" "command-line switch"_Run_options.html to change the
@ -207,7 +207,7 @@ mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half co
NOTE: MPI tasks and threads should be bound to cores as described
above for CPUs.
NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
NOTE: To build with Kokkos support for Intel Xeon Phi co-processors
such as Knight's Corner (KNC), your system must be configured to use
them in "native" mode, not "offload" mode like the USER-INTEL package
supports.

4
doc/src/Speed_omp.txt
View File

@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l
The system has a spatially inhomogeneous particle density which does
not map well to the "domain decomposition scheme"_processors.html or
"load-balancing"_balance.html options that LAMMPS provides. This is
because multi-threading achives parallelism over the number of
because multi-threading achieves parallelism over the number of
particles, not via their distribution in space. :l
A machine is being used in "capability mode", i.e. near the point
@ -143,7 +143,7 @@ the performance-limiting factor. Using multi-threading allows less
MPI tasks to be invoked and can speed-up the long-range solver, while
increasing overall performance by parallelizing the pairwise and
bonded calculations via OpenMP. Likewise additional speedup can be
sometimes be achived by increasing the length of the Coulombic cutoff
sometimes be achieved by increasing the length of the Coulombic cutoff
and thus reducing the work done by the long-range solver. Using the
"run_style verlet/split"_run_style.html command, which is compatible
with the USER-OMP package, is an alternative way to reduce the number

4
doc/src/Speed_packages.txt
View File

@ -14,7 +14,7 @@ Accelerated versions of various "pair_style"_pair_style.html,
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
co-processors.
All of these commands are in packages provided with LAMMPS. An
overview of packages is give on the "Packages"_Packages.html doc
@ -161,7 +161,7 @@ package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
co-processors. This can result in additional speedup over 2x depending
on the hardware configuration. :l
Styles with a "kk" suffix are part of the KOKKOS package, and can be

8
doc/src/Tools.txt
View File

@ -163,7 +163,7 @@ for the "chain benchmark"_Speed_bench.html.
colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
The colvars directory contains a collection of tools for post-processing
data produced by the colvars collective variable library.
To compile the tools, edit the makefile for your system and run "make".
@ -406,15 +406,15 @@ supports it. It has its own WWW page at
msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
Insight MD code, formerly MSI/Biosym and its Discover MD code).
input and data files from BIOVIA's Materias Studio files (formerly
Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code).
This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). Several people contributed changes
to remove bugs and adapt its output to changes in LAMMPS.
This tool has several known limitations and is no longer under active
development, so there are no changes except for the occasional bugfix.
development, so there are no changes except for the occasional bug fix.
See the README file in the tools/msi2lmp folder for more information.

2
doc/src/angle_sdk.txt
View File

@ -28,7 +28,7 @@ The {sdk} angle style is a combination of the harmonic angle potential,
where theta0 is the equilibrium value of the angle and K a prefactor,
with the {repulsive} part of the non-bonded {lj/sdk} pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parametrization using the
coarse grained MD simulations with the CMM parameterization using the
"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style
{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.

2
doc/src/atom_style.txt
View File

@ -87,7 +87,7 @@ quantities.
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{peri} | mass, volume | mesoscopic Peridynamic models |
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
{sphere} | diameter, mass, angular velocity | granular models |
{spin} | magnetic moment | system with magnetic particles |

8
doc/src/balance.txt
View File

@ -247,7 +247,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the {stopthresh}
criterion is met.
A rebalance operation in a single dimension is performed using a
A re-balance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning for a single value, except
@ -261,11 +261,11 @@ information, so that they become closer together over time. Thus as
the recursion progresses, the count of particles on either side of the
plane gets closer to the target value.
Once the rebalancing is complete and final processor sub-domains
Once the re-balancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and
the balance procedure ends.
NOTE: At each rebalance operation, the bisectioning for each cutting
NOTE: At each re-balance operation, the bisectioning for each cutting
plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
@ -348,7 +348,7 @@ specified groups, its weight is not changed. If it belongs to
multiple groups, its weight is the product of the weight factors.
This weight style is useful in combination with pair style
"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody
"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body
potential with a fast pair-wise potential. It is also useful when
using "run_style respa"_run_style.html where some portions of the
system have many bonded interactions and others none. It assumes that

2
doc/src/bond_oxdna.txt
View File

@ -52,7 +52,7 @@ hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparametrizing the entire model.
be changed without reparameterizing the entire model.
Example input and data files for DNA duplexes can be found in
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python

2
doc/src/comm_modify.txt
View File

@ -154,6 +154,6 @@ Communication mode {multi} is currently only available for
[Default:]
The option defauls are mode = single, group = all, cutoff = 0.0, vel =
The option defaults are mode = single, group = all, cutoff = 0.0, vel =
no. The cutoff default of 0.0 means that ghost cutoff = neighbor
cutoff = pairwise force cutoff + neighbor skin.

2
doc/src/compute.txt
View File

@ -309,7 +309,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
"temp/uef"_compute_temp_uef.html -
"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
"xrd"_compute_xrd.html - :ul

62
doc/src/compute_adf.txt
View File

@ -33,22 +33,22 @@ keyword = {ordinate} :l
compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
1 1 2 0.0 1.2 0.0 1.5 &
1 2 2 0.0 1.5 0.0 1.5 &
1 2 2 0.0 1.5 0.0 1.5 &
2 1 1 0.0 1.2 0.0 1.2 &
2 1 2 0.0 1.5 2.0 3.5 &
2 2 2 2.0 3.5 2.0 3.5
2 2 2 2.0 3.5 2.0 3.5
compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5
compute 1 fluid adf 32 :pre
[Description:]
Define a computation that calculates one or more angular distribution functions
(ADF) for a group of particles. Each ADF is calculated in histogram form
(ADF) for a group of particles. Each ADF is calculated in histogram form
by measuring the angle formed by a central atom and two neighbor atoms and
binning these angles into {Nbin} bins.
Only neighbors for which {Rinner} < {R} < {Router} are counted, where
{Rinner} and {Router} are specified separately for the first and second
neighbor atom in each requested ADF.
neighbor atom in each requested ADF.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
@ -66,18 +66,18 @@ the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
NOTE: If you request any outer cutoff {Router} > force cutoff, or if no
NOTE: If you request any outer cutoff {Router} > force cutoff, or if no
pair style is defined, e.g. the "rerun"_rerun.html command is being used to
post-process a dump file of snapshots you must insure ghost atom information
out to the largest value of {Router} + {skin} is communicated, via the
"comm_modify cutoff"_comm_modify.html command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The {skin} value
is what is specified with the "neighbor"_neighbor.html command.
post-process a dump file of snapshots you must insure ghost atom information
out to the largest value of {Router} + {skin} is communicated, via the
"comm_modify cutoff"_comm_modify.html command, else the ADF computation
cannot be performed, and LAMMPS will give an error message. The {skin} value
is what is specified with the "neighbor"_neighbor.html 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
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 2nd 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
@ -88,13 +88,13 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st 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}
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
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
in the range of types represented by {ktypeN}.
one neighbor in the range of types represented by {jtypeN} and another neighbor
in the range of types represented by {ktypeN}.
If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then
LAMMPS will generate a single ADF for all atoms in the group.
@ -106,13 +106,13 @@ Such an ADF is both uninformative and
extremely expensive to compute. For example, with liquid water
with a 10 A force cutoff, there are 80,000 angles per atom.
In addition, most of the interesting angular structure occurs for
neighbors that are the closest to the central atom, involving
neighbors that are the closest to the central atom, involving
just a few dozen angles.
Angles for each ADF are generated by double-looping over the list of
neighbors of each central atom I,
just as they would be in the force calculation for
a threebody potential such as "Stillinger-Weber"_pair_sw.html.
Angles for each ADF are generated by double-looping over the list of
neighbors of each central atom I,
just as they would be in the force calculation for
a three-body potential such as "Stillinger-Weber"_pair_sw.html.
The angle formed by central atom I and neighbor atoms J and K is included in an
ADF if the following criteria are met:
@ -121,12 +121,12 @@ the distance between atoms I,J is between Rjinner and Rjouter
the distance between atoms I,K is between Rkinner and Rkouter
the type of the I atom matches itypeN (one or a range of types)
atoms I,J,K are distinct
the type of the J atom matches jtypeN (one or a range of types)
the type of the J atom matches jtypeN (one or a range of types)
the type of the K atom matches ktypeN (one or a range of types) :ul
Each unique angle satisfying the above criteria is counted only once, regardless
of whether either or both of the neighbor atoms making up the
angle appear in both the J and K lists.
angle appear in both the J and K lists.
It is OK if a particular angle is included in more than
one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN}
arguments are specified.
@ -146,15 +146,15 @@ number radial distribution function.
The {ordinate} optional keyword determines
whether the bins are of uniform angular size from zero
to 180 ({degree}), zero to Pi ({radian}), or the
to 180 ({degree}), zero to Pi ({radian}), or the
cosine of the angle uniform in the range \[-1,1\] ({cosine}).
{cosine} has the advantage of eliminating the {acos()} function
call, which speeds up the compute by 2-3x, and it is also preferred
on physical grounds, because the for uniformly distributed particles
on physical grounds, because the for uniformly distributed particles
in 3D, the angular probability density w.r.t dtheta is
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
the integral is 1.
The simplest way to output the results of the compute adf calculation
@ -170,7 +170,7 @@ This compute calculates a global array with the number of rows =
{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the
number of I,J,K triples specified. The first column has the bin
coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN})
the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN})
interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
the "Howto output"_Howto_output.html doc page for an overview of
@ -181,15 +181,15 @@ The array values calculated by this compute are all "intensive".
The first column of array values is the angle-related ordinate, either
the angle in degrees or radians, or the cosine of the angle. Each
subsequent pair of columns gives the first and second kinds of ADF
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
in the first ADF column are normalized numbers >= 0.0,
whose integral w.r.t. the ordinate is 1,
i.e. the first ADF is a normalized probability distribution.
i.e. the first ADF is a normalized probability distribution.
The values in the second ADF column are also numbers >= 0.0.
They are the cumulative density distribution of angles per atom.
By definition, this ADF is monotonically increasing from zero to
a maximum value equal to the average total number of
angles per atom satisfying the ADF criteria.
angles per atom satisfying the ADF criteria.
[Restrictions:]
@ -200,7 +200,7 @@ distances, you can use the "rerun"_rerun.html command to post-process
a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren't running dynamics and thus are not changing
your model.
your model.
[Related commands:]

2
doc/src/compute_basal_atom.txt
View File

@ -28,7 +28,7 @@ The results enable efficient identification and characterization of
twins and grains in hexagonal close-packed structures.
The output of the compute is thus the 3 components of a unit vector
associdate with each atom. The components are set to 0.0 for
associated with each atom. The components are set to 0.0 for
atoms not in the group.
Details of the calculation are given in "(Barrett)"_#Barrett.

2
doc/src/compute_bond_local.txt
View File

@ -68,7 +68,7 @@ in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms along the bond
direction, after the COM velocity has been subtracted from each.
The value {engrot} is the rotationsl kinetic energy of the two atoms
The value {engrot} is the rotational kinetic energy of the two atoms
in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms perpendicular to
the bond direction, after the COM velocity has been subtracted from

2
doc/src/compute_chunk_atom.txt
View File

@ -210,7 +210,7 @@ between {crmin} and {crmax}. For example, if {crmin} = 1.0 and
{crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r <
2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in
the radial dimensions is the same whether the simulation box is
orthogonal or triclinic; i.e. the concetric circles are not tilted or
orthogonal or triclinic; i.e. the concentric circles are not tilted or
scaled differently in the two different dimensions to transform them
into ellipses.

2
doc/src/compute_cna_atom.txt
View File

@ -33,7 +33,7 @@ Currently, there are five kinds of CNA patterns LAMMPS recognizes:
fcc = 1
hcp = 2
bcc = 3
icosohedral = 4
icosahedral = 4
unknown = 5 :ul
The value of the CNA pattern will be 0 for atoms not in the specified

2
doc/src/compute_damage_atom.txt
View File

@ -26,7 +26,7 @@ in a group. This is a quantity relevant for "Peridynamics
models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf
for an overview of LAMMPS commands for Peridynamics modeling.
The "damage" of a Peridymaics particles is based on the bond breakage
The "damage" of a Peridynamics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged.

2
doc/src/compute_displace_atom.txt
View File

@ -57,7 +57,7 @@ correctly with time=0 atom coordinates from the restart file.
:line
The {refresh} option can be used in conjuction with the "dump_modify
The {refresh} option can be used in conjunction with the "dump_modify
refresh" command to generate incremental dump files.
The definition and motivation of an incremental dump file is as

4
doc/src/compute_heat_flux.txt
View File

@ -82,11 +82,11 @@ first term in the equation for J above.
The heat flux can be output every so many timesteps (e.g. via the
"thermo_style custom"_thermo_style.html command). Then as a
post-processing operation, an autocorrelation can be performed, its
post-processing operation, an auto-correlation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.
The "fix ave/correlate"_fix_ave_correlate.html command can calculate
the autocorrelation. The trap() function in the
the auto-correlation. The trap() function in the
"variable"_variable.html command can calculate the integral.
An example LAMMPS input script for solid Ar is appended below. The

2
doc/src/compute_msd.txt
View File

@ -50,7 +50,7 @@ The value of the displacement will be
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
displacement of each atom is calculated.
If the {average} option is set to {yes} then the reference position of
an atom is based on the average position of that atom, corrected for

2
doc/src/compute_msd_nongauss.txt
View File

@ -48,7 +48,7 @@ others.
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
displacement of each atom is calculated.
See the "compute msd"_compute_msd.html doc page for further important
NOTEs, which also apply to this compute.

2
doc/src/compute_pair.txt
View File

@ -15,7 +15,7 @@ compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
pair = style name of this compute command :l
pstyle = style name of a pair style that calculates additional values :l
nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l
nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a hybrid style :l
{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l
:ule

2
doc/src/compute_plasticity_atom.txt
View File

@ -30,7 +30,7 @@ The plasticity for a Peridynamic particle is the so-called consistency
parameter (lambda). For elastic deformation lambda = 0, otherwise
lambda > 0 for plastic deformation. For details, see
"(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS
distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
distribution in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
This command can be invoked for one of the Peridynamic "pair
styles"_pair_peri.html: peri/eps.

4
doc/src/compute_pressure.txt
View File

@ -40,7 +40,7 @@ below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), and V is the system
volume (or area in 2d). The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
manybody, and long-range interactions, where r_i and f_i are the
many-body, and long-range interactions, where r_i and f_i are the
position and force vector of atom i, and the black dot indicates a dot
product. When periodic boundary conditions are used, N' necessarily
includes periodic image (ghost) atoms outside the central box, and the
@ -68,7 +68,7 @@ compute temperature or ke and/or the virial. The {virial} keyword
means include all terms except the kinetic energy {ke}.
Details of how LAMMPS computes the virial efficiently for the entire
system, including for manybody potentials and accounting for the
system, including for many-body potentials and accounting for the
effects of periodic boundary conditions are discussed in
"(Thompson)"_#Thompson1.

2
doc/src/compute_pressure_cylinder.txt
View File

@ -58,7 +58,7 @@ This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pair-wise force
calculations not available for most manybody pair styles. K-space
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included
and may be calculated from the number density output by P_kin=density*k*T.

6
doc/src/compute_property_atom.txt
View File

@ -19,7 +19,7 @@ input = one or more atom attributes :l
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
sp, spx, spy, spz, fmx, fmy, fmz,
sp, spx, spy, spz, fmx, fmy, fmz,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
@ -158,8 +158,8 @@ corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.
For the spin quantities, sp is in the units of the Bohr magneton, spx,
spy, and spz are adimensional quantities, and fmx, fmy and fmz are
given in rad.THz.
spy, and spz are unitless quantities, and fmx, fmy and fmz are given
in rad/THz.
[Restrictions:] none

2
doc/src/compute_ptm_atom.txt
View File

@ -80,7 +80,7 @@ too frequently or to have multiple compute/dump commands, each with a
[Output info:]
This compute calculates a per-atom arry, which can be accessed by
This compute calculates a per-atom array, which can be accessed by
any command that uses per-atom values from a compute as input. See
the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.

2
doc/src/compute_reduce.txt
View File

@ -61,7 +61,7 @@ or {max} options find the minimum or maximum value across all vector
values. The {ave} setting adds the vector values into a global total,
then divides by the number of values in the vector. The {sumsq}
option sums the square of the values in the vector into a global
total. The {avesq} setting does the same as {sumsq}, then divdes the
total. The {avesq} setting does the same as {sumsq}, then divides the
sum of squares by the number of values. The last two options can be
useful for calculating the variance of some quantity, e.g. variance =
sumsq - ave^2.

2
doc/src/compute_reduce_chunk.txt
View File

@ -137,7 +137,7 @@ compute micelle all chunk/atom c_spread compress yes :pre
Further analysis on a per-micelle basis can now be performed using any
of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html
doc page. E.g. count the number of atoms in each micelle, calculate
its center or mass, shape (moments of intertia), radius of gyration,
its center or mass, shape (moments of inertia), radius of gyration,
etc.
compute prop all property/chunk micelle count

2
doc/src/compute_rigid_local.txt
View File

@ -106,7 +106,7 @@ There are two options for outputting the coordinates of the center of
mass (COM) of the body. The {x}, {y}, {z} attributes write the COM
"unscaled", in the appropriate distance "units"_units.html (Angstroms,
sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
the image flags for each atobody. Unwrapped means that if the body
the image flags for each body. Unwrapped means that if the body
COM has passed thru a periodic boundary one or more times, the value
is generated what the COM coordinate would be if it had not been
wrapped back into the periodic box.

2
doc/src/compute_smd_hourglass_error.txt
View File

@ -29,7 +29,7 @@ within the neighborhood of the central node and the deformation
gradient, the approximated relative separation will coincide with the
actual relative separation of the particles i and j in the deformed
configuration. This compute is only really useful for debugging the
hourglass control mechanim which is part of the Total-Lagrangian SPH
hourglass control mechanism which is part of the Total-Lagrangian SPH
pair style.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth

2
doc/src/compute_smd_tlsph_defgrad.txt
View File

@ -30,7 +30,7 @@ Mach Dynamics in LAMMPS.
[Output info:]
This compute outputss a per-particle vector of vectors (tensors),
This compute outputs a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
from a compute as input. See the "Howto output"_Howto_output.html doc
page for an overview of LAMMPS output options.

2
doc/src/compute_smd_tlsph_shape.txt
View File

@ -38,7 +38,7 @@ overview of LAMMPS output options.
The per-particle vector has 7 entries. The first three entries
correspond to the lengths of the ellipsoid's axes and have units of
length. These axis valus are computed as the contact radius times the
length. These axis values are computed as the contact radius times the
xx, yy, or zz components of the Green-Lagrange strain tensor
associated with the particle. The next 4 values are quaternions
(order: q, x, y, z) which describe the spatial rotation of the

4
doc/src/compute_stress_atom.txt
View File

@ -73,9 +73,9 @@ Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.
Details of how LAMMPS computes the virial for individual atoms for
either pairwise or manybody potentials, and including the effects of
either pairwise or many-body potentials, and including the effects of
periodic boundary conditions is discussed in "(Thompson)"_#Thompson2.
The basic idea for manybody potentials is to treat each component of
The basic idea for many-body potentials is to treat each component of
the force computation between a small cluster of atoms in the same
manner as in the formula above for bond, angle, dihedral, etc
interactions. Namely the quantity R dot F is summed over the atoms in

2
doc/src/compute_tally.txt
View File

@ -47,7 +47,7 @@ the based classes of LAMMPS.
The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
manybody interactions. On the other hand, the computation does not
many-body interactions. On the other hand, the computation does not
have to compute forces or energies a second time and thus can be much
more efficient. The callback mechanism allows to write more complex
pairwise property computations.

2
doc/src/compute_temp_asphere.txt
View File

@ -60,7 +60,7 @@ same. If it does not rotate around the axis perpendicular to its
circular cross section, then it should have 5 dof instead of 6 in 3d.
The latter is the case for uniaxial ellipsoids in a "GayBerne
model"_pair_gayberne.html since there is no induced torque around the
optical axis. It will also be the case for biaxial ellipsoids when
optical axis. It will also be the case for bi-axial ellipsoids when
exactly two of the semiaxes have the same length and the corresponding
relative well depths are equal.

2
doc/src/compute_temp_chunk.txt
View File

@ -118,7 +118,7 @@ or "fix rigid"_fix_rigid.html. This is because those degrees of
freedom (e.g. a constrained bond) could apply to sets of atoms that
are both included and excluded from a specific chunk, and hence the
concept is somewhat ill-defined. In some cases, you can use the
{adof} and {cdof} keywords to adjust the calculated degress of freedom
{adof} and {cdof} keywords to adjust the calculated degrees of freedom
appropriately, as explained below.
Note that the per-chunk temperature calculated by this compute and the

2
doc/src/compute_temp_cs.txt
View File

@ -74,7 +74,7 @@ relative to the COM velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining COM
velocity will be performed, and the bias will be added back in. This
means the thermostating will effectively be performed on the
means the thermostatting will effectively be performed on the
core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include "fix
nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix

2
doc/src/compute_ti.txt
View File

@ -45,7 +45,7 @@ described in "Eike"_#Eike.
Typically this compute will be used in conjunction with the "fix
adapt"_fix_adapt.html command which can perform alchemical
transformations by adusting the strength of an interaction potential
transformations by adjusting the strength of an interaction potential
as a simulation runs, as defined by one or more
"pair_style"_pair_style.html or "kspace_style"_kspace_style.html
commands. This scaling is done via a prefactor on the energy, forces,

2
doc/src/create_box.txt
View File

@ -58,7 +58,7 @@ edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or
positive or negative values and are called "tilt factors" because they
are the amount of displacement applied to faces of an originally
orthogonal box to transform it into the parallelipiped.
orthogonal box to transform it into the parallelepiped.
By default, a {prism} region used with the create_box command must
have tilt factors (xy,xz,yz) that do not skew the box more than half

4
doc/src/dihedral_charmm.txt
View File

@ -41,7 +41,7 @@ field.
NOTE: The newer {charmmfsw} style was released in March 2017. We
recommend it be used instead of the older {charmm} style when running
a simulation with the CHARMM force field, either with long-range
Coulombics or a Coulomb cutoff, via the "pair_style
Coulombics or a Coulombic cutoff, via the "pair_style
lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
Otherwise the older {charmm} style is fine to use. See the discussion
@ -87,7 +87,7 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
default). Otherwise 1-4 non-bonded interactions in dihedrals will be
computed twice.
For simulations using the CHARMM force field with a Coulomb cutoff,
For simulations using the CHARMM force field with a Coulombic cutoff,
the difference between the {charmm} and {charmmfsw} styles is in the
computation of the 1-4 non-bond interactions, though only if the
distance between the two atoms is within the switching region of the

6
doc/src/dump_h5md.txt
View File

@ -17,7 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l
h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file.h5 = name of file to write to :l
args = list of data elements to dump, with their dump "subintervals"
args = list of data elements to dump, with their dump "sub-intervals"
position options
image
velocity options
@ -63,7 +63,7 @@ another particle group must specify {create_group yes}.
:link(h5md,http://nongnu.org/h5md/)
Each data element is written every N*N_element steps. For {image}, no
subinterval is needed as it must be present at the same interval as
sub-interval is needed as it must be present at the same interval as
{position}. {image} must be given after {position} in any case. The
box information (edges in each dimension) is stored at the same
interval than the {position} element, if present. Else it is stored
@ -76,7 +76,7 @@ written to a dump file may be slightly outside the simulation box.
[Use from write_dump:]
It is possible to use this dump style with the
"write_dump"_write_dump.html command. In this case, the subintervals
"write_dump"_write_dump.html command. In this case, the sub-intervals
must not be set at all. The write_dump command can be used either to
create a new file or to add current data to an existing dump file by
using the {file_from} keyword.

11
doc/src/dump_image.txt
View File

@ -541,10 +541,11 @@ a) Use the ImageMagick convert program. :ulb,l
% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg :pre
Animated GIF files from ImageMagick are unoptimized. You can use a
program like gifsicle to optimize and massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with rather
inefficient compression and low quality.
Animated GIF files from ImageMagick are not optimized. You can use
a program like gifsicle to optimize and thus massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with a rather
inefficient compression and low quality compared to more modern
compression styles like MPEG-4, H.264, VP8, VP9, H.265 and so on.
b) Use QuickTime. :l
@ -564,7 +565,7 @@ allows extremely flexible encoding and decoding of movies.
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre
Frontends for FFmpeg exist for multiple platforms. For more
Front ends for FFmpeg exist for multiple platforms. For more
information see the "FFmpeg homepage"_http://www.ffmpeg.org/
:ule

4
doc/src/dump_modify.txt
View File

@ -201,7 +201,7 @@ atom type (1 to Ntype) in the simulation. The same element name can
be given to multiple atom types.
In the case of {xyz} format dumps, there are no restrictions to what
label can be used as an element name. Any whitespace separated text
label can be used as an element name. Any white-space separated text
will be accepted.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
@ -667,7 +667,7 @@ command, when its atom diameter setting is {type}, to set the size
that atoms of each type will be drawn in the image. The specified
{type} should be an integer from 1 to Ntypes. As with the {acolor}
keyword, a wildcard asterisk can be used as part of the {type}
argument to specify a range of atomt types. The specified {diam} is
argument to specify a range of atom types. The specified {diam} is
the size in whatever distance "units"_units.html the input script is
using, e.g. Angstroms.

2
doc/src/fix.txt
View File

@ -202,7 +202,7 @@ accelerated styles exist.
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"edpd/source"_fix_dpd_source.html -
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - ehanced heat exchange algorithm
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
"eos/cv"_fix_eos_cv.html -
"eos/table"_fix_eos_table.html -

4
doc/src/fix_append_atoms.txt
View File

@ -28,7 +28,7 @@ keyword = {basis} or {size} or {freq} or {temp} or {random} or {units} :l
target = target temperature for the region between zhi-extent and zhi (temperature units)
damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
extent = extent of thermostatted region (distance units)
{random} args = xmax ymax zmax seed
{xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units)
{seed} = random number seed for random displacement
@ -68,7 +68,7 @@ be added.
The {random} keyword will give the atoms random displacements around
their lattice points to simulate some initial temperature.
The {temp} keyword will cause a region to be thermostated with a
The {temp} keyword will cause a region to be thermostatted with a
Langevin thermostat on the zhi boundary. The size of the region is
measured from zhi and is set with the {extent} argument.

2
doc/src/fix_ave_chunk.txt
View File

@ -240,7 +240,7 @@ shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because
those degrees of freedom (e.g. a constrained bond) could apply to sets
of atoms that are both included and excluded from a specific chunk,
and hence the concept is somewhat ill-defined. In some cases, you can
use the {adof} and {cdof} keywords to adjust the calculated degress of
use the {adof} and {cdof} keywords to adjust the calculated degrees of
freedom appropriately, as explained below.
Also note that a bias can be subtracted from atom velocities before

2
doc/src/fix_ave_time.txt
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@ -133,7 +133,7 @@ fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rd
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a mlutiple of {Nfreq}. The average is over {Nrepeat}
that are a multiple of {Nfreq}. The average is over {Nrepeat}
quantities, computed in the preceding portion of the simulation every
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps

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