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Minor updates in documentation and setup tool, merge before upgrade to oxDNA2

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This commit is contained in:
Oliver Henrich
2017-03-14 11:39:09 +00:00
parent 23b8287933 f871ecdc67
commit 7a75cd111c
551 changed files with 15121 additions and 4619 deletions
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2
bench/FERMI/README
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@ -14,7 +14,7 @@ lmp_linux_mixed
lmp_linux_double
The precision (single, mixed, double) refers to the GPU and USER-CUDA
pacakge precision. See the README files in the lib/gpu and lib/cuda
package precision. See the README files in the lib/gpu and lib/cuda
directories for instructions on how to build the packages with
different precisions. The GPU and USER-CUDA sub-sections of the
doc/Section_accelerate.html file also describes this process.

1
doc/.gitignore vendored
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@ -1,4 +1,5 @@
/html
/spelling
/LAMMPS.epub
/LAMMPS.mobi
/Manual.pdf

17
doc/Makefile
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@ -22,7 +22,7 @@ endif
SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
.PHONY: help clean-all clean epub html pdf old venv
.PHONY: help clean-all clean epub html pdf old venv spelling
# ------------------------------------------
@ -44,6 +44,10 @@ clean-all:
clean:
rm -rf $(RSTDIR) html
rm -rf spelling
clean-spelling:
rm -rf spelling
html: $(OBJECTS)
@(\
@ -64,6 +68,17 @@ html: $(OBJECTS)
@rm -rf html/USER/*/*.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
@(\
. $(VENV)/bin/activate ;\
pip install sphinxcontrib-spelling ;\
cp -r src/* $(RSTDIR)/ ;\
cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
deactivate ;\
)
@echo "Spell check finished."
epub: $(OBJECTS)
@mkdir -p epub
@rm -f LAMMPS.epub

12
doc/src/2001/input_commands.html
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@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake",
entirely rigid (e.g. water)
the angletype option enables an additional check when SHAKE constraints
are computed: if a cluster is of size 3 and both bonds in
the cluster are of a bondtype specified by the 2nd paramter of
the cluster are of a bondtype specified by the 2nd parameter of
angletype, then the cluster is SHAKEn with an additional angle
constraint that makes it rigid, using the equilibrium angle appropriate
to the specified angletype
@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely
since they will not be SHAKEn but neither will the angle force by computed
for style region, a coeff of INF means + or - infinity (all the way
to the boundary)
an atom can be assigned to multiple constraints, the contraints will be
an atom can be assigned to multiple constraints, the constraints will be
applied in the reverse order they are assigned to that atom
(e.g. each timestep, the last fix assigned to an atom will be applied
to it first, then the next-to-last applied second, etc)
@ -689,7 +689,7 @@ coeffs: types
remainder
no other parameters required
used with "create temp" commmand to initialize velocities of atoms
used with "create temp" command to initialize velocities of atoms
by default, the "create temp" command initializes the velocities of all atoms,
this command limits the initialization to a group of atoms
this command is only in force for the next "create temp" command, any
@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are
applied when atoms move except for the following
fixes associated with temperature control are not allowed
(rescale, hoover/drag, langevin)
the minimizer does not invoke the "fix style shake" contraints on
the minimizer does not invoke the "fix style shake" constraints on
bond lengths
the minimizer does not invoke pressure control or volume control settings
for good convergence, should specify use of smooth nonbond force fields
@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
specifed mesh size will override the default
specified mesh size will override the default
</PRE>
<HR>
<H3>
@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files
when the minimizer is invoked this command means create a restart file
at the end of the minimization with the filename filename.timestep.min
a restart file stores atom and force-field information in binary form
allows program to restart from where it left off (see &quot;read restart&quot; commmand)
allows program to restart from where it left off (see &quot;read restart&quot; command)
Default = 0
</PRE>

4
doc/src/99/basics.html
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@ -167,7 +167,7 @@ tool on the small-system data file.</P>
<P>
(6) flow</P>
<P>
2-d flow of Lennard-Jones atoms in a channel using various contraint
2-d flow of Lennard-Jones atoms in a channel using various constraint
options.</P>
<P>
(7) polymer</P>
@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f
(compile and link with print.c) which can be used to generate random
initial polymer configurations for bead-spring models like those used
in examples/polymer. It uses an input polymer definition file (see
examples/polymer for two sample def files) that specfies how many
examples/polymer for two sample def files) that specifies how many
chains of what length, a random number seed, etc.</P>
</BODY>
</HTML>

2
doc/src/99/crib.html
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@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.</P>
<LI>
maxtype = max # of atom types
<LI>
maxbond = max # of bonds to compute on one procesor
maxbond = max # of bonds to compute on one processor
<LI>
maxangle = max # of angles to compute on one processor
<LI>

8
doc/src/99/input_commands.html
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@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint
use appropriate number of coeffs for a particular style
the constraint itself is defined by the &quot;fix style&quot; command
multiple groups of atoms can be assigned to the same constraint
an atom can be assigned to multiple constraints, the contraints will be
an atom can be assigned to multiple constraints, the constraints will be
applied in the reverse order they are assigned to that atom
(e.g. each timestep, the last fix assigned to an atom will be applied
to it first, then the next-to-last applied second, etc)
@ -477,7 +477,7 @@ coeffs: types
remainder
no other parameters required
used with &quot;create temp&quot; commmand to initialize velocities of atoms
used with &quot;create temp&quot; command to initialize velocities of atoms
by default, the &quot;create temp&quot; command initializes the velocities of all atoms,
this command limits the initialization to a group of atoms
this command is only in force for the next &quot;create temp&quot; command, any
@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
specifed mesh size will override the default
specified mesh size will override the default
Default = none
</PRE>
@ -1343,7 +1343,7 @@ value of 0 means never create one
program will toggle between 2 filenames as the run progresses
so always have at least one good file even if the program dies in mid-write
restart file stores atom positions and velocities in binary form
allows program to restart from where it left off (see &quot;read restart&quot; commmand)
allows program to restart from where it left off (see &quot;read restart&quot; command)
Default = 0
</PRE>

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doc/src/Eqs/pair_kolmogorov_crespi_z.tex Normal file
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@ -0,0 +1,13 @@
\documentclass[12pt]{article}
\thispagestyle{empty}
\begin{document}
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
\rho_{ij}^2 = \rho_{ji}^2 & = & x_{ij}^2 + y_{ij}^2 ~\hspace{2cm} (\mathbf{n_i}\equiv\hat \mathbf{z})\\
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right) ^{2n}
\end{eqnarray*}
\end{document}

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="21 Feb 2017 version">
<META NAME="docnumber" CONTENT="10 Mar 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
21 Feb 2017 version :c,h4
10 Mar 2017 version :c,h4
Version info: :h4

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doc/src/Section_commands.txt
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@ -281,12 +281,12 @@ the "minimize"_minimize.html command. A parallel tempering
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. The
This section lists core LAMMPS commands, grouped by category.
The "next section"_#cmd_5 lists all commands alphabetically. The
next section also includes (long) lists of style options for entries
that appear in the following categories as a single command (fix,
compute, pair, etc). Commands that are added by user packages are not
included in these categories, but they are in the next section.
included in the categories here, but they are in the next section.
Initialization:
@ -361,7 +361,7 @@ Settings:
"timer"_timer.html,
"timestep"_timestep.html
Operations within timestepping (fixes) and diagnositics (computes):
Operations within timestepping (fixes) and diagnostics (computes):
"compute"_compute.html,
"compute_modify"_compute_modify.html,
@ -1016,6 +1016,7 @@ package"_Section_start.html#start_3.
"eff/cut"_pair_eff.html,
"exp6/rx"_pair_exp6_rx.html,
"gauss/cut"_pair_gauss.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lennard/mdf"_pair_mdf.html,
"list"_pair_list.html,
"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
@ -1091,7 +1092,7 @@ package"_Section_start.html#start_3.
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
:line

122
doc/src/Section_errors.txt
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@ -574,11 +574,11 @@ group of atoms correctly. :dd
{Bad quadratic solve for particle/line collision} :dt
This is an internal error. It should nornally not occur. :dd
This is an internal error. It should normally not occur. :dd
{Bad quadratic solve for particle/tri collision} :dt
This is an internal error. It should nornally not occur. :dd
This is an internal error. It should normally not occur. :dd
{Bad real space Coulomb cutoff in fix tune/kspace} :dt
@ -912,7 +912,7 @@ Atoms can not be added afterwards to this fix option. :dd
{Cannot append atoms to a triclinic box} :dt
The simulation box must be defined with edges alligned with the
The simulation box must be defined with edges aligned with the
Cartesian axes. :dd
{Cannot balance in z dimension for 2d simulation} :dt
@ -992,7 +992,7 @@ file. :dd
LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
factor that partitions the computation between real space and k-space
for Disptersion interactions. :dd
for Dispersion interactions. :dd
{Cannot create an atom map unless atoms have IDs} :dt
@ -1327,7 +1327,7 @@ Self-explanatory. :dd
This file is created when you use some LAMMPS features, to indicate
what paper you should cite on behalf of those who implemented
the feature. Check that you have write priveleges into the directory
the feature. Check that you have write privileges into the directory
you are running in. :dd
{Cannot open log.lammps for writing} :dt
@ -2005,7 +2005,7 @@ Self-explanatory. :dd
{Cannot use fix reax/bonds without pair_style reax} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt
@ -2088,7 +2088,7 @@ Self-explanatory. :dd
{Cannot use lines with fix srd unless overlap is set} :dt
This is because line segements are connected to each other. :dd
This is because line segments are connected to each other. :dd
{Cannot use multiple fix wall commands with pair brownian} :dt
@ -2131,7 +2131,7 @@ Self-explanatory. :dd
{Cannot use newton pair with born/gpu pair style} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Cannot use newton pair with buck/coul/cut/gpu pair style} :dt
@ -2291,7 +2291,7 @@ Self-explanatory. :dd
{Cannot use newton pair with zbl/gpu pair style} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Cannot use non-zero forces in an energy minimization} :dt
@ -2641,11 +2641,11 @@ uses a pairwise neighbor list. :dd
{Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt
Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd
Radius cannot be bigger than 1/2 of a non-axis periodic dimension. :dd
{Compute chunk/atom bin/sphere radius is too large for periodic box} :dt
Radius cannot be bigger than 1/2 of any periodic dimention. :dd
Radius cannot be bigger than 1/2 of any periodic dimension. :dd
{Compute chunk/atom compute array is accessed out-of-range} :dt
@ -2706,15 +2706,15 @@ It will only store IDs if its compress option is enabled. :dd
{Compute chunk/atom stores no coord1 for compute property/chunk} :dt
Only certain binning options for comptue chunk/atom store coordinates. :dd
Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom stores no coord2 for compute property/chunk} :dt
Only certain binning options for comptue chunk/atom store coordinates. :dd
Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom stores no coord3 for compute property/chunk} :dt
Only certain binning options for comptue chunk/atom store coordinates. :dd
Only certain binning options for compute chunk/atom store coordinates. :dd
{Compute chunk/atom variable is not atom-style variable} :dt
@ -2735,11 +2735,11 @@ is used to find clusters. :dd
{Compute cna/atom cutoff is longer than pairwise cutoff} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute cna/atom requires a pair style be defined} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute com/chunk does not use chunk/atom compute} :dt
@ -2747,7 +2747,7 @@ The style of the specified compute is not chunk/atom. :dd
{Compute contact/atom requires a pair style be defined} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute contact/atom requires atom style sphere} :dt
@ -2760,7 +2760,7 @@ since those atoms are not in the neighbor list. :dd
{Compute coord/atom requires a pair style be defined} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute damage/atom requires peridynamic potential} :dt
@ -2790,7 +2790,7 @@ Self-explanatory. :dd
{Compute erotate/asphere requires extended particles} :dt
This compute cannot be used with point paritlces. :dd
This compute cannot be used with point particles. :dd
{Compute erotate/rigid with non-rigid fix-ID} :dt
@ -2835,7 +2835,7 @@ Cannot compute order parameter beyond cutoff. :dd
{Compute hexorder/atom requires a pair style be defined} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute improper/local used when impropers are not allowed} :dt
@ -2881,11 +2881,11 @@ Cannot compute order parameter beyond cutoff. :dd
{Compute orientorder/atom requires a pair style be defined} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Compute pair must use group all} :dt
Pair styles accumlate energy on all atoms. :dd
Pair styles accumulate energy on all atoms. :dd
{Compute pe must use group all} :dt
@ -2935,7 +2935,7 @@ The style of the specified compute is not chunk/atom. :dd
{Compute property/local cannot use these inputs together} :dt
Only inputs that generate the same number of datums can be used
togther. E.g. bond and angle quantities cannot be mixed. :dd
together. E.g. bond and angle quantities cannot be mixed. :dd
{Compute property/local does not (yet) work with atom_style template} :dt
@ -3079,7 +3079,7 @@ Self-explanatory. :dd
{Compute temp/asphere requires extended particles} :dt
This compute cannot be used with point paritlces. :dd
This compute cannot be used with point particles. :dd
{Compute temp/body requires atom style body} :dt
@ -3524,12 +3524,12 @@ path and name are correct. :dd
{Could not process Python file} :dt
The Python code in the specified file was not run sucessfully by
The Python code in the specified file was not run successfully by
Python, probably due to errors in the Python code. :dd
{Could not process Python string} :dt
The Python code in the here string was not run sucessfully by Python,
The Python code in the here string was not run successfully by Python,
probably due to errors in the Python code. :dd
{Coulomb PPPMDisp order has been reduced below minorder} :dt
@ -3638,7 +3638,7 @@ Self-explanatory. :dd
{Cutoffs missing in pair_style buck/long/coul/long} :dt
Self-exlanatory. :dd
Self-explanatory. :dd
{Cutoffs missing in pair_style lj/long/coul/long} :dt
@ -4385,7 +4385,7 @@ Self-explanatory. :dd
{Fix ave/chunk does not use chunk/atom compute} :dt
The specified conpute is not for a compute chunk/atom command. :dd
The specified compute is not for a compute chunk/atom command. :dd
{Fix ave/chunk fix does not calculate a per-atom array} :dt
@ -4617,11 +4617,11 @@ An index for the array is out of bounds. :dd
{Fix ave/time compute does not calculate a scalar} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Fix ave/time compute does not calculate a vector} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Fix ave/time compute does not calculate an array} :dt
@ -4970,7 +4970,7 @@ Self-explanatory. :dd
{Fix langevin angmom requires extended particles} :dt
This fix option cannot be used with point paritlces. :dd
This fix option cannot be used with point particles. :dd
{Fix langevin omega is not yet implemented with kokkos} :dt
@ -6171,7 +6171,7 @@ map command will force an atom map to be created. :dd
{Initial temperatures not all set in fix ttm} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Input line quote not followed by whitespace} :dt
@ -6199,7 +6199,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd
{Insufficient Jacobi rotations for triangle} :dt
The calculation of the intertia tensor of the triangle failed. This
The calculation of the inertia tensor of the triangle failed. This
should not happen if it is a reasonably shaped triangle. :dd
{Insufficient memory on accelerator} :dt
@ -6463,15 +6463,15 @@ Self-explanatory. :dd
{Invalid attribute in dump custom command} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Invalid attribute in dump local command} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Invalid attribute in dump modify command} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Invalid basis setting in create_atoms command} :dt
@ -6737,7 +6737,7 @@ or cause multiple files to be written. :dd
Filenames used with the dump xyz style cannot be binary or cause files
to be written by each processor. :dd
{Invalid dump_modify threshhold operator} :dt
{Invalid dump_modify threshold operator} :dt
Operator keyword used for threshold specification in not recognized. :dd
@ -6751,7 +6751,7 @@ The fix is not recognized. :dd
{Invalid fix ave/time off column} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Invalid fix box/relax command for a 2d simulation} :dt
@ -7313,7 +7313,7 @@ Self-explanatory. Check the input script or data file. :dd
{LJ6 off not supported in pair_style buck/long/coul/long} :dt
Self-exlanatory. :dd
Self-explanatory. :dd
{Label wasn't found in input script} :dt
@ -7361,7 +7361,7 @@ This should not occur. Report the problem to the developers. :dd
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
box, or moved futher than one processor's sub-domain away before
box, or moved further than one processor's sub-domain away before
reneighboring. :dd
{MEAM library error %d} :dt
@ -7526,7 +7526,7 @@ Self-explanatory. :dd
{Molecule template ID for create_atoms does not exist} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Molecule template ID for fix deposit does not exist} :dt
@ -7552,7 +7552,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Molecule toplogy/atom exceeds system topology/atom} :dt
{Molecule topology/atom exceeds system topology/atom} :dt
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
@ -7792,7 +7792,7 @@ Self-explanatory. :dd
{Must use variable energy with fix addforce} :dt
Must define an energy vartiable when applyting a dynamic
Must define an energy variable when applying a dynamic
force during minimization. :dd
{Must use variable energy with fix efield} :dt
@ -8042,7 +8042,7 @@ Self-explanatory. :dd
{Non digit character between brackets in variable} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Non integer # of swaps in temper command} :dt
@ -8663,7 +8663,7 @@ not be invoked by bond_style quartic. :dd
{Pair style does not support compute group/group} :dt
The pair_style does not have a single() function, so it cannot be
invokded by the compute group/group command. :dd
invoked by the compute group/group command. :dd
{Pair style does not support compute pair/local} :dt
@ -8948,11 +8948,11 @@ Self-explanatory. :dd
{Pair yukawa/colloid requires atom style sphere} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Pair yukawa/colloid requires atoms with same type have same radius} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Pair yukawa/colloid/gpu requires atom style sphere} :dt
@ -9166,7 +9166,7 @@ Self-explanatory. :dd
{Python function evaluation failed} :dt
The Python function did not run succesfully and/or did not return a
The Python function did not run successfully and/or did not return a
value (if it is supposed to return a value). This is probably due to
some error condition in the function. :dd
@ -10025,7 +10025,7 @@ make sense in between runs. :dd
{Threshhold for an atom property that isn't allocated} :dt
A dump threshhold has been requested on a quantity that is
A dump threshold has been requested on a quantity that is
not defined by the atom style used in this simulation. :dd
{Timestep must be >= 0} :dt
@ -10087,7 +10087,7 @@ to a large size. :dd
{Too many atom triplets for pair bop} :dt
The number of three atom groups for angle determinations exceeds the
expected number. Check your atomic structrure to ensure that it is
expected number. Check your atomic structure to ensure that it is
realistic. :dd
{Too many atoms for dump dcd} :dt
@ -10155,7 +10155,7 @@ to a large size. :dd
{Too many timesteps} :dt
The cummulative timesteps must fit in a 64-bit integer. :dd
The cumulative timesteps must fit in a 64-bit integer. :dd
{Too many timesteps for NEB} :dt
@ -10654,7 +10654,7 @@ Only atom-style variables can be used. :dd
{Variable for region cylinder is invalid style} :dt
Only equal-style varaibles are allowed. :dd
Only equal-style variables are allowed. :dd
{Variable for region is invalid style} :dt
@ -10666,7 +10666,7 @@ Self-explanatory. :dd
{Variable for region sphere is invalid style} :dt
Only equal-style varaibles are allowed. :dd
Only equal-style variables are allowed. :dd
{Variable for restart is invalid style} :dt
@ -10707,7 +10707,7 @@ Self-explanatory. :dd
{Variable has circular dependency} :dt
A circular dependency is when variable "a" in used by variable "b" and
variable "b" is also used by varaible "a". Circular dependencies with
variable "b" is also used by variable "a". Circular dependencies with
longer chains of dependence are also not allowed. :dd
{Variable name between brackets must be alphanumeric or underscore characters} :dt
@ -10796,7 +10796,7 @@ Self-explanatory. :dd
{Variable name for fix deform does not exist} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Variable name for fix efield does not exist} :dt
@ -11083,7 +11083,7 @@ for a dihedral) and adding a small amount of stretch. :dd
{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
Self-explantory. :dd
Self-explanatory. :dd
{Calling write_dump before a full system init.} :dt
@ -11414,7 +11414,7 @@ The command options you have used caused atoms to be lost. :dd
Lost atoms are checked for each time thermo output is done. See the
thermo_modify lost command for options. Lost atoms usually indicate
bad dynamics, e.g. atoms have been blown far out of the simulation
box, or moved futher than one processor's sub-domain away before
box, or moved further than one processor's sub-domain away before
reneighboring. :dd
{MSM mesh too small, increasing to 2 points in each direction} :dt
@ -11452,7 +11452,7 @@ i.e. the first molecule in the template. :dd
{Molecule template for fix shake has multiple molecules} :dt
The fix shake command will only recoginze molecules of a single
The fix shake command will only recognize molecules of a single
type, i.e. the first molecule in the template. :dd
{More than one compute centro/atom} :dt
@ -11537,7 +11537,7 @@ neigh_modify exclude command. :dd
If a thermo_style command is used after a thermo_modify command, the
settings changed by the thermo_modify command will be reset to their
default values. This is because the thermo_modify commmand acts on
default values. This is because the thermo_modify command acts on
the currently defined thermo style, and a thermo_style command creates
a new style. :dd
@ -11589,7 +11589,7 @@ This may not be what you intended. :dd
{One or more dynamic groups may not be updated at correct point in timestep} :dt
If there are other fixes that act immediately after the intitial stage
If there are other fixes that act immediately after the initial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
fixes. This will insure that dynamic group assignments are made
@ -11886,7 +11886,7 @@ Self-explanatory. :dd
{Using largest cutoff for buck/long/coul/long} :dt
Self-exlanatory. :dd
Self-explanatory. :dd
{Using largest cutoff for lj/long/coul/long} :dt

2
doc/src/Section_history.txt
View File

@ -37,7 +37,7 @@ pitfalls or alternatives.
Please see some of the closed issues for examples of how to
suggest code enhancements, submit proposed changes, or report
possible bugs and how they are resoved.
possible bugs and how they are resolved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send

52
doc/src/Section_howto.txt
View File

@ -573,7 +573,7 @@ LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
Note that the when using the TIP4P pair style, the neighobr list
Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
@ -618,7 +618,7 @@ any of the parameters above, though it becomes a different model in
that mode of usage.
The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:
the partial charge assignments change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
@ -863,7 +863,7 @@ boundary conditions in specific dimensions. See the command doc pages
for details.
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simluation box is created. This happens in one of 3 ways.
time the simulation box is created. This happens in one of 3 ways.
If the "create_box"_create_box.html command is used with a region of
style {prism}, then a triclinic box is setup. See the
"region"_region.html command for details. If the
@ -982,10 +982,10 @@ 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 dyanamics via the "fix
A second use is to run Parinello-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 analalog for an "energy minimization"_minimize.html is
tensor. The analog for an "energy minimization"_minimize.html is
the "fix box/relax"_fix_box_relax.html command.
A third use is to shear a bulk solid to study the response of the
@ -1392,7 +1392,7 @@ custom"_dump.html command.
There is also a "dump local"_dump.html format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumuerate the local values. Two additional kinds of
specified to enumerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
provides the values to be output. In each case, the compute or fix
@ -1525,7 +1525,7 @@ Variables that generate values to output :h5,link(variable)
"Variables"_variable.html defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
atomfile-style variables generate a global scalar value, global vector
or values, or a per-atom vector, resepctively, when accessed. The
or values, or a per-atom vector, respectively, when accessed. The
formulas used to define these variables can contain references to the
thermodynamic keywords and to global and per-atom data generated by
computes, fixes, and other variables. The values generated by
@ -1585,7 +1585,7 @@ Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
@ -1640,14 +1640,14 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
DPD thermostatting alters pairwise interactions in a manner analagous
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
Any of the thermostatting fixes can use temperature computes that
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
caluclated with the velocity bias removed. Second, the thermostat
calculated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle's
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
@ -1888,7 +1888,7 @@ instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
used to instantiate LAMMPS, and MPI is initialzed if necessary.
used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
@ -1976,7 +1976,7 @@ The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects atom info of the requested type (atom coords,
types, forces, etc) from all procsesors, orders them by atom ID, and
types, forces, etc) from all processors, orders them by atom ID, and
returns a full list to each calling processor. The scatter function
does the inverse. It distributes the same kinds of values,
passed by the caller, to each atom owned by individual processors.
@ -2013,7 +2013,7 @@ a simple Lennard-Jones fluid model. Also, see "this
section"_Section_howto.html#howto_21 of the manual for an analogous
discussion for viscosity.
The thermal conducitivity tensor kappa is a measure of the propensity
The thermal conductivity tensor kappa is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
@ -2099,7 +2099,7 @@ and grad(Vstream) is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
The first method is to perform a non-equlibrium MD (NEMD) simulation
The first method is to perform a non-equilibrium MD (NEMD) simulation
by shearing the simulation box via the "fix deform"_fix_deform.html
command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
thermostat the fluid via the SLLOD equations of motion.
@ -2125,7 +2125,7 @@ the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
swapped between atoms in two different layers of the simulation box in
a different dimension. This induces a velocity gradient which can be
monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
The fix tallies the cummulative momentum transfer that it performs.
The fix tallies the cumulative momentum transfer that it performs.
See the "fix viscosity"_fix_viscosity.html command for details.
The fourth method is based on the Green-Kubo (GK) formula which
@ -2268,7 +2268,7 @@ atoms with same local defect structure | chunk ID = output of "compute centro/at
Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple intergers.
scales the floating point value to spread it across multiple integers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
@ -2353,7 +2353,7 @@ largest cluster or fastest diffusing molecule. :l
Example calculations with chunks :h5
Here are eaxmples using chunk commands to calculate various
Here are examples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
@ -2424,7 +2424,7 @@ which both have their up- and downsides.
The first approach is to set desired real-space an kspace accuracies
via the {kspace_modify force/disp/real} and {kspace_modify
force/disp/kspace} commands. Note that the accuracies have to be
specified in force units and are thus dependend on the chosen unit
specified in force units and are thus dependent on the chosen unit
settings. For real units, 0.0001 and 0.002 seem to provide reasonable
accurate and efficient computations for the real-space and kspace
accuracies. 0.002 and 0.05 work well for most systems using lj
@ -2444,7 +2444,7 @@ performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parametes that provide accurate and fast computations for
parameters that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
@ -2478,7 +2478,7 @@ arithmetic mixing rule substantially increases the computational cost.
The computational overhead can be reduced using the {kspace_modify
mix/disp geom} and {kspace_modify splittol} commands. The first
command simply enforces geometric mixing of the dispersion
coeffiecients in kspace computations. This introduces some error in
coefficients in kspace computations. This introduces some error in
the computations but will also significantly speed-up the
simulations. The second keyword sets the accuracy with which the
dispersion coefficients are approximated using a matrix factorization
@ -2497,7 +2497,7 @@ to specify this command explicitly.
6.25 Polarizable models :link(howto_25),h4
In polarizable force fields the charge distributions in molecules and
materials respond to their electrostatic environements. Polarizable
materials respond to their electrostatic environments. Polarizable
systems can be simulated in LAMMPS using three methods:
the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
@ -2551,7 +2551,7 @@ this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the poarizable models and the simulation
choosing the parameters of the polarizable models and the simulation
conditions.
In the core-shell model the vibration of the shells is kept faster
@ -2727,18 +2727,18 @@ 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.
Therefore it is recomendable to use the "fix
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
prevent any drift.
When intializing the velocities of a system with core/shell pairs, it
When initializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the {bias} keyword of the
"velocity create"_velocity.html command and assigning the "compute
temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
"velocity"_velocity.html commmand, e.g.
"velocity"_velocity.html command, e.g.
velocity all create 1427 134 bias yes temp CSequ
velocity all scale 1427 temp CSequ :pre
@ -2808,7 +2808,7 @@ CS-Info # header of additional section :pre
6.27 Drude induced dipoles :link(howto_27),h4
The thermalized Drude model, similarly to the "core-shell"_#howto_26
model, representes induced dipoles by a pair of charges (the core atom
model, represents induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
("Lamoureux and Roux"_#howto-Lamoureux):

22
doc/src/Section_modify.txt
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@ -159,17 +159,17 @@ pack_comm_vel: add velocity info to communication buffer (required)
pack_comm_hybrid: store extra info unique to this atom style (optional)
unpack_comm: retrieve an atom's info from the buffer (required)
unpack_comm_vel: also retrieve velocity info (required)
unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
unpack_comm_hybrid: retrieve extra info unique to this atom style (optional)
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
pack_reverse_hybrid: store extra info unique to this atom style (optional)
unpack_reverse: retrieve an atom's info from the buffer (required)
unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional)
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
pack_border_vel: add velocity info to buffer (required)
pack_border_hybrid: store extra info unique to this atom style (optional)
unpack_border: retrieve an atom's info from the buffer (required)
unpack_border_vel: also retrieve velocity info (required)
unpack_border_hybrid: retreive extra info unique to this atom style (optional)
unpack_border_hybrid: retrieve extra info unique to this atom style (optional)
pack_exchange: store all an atom's info to migrate to another processor (required)
unpack_exchange: retrieve an atom's info from the buffer (required)
size_restart: number of restart quantities associated with proc's atoms (required)
@ -369,7 +369,7 @@ pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
@ -517,7 +517,7 @@ 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
shape_update : change region shape if set by time-depedent variable :tb(s=:)
shape_update : change region shape if set by time-dependent variable :tb(s=:)
:line
@ -601,16 +601,16 @@ Adding keywords for the "thermo_style custom"_thermo_style.html command
"here"_Section_modify.html#mod_13 on this page.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaulate() method. Search for
editing one section of the Variable::evaluate() method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
Variable::evaulate() method. Search for the word "customize" to find
Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaulate() method. Search for the word "customize"
of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new "compute styles"_compute.html (whose calculated values can
@ -740,7 +740,7 @@ entry to add to the USER-MISC/README file in that dir, along with the
contribute several individual features. :l
If you want your contribution to be added as a user-contribution and
it is several related featues, it is probably best to make it a user
it is several related features, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
@ -785,10 +785,10 @@ file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
prerequiste for building the HTML format files are Python 3.x and
prerequisite for building the HTML format files are Python 3.x and
virtualenv, the requirement for generating the PDF format manual
is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
"make html" and carefully inspect and proofread the resuling HTML format
"make html" and carefully inspect and proofread the resulting HTML format
doc page before submitting your code. :l
For a new package (or even a single command) you should include one or

22
doc/src/Section_packages.txt
View File

@ -94,7 +94,7 @@ Package, Description, Author(s), Doc page, Example, Library
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
responsible for creating and maintaining the package.
(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
which were created by Amit Kumar and Michael Bybee from Jonathan
@ -462,7 +462,7 @@ options you are optimizing for: CPU acceleration via OpenMP, GPU
acceleration, or Intel Xeon Phi. (You can build multiple times to
create LAMMPS executables for different hardware.) It also requires a
C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is
used, and an appopriate KOKKOS_ARCH setting should be made in your
used, and an appropriate KOKKOS_ARCH setting should be made in your
Makefile.machine for your GPU hardware and NVIDIA software.
The simplest way to do this is to use Makefile.kokkos_cuda or
@ -955,8 +955,8 @@ multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica
dynamics (PRD), temperature accelerated dynamics (TAD), parallel
tempering, and a verlet/split algorithm for performing long-range
Coulombics on one set of processors, and the remainded of the force
field calcalation on another set.
Coulombics on one set of processors, and the remainder of the force
field calculation on another set.
To install via make or Make.py:
@ -1176,7 +1176,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
responsible for creating and maintaining the package.
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
@ -1295,13 +1295,13 @@ integrators with improved stability.
See these doc pages to get started:
"bond_style oxdna_fene"_bond_oxdna_fene.html
"pair_style oxdna_excv"_pair_oxdna_excv.html
"bond_style oxdna/fene"_bond_oxdna.html
"pair_style oxdna/..."_pair_oxdna.html
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
Supporting info: /src/USER-CGDNA/README, "bond_style
oxdna_fene"_bond_oxdna_fene.html, "pair_style
oxdna_excv"_pair_oxdna_excv.html, "fix
oxdna/fene"_bond_oxdna.html, "pair_style
oxdna/..."_pair_oxdna.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html
Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
@ -1778,7 +1778,7 @@ particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
For technical details about this implementation of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
@ -1848,7 +1848,7 @@ See this doc page to get started:
The persons who created the USER-SMTBQ package are Nicolas Salles,
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
them directly if you have any questions.
Examples: examples/USER/smtbq

2
doc/src/Section_perf.txt
View File

@ -69,7 +69,7 @@ bench/in.lj input script.
For all the benchmarks, a useful metric is the CPU cost per atom per
timestep. Since performance scales roughly linearly with problem size
and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained
potentials), the run time of any problem using the same model (atom
style, force field, cutoff, etc) can then be estimated.

14
doc/src/Section_python.txt
View File

@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python.
Section 11.8 gives some examples of coupling LAMMPS to other tools via
Python. For example, LAMMPS can easily be coupled to a GUI or other
visualization tools that display graphs or animations in real time as
LAMMPS runs. Examples of such scripts are inlcluded in the python
LAMMPS runs. Examples of such scripts are included in the python
directory.
Two advantages of using Python to run LAMMPS are how concise the
@ -177,7 +177,7 @@ 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 preceeding section (11.1)
must also follow the steps overviewed in the preceding section (11.1)
for running LAMMPS from Python. 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.
@ -325,7 +325,7 @@ sudo python setup.py install :pre
Again, the "sudo" is only needed if required to copy PyPar files into
your Python distribution's site-packages directory.
If you have successully installed PyPar, you should be able to run
If you have successfully installed PyPar, you should be able to run
Python and type
import pypar :pre
@ -369,7 +369,7 @@ user privilege into the user local directory type
python setup.py install --user :pre
If you have successully installed mpi4py, you should be able to run
If you have successfully installed mpi4py, you should be able to run
Python and type
from mpi4py import MPI :pre
@ -610,7 +610,7 @@ lmp = lammps() :pre
create an instance of LAMMPS, wrapped in a Python class by the lammps
Python module, and return an instance of the Python class as lmp. It
is used to make all subequent calls to the LAMMPS library.
is used to make all subsequent calls to the LAMMPS library.
Additional arguments to lammps() can be used to tell Python the name
of the shared library to load or to pass arguments to the LAMMPS
@ -662,7 +662,7 @@ or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
local data calculated by the compute or fix can be accessed. What is
returned depends on whether the compute or fix calculates a scalar or
vector or array. For a scalar, a single double value is returned. If
the compute or fix calculates a vector or array, a pointer to the
@ -774,7 +774,7 @@ demo.py, invoke various LAMMPS library interface routines,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
plot.py, real-time temperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)

24
doc/src/Section_start.txt
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@ -80,7 +80,7 @@ This section has the following sub-sections:
Read this first :h5,link(start_2_1)
If you want to avoid building LAMMPS yourself, read the preceeding
If you want to avoid building LAMMPS yourself, read the preceding
section about options available for downloading and installing
executables. Details are discussed on the "download"_download page.
@ -251,7 +251,7 @@ re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:
within the LAMMPS code. The options that are currently recognized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
@ -362,7 +362,7 @@ installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
environements, you may simply need to include the correct module in
environments, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
@ -430,7 +430,7 @@ use the KISS library described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include
for their compile/link environments, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
@ -450,7 +450,7 @@ you must also manually specify the correct library, namely -lsfftw or
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
calculations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
@ -682,7 +682,7 @@ various make commands that can be used to manipulate packages.
If you use a command in a LAMMPS input script that is part of a
package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown.
Every command's doc page specfies if it is part of a package. You can
Every command's doc page specifies if it is part of a package. You can
also type
lmp_machine -h :pre
@ -1008,7 +1008,7 @@ Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
rename if desired. Likewise it creates an executable named
src/lmp_auto, which you can rename using the -o switch if desired.
The most recently executed Make.py commmand is saved in
The most recently executed Make.py command is saved in
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
the last command, or you can save a sequence of one or more Make.py
commands to a file and invoke the file of commands using "-r". You
@ -1064,7 +1064,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
can link to dyamically. It will also create a soft link liblammps.so,
can link to dynamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
@ -1416,8 +1416,8 @@ LAMMPS is compiled with CUDA=yes.
numa Nm :pre
This option is only relevant when using pthreads with hwloc support.
In this case Nm defines the number of NUMA regions (typicaly sockets)
on a node which will be utilizied by a single MPI rank. By default Nm
In this case Nm defines the number of NUMA regions (typically sockets)
on a node which will be utilized by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
@ -1481,7 +1481,7 @@ replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
To run multiple independent simulatoins from one input script, using
To run multiple independent simulations from one input script, using
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
@ -1760,7 +1760,7 @@ The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other,
similar MD codes. The {CPU use} line provides the CPU utilzation per
similar MD codes. The {CPU use} line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1 of no OpenMP). Lower numbers correspond to delays due
to file I/O or insufficient thread utilization.

2
doc/src/Section_tools.txt
View File

@ -471,7 +471,7 @@ These tools were written by Aidan Thompson at Sandia.
restart2data tool :h4,link(restart)
NOTE: This tool is now obsolete and is not included in the current
LAMMPS distribution. This is becaues there is now a
LAMMPS distribution. This is because there is now a
"write_data"_write_data.html command, which can create a data file
from within an input script. Running LAMMPS with the "-r"
"command-line switch"_Section_start.html#start_7 as follows:

2
doc/src/USER/atc/man_consistent_fe_initialization.html
View File

@ -27,7 +27,7 @@
syntax</a></h2>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>

6
doc/src/accelerate_intel.txt
View File

@ -20,7 +20,7 @@ coprocessors 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
twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and coprocessor cores simulataneously.
LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
[Currently Available USER-INTEL Styles:]
@ -115,7 +115,7 @@ coprocessor 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.
Although any compiler can be used with the USER-INTEL pacakge,
Although any compiler can be used with the USER-INTEL package,
currently, vectorization directives are disabled by default when
not using Intel compilers due to lack of standard support and
observations of decreased performance. The OpenMP standard now
@ -428,7 +428,7 @@ to the card. This allows for overlap of MPI communication of forces
with computation on the coprocessor 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
explictly.
explicitly.
When using offload with CPU Hyper-Threading disabled, it may help
performance to use fewer MPI tasks and OpenMP threads than available

8
doc/src/accelerate_kokkos.txt
View File

@ -217,7 +217,7 @@ best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
significantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper
@ -234,7 +234,7 @@ provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in "Section 5.3"_Section_accelerate.html#acc_3.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an
Intel Phi processor.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
@ -272,7 +272,7 @@ coprocessor support you need to insure there are one or more MPI tasks
per coprocessor, and choose the number of coprocessor threads to use
per MPI task (via the "-k" command-line switch discussed below). The
product of MPI tasks * coprocessor threads/task should not exceed the
maximum number of threads the coproprocessor is designed to run,
maximum number of threads the coprocessor is designed to run,
otherwise performance will suffer. This value is 240 for current
generation Xeon Phi(TM) chips, which is 60 physical cores * 4
threads/core. Note that with the KOKKOS package you do not need to
@ -333,7 +333,7 @@ device=CUDA are the same.
You must still use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
specify its additional arguments for hardware options appopriate to
specify its additional arguments for hardware options appropriate to
your system, as documented above.
Use the "suffix kk"_suffix.html command, or you can explicitly add a

2
doc/src/angle_hybrid.txt
View File

@ -81,7 +81,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
[Related commands:]

8
doc/src/atom_modify.txt
View File

@ -103,7 +103,7 @@ turns off the {first} option.
It is OK to use the {first} keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simullation
your input script. LAMMPS does not use the group until a simulation
is run.
The {sort} keyword turns on a spatial sorting or reordering of atoms
@ -116,7 +116,7 @@ various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.
Reordering is peformed every {Nfreq} timesteps during a dynamics run
Reordering is performed every {Nfreq} timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
@ -130,7 +130,7 @@ the processor's 1d list of atoms.
The goal of this procedure is for atoms to put atoms close to each
other in the processor's one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise intereractions and neighbor lists are computed. Note that if
pairwise interactions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.
@ -138,7 +138,7 @@ cache locality will be undermined.
NOTE: Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
to diverging trajectories over time when comparing two simulations.
Various commands, particularly those which use random numbers
(e.g. "velocity create"_velocity.html, and "fix
langevin"_fix_langevin.html), may generate (statistically identical)

10
doc/src/atom_style.txt
View File

@ -115,7 +115,7 @@ particle.
For the {ellipsoid} style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the {dipole} style, a point dipole is defined for each point
@ -149,7 +149,7 @@ Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetretating each other.
individual physical bodies from penetrating each other.
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
@ -165,7 +165,7 @@ For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The {template} style allows molecular topolgy (bonds,angles,etc) to be
The {template} style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the "molecule"_molecule.html
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
@ -195,7 +195,7 @@ the {bstyle} argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
The "body"_body.html doc page descibes the body styles LAMMPS
The "body"_body.html doc page describes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent. For all styles, each body particle stores
moments of inertia and a quaternion 4-vector, so that its orientation
@ -280,7 +280,7 @@ The {dpd} style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The {meso} style is part of the USER-SPH package for smoothed particle
hydrodyanmics (SPH). See "this PDF
hydrodynamics (SPH). See "this PDF
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
The {wavepacket} style is part of the USER-AWPMD package for the

56
doc/src/balance.txt
View File

@ -12,7 +12,7 @@ balance command :h3
balance thresh style args ... keyword args ... :pre
thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l
thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l
one style/arg pair can be used (or multiple for {x},{y},{z}) :l
style = {x} or {y} or {z} or {shift} or {rcb} :l
{x} args = {uniform} or Px-1 numbers between 0 and 1
@ -30,7 +30,7 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l
{shift} args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshhold is reached
stopthresh = stop balancing when this imbalance threshold is reached
{rcb} args = none :pre
zero or more keyword/arg pairs may be appended :l
keyword = {weight} or {out} :l
@ -76,13 +76,13 @@ sub-domain sizes and shapes on-the-fly during a "run"_run.html.
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or when
the computational cost varies signficantly between different
the computational cost varies significantly between different
particles. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or "hybrid pair
style simulations"_pair_hybrid.html which combine pair styles with
different computational cost. In these cases, the LAMMPS default of
dividing the simulation box volume into a regular-spaced grid of 3d
bricks, with one equal-volume sub-domain per procesor, may assign
bricks, with one equal-volume sub-domain per processor, may assign
numbers of particles per processor in a way that the computational
effort varies significantly. This can lead to poor performance when
the simulation is run in parallel.
@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
which typically inducces a diffrent number of atoms assigned to each
which typically induces a different number of atoms assigned to each
processor. Details on the various weighting options and examples for
how they can be used are "given below"_#weighted_balance.
@ -222,7 +222,7 @@ listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
there are 2 procesors in the x dimension, you specify a single value
there are 2 processors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
@ -266,7 +266,7 @@ assigned, particles are migrated to their new owning processor, and
the balance procedure ends.
NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
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
{Niter} is specified as 10, the cutting plane will typically be
@ -286,24 +286,32 @@ above. It performs a recursive coordinate bisectioning (RCB) of the
simulation domain. The basic idea is as follows.
The simulation domain is cut into 2 boxes by an axis-aligned cut in
the longest dimension, leaving one new box on either side of the cut.
All the processors are also partitioned into 2 groups, half assigned
to the box on the lower side of the cut, and half to the box on the
upper side. (If the processor count is odd, one side gets an extra
processor.) The cut is positioned so that the number of particles in
the lower box is exactly the number that the processors assigned to
that box should own for load balance to be perfect. This also makes
load balance for the upper box perfect. The positioning is done
iteratively, by a bisectioning method. Note that counting particles
on either side of the cut requires communication between all
processors at each iteration.
one of the dimensions, leaving one new sub-box on either side of the
cut. Which dimension is chosen for the cut depends on the particle
(weight) distribution within the parent box. Normally the longest
dimension of the box is cut, but if all (or most) of the particles are
at one end of the box, a cut may be performed in another dimension to
induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
shape.
After the cut is made, all the processors are also partitioned into 2
groups, half assigned to the box on the lower side of the cut, and
half to the box on the upper side. (If the processor count is odd,
one side gets an extra processor.) The cut is positioned so that the
number of (weighted) particles in the lower box is exactly the number
that the processors assigned to that box should own for load balance
to be perfect. This also makes load balance for the upper box
perfect. The positioning of the cut is done iteratively, by a
bisectioning method (median search). Note that counting particles on
either side of the cut requires communication between all processors
at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the particles
in the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the
assigned to each box make a new cut in one dimension of that box,
splitting the box, the subset of processors, and the particles in the
box in two. The recursion continues until every processor is assigned
a sub-box of the entire simulation domain, and owns the (weighted)
particles in that sub-box.
:line
@ -368,7 +376,7 @@ of about 0.8 often results in the best performance, since the number
of neighbors is likely to overestimate the ideal weight.
This weight style is useful for systems where there are different
cutoffs used for different pairs of interations, or the density
cutoffs used for different pairs of interactions, or the density
fluctuates, or a large number of particles are in the vicinity of a
wall, or a combination of these effects. If a simulation uses
multiple neighbor lists, this weight style will use the first suitable
@ -402,7 +410,7 @@ decrease the weights so that the ratio of max weight to min weight
decreases by {factor}. In both cases the intermediate weight values
increase/decrease proportionally as well. A value = 1.0 has no effect
on the {time} weights. As a rule of thumb, effective values to use
are typicall between 0.5 and 1.2. Note that the timer quantities
are typically between 0.5 and 1.2. Note that the timer quantities
mentioned above can be affected by communication which occurs in the
middle of the operations, e.g. pair styles with intermediate exchange
of data witin the force computation, and likewise for KSpace solves.

8
doc/src/body.txt
View File

@ -82,7 +82,7 @@ internal stress that induces fragmentation :ul
then the interaction between pairs of particles is likely to be more
complex than the summation of simple sub-particle interactions. An
example is contact or frictional forces between particles with planar
sufaces that inter-penetrate.
surfaces that inter-penetrate.
These are additional LAMMPS commands that can be used with body
particles of different styles
@ -105,7 +105,7 @@ in the sections below.
The {nparticle} body style represents body particles as a rigid body
with a variable number N of sub-particles. It is provided as a
vanillia, prototypical example of a body particle, although as
vanilla, prototypical example of a body particle, although as
mentioned above, the "fix rigid"_fix_rigid.html command already
duplicates its functionality.
@ -140,7 +140,7 @@ for more details.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the prinicpal axes of the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle. The
@ -218,7 +218,7 @@ wish; see the "read_data"_read_data.html command for more details.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the prinicpal axes of the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass

2
doc/src/bond_hybrid.txt
View File

@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
[Related commands:]

20
doc/src/bond_oxdna_fene.txt → doc/src/bond_oxdna.txt
View File

@ -6,20 +6,20 @@
:line
bond_style oxdna_fene command :h3
bond_style oxdna/fene command :h3
[Syntax:]
bond_style oxdna_fene :pre
bond_style oxdna/fene :pre
[Examples:]
bond_style oxdna_fene
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 :pre
[Description:]
The {oxdna_fene} bond style uses the potential
The {oxdna/fene} bond style uses the potential
:c,image(Eqs/bond_oxdna_fene.jpg)
@ -37,14 +37,14 @@ Delta (distance)
r0 (distance) :ul
NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of
"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients
for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"pair_style oxdna/excv"_pair_oxdna.html). The coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
A technical report with more information on the model, the structure of the input file,
the setup tool and the performance of the LAMMPS-implementation of oxDNA
can be found "here"_PDF/USER-CGDNA-overview.pdf.
@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
[Default:] none

2
doc/src/bonds.txt
View File

@ -15,7 +15,7 @@ Bond Styles :h1
bond_morse
bond_none
bond_nonlinear
bond_oxdna_fene
bond_oxdna
bond_quartic
bond_table
bond_zero

10
doc/src/change_box.txt
View File

@ -101,11 +101,11 @@ Instead you could do something like this, assuming the simulation box
is non-periodic and atoms extend from 0 to 20 in all dimensions:
change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre
create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre
change_box all x final -10 20 boundary f s s
create_atoms 1 single -5 5 5
change_box boundary s s s # this will work :pre
change_box all boundary s s s # this will work :pre
NOTE: Unlike the earlier "displace_box" version of this command, atom
remapping is NOT performed by default. This command allows remapping
@ -258,8 +258,8 @@ command.
:line
The {ortho} and {triclinic} keywords convert the simulation box to be
orthogonal or triclinic (non-orthongonal). See "this
section"_Section_howto#howto_13 for a discussion of how non-orthongal
orthogonal or triclinic (non-orthogonal). See "this
section"_Section_howto#howto_13 for a discussion of how non-orthogonal
boxes are represented in LAMMPS.
The simulation box is defined as either orthogonal or triclinic when
@ -289,7 +289,7 @@ the create_box command is encountered in the input script.
The {remap} keyword remaps atom coordinates from the last saved box
size/shape to the current box state. For example, if you stretch the
box in the x dimension or tilt it in the xy plane via the {x} and {xy}
keywords, then the {remap} commmand will dilate or tilt the atoms to
keywords, then the {remap} command will dilate or tilt the atoms to
conform to the new box size/shape, as if the atoms moved with the box
as it deformed.

2
doc/src/comm_style.txt
View File

@ -39,7 +39,7 @@ sizes and shapes. Again there is one tile per processor. To acquire
information for nearby atoms, communication must now be done with a
more complex pattern of neighboring processors.
Note that this command does not actually define a partitoining of the
Note that this command does not actually define a partitioning of the
simulation box (a domain decomposition), rather it determines what
kinds of decompositions are allowed and the pattern of communication
used to enable the decomposition. A decomposition is created when the

2
doc/src/compute.txt
View File

@ -235,7 +235,7 @@ section of "this page"_Section_commands.html#cmd_5.
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
"ti"_compute_ti.html - thermodyanmic integration free energy values
"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
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk

2
doc/src/compute_angmom_chunk.txt
View File

@ -22,7 +22,7 @@ compute 1 fluid angmom/chunk molchunk :pre
[Description:]
Define a computation that calculates the angular momemtum of multiple
Define a computation that calculates the angular momentum of multiple
chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute

6
doc/src/compute_centro_atom.txt
View File

@ -18,8 +18,8 @@ lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l
zero or more keyword/value pairs may be appended :l
keyword = {axes} :l
{axes} value = {no} or {yes}
{no} = do not calulate 3 symmetry axes
{yes} = calulate 3 symmetry axes :pre
{no} = do not calculate 3 symmetry axes
{yes} = calculate 3 symmetry axes :pre
:ule
[Examples:]
@ -108,7 +108,7 @@ symmetry axis, followed by the second, and third symmetry axes in
columns 5-7 and 8-10.
The centrosymmetry values are unitless values >= 0.0. Their magnitude
depends on the lattice style due to the number of contibuting neighbor
depends on the lattice style due to the number of contributing neighbor
pairs in the summation in the formula above. And it depends on the
local defects surrounding the central atom, as described above. For
the {axes yes} case, the vector components are also unitless, since

6
doc/src/compute_chunk_atom.txt
View File

@ -386,7 +386,7 @@ If {compress yes} is set, and the {compress} keyword comes before the
{limit} keyword, the compression operation is performed first, as
described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
preceeding paragraph. Note that in this case, all atoms will end up
preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
compute/fix/variable value) may have been > {Nc}, because of the
compression operation.
@ -459,7 +459,7 @@ The original chunk IDs (before renumbering) can be accessed by the
which outputs the original IDs as one of the columns in its global
output array. For example, using the "compute cluster/atom" command
discussed above, the original 5 unique chunk IDs might be atom IDs
(27,4982,58374,857838,1000000). After compresion, these will be
(27,4982,58374,857838,1000000). After compression, these will be
renumbered to (1,2,3,4,5). The original values (27,...,1000000) can
be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command,
or by using the "fix ave/time"_fix_ave_time.html command in
@ -538,7 +538,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to
to the first or last bin in both the radial and axis dimensions. If
{discard} is set to {mixed}, which is the default, the radial
dimension is treated the same as for {discard} = no. But for the axis
dimensinon, it will only have its chunk ID set to the first or last
dimension, it will only have its chunk ID set to the first or last
bin if bins extend to the simulation box boundary in the axis
dimension. This is the case if the {bound} keyword settings are
{lower} and {upper}, which is the default. If the {bound} keyword

2
doc/src/compute_cna_atom.txt
View File

@ -42,7 +42,7 @@ performed on mono-component systems.
The CNA calculation can be sensitive to the specified cutoff value.
You should insure the appropriate nearest neighbors of an atom are
found within the cutoff distance for the presumed crystal strucure.
found within the cutoff distance for the presumed crystal structure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
obtain a good cutoff distance:

2
doc/src/compute_com.txt
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@ -25,7 +25,7 @@ Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.
A vector of three quantites is calculated by this compute, which
A vector of three quantities is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
NOTE: The coordinates of an atom contribute to the center-of-mass in

2
doc/src/compute_coord_atom.txt
View File

@ -70,7 +70,7 @@ The ID of the previously specified "compute
orientorder/atom"_compute_orientorder/atom command is specified as
{orientorderID}. The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
described in its documenation. Note that orientorder/atom compute
described in its documentation. Note that orientorder/atom compute
defines its own criteria for identifying neighboring atoms. If the
scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
orientorder/atom compute is larger than the specified {threshold},

2
doc/src/compute_damage_atom.txt
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@ -47,7 +47,7 @@ any command that uses per-atom values from a compute as input. See
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values are unitlesss numbers (damage) >= 0.0.
The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]

2
doc/src/compute_dilatation_atom.txt
View File

@ -50,7 +50,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
The per-atom vector values are unitlesss numbers (theta) >= 0.0.
The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]

2
doc/src/compute_displace_atom.txt
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@ -25,7 +25,7 @@ Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.
A vector of four quantites per atom is calculated by this compute.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).

4
doc/src/compute_event_displace.txt
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@ -14,7 +14,7 @@ compute ID group-ID event/displace threshold :pre
ID, group-ID are documented in "compute"_compute.html command
event/displace = style name of this compute command
threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul
threshold = minimum distance any particle must move to trigger an event (distance units) :ul
[Examples:]
@ -37,7 +37,7 @@ further than the threshold distance.
NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false postives."
local atom displacements and may generate "false positives."
[Output info:]

6
doc/src/compute_global_atom.txt
View File

@ -55,7 +55,7 @@ M is the actual length of the input vector, then an output value of
0.0 is assigned to the atom.
An example of how this command is useful, is in the context of
"chunks" which are static or dyanmic subsets of atoms. The "compute
"chunks" which are static or dynamic subsets of atoms. The "compute
chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
to each atom. It's output can be used as the {index} parameter for
this command. Various other computes with "chunk" in their style
@ -192,7 +192,7 @@ reference thermodynamic keywords and various other attributes of
atoms, or invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of generating a vector of
global quantities which the {index} parameter will reference for
assignement of global values to atoms.
assignment of global values to atoms.
:line
@ -207,7 +207,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector or array values will be in whatever units the
corresponsing input values are in.
corresponding input values are in.
[Restrictions:] none

4
doc/src/compute_heat_flux.txt
View File

@ -38,7 +38,7 @@ subtracted to a group of atoms.
The compute takes three arguments which are IDs of other
"computes"_compute.html. One calculates per-atom kinetic energy
({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
third calcualtes per-atom stress ({stress-ID}).
third calculates per-atom stress ({stress-ID}).
NOTE: These other computes should provide values for all the atoms in
the group this compute specifies. That means the other computes could
@ -83,7 +83,7 @@ The heat flux can be output every so many timesteps (e.g. via the
post-processing operation, an autocorrelation can be performed, its
integral estimated, and the Green-Kubo formula above evaluated.
The "fix ave/correlate"_fix_ave_correlate.html command can calclate
The "fix ave/correlate"_fix_ave_correlate.html command can calculate
the autocorrelation. The trap() function in the
"variable"_variable.html command can calculate the integral.

2
doc/src/compute_inertia_chunk.txt
View File

@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
defined and examples of how they can be used to measure properties of
a system.
This compute calculates the 6 components of the symmetric intertia
This compute calculates the 6 components of the symmetric inertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
calculation includes all effects due to atoms passing thru periodic
boundaries.

2
doc/src/compute_msd.txt
View File

@ -33,7 +33,7 @@ passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the "compute
msd/nongauss"_compute_msd_nongauss.html command.
A vector of four quantites is calculated by this compute. The first 3
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and

2
doc/src/compute_msd_chunk.txt
View File

@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
defined and examples of how they can be used to measure properties of
a system.
Four quantites are calculated by this compute for each chunk. The
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These

6
doc/src/compute_msd_nongauss.txt
View File

@ -30,12 +30,12 @@ Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.
A vector of three quantites is calculated by this compute. The first
A vector of three quantities is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
group. The 3rd component is the nonGaussian diffusion parameter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.
:c,image(Eqs/compute_msd_nongauss.jpg)
@ -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 calcluated.
displacment of each atom is calculated.
See the "compute msd"_compute_msd.html doc page for further important
NOTEs, which also apply to this compute.

4
doc/src/compute_pair.txt
View File

@ -43,7 +43,7 @@ style van der Waals interaction or not) is tallied in {evdwl}. If
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
specfied as {evdwl} or {ecoul}, then just that portion of the energy
specified as {evdwl} or {ecoul}, then just that portion of the energy
is stored as a global scalar.
NOTE: The energy returned by the {evdwl} keyword does not include tail
@ -52,7 +52,7 @@ corrections, even if they are enabled via the
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into a dozen or so components is tallied by the
"pair_style reax"_pair_reax.html commmand. These values (1 or more)
"pair_style reax"_pair_reax.html command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
"individual pair styles"_pair_style.html for info on these values.

2
doc/src/compute_pair_local.txt
View File

@ -47,7 +47,7 @@ force cutoff distance for that interaction, as defined by the
"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
commands.
The value {dist} is the distance bewteen the pair of atoms.
The value {dist} is the distance between the pair of atoms.
The value {eng} is the interaction energy for the pair of atoms.

2
doc/src/compute_pe_atom.txt
View File

@ -51,7 +51,7 @@ these terms is included in the pair energy, not the dihedral energy.
The KSpace contribution is calculated using the method in
"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
as specified by the "kspace_style pppm"_kspace_style.html command.
For PPPM, the calcluation requires 1 extra FFT each timestep that
For PPPM, the calculation requires 1 extra FFT each timestep that
per-atom energy is calculated. This "document"_PDF/kspace.pdf
describes how the long-range per-atom energy calculation is performed.

2
doc/src/compute_plasticity_atom.txt
View File

@ -44,7 +44,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]

2
doc/src/compute_pressure.txt
View File

@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias.
Also note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various "compute
is calculated by the temperature compute. See the various "compute
temperature"_compute.html styles for details.
A compute of this style with the ID of "thermo_press" is created when

2
doc/src/compute_property_chunk.txt
View File

@ -64,7 +64,7 @@ can only be used if the {compress} keyword was set to {yes} for the
"compute chunk/atom"_compute_chunk_atom.html command referenced by
chunkID. This means that the original chunk IDs (e.g. molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned
to them. Thus a compresed chunk ID of 3 may correspond to an original
to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The {id} attribute will
then be 415 for the 3rd chunk.

2
doc/src/compute_rdf.txt
View File

@ -73,7 +73,7 @@ post-process a dump file to calculate it. This is because using the
which may slow down your simulation. If you specify a {Rcut} <= force
cutoff, you will force an additional neighbor list to be built at
every timestep this command is invoked (or every reneighboring
timestep, whichever is less frequent), which is inefficent. LAMMPS
timestep, whichever is less frequent), which is inefficient. LAMMPS
will warn you if this is the case. If you specify a {Rcut} > force
cutoff, you must insure ghost atom information out to {Rcut} + {skin}
is communicated, via the "comm_modify cutoff"_comm_modify.html

2
doc/src/compute_rigid_local.txt
View File

@ -123,7 +123,7 @@ The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of
the COM velocity and force on the COM of the body.
The {omegax}, {omegay}, and {omegaz} attributes are the angular
velocity componennts of the body around its COM.
velocity components of the body around its COM.
The {angmomx}, {angmomy}, and {angmomz} attributes are the angular
momentum components of the body around its COM.

2
doc/src/compute_saed.txt
View File

@ -93,7 +93,7 @@ parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
example 3D intestiety data and the intersection of a \[010\] zone axis
example 3D intensity data and the intersection of a \[010\] zone axis
in the below image.
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)

2
doc/src/compute_smd_ulsph_num_neighs.txt
View File

@ -35,7 +35,7 @@ any command that uses per-particle values from a compute as input.
See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle values will be given dimentionless, see "units"_units.html.
The per-particle values will be given dimensionless, see "units"_units.html.
[Restrictions:]

2
doc/src/compute_stress_atom.txt
View File

@ -92,7 +92,7 @@ The KSpace contribution is calculated using the method in
"(Heyes)"_#Heyes for the Ewald method and by the methodology described
in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified
by the "kspace_style pppm"_kspace_style.html command. Note that for
PPPM, the calcluation requires 6 extra FFTs each timestep that
PPPM, the calculation requires 6 extra FFTs each timestep that
per-atom stress is calculated. Thus it can significantly increase the
cost of the PPPM calculation if it is needed on a large fraction of
the simulation timesteps.

2
doc/src/compute_temp_asphere.txt
View File

@ -138,7 +138,7 @@ This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This compute requires that atoms store angular momementum and a
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.

2
doc/src/compute_temp_body.txt
View File

@ -120,7 +120,7 @@ This compute is part of the BODY package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This compute requires that atoms store angular momementum and a
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.

6
doc/src/compute_temp_chunk.txt
View File

@ -44,7 +44,7 @@ compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre
Define a computation that calculates the temperature of a group of
atoms that are also in chunks, after optionally subtracting out the
center-of-mass velocity of each chunk. By specifying optional values,
it can also calulate the per-chunk temperature or energies of the
it can also calculate the per-chunk temperature or energies of the
multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute
@ -122,7 +122,7 @@ concept is somewhat ill-defined. In some cases, you can use the
{adof} and {cdof} keywords to adjust the calculated degress of freedom
appropriately, as explained below.
Note that the per-chunk temperature calulated by this compute and the
Note that the per-chunk temperature calculated by this compute and the
"fix ave/chunk temp"_fix_ave_chunk.html command can be different.
This compute calculates the temperature for each chunk for a single
snapshot. Fix ave/chunk can do that but can also time average those
@ -208,7 +208,7 @@ This compute also optionally calculates a global array, if one or more
of the optional values are specified. The number of rows in the array
= the number of chunks {Nchunk} as calculated by the specified
"compute chunk/atom"_compute_chunk_atom.html command. The number of
columns is the number of specifed values (1 or more). These values
columns is the number of specified values (1 or more). These values
can be accessed by any command that uses global array values from a
compute as input. Again, see "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output

2
doc/src/compute_temp_profile.txt
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@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
NOTE: When using the {out} keyword with a value of {bin}, the
calculated temperature for each bin does not include the
degrees-of-freedom adjustment described in the preceeding paragraph,
degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the {extra} option, which is applied to each bin.

2
doc/src/compute_vacf.txt
View File

@ -27,7 +27,7 @@ function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
A vector of four quantites is calculated by this compute. The first 3
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial

4
doc/src/compute_voronoi_atom.txt
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@ -217,6 +217,10 @@ This compute is part of the VORONOI package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
It also requiers you have a copy of the Voro++ library built and
installed on your system. See instructions on obtaining and
installing the Voro++ software in the src/VORONOI/README file.
[Related commands:]
"dump custom"_dump.html, "dump local"_dump.html

13
doc/src/create_atoms.txt
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@ -101,7 +101,7 @@ positions.
For the {random} style, N particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
speficied random number {seed}, resulting in the same set of particles
specified random number {seed}, resulting in the same set of particles
coordinates, independent of how many processors are being used in the
simulation. If the {region-ID} argument is specified as NULL, then
the created particles will be anywhere in the simulation box. If a
@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules
are being added. The "delete_atoms"_delete_atoms.html command can be
used to remove overlapping atoms or molecules.
NOTE: You cannot use any of the styles explained above to create atoms
that are outside the simulation box; they will just be ignored by
LAMMPS. This is true even if you are using shrink-wrapped box
boundaries, as specified by the "boundary"_boundary.html command.
However, you can first use the "change_box"_change_box.html command to
temporarily expand the box, then add atoms via create_atoms, then
finally use change_box command again if needed to re-shrink-wrap the
new atoms. See the "change_box"_change_box.html doc page for an
example of how to do this, using the create_atoms {single} style to
insert a new atom outside the current simulation box.
:line
Individual atoms are inserted by this command, unless the {mol}

2
doc/src/dihedral_hybrid.txt
View File

@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart files"_restart.html. Thus when restarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
[Related commands:]

4
doc/src/dump.txt
View File

@ -225,7 +225,7 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See "this
of xlo, etc, since they represent a bounding box. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
@ -545,7 +545,7 @@ that the coordinate values may be far outside the box bounds printed
with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using
{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding cooordinate increased or decreased by 1.0.
have the corresponding coordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix}, {iy}, {iz}
attributes. For periodic dimensions, they specify which image of the

4
doc/src/dump_custom_vtk.txt
View File

@ -211,7 +211,7 @@ charge.
There are several options for outputting atom coordinates. The {x},
{y}, {z} attributes are used to write atom coordinates "unscaled", in
the appropriate distance "units"_units.html (Angstroms, sigma, etc).
Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the
Additionally, you can use {xs}, {ys}, {zs} if you want to also save the
coordinates "scaled" to the box size, so that each value is 0.0 to
1.0. If the simulation box is triclinic (tilted), then all atom
coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you
@ -224,7 +224,7 @@ values may be far outside the box bounds printed with the snapshot.
Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
that the unwrapped coordinates are scaled by the box size. Atoms that
have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
coordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix}, {iy}, {iz}
attributes. For periodic dimensions, they specify which image of the

16
doc/src/dump_image.txt
View File

@ -99,7 +99,7 @@ included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
below. Other dump styles store snapshots of numerical data asociated
below. Other dump styles store snapshots of numerical data associated
with atoms in various formats, as discussed on the "dump"_dump.html
doc page.
@ -237,7 +237,7 @@ diameter, which can be used as the {diameter} setting.
:line
The various kewords listed above control how the image is rendered.
The various keywords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
@ -261,7 +261,7 @@ the input script defines, e.g. Angstroms.
The {bond} keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
(e.g. region, threshhold settings of the
(e.g. region, threshold settings of the
"dump_modify"_dump_modify.html command). By default, bonds are drawn
if they are defined in the input data file as read by the
"read_data"_read_data.html command. Using {none} for both the bond
@ -356,7 +356,7 @@ is used to define body particles with internal state
body style. If this keyword is not used, such particles will be drawn
as spheres, the same as if they were regular atoms.
The "body"_body.html doc page descibes the body styles LAMMPS
The "body"_body.html doc page describes the body styles LAMMPS
currently supports, and provides more details as to the kind of body
particles they represent and how they are drawn by this dump image
command. For all the body styles, individual atoms can be either a
@ -442,7 +442,7 @@ degrees.
The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
@ -476,8 +476,8 @@ smaller. {Zfactor} must be a value > 0.0.
The {persp} keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A {pfactor} value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A {pfactor}
of 0.0 means that parallel lines will meet at infinity (1.0/pfactor),
which is an orthographic rendering with no perspective. A {pfactor}
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
value > 1 will create a highly skewed image with a large amount of
perspective.
@ -638,7 +638,7 @@ pipe:: Input/output error :pre
which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
and 2 format streams) have video bandwith limits that can be crossed
and 2 format streams) have video bandwidth limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:

4
doc/src/dump_modify.txt
View File

@ -426,7 +426,7 @@ regions.
The {scale} keyword applies only to the dump {atom} style. A scale
value of {yes} means atom coords are written in normalized units from
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
0.0 to 1.0 in each box dimension. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of {no} means they are written in absolute distance units
(e.g. Angstroms or sigma).
@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values
which may be useful for the comparision operator. Boolean values can
which may be useful for the comparison operator. Boolean values can
be generated by variable formulas that use comparison or Boolean math
operators or special functions like gmask() and rmask() and grmask().
See the "variable"_variable.html command doc page for details.

8
doc/src/fix_ave_chunk.txt
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@ -67,7 +67,7 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
[NOTE:]
If you are trying to replace a deprectated fix ave/spatial command
If you are trying to replace a deprecated fix ave/spatial command
with the newer, more flexible fix ave/chunk and "compute
chunk/atom"_compute_chunk_atom.html commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
@ -189,7 +189,7 @@ chunk/atom"_compute_chunk_atom.html command must remain constant. If
the {ave} keyword is set to {running} or {window} then {Nchunk} must
remain constant for the duration of the simulation. This fix forces
the chunk/atom compute specified by chunkID to hold {Nchunk} constant
for the appropriate time windows, by not allowing it to re-calcualte
for the appropriate time windows, by not allowing it to re-calculate
{Nchunk}, which can also affect how it assigns chunk IDs to atoms.
More details are given on the "compute
chunk/atom"_compute_chunk_atom.html doc page.
@ -301,7 +301,7 @@ sample values" divided by {Nrepeat}. In other words it is an average
of an average.
If the {norm} setting is {none}, a similar computation as for the
{sample} seting is done, except the individual "average sample values"
{sample} setting is done, except the individual "average sample values"
are "summed sample values". A summed sample value is simply the chunk
value summed over atoms in the sample, without dividing by the number
of atoms in the sample. The output value for the chunk on the
@ -410,7 +410,7 @@ chunk/atom"_compute_chunk_atom.html command supports them. The OrigID
column is only used if the {compress} keyword was set to {yes} for the
"compute chunk/atom"_compute_chunk_atom.html command. This means that
the original chunk IDs (e.g. molecule IDs) will have been compressed
to remove chunk IDs with no atoms assigned to them. Thus a compresed
to remove chunk IDs with no atoms assigned to them. Thus a compressed
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
415. The OrigID column will list 415 for the 3rd chunk.

4
doc/src/fix_ave_correlate.txt
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@ -64,7 +64,7 @@ fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
[Description:]
Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
calculate time correlations between them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
@ -219,7 +219,7 @@ to {upper} then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
If {type} is set
to {lower} then each input value is correlated with every preceeding
to {lower} then each input value is correlated with every preceding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
If {type} is set to {auto/upper} then each input value is correlated

6
doc/src/fix_ave_time.txt
View File

@ -33,7 +33,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title
vector = all input values are global vectors or global arrays
{ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{start} args = Nstart
Nstart = start averaging on this timestep
@ -223,7 +223,7 @@ output as-is without further averaging.
If the {ave} setting is {running}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a
cummulative sense before being output. Each output value is thus the
cumulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the "unfix"_unfix.html
@ -320,7 +320,7 @@ input values are averaged and {mode} = vector. The global array has #
of rows = length of the input vectors and # of columns = number of
inputs.
If the fix prouduces a scalar or vector, then the scalar and each
If the fix produces a scalar or vector, then the scalar and each
element of the vector can be either "intensive" or "extensive",
depending on whether the values contributing to the scalar or vector
element are "intensive" or "extensive". If the fix produces an array,

18
doc/src/fix_balance.txt
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@ -15,12 +15,12 @@ fix ID group-ID balance Nfreq thresh style args keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
balance = style name of this fix command :l
Nfreq = perform dynamic load balancing every this many steps :l
thresh = imbalance threshhold that must be exceeded to perform a re-balance :l
thresh = imbalance threshold that must be exceeded to perform a re-balance :l
style = {shift} or {rcb} :l
shift args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshhold is reached
stopthresh = stop balancing when this imbalance threshold is reached
{rcb} args = none :pre
zero or more keyword/arg pairs may be appended :l
keyword = {weight} or {out} :l
@ -63,14 +63,14 @@ perform "static" balancing, before or between runs, see the
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
where the computational cost varies signficantly between different
where the computational cost varies significantly between different
atoms. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or
"hybrid pair style simulations"_pair_hybrid.html which combine
pair styles with different computational cost. In these cases, the
LAMMPS default of dividing the simulation box volume into a
regular-spaced grid of 3d bricks, with one equal-volume sub-domain
per procesor, may assign numbers of particles per processor in a
per processor, may assign numbers of particles per processor in a
way that the computational effort varies significantly. This can
lead to poor performance when the simulation is run in parallel.
@ -78,7 +78,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
which typically inducces a diffrent number of atoms assigned to each
which typically induces a different number of atoms assigned to each
processor.
NOTE: The weighting options listed above are documented with the
@ -216,7 +216,7 @@ for a single value, except that the bounds used for each bisectioning
take advantage of information from neighboring cuts if possible, as
well as counts of particles at the bounds on either side of each cuts,
which themselves were cuts in previous iterations. The latter is used
to infer a density of pariticles near each of the current cuts. At
to infer a density of particles near each of the current cuts. At
each iteration, the count of particles on either side of each plane is
tallied. If the counts do not match the target value for the plane,
the position of the cut is adjusted based on the local density. The
@ -239,7 +239,7 @@ assigned, particles migrate to their new owning processor as part of
the normal reneighboring procedure.
NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
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 based on the local density, as
described above, which should typically be 1/2 or more every
@ -249,7 +249,7 @@ typically be positioned to better than 1 part in 1000 accuracy
be accurate to better than 1 part in a million. Thus there is no need
to set {Niter} to a large value. This is especially true if you are
rebalancing often enough that each time you expect only an incremental
adjustement in the cutting planes is necessary. LAMMPS will check if
adjustment in the cutting planes is necessary. LAMMPS will check if
the threshold accuracy is reached (in a dimension) is less iterations
than {Niter} and exit early.
@ -275,7 +275,7 @@ at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the atoms in
box, splitting the box, the subset of processors, and the atoms in
the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the atoms
in that sub-box.

6
doc/src/fix_bond_break.txt
View File

@ -79,8 +79,8 @@ part of bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though one molecule
becomes two moleclues due to the broken bond, all atoms in both new
moleclues retain their original molecule IDs.
becomes two molecules due to the broken bond, all atoms in both new
molecules retain their original molecule IDs.
Computationally, each timestep this fix operates, it loops over all
the bonds in the system and computes distances between pairs of bonded
@ -122,7 +122,7 @@ by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds broken on the most recent breakage timestep
(2) cummulative # of bonds broken :ul
(2) cumulative # of bonds broken :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy

6
doc/src/fix_bond_create.txt
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@ -118,8 +118,8 @@ of new bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though two molecules
become one moleclue due to the created bond, all atoms in the new
moleclue retain their original molecule IDs.
become one molecule due to the created bond, all atoms in the new
molecule retain their original molecule IDs.
If the {atype} keyword is used and if an angle potential is defined
via the "angle_style"_angle_style.html command, then any new 3-body
@ -218,7 +218,7 @@ by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds created on the most recent creation timestep
(2) cummulative # of bonds created :ul
(2) cumulative # of bonds created :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy

10
doc/src/fix_bond_swap.txt
View File

@ -81,7 +81,7 @@ by this processor on this timestep.
The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the "read_data"_read_data.html comand.
in the data file, read by the "read_data"_read_data.html command.
Consider a system of 6-mer chains. You have 2 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve chain length. For a particular momoner there will
@ -124,7 +124,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
@ -151,8 +151,8 @@ the Boltzmann criterion.
This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The first component of the
vector is the cummulative number of swaps performed by all processors.
The second component of the vector is the cummulative number of swaps
vector is the cumulative number of swaps performed by all processors.
The second component of the vector is the cumulative number of swaps
attempted (whether accepted or rejected). Note that a swap "attempt"
only occurs when swap partners meeting the criteria described above
are found on a particular timestep. The vector values calculated by
@ -168,7 +168,7 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The setings of the "special_bond" command must be 0,1,1 in order to
The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
harmonic bonds. This means that pairwise interactions between bonded
atoms are turned off, but are turned on between atoms two or three

6
doc/src/fix_box_relax.txt
View File

@ -54,7 +54,7 @@ The external pressure tensor is specified using one or more of the
keywords. These keywords give you the ability to specify all 6
components of an external stress tensor, and to couple various of
these components together so that the dimensions they represent are
varied together during the mimimization.
varied together during the minimization.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
@ -103,7 +103,7 @@ far. In all cases, the particle positions at each iteration are
unaffected by the chosen value, except that all particles are
displaced by the same amount, different on each iteration.
NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz}
NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz}
can sometimes result in arbitrarily large values of the tilt factors,
i.e. a dramatically deformed simulation box. This typically indicates
that there is something badly wrong with how the simulation was
@ -122,7 +122,7 @@ well-defined minimization problem. This is because the objective
function being minimized changes if the box size/shape changes. In
practice this means the minimizer can get "stuck" before you have
reached the desired tolerance. The solution to this is to restart the
minmizer from the new adjusted box size/shape, since that creates a
minimizer from the new adjusted box size/shape, since that creates a
new objective function valid for the new box size/shape. Repeat as
necessary until the box size/shape has reached its new equilibrium.

2
doc/src/fix_cmap.txt
View File

@ -44,7 +44,7 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
dihedrals, etc. Specically it should have a line like this
dihedrals, etc. Specially it should have a line like this
in its header section:
N crossterms :pre

4
doc/src/fix_colvars.txt
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@ -59,7 +59,7 @@ always apply to the entire system and there can only be one instance
of the colvars fix at a time. The colvars fix will only communicate
the minimum information necessary and the colvars library supports
multiple, completely independent collective variables, so there is
no restriction to functionaliry by limiting the number of colvars fixes.
no restriction to functionality by limiting the number of colvars fixes.
The {input} keyword allows to specify a state file that would contain
the restart information required in order to continue a calculation from
@ -100,7 +100,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]

4
doc/src/fix_controller.txt
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@ -107,7 +107,7 @@ When choosing the values of the four constants, it is best to first
pick a value and sign for {alpha} that is consistent with the
magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp}
should then be tested over a large positive range keeping {Ki}={Kd}=0.
A good value for {Kp} will produce a fast reponse in {pvar}, without
A good value for {Kp} will produce a fast response in {pvar}, without
overshooting the {setpoint}. For many applications, proportional
feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
there is a substantial lag time in the response of {pvar} to a change
@ -175,7 +175,7 @@ equal-style versus internal-style variable interchangeably.
[Restart, fix_modify, output, run start/stop, minimize info:]
Currenlty, no information about this fix is written to "binary restart
Currently, no information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.

4
doc/src/fix_deform.txt
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@ -580,10 +580,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the "boundary"_boundary.html comamnd.
shrink-wrapped via the "boundary"_boundary.html command.
You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
xy) that is shrink-wrapped via the "boundary"_boundary.html command.
[Related commands:]

6
doc/src/fix_deposit.txt
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@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
deposit = style name of this fix command :l
N = # of atoms or molecules to insert :l
type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
M = insert a single atom or molecule every M steps :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
@ -140,7 +140,7 @@ the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are
{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
time a molecule is deposited, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
@ -192,7 +192,7 @@ LAMMPS prints a warning message.
NOTE: If you are inserting finite size particles or a molecule or
rigid body consisting of finite-size particles, then you should
typically set R larger than the distance at which any inserted
particle may overlap with either a previouly inserted particle or an
particle may overlap with either a previously inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.

2
doc/src/fix_eos_table.txt
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@ -17,7 +17,7 @@ eos/table = style name of this fix command
style = {linear} = method of interpolation
file = filename containing the tabulated equation of state
N = use N values in {linear} tables
keyword = name of table keyword correponding to table file :ul
keyword = name of table keyword corresponding to table file :ul
[Examples:]

2
doc/src/fix_eos_table_rx.txt
View File

@ -17,7 +17,7 @@ eos/table/rx = style name of this fix command
style = {linear} = method of interpolation
file1 = filename containing the tabulated equation of state
N = use N values in {linear} tables
keyword = name of table keyword correponding to table file
keyword = name of table keyword corresponding to table file
file2 = filename containing the heats of formation of each species (optional)
deltaHf = heat of formation for a single species in energy units (optional)
energyCorr = energy correction in energy units (optional)

6
doc/src/fix_evaporate.txt
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@ -31,9 +31,9 @@ fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
[Description:]
Remove M atoms from the simulation every N steps. This can be used,
for example, to model evaporation of solvent particles or moleclues
for example, to model evaporation of solvent particles or molecules
(i.e. drying) of a system. Every N steps, the number of atoms in the
fix group and within the specifed region are counted. M of these are
fix group and within the specified region are counted. M of these are
chosen at random and deleted. If there are less than M eligible
particles, then all of them are deleted.
@ -74,7 +74,7 @@ are relevant to this fix.
This fix computes a global scalar, which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative number of deleted atoms. The scalar value calculated by
cumulative number of deleted atoms. The scalar value calculated by
this fix is "intensive".
No parameter of this fix can be used with the {start/stop} keywords of

4
doc/src/fix_gle.txt
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@ -62,7 +62,7 @@ as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
optimal for a given application and the system of choice can be
obtained from "(GLE4MD)"_#GLE4MD.
Equilibrium sampling a temperature T is obtained by specifiying the
Equilibrium sampling a temperature T is obtained by specifying the
target value as the {Tstart} and {Tstop} arguments, so that the diffusion
matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
@ -116,7 +116,7 @@ output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
[Restrictions:]

2
doc/src/fix_gravity.txt
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@ -76,7 +76,7 @@ specified as an equal-style "variable"_variable.html. If the value is
a variable, it should be specified as v_name, where name is the
variable name. In this case, the variable will be evaluated each
timestep, and its value used to determine the quantity. You should
insure that the variable calculates a result in the approriate units,
insure that the variable calculates a result in the appropriate units,
e.g. force/mass or degrees.
Equal-style variables can specify formulas with various mathematical

54
doc/src/fix_halt.txt
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@ -15,15 +15,16 @@ fix ID group-ID halt N attribute operator avalue keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
halt = style name of this fix command :l
N = check halt condition every N steps :l
attribute = hstyle or v_name :l
hstyle = {bondmax}
attribute = {bondmax} or {tlimit} or v_name :l
bondmax = length of longest bond in the system
tlimit = elapsed CPU time
v_name = name of "equal-style variable"_variable.html :pre
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
avalue = numeric value to compare attribute to :l
string = text string to print with optional variable names :l
zero or more keyword/value pairs may be appended :l
keyword = {error} :l
{error} value = {hard} or {soft} or {continue} :pre
keyword = {error} or {message} :l
{error} value = {hard} or {soft} or {continue}
{message} value = {yes} or {no} :pre
:ule
[Examples:]
@ -40,14 +41,33 @@ specified by the "run"_run.html or "minimize"_minimize.html command.
The specified group-ID is ignored by this fix.
The specified {attribute} can be one of the {hstyle} options listed
above, or an "equal-style variable"_variable.html referenced as
{v_name}, where "name" is the name of a variable that has been defined
previously in the input script.
The specified {attribute} can be one of the options listed above,
namely {bondmax} or {tlimit}, or an "equal-style
variable"_variable.html referenced as {v_name}, where "name" is the
name of a variable that has been defined previously in the input
script.
The only {hstyle} option currently implemented is {bondmax}. This
will loop over all bonds in the system, compute their current
lengths, and set {attribute} to the longest bond distance.
The {bondmax} attribute will loop over all bonds in the system,
compute their current lengths, and set {attribute} to the longest bond
distance.
The {tlimit} attribute queries the elapsed CPU time (in seconds) since
the current run began, and sets {attribute} to that value. This is an
alternative way to limit the length of a simulation run, similar to
the "timer"_timer.html timeout command. There are two differences in
using this method versus the timer command option. The first is that
the clock starts at the beginning of the current run (not when the
timer or fix command is specified), so that any setup time for the run
is not included in the elapsed time. The second is that the timer
invocation and syncing across all processors (via MPI_Allreduce) is
not performed once every {N} steps by this command. Instead it is
performed (typically) only a small number of times and the elapsed
times are used to predict when the end-of-the-run will be. Both of
these attributes can be useful when performing benchmark calculations
for a desired length of time with minmimal overhead. For example, if
a run is performing 1000s of timesteps/sec, the overhead for syncing
the timer frequently across a large number of processors may be
non-negligble.
Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate
@ -100,6 +120,14 @@ Note that you may wish use the "unfix"_unfix.html command on the fix
halt ID, so that the same condition is not immediately triggered in a
subsequent run.
The optional {message} keyword determines whether a message is printed
to the screen and logfile when the half condition is triggered. If
{message} is set to yes, a one line message with the values that
triggered the halt is printed. If {message} is set to no, no message
is printed; the run simply exits. The latter may be desirable for
post-processing tools that extract thermodyanmic information from log
files.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
@ -118,4 +146,4 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Default:]
The option defaults are error = hard.
The option defaults are error = hard and message = yes.

4
doc/src/fix_indent.txt
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@ -107,7 +107,7 @@ fashion. For the latter, see the {start} and {stop} keywords of the
"run"_run.html command and the {elaplong} keyword of "thermo_style
custom"_thermo_style.html for details.
For example, if a spherical indenter's x-position is specfied as v_x,
For example, if a spherical indenter's x-position is specified as v_x,
then this variable definition will keep it's center at a relative
position in the simulation box, 1/4 of the way from the left edge to
the right edge, even if the box size changes:
@ -121,7 +121,7 @@ variable x equal "2.5 + 5*elaplong*dt"
variable x equal vdisplace(2.5,5) :pre
If a spherical indenter's radius is specified as v_r, then these
variable definitions will grow the size of the indenter at a specfied
variable definitions will grow the size of the indenter at a specified
rate.
variable r0 equal 0.0

2
doc/src/fix_langevin.txt
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@ -307,7 +307,7 @@ setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.

2
doc/src/fix_langevin_eff.txt
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@ -80,7 +80,7 @@ setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
cumulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.

2
doc/src/fix_lb_fluid.txt
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@ -328,7 +328,7 @@ fix must be used in conjunction with the
"lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is
set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or
one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or
"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specifiy
"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify
their own value for the force coupling constant.
[Related commands:]

2
doc/src/fix_modify.txt
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@ -53,7 +53,7 @@ default method for computing P.
For fixes that calculate a contribution to the potential energy of the
system, the {energy} keyword will include that contribution in
thermodynamic output of potential energy. This is because the {energy
yes} setting must be specfied to include the fix's global or per-atom
yes} setting must be specified to include the fix's global or per-atom
energy in the calculation performed by the "compute
pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
commands. See the "thermo_style"_thermo_style.html command for info

4
doc/src/fix_move.txt
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@ -58,7 +58,7 @@ nve"_fix_nve.html command). It is up to you to decide whether
periodic boundaries are appropriate with the kind of atom motion you
are prescribing with this fix.
NOTE: As dicsussed below, atoms are moved relative to their initial
NOTE: As discussed below, atoms are moved relative to their initial
position at the time the fix is specified. These initial coordinates
are stored by the fix in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
@ -131,7 +131,7 @@ This style also sets the velocity of each atom to (omega cross Rperp)
where omega is its angular velocity around the rotation axis and Rperp
is a perpendicular vector from the rotation axis to the atom. If the
defined "atom_style"_atom_style.html assigns an angular velocity or
angular moementum or orientation to each atom ("atom
angular momentum or orientation to each atom ("atom
styles"_atom_style.html sphere, ellipsoid, line, tri, body), then
those properties are also updated appropriately to correspond to the
atom's motion and rotation over time.

4
doc/src/fix_mscg.txt
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@ -83,7 +83,7 @@ produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges.
The force matching functionality (step 5) outputs tabulated force
files for every interaction in the system. Other diagnostic files can
also be output depending on the paramters in the MS-CG library input
also be output depending on the parameters in the MS-CG library input
script. Again, see the documentation provided with the MS-CG library
for more info.
@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
dependencies, which are describd in its documentation.
dependencies, which are described in its documentation.
Currently, the MS-CG library is not setup to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run

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