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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
\end{eqnarray*}
\end{document}

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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="20 Apr 2018 version">
<META NAME="docnumber" CONTENT="11 May 2018 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>
@ -19,7 +19,7 @@
:line
LAMMPS Documentation :c,h1
20 Apr 2018 version :c,h2
11 May 2018 version :c,h2
Version info: :h3

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@ -684,6 +684,7 @@ package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
"bond/react"_fix_bond_react.html,
"colvars"_fix_colvars.html,
"dpd/energy (k)"_fix_dpd_energy.html,
"drude"_fix_drude.html,
@ -1211,7 +1212,8 @@ package"_Section_start.html#start_3.
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html :tb(c=4,ea=c)
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line

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doc/src/Section_packages.txt
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@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
:line
USER-BOCS package :link(USER-BOCS),h4
[Contents:]
This package provides "fix bocs"_fix_bocs.html, a modified version
of "fix npt"_fix_nh.html which includes the pressure correction to
the barostat as outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
[Install or un-install:]
make yes-user-bocs
make machine :pre
make no-user-bocs
make machine :pre
[Supporting info:]
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
See the following reference for information about the entire package:
Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
Example inputs are in the examples/USER/bocs folder.
:line
USER-CGDNA package :link(USER-CGDNA),h4
[Contents:]

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@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
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.
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich2)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

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@ -10,19 +10,29 @@ compute ackland/atom command :h3
[Syntax:]
compute ID group-ID ackland/atom :pre
compute ID group-ID ackland/atom keyword/value :pre
ID, group-ID are documented in "compute"_compute.html command
ackland/atom = style name of this compute command :ul
ID, group-ID are documented in "compute"_compute.html command :ulb,l
ackland/atom = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {legacy} :l
{legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
:ule
[Examples:]
compute 1 all ackland/atom :pre
compute 1 all ackland/atom
compute 1 all ackland/atom legacy yes :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to the formulation given in "(Ackland)"_#Ackland.
Historically, LAMMPS had two, slightly different implementations of
the algorithm from the paper. With the {legacy} keyword, it is
possible to switch between the pre-2015 ({legacy yes}) and post-2015
implemention ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
@ -66,7 +76,8 @@ integers defined above.
"compute centro/atom"_compute_centro_atom.html
[Default:] none
[Default:]
The keyword {legacy} defaults to {no}.
:line

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@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
displace/atom = style name of this compute command :l
zero or more keyword/arg pairs may be appended :l
keyword = {refresh} :
keyword = {refresh} :l
{replace} arg = name of per-atom variable :pre
:ule

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@ -161,9 +161,9 @@ function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
the calculated bispectrum components. This optional keyword is only
available for compute {sna/atom}, as {snad/atom} and {snav/atom}
are unaffected by the removal of constant terms.
the calculated bispectrum components. This optional keyword
normally only affects compute {sna/atom}. However, when
{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.
The keyword {quadraticflag} determines whether or not the
quadratic analogs to the bispectrum quantities are generated.
@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
If the {quadratic} keyword value is set to 1, then additional
columns are appended to each per-atom array, corresponding to
columns are generated, corresponding to
the products of all distinct pairs of bispectrum components. If the
number of bispectrum components is {K}, then the number of distinct pairs
is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same
ordering of sub-blocks as was used for the bispectrum
components. Within each sub-block, the ordering is upper-triangular,
(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
is {K}({K}+1)/2.
For compute {sna/atom} these columns are appended to existing {K} columns.
The ordering of quadratic terms is upper-triangular,
(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}).
For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2
additional columns is inserted directly after each of sub-block
of linear terms i.e. linear and quadratic terms are contiguous.
So the nesting order from inside to outside is bispectrum component,
linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
from a compute as input. See "Section

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style table/cut command :h3
[Syntax:]
dihedral_style table/cut style Ntable :pre
style = {linear} or {spline} = method of interpolation
Ntable = size of the internal lookup table :ul
[Examples:]
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre
[Description:]
The {table/cut} dihedral style creates interpolation tables of length
{Ntable} from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". In addition, an
analytic cutoff that is quadratic in the bond-angle (theta) is applied
in order to regularize the dihedral interaction. The dihedral table
files are read by the "dihedral_coeff"_dihedral_coeff.html command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
{Ntable} dihedral angles. During a simulation, these tables are used
to interpolate energy and force values on individual atoms as
needed. The interpolation is done in one of 2 styles: {linear} or
{spline}.
For the {linear} style, the dihedral angle (phi) is used to find 2
surrounding table values from which an energy or its derivative is
computed by linear interpolation.
For the {spline} style, cubic spline coefficients are computed and
stored at each of the {Ntable} evenly-spaced values in the
interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the "dihedral_coeff"_dihedral_coeff.html command as in the example
above.
style (aat)
cutoff prefactor
cutoff angle1
cutoff angle2
filename
keyword :ul
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
:c,image(Eqs/dihedral_table_cut.jpg)
The cutoff specifies an prefactor to the cutoff function. While this value
would ordinarily equal 1 there may be situations where the value should change.
The cutoff angle1 specifies the angle (in degrees) below which the dihedral
interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between angle1 and angle2, which is the angle at
which the cutoff function drops to zero. The value of zero effectively "turns
off" the dihedral interaction.
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
:line
The format of a tabulated file is as follows (without the
parenthesized comments). It can begin with one or more comment
or blank lines.
# Table of the potential and its negative derivative :pre
DIH_TABLE1 (keyword is the first text on line)
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
(blank line)
1 -168.0 -1.40351172223 0.0423346818422
2 -156.0 -1.70447981034 0.00811786522531
3 -144.0 -1.62956100432 -0.0184129719987
...
30 180.0 -0.707106781187 0.0719306095245 :pre
# Example 2: table of the potential. Forces omitted :pre
DIH_TABLE2
N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
1 -168.0 -1.40351172223
2 -156.0 -1.70447981034
3 -144.0 -1.62956100432
...
30 180.0 -0.707106781187 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in
any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value, the 3rd value is the energy (in energy units), and
the 4th is -dE/d(phi) also in energy units). The 3rd term is the
energy of the 4-atom configuration for the specified angle. The 4th
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
are still energy, not force. The dihedral angle values must increase
from one line to the next.
Dihedral table splines are cyclic. There is no discontinuity at 180
degrees (or at any other angle). Although in the examples above, the
angles range from -180 to 180 degrees, in general, the first angle in
the list can have any value (positive, zero, or negative). However
the {range} of angles represented in the table must be {strictly} less
than 360 degrees (2pi radians) to avoid angle overlap. (You may not
supply entries in the table for both 180 and -180, for example.) If
the user's table covers only a narrow range of dihedral angles,
strange numerical behavior can occur in the large remaining gap.
[Parameters:]
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the N
specified in the "dihedral_style table"_dihedral_style.html command.
Let {Ntable} is the number of table entries requested dihedral_style
command, and let {Nfile} be the parameter following "N" in the
tabulated file ("30" in the sparse example above). What LAMMPS does
is a preliminary interpolation by creating splines using the {Nfile}
tabulated values as nodal points. It uses these to interpolate as
needed to generate energy and derivative values at {Ntable} different
points (which are evenly spaced over a 360 degree range, even if the
angles in the file are not). The resulting tables of length {Ntable}
are then used as described above, when computing energy and force for
individual dihedral angles and their atoms. This means that if you
want the interpolation tables of length {Ntable} to match exactly what
is in the tabulated file (with effectively nopreliminary
interpolation), you should set {Ntable} = {Nfile}. To insure the
nodal points in the user's file are aligned with the interpolated
table entries, the angles in the table should be integer multiples of
360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the 4th column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the 3rd column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the 4th column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the the {Ntable} different entries in the
interpolated energy table to a file to make sure that the interpolated
function agrees with the user's expectations. (Note: You can
temporarily increase the {Ntable} parameter to a high value for this
purpose. "{Ntable}" is explained above.)
The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
It is followed by a filename, and it allows the user to check the
interpolated force table. This option is available even if the user
selected the "NOF" option.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html
[Default:] none
:link(dihedralcut-Salerno)
[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

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@ -19,6 +19,7 @@ Dihedral Styles :h1
dihedral_quadratic
dihedral_spherical
dihedral_table
dihedral_table_cut
dihedral_zero
dihedral_charmm
dihedral_class2

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doc/src/dump_modify.txt
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@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
these keywords apply to various dump styles :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
{image} arg = {yes} or {no}
{label} arg = string
string = character string (e.g. BONDS) to use in header of dump local file
{maxfiles} arg = Fmax
Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
{nfile} arg = Nf
Nf = write this many files, one from each of Nf processors
{pad} arg = Nchar = # of characters to convert timestep to
@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
:line
The {maxfiles} keyword can only be used when a '*' wildcard is
included in the dump file name, i.e. when writing a new file(s) for
each snapshot. The specified {Fmax} is how many snapshots will be
kept. Once this number is reached, the file(s) containing the oldest
snapshot is deleted before a new dump file is written. If the
specified {Fmax} <= 0, then all files are retained.
This can be useful for debugging, especially if you don't know on what
timestep something bad will happen, e.g. when LAMMPS will exit with an
error. You can dump every timestep, and limit the number of dump
files produced, even if you run for 1000s of steps.
:line
The {nfile} or {fileper} keywords can be used in conjunction with the
"%" wildcard character in the specified dump file name, for all dump
styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@ -901,6 +917,7 @@ flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
maxifiles = -1
nfile = 1
pad = 0
pbc = no

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@ -0,0 +1,112 @@
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bocs command :h3
[Syntax:]
fix ID group-ID bocs keyword values ... :pre
keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
{temp} values = Tstart Tstop Tdamp
{cgiso} values = Pstart Pstop Pdamp
{basis set}
{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
{linear_spline} values = input_filename
{cubic_spline} values = input_filename :pre
:ule
[Examples:]
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
thermo_modify press 1_press :pre
[Description:]
These commands incorporate a pressure correction as described by
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
The first half of the command mimics a standard fix npt command:
fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
The two differences are replacing {npt} with {bocs}, and replacing
{iso}/{aniso}/{etc} with {cgiso}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:
Volume_i, PressureCorrection_i :pre
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
With the {analytic} option, the arguments are as follows:
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.
[Restrictions:]
As this is computing a (modified) pressure, group-ID should be {all}.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
By default, LAMMPS will still report the normal value for the pressure
if the pressure is printed via a {thermo} command, or if the pressures
are written to a file every so often. In order to have LAMMPS report the
modified pressure, you must include the {thermo_modify} command given in
the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
This fix is part of the USER-BOCS 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.
[Related:]
For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on github"_bocsgithub and read the release
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
:link(bocsgithub,https://github.com/noid-group/BOCS)
:line
:link(bocs-Dunn1)
[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
:link(bocs-Martyna)
[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
:link(bocs-Dunn2)
[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).

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@ -0,0 +1,332 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bond/react command :h3
[Syntax:]
fix ID group-ID bond/react common_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
... :pre
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
bond/react = style name of this fix command :l
zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
these apply to all reaction specifications (below) :l
common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization
{yes} = perform reaction site stabilization
{group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
{xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
react = mandatory argument indicating new reaction specification :l
react-ID = user-assigned name for the reaction :l
react-group-ID = only atoms in this group are available for the reaction :l
Nevery = attempt reaction every this many steps :l
Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l
individual_keyword = {prob} or {stabilize_steps} :l
{prob} values = fraction seed
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
{stabilize_steps} value = timesteps
timesteps = number of timesteps to apply internally created nve/limit.html :pre
:ule
[Examples:]
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
molecule mol1 pre_reacted_rxn1.txt
molecule mol2 post_reacted_rxn1.txt
molecule mol3 pre_reacted_rxn2.txt
molecule mol4 post_reacted_rxn2.txt
fix 5 all bond/react stabilization yes nvt_grp .03 &
react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
[Description:]
Initiate complex covalent bonding (topology) changes. These topology
changes will be referred to as 'reactions' throughout this
documentation. Topology changes are defined in pre- and post-reaction
molecule templates and can include creation and deletion of bonds,
angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
atom-types, or atomic charges.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
determine bonding changes a priori. Rather, it uses a distance-based
probabilistic criteria to effect predetermined topology changes in
simulations using standard force fields.
This fix was created to facilitate the dynamic creation of polymeric,
amorphous or highly-crosslinked systems. A suggested workflow for
using this fix is: 1) identify a reaction to be simulated 2) build a
molecule template of the reaction site before the reaction has
occurred 3) build a molecule template of the reaction site after the
reaction has occurred 4) create a map that relates the
template-atom-IDs of each atom between pre- and post-reaction molecule
templates 5) fill a simulation box with molecules and run a simulation
with fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple {react}
arguments to a single 'fix bond/react' command. This syntax is
necessary because the 'common keywords' are applied to all reactions.
The {stabilization} keyword enables reaction site stabilization.
Reaction site stabilization is performed by including reacting atoms
in an internally created fix "nve/limit"_fix_nve_limit.html time
integrator for a set number of timesteps given by the
{stabilize_steps} keyword. While reacting atoms are being time
integrated by the internal nve/limit, they are prevented from being
involved in any new reactions. The {xmax} value keyword should
typically be set to the maximum distance that non-reacting atoms move
during the simulation.
The group-ID set using the {stabilization} keyword should be a
previously unused group-ID. It cannot be specified as 'all'. The fix
bond/react command creates a "dynamic group"_group.html of this name
that includes all non-reacting atoms. This dynamic group-ID should
then be used by a subsequent system-wide time integrator such as nvt,
npt, or nve, as shown in the second example above. It is currently
necessary to place the time integration command after the fix
bond/react command due to the internal dynamic grouping performed by
fix bond/react.
NOTE: The internally created group currently applies to all atoms in
the system, i.e. you should generally not have a separate thermostat
which acts on the 'all' group.
The following comments pertain to each {react} argument:
A check for possible new reaction sites is performed every {Nevery}
timesteps.
Two conditions must be met for a reaction to occur. First a bonding
atom pair must be identified. Second, the topology surrounding the
bonding atom pair must match the topology of the pre-reaction
template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms within the specified react-group-ID of type
typei and typej must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
chosen. Then, if both an atomi and atomj have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
reactions that involve a given atom on the same timestep. If this is
the case, only one such reaction is permitted to occur. This reaction
is chosen randomly from all potential reactions. This capability
allows e.g. for different reaction pathways to proceed from identical
reaction sites with user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
surrounding topology. As described below, the bonding atom pairs of
the pre-reacted template are specified by atom ID in the map file. The
pre-reacted molecule template should contain as few atoms as possible
while still completely describing the topology of all atoms affected
by the reaction. For example, if the force field contains dihedrals,
the pre-reacted template should contain any atom within three bonds of
reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the
rest of a long polymer chain. These are referred to as edge atoms, and
are also specified in the map file.
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template
must be the same as those of a potential reaction site in the
simulation. A detailed discussion of matching molecule template atom
types with the simulation is provided on the "molecule"_molecule.html
command page.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It
must contain the same number of atoms as the pre-reacted template. A
one-to-one correspondence between the atom IDs in the pre- and
post-reacted templates is specified in the map file as described
below. Note that during a reaction, an atom, bond, etc. type may
change to one that was previously not present in the simulation. These
new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
"molecule"_molecule.html command page.
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and one optional keyword. The mandatory
keyword is 'equivalences' and the optional keyword is 'edgeIDs':
N {equivalences} = # of atoms N in the reaction molecule templates
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
The body of the map file contains two mandatory sections and one
optional section. The first mandatory section begins with the keyword
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
pre-reacted molecule template. The second mandatory section begins
with the keyword 'Equivalences' and lists a one-to-one correspondence
between atom IDs of the pre- and post-reacted templates. The first
column is an atom ID of the pre-reacted molecule template, and the
second column is the corresponding atom ID of the post-reacted
molecule template. The optional section begins with the keyword
'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
molecule template.
A sample map file is given below:
:line
# this is a map file :pre
2 edgeIDs
7 equivalences :pre
BondingIDs :pre
3
5 :pre
EdgeIDs :pre
1
7 :pre
Equivalences :pre
1 1
2 2
3 3
4 4
5 5
6 6
7 7 :pre
:line
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
angles, dihedrals or impropers are supported.
A few capabilities to note: 1) You may specify as many {react}
arguments as desired. For example, you could break down a complicated
reaction mechanism into several reaction steps, each defined by its
own {react} argument. 2) While typically a bond is formed or removed
between the bonding atom pairs specified in the pre-reacted molecule
template, this is not required. 3) By reversing the order of the pre-
and post- reacted molecule templates in another {react} argument, you
can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
it occurs.
The {prob} keyword can affect whether an eligible reaction actually
occurs. The fraction setting must be a value between 0.0 and 1.0. A
uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction.
The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
overall system thermostat.
In order to produce the most physical behavior, this 'reaction site
equilibration time' should be tuned to be as small as possible while
retaining stability for a given system or reaction step. After a
limited number of case studies, this number has been set to a default
of 60 timesteps. Ideally, it should be individually tuned for each fix
reaction step. Note that in some situations, decreasing rather than
increasing this parameter will result in an increase in stability.
A few other considerations:
It may be beneficial to ensure reacting atoms are at a certain
temperature before being released to the overall thermostat. For this,
you can use the internally-created dynamic group named
"bond_react_MASTER_group." For example, adding the following command
would thermostat the group of all atoms currently involved in a
reaction:
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
NOTE: This command must be added after the fix bond/react command, and
will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
neighbor lists (for bond-forming reactions) and computes distances
between pairs of atoms in the list. It also communicates between
neighboring processors to coordinate which bonds are created and/or
removed. All of these operations increase the cost of a timestep. Thus
you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the dump
local command.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html, aside from internally-created per-atom
properties. None of the "fix_modify"_fix_modify.html options are
relevant to this fix.
This fix computes one statistic for each {react} argument that it
stores in a global vector, of length 'number of react arguments', that
can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated by
this fix are "intensive".
These is 1 quantity for each react argument:
(1) cumulative # of reactions occurred :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
minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC 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.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix
bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
"dump local"_dump.html, "special_bonds"_special_bonds.html
[Default:]
The option defaults are stabilization = no, stabilize_steps = 60
:line
:link(Gissinger)
[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).

2
doc/src/fix_langevin_drude.txt
View File

@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the
self-consistent minimization. It must however be high enough, so that
the dipoles can follow the local electric field exerted by the
neighbouring atoms. The optimal value probably depends on the
neighboring atoms. The optimal value probably depends on the
temperature of the centers of mass and on the mass of the Drude
particles.

36
doc/src/fix_modify.txt
View File

@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre
fix-ID = ID of the fix to modify :ulb,l
one or more keyword/value pairs may be appended :l
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{energy} value = {yes} or {no}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
{bodyforces} value = {early} or {late}
early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
[Examples:]
@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the
relaxation criteria, although this seems unlikely.
NOTE: This option is only supported by fixes that explicitly say
so. For some of these (e.g. the
"fix shake"_fix_shake.html command) the default setting is
{virial yes}, for others it is {virial no}.
so. For some of these (e.g. the "fix shake"_fix_shake.html command)
the default setting is {virial yes}, for others it is {virial no}.
For fixes that set or modify forces, it may be possible to select at
which "r-RESPA"_run_style.html level the fix operates via the {respa}
@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify
dynamic/dof"_compute_modify.html command for a similar way to insure
correct temperature normalization for those thermostats.
The {bodyforces} keyword determines whether the forces and torques
acting on rigid bodies are computed {early} at the post-force stage of
each timestep (right after per-atom forces have been computed and
communicated among processors), or {late} at the final-integrate stage
of each timestep (after any other fixes have finished their post-force
tasks). Only the rigid-body integration fixes use this option, which
includes "fix rigid"_fix_rigid.html and "fix
rigid/small"_fix_rigid.html, and their variants, and also "fix
poems"_fix_poems.html.
The default is {late}. If there are other fixes that add forces to
individual atoms, then the rigid-body constraints will include these
forces when time-integrating the rigid bodies. If {early} is
specified, then new fixes can be written that use or modify the
per-body force and torque, before time-integration of the rigid bodies
occurs. Note however this has the side effect, that fixes such as
"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
"fix spring"_fix_spring.html, which add forces to individual atoms
will have no effect on the motion of the rigid bodies if they are
specified in the input script after the fix rigid command. LAMMPS
will give a warning if that is the case.
[Restrictions:] none
[Related commands:]
@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
[Default:]
The option defaults are temp = ID defined by fix, press = ID defined
by fix, energy = no, virial = different for each fix style, respa = 0.
by fix, energy = no, virial = different for each fix style, respa = 0,
bodyforce = late.

18
doc/src/fix_poems.txt
View File

@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
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. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. 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 minimization"_minimize.html.
files"_restart.html.
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
this fix style to set whether per-body forces and torques are computed
early or late in a timestep, i.e. at the post-force stage or at the
final-integrate stage, respectively.
No global or per-atom quantities are stored by this fix for access by
various "output commands"_Section_howto.html#howto_15. 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
minimization"_minimize.html.
[Restrictions:]

2
doc/src/fix_reax_bonds.txt
View File

@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
The specified group-ID is ignored by this fix.
The format of the output file should be reasonably self-explanatory.
The meaning of the column header abbreviations is as follows:

29
doc/src/fix_restrain.txt
View File

@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi0 = equilibrium dihedral angle phi (degrees) :pre
phi0 = equilibrium dihedral angle phi (degrees)
keyword/value = optional keyword value pairs. supported keyword/value pairs:
{mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
:ule
[Examples:]
@ -155,11 +157,13 @@ associated with the restraint is
with the following coefficients:
K (energy)
n = 1
n (multiplicity, >= 0)
d (degrees) = phi0 + 180 :ul
K and phi0 are specified with the fix. Note that the value of n is
hard-wired to 1. Also note that the energy will be a minimum when the
K and phi0 are specified with the fix. Note that the value of the
dihedral multiplicity {n} is set by default to 1. You can use the
optional {mult} keyword to set it to a different positive integer.
Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.
:line
@ -183,10 +187,17 @@ added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for 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
potential energy for all the restraints as discussed above. The scalar
value calculated by this fix is "extensive".
This fix computes a global scalar and a global vector of length 3, which
can be accessed by various "output commands"_Section_howto.html#howto_15.
The scalar is the total potential energy for {all} the restraints as
discussed above. The vector values are the sum of contributions to the
following individual categories:
1 = bond energy
2 = angle energy
3 = dihedral energy :ul
The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.

13
doc/src/fix_rigid.txt
View File

@ -223,10 +223,10 @@ via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule} or {custom}, you can define a system that has
no rigid bodies initially. This is useful when you are using the {mol}
keyword in conjunction with another fix that is adding rigid bodies
on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
"fix pour"_fix_pour.html.
no rigid bodies initially. This is useful when you are using the
{mol} keyword in conjunction with another fix that is adding rigid
bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
or "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@ -742,6 +742,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2
NVT rigid fixes do not use any external compute to compute
instantaneous temperature.
The "fix_modify"_fix_modify.html {bodyforces} option is supported by
all rigid styles to set whether per-body forces and torques are
computed early or late in a timestep, i.e. at the post-force stage or
at the final-integrate stage or the timestep, respectively.
The 2 NVE rigid fixes compute a global scalar which can be accessed by
various "output commands"_Section_howto.html#howto_15. The scalar
value calculated by these fixes is "intensive". The scalar is the

2
doc/src/fixes.txt
View File

@ -20,9 +20,11 @@ Fixes :h1
fix_ave_time
fix_aveforce
fix_balance
fix_bocs
fix_bond_break
fix_bond_create
fix_bond_swap
fix_bond_react
fix_box_relax
fix_cmap
fix_colvars

3
doc/src/lammps.book
View File

@ -135,8 +135,10 @@ fix_ave_histo.html
fix_ave_time.html
fix_aveforce.html
fix_balance.html
fix_bocs.html
fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
fix_cmap.html
@ -580,6 +582,7 @@ dihedral_opls.html
dihedral_quadratic.html
dihedral_spherical.html
dihedral_table.html
dihedral_table_cut.html
dihedral_zero.html
lammps_commands_improper.html

2
doc/src/pair_kolmogorov_crespi_z.txt
View File

@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above.
This potential is intended for interactions between two layers of graphene.
Therefore, to avoid interaction between layers in multi-layered materials,
each layer should have a separate atom type and interactions should only
be computed between atom types of neighbouring layers.
be computed between atom types of neighboring layers.
The parameter file (e.g. CC.KC), is intended for use with metal
"units"_units.html, with energies in meV. An additional parameter, {S},

11
doc/src/pair_oxdna.txt
View File

@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
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.
Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich1)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc1)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

11
doc/src/pair_oxdna2.txt
View File

@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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/.
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.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc2)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).