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<H2>
LAMMPS</H2>
<P>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 2001 version, written in F90,
which has been superceded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>
LAMMPS is a classical molecular dynamics code designed for simulating
molecular and atomic systems on parallel computers using
spatial-decomposition techniques. It runs on any parallel platform that
supports F90 and the MPI message-passing library or on single-processor
workstations.</P>
<P>
LAMMPS 2001 is copyrighted code that is distributed freely as
open-source software under the GNU Public License (GPL). See the
LICENSE file or <A HREF="http://www.gnu.org">www.gnu.org</A> for more
details. Basically the GPL allows you as a user to use, modify, or
distribute LAMMPS however you wish, so long as any software you
distribute remains under the GPL.
<P>
Features of LAMMPS 2001 include:</P>
<UL>
<LI>
short-range pairwise Lennard-Jones and Coulombic interactions
<LI>
long-range Coulombic interactions via Ewald or PPPM (particle-mesh
Ewald)
<LI>
short-range harmonic bond potentials (bond, angle, torsion, improper)
<LI>
short-range class II (cross-term) molecular potentials
<LI>
NVE, NVT, NPT dynamics
<LI>
constraints on atoms or groups of atoms
<LI>
rRESPA long-timescale integrator
<LI>
energy minimizer (Hessian-free truncated Newton method)
</UL>
<P>
For users of LAMMPS 99, this version is written in F90 to take
advantage of dynamic memory allocation. This means the user does not
have to fiddle with parameter settings and re-compile the code so
often for different problems. This enhancment means there are new
rules for the ordering of commands in a LAMMPS input script, as well
as a few new commands to guide the memory allocator. Users should read
the beginning sections of the <A
HREF="input_commands.html">input_commands</A> file for an
explanation.</P>
<P>
More details about the code can be found <A
HREF="#_cch3_930958294">here</A>, in the HTML- or text-based
documentation. The LAMMPS Web page is at <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">www.cs.sandia.gov/~sjplimp/lammps.html</A>
, which includes benchmark timings and a list of papers written using
LAMMPS results. They illustrate the kinds of scientific problems that
can be modeled with LAMMPS. These two papers describe the parallel
algorithms used in the code. Please cite these if you incorporate
LAMMPS results in your work. And if you send me citations for your
papers, I'll be pleased to add them to the LAMMPS WWW page.
</P>
<P>
S. J. Plimpton, R. Pollock, M. Stevens, &quot;Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations&quot;, in Proc of
the Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN, March 1997.</P>
<P>
S. J. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J Comp Phys, 117, 1-19 (1995).</P>
<P>
LAMMPS was originally developed as part of a 5-way CRADA collaboration
between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and
Dupont) and 2 DoE laboratories (Sandia National Laboratories and
Lawrence Livermore National Laboratories).</P>
<P>
The primary author of LAMMPS is Steve Plimpton, but others have written
or worked on significant portions of the code:</P>
<UL>
<LI>
Roy Pollock (LLNL): Ewald, PPPM solvers
<LI>
Mark Stevens (Sandia): rRESPA, NPT integrators
<LI>
Eric Simon (Cray Research): class II force fields
<LI>
Todd Plantenga (Sandia): energy minimizer
<LI>
Steve Lustig (Dupont): msi2lmp tool
<LI>
Mike Peachey (Cray Research): msi2lmp tool
</UL>
<P>
Other CRADA partners involved in the design and testing of LAMMPS are </P>
<UL>
<LI>
John Carpenter (Cray Research)
<LI>
Terry Stouch (Bristol-Myers Squibb)
<LI>
Jim Belak (LLNL)
</UL>
<P>
If you have questions about LAMMPS, please contact me:
</P>
<DL>
<DT>
Steve Plimpton
<DD>
sjplimp@sandia.gov
<DD>
www.cs.sandia.gov/~sjplimp
<DD>
Sandia National Labs
<DD>
Albuquerque, NM 87185
</DL>
<HR>
<H3>
<A NAME="_cch3_930958294">More Information about LAMMPS</A></H3>
<DIR>
<LI>
<A HREF="basics.html">Basics</A>
<DIR>
<LI>
how to make, run, and test LAMMPS with the example problems
</DIR>
<LI>
<A HREF="input_commands.html">Input Commands</A>
<DIR>
<LI>
a complete listing of input commands used by LAMMPS
</DIR>
<LI>
<A HREF="data_format.html">Data Format</A>
<DIR>
<LI>
the data file format used by LAMMPS
</DIR>
<LI>
<A HREF="force_fields.html">Force Fields</A>
<DIR>
<LI>
the equations LAMMPS uses to compute force-fields
</DIR>
<LI>
<A HREF="units.html">Units</A>
<DIR>
<LI>
the input/output and internal units for LAMMPS variables
</DIR>
<LI>
<A HREF="history.html">History</A>
<DIR>
<LI>
a brief timeline of features added to LAMMPS
</DIR>
<LI>
<A HREF="deficiencies.html">Deficiencies</A>
<DIR>
<LI>
features LAMMPS does not (yet) have
</DIR>
</DIR>
</BODY>
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<H2>
Basics of Using LAMMPS</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<UL>
<LI>
<A HREF="#_cch3_931273040">Distribution</A>
<LI>
<A HREF="#_cch3_930327142">Making LAMMPS</A>
<LI>
<A HREF="#_cch3_930327155">Running LAMMPS</A>
<LI>
<A HREF="#_cch3_930759879">Examples</A>
<LI>
<A HREF="#_cch3_931282515">Other Tools</A>
<LI>
<A HREF="#_cch3_931282000">Extending LAMMPS</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_931273040">Distribution</A></H3>
<P>
When you unzip/untar the LAMMPS distribution you should have several
directories: </P>
<UL>
<LI>
src = source files for LAMMPS
<LI>
doc = HTML documentation
<LI>
examples = sample problems with inputs and outputs
<LI>
tools = serial program for creating and massaging LAMMPS data files
<LI>
converters = msi2lmp, lmp2arc, amber = codes & scripts for converting
between MSI/Discover, AMBER, and LAMMPS formats
</UL>
<HR>
<H3>
<A NAME="_cch3_930327142">Making LAMMPS</A></H3>
<P>
The src directory contains the F90 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
<P>
make machine</P>
<P>
from within the src directoy. E.g. "make sgi" or "make t3e". This
should create an executable such as lmp_sgi or lmp_t3e. For optimal
performance you'll want to use a good F90 compiler to make LAMMPS; on
Linux boxes I've been told the Leahy F90 compiler is a good choice.
(If you don't have an F90 compiler, I can give you an older F77-based
version of LAMMPS 99, but you'll lose the dynamic memory and some
other new features in LAMMPS 2001.)</P>
<P>
In the src directory, there is one top-level Makefile and several
low-level machine-specific files named Makefile.xxx where xxx = the
machine name. If a low-level Makefile exists for your platform, you do
not need to edit the top-level Makefile. However you should check the
system-specific section of the low-level Makefile to insure the
various paths are correct for your environment. If a low-level
Makefile does not exist for your platform, you will need to add a
suitable target to the top-level Makefile. You will also need to
create a new low-level Makefile using one of the existing ones as a
template. If you wish to make LAMMPS for a single-processor
workstation that doesn't have an installed MPI library, you can
specify the "serial" target which uses a directory of MPI stubs to
link against - e.g. &quot;make serial&quot;. You will need to make the
stub library (type &quot;make&quot; in STUBS directory) for your
workstation before doing this.</P>
<P>
Note that the two-level Makefile system allows you to make LAMMPS for
multiple platforms. Each target creates its own object directory for
separate storage of its *.o files.</P>
<P>
There are a few compiler switches of interest which can be specified
in the low-level Makefiles. If you use a F90FLAGS switch of -DSYNC
then synchronization calls will be made before the timing routines in
integrate.f. This may slow down the code slightly, but will make the
individual timings reported at the end of a run more accurate. The
F90FLAGS setting of -DSENDRECV will use MPI_Sendrecv calls for data
exchange between processors instead of MPI_Irecv, MPI_Send,
MPI_Wait. Sendrecv is often slower, but on some platforms can be
faster, so it is worth trying, particularly if your communication
timings seem slow.</P>
<P>
The CCFLAGS setting in the low-level Makefiles requires a FFT setting,
for example -DFFT_SGI or -DFFT_T3E. This is for inclusion of the
appropriate machine-specific native 1-d FFT libraries on various
platforms. Currently, the supported machines and switches (used in
fft_3d.c) are FFT_SGI, FFT_DEC, FFT_INTEL, FFT_T3E, and FFT_FFTW. The
latter is a publicly available portable FFT library, <A
HREF="http://www.fftw.org">FFTW</A>, which you can install on any
machine. If none of these options is suitable for your machine, please
contact me, and we'll discuss how to add the capability to call your
machine's native FFT library. You can also use FFT_NONE if you have no
need to use the PPPM option in LAMMPS.</P>
<P>
For Linux and T3E compilation, there is a also a CCFLAGS setting for KLUDGE
needed (see Makefile.linux and Makefile.t3e). This is to enable F90 to
call C with appropriate underscores added to C function names.
<HR>
<H3>
<A NAME="_cch3_930327155">Running LAMMPS</A></H3>
<P>
LAMMPS is run by redirecting a text file (script) of input commands into it.</P>
<P>
lmp_sgi &lt; in.lj</P>
<P>
lmp_t3e &lt; in.lj</P>
<P>
The script file contains commands that specify the parameters for the
simulation as well as to read other necessary files such as a data file
that describes the initial atom positions, molecular topology, and
force-field parameters. The <A HREF="input_commands.html">input_commands</A>
page describes all the possible commands that can be used. The <A
HREF="data_format.html">data_format</A> page describes the format of
the data file. </P>
<P>
LAMMPS can be run on any number of processors, including a single
processor. In principle you should get identical answers on any number
of processors and on any machine. In practice, numerical round-off can
cause slight differences and eventual divergence of dynamical
trajectories. </P>
<P>
When LAMMPS runs, it estimates the array sizes it should allocate based
on the problem you are simulating and the number of processors you
are running on. If you run out of physical memory, you will get a F90
allocation error and the code should hang or crash. The only thing you
can do about this is run on more processors or run a smaller problem. If
you get an error message to the screen about &quot;boosting&quot;
something, it means LAMMPS under-estimated the size needed for one (or
more) data arrays. The &quot;extra memory&quot; command can be used in
the input script to augment these sizes at run time. A few arrays are
hard-wired to sizes that should be sufficient for most users. These are
specified with parameter settings in the global.f file. If you get a
message to &quot;boost&quot; one of these parameters you will have to
change it and re-compile LAMMPS.</P>
<P>
Some LAMMPS errors are detected at setup; others like neighbor list
overflow may not occur until the middle of a run. Except for F90
allocation errors which may cause the code to hang (with an error
message) since only one processor may incur the error, LAMMPS should
always print a message to the screen and exit gracefully when it
encounters a fatal error. If the code ever crashes or hangs without
spitting out an error message first, it's probably a bug, so let me
know about it. Of course this applies to algorithmic or parallelism
issues, not to physics mistakes, like specifying too big a timestep or
putting 2 atoms on top of each other! One exception is that different
MPI implementations handle buffering of messages differently. If the
code hangs without an error message, it may be that you need to
specify an MPI setting or two (usually via an environment variable) to
enable buffering or boost the sizes of messages that can be
buffered.</P>
<HR>
<H3>
<A NAME="_cch3_930759879">Examples</A></H3>
<P>
There are several directories of sample problems in the examples
directory. All of them use an input file (in.*) of commands and a data
file (data.*) of initial atomic coordinates and produce one or more
output files. Sample outputs on different machines and numbers of
processors are included to compare your answers to. See the README
file in the examples sub-directory for more information on what LAMMPS
features the examples illustrate.</P>
<P>
(1) lj = atomic simulations of Lennard-Jones systems.
<P>
(2) class2 = phenyalanine molecule using the DISCOVER cff95 class 2
force field.
<P>
(3) lc = liquid crystal molecules with various Coulombic options and
periodicity settings.
<P>
(4) flow = 2d flow of Lennard-Jones atoms in a channel using various
constraint options.
<P>
(5) polymer = bead-spring polymer models with one or two chain types.
</P>
<HR>
<H3>
<A NAME="_cch3_931282515">Other Tools</A></H3>
<P>
The converters directory has source code and scripts for tools that
perform input/output file conversions between MSI Discover, AMBER, and
LAMMPS formats. See the README files for the individual tools for
additional information.
<P>
The tools directory has several serial programs that create and
massage LAMMPS data files.
<P>
(1) setup_chain.f = create a data file of polymer bead-spring chains
<P>
(2) setup_lj.f = create a data file of an atomic LJ mixture of species
<P>
(3) setup_flow_2d.f = create a 2d data file of LJ particles with walls for
a flow simulation
<P>
(4) replicate.c = replicate or scale an existing data file into a new one
<P>
(5) peek_restart.f = print-out info from a binary LAMMPS restart file
<P>
(6) restart2data.f = convert a binary LAMMPS restart file into a text data file
<P>
See the comments at the top of each source file for information on how
to use the tool.
<HR>
<H3>
<A NAME="_cch3_931282000">Extending LAMMPS</A></H3>
<P>
User-written routines can be compiled and linked with LAMMPS, then
invoked with the "diagnostic" command as LAMMPS runs. These routines
can be used for on-the-fly diagnostics or a variety of other purposes.
The examples/lc directory shows an example of using the diagnostic
command with the in.lc.big.fixes input script. A sample diagnostic
routine is given there also: diagnostic_temp_molecules.f.
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<H2>
LAMMPS Data Format</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
<P>
This file describes the format of the data file read into LAMMPS with
the &quot;read data&quot; command. The data file contains basic
information about the size of the problem to be run, the initial atomic
coordinates, molecular topology, and (optionally) force-field
coefficients. It will be easiest to understand this file if you read it
while looking at a sample data file from the examples.</P>
<P>
This page has 2 sections:</P>
<UL>
<LI>
<A HREF="#_cch3_930958962">Rules for formatting the Data File</A>
<LI>
<A HREF="#_cch3_930958969">Sample file with Annotations</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
<P>
Blank lines are important. After the header section, new entries are
separated by blank lines. </P>
<P>
Indentation and space between words/numbers on one line is not
important except that keywords (e.g. Masses, Bond Coeffs) must be
left-justified and capitalized as shown. </P>
<P>
The header section (thru box bounds) must appear first in the file, the
remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come
in any order. </P>
<P>
These entries must be in the file: header section, Masses, Atoms. </P>
<P>
These entries must be in the file if there are a non-zero number of
them: Bonds, Angles, Dihedrals, Impropers. Force field coefficients
can be specified in the input script, so do not have to appear in the
data file. The one exception to this is class 2 force field
coefficients which can only be specified in the data file.
<P>
The Nonbond Coeffs entry contains one line for each atom type. These
are the coefficients for an interaction between 2 atoms of the same
type. The cross-type coeffs are computed by the appropriate class I or
class II mixing rules, or can be specified explicitly using the
&quot;nonbond coeff&quot; command in the input command script. See the <A
HREF="force_fields.html">force_fields</A> page for more information. </P>
<P>
In the Atoms entry, the atoms can be in any order so long as there are
N entries. The 1st number on the line is the atom-tag (number from 1 to
N) which is used to identify the atom throughout the simulation. The
molecule-tag is a second identifier which is attached to the atom; it
can be 0, or a counter for the molecule the atom is part of, or any
other number you wish. The q value is the charge of the atom in
electron units (e.g. +1 for a proton). The xyz values are the initial
position of the atom. For 2-d simulations specify z as 0.0.</P>
<P>
The final 3 nx,ny,nz values on a line of the Atoms entry are optional.
LAMMPS only reads them if the &quot;true flag&quot; command is
specified in the input command script. Otherwise they are initialized
to 0 by LAMMPS. Their meaning, for each dimension, is that
&quot;n&quot; box-lengths are added to xyz to get the atom's
&quot;true&quot; un-remapped position. This can be useful in pre- or
post-processing to enable the unwrapping of long-chained molecules
which wind thru the periodic box one or more times. The value of
&quot;n&quot; can be positive, negative, or zero. For 2-d simulations
specify nz as 0. </P>
<P>
Atom velocities are initialized to 0.0 if there is no Velocities entry.
In the Velocities entry, the atoms can be in any order so long as there
are N entries. The 1st number on the line is the atom-tag (number from
1 to N) which is used to identify the atom which the given velocity
will be assigned to.</P>
<P>
Entries for Velocities, Bonds, Angles, Dihedrals, Impropers must appear
in the file after an Atoms entry.</P>
<P>
For simulations with periodic boundary conditions, xyz coords are
remapped into the periodic box (from as far away as needed), so the
initial coordinates need not be inside the box. The nx,ny,nz values
(as read in or as set to zero by LAMMPS) are appropriately adjusted by
this remapping. </P>
<P>
The number of coefficients specified on each line of coefficient
entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
&quot;style&quot; of interaction. This must be specified in the input
command script before the "read data" command is issued, unless the
default is used. See the <A
HREF="input_commands.html">input_commands</A> page for a description
of the various style options. The <A HREF="input_commands.html">input_commands</A>
and <A HREF="force_fields.html">force_fields</A> pages explain the
meaning and valid values for each of the coefficients. </P>
<HR>
<H3>
<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
<P>
Here is a sample file with annotations in parenthesis and lengthy
sections replaced by dots (...). Note that the blank lines are
important in this example.</P>
<PRE>
LAMMPS Description (1st line of file)
100 atoms (this must be the 3rd line, 1st 2 lines are ignored)
95 bonds (# of bonds to be simulated)
50 angles (include these lines even if number = 0)
30 dihedrals
20 impropers
5 atom types (# of nonbond atom types)
10 bond types (# of bond types = sets of bond coefficients)
18 angle types
20 dihedral types (do not include a bond,angle,dihedral,improper type
2 improper types line if number of bonds,angles,etc is 0)
-0.5 0.5 xlo xhi (for periodic systems this is box size,
-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)
-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)
Masses
1 mass
...
N mass (N = # of atom types)
Nonbond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of atom types)
Bond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of bond types)
Angle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
Dihedral Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
Improper Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of improper types)
BondBond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
BondAngle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
MiddleBondTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
EndBondTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleAngleTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
BondBond13 Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleAngle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of improper types)
Atoms
1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -
... see &quot;true flag&quot; input command)
...
N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)
Velocities
1 vx vy vz
...
...
N vx vy vz (N = # of atoms)
Bonds
1 bond-type atom-1 atom-2
...
N bond-type atom-1 atom-2 (N = # of bonds)
Angles
1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)
...
N angle-type atom-1 atom-2 atom-3 (N = # of angles)
Dihedrals
1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)
...
N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)
Impropers
1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-2 is central atom)
...
N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)
</PRE>
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<H2>
LAMMPS Deficiencies</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<P>
This is a brief list of features lacking in the current version of
LAMMPS. Some of these deficiencies are because of lack of
time/interest; others are just hard!</P>
<UL>
<LI>
The calculation of pressure does not include a long-range Van der Waals
correction. This would be a constant for constant volume simulations
but is a source of error for constant pressure simulations where
the box-size varies dynamically.
<LI>
The smoothed Coulomb style cannot be used with class 2 force fields.
<LI>
The minimizer does not work with constant pressure conditions, nor
for some kinds of fixes (constraints).
<LI>
No support for non-rectilinear boxes (e.g. Parinello-Rahman
pressure control).
<LI>
SHAKE fixes cannot be combined with rREPSA.
<LI>
In the current F90 version of LAMMPS, Ewald computations are 2x slower
on some machines than they were in the earlier F77 version. This is
probably because of F90 compiler treatment of allocatable arrays. This
slowdown is not an issue with PPPM, which is more commonly used anyway.
<LI>
LAMMPS uses a spatial-decomposition of the simulation domain, but no
other load-balancing -- thus some geometries or density fluctuations can
lead to load imbalance on a parallel machine.
</UL>
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<H2>
LAMMPS Force Fields</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
<P>
This file outlines the force-field formulas used in LAMMPS. Read this
file in conjunction with the <A HREF="data_format.html">data_format</A>
and <A HREF="units.html">units</A> files.</P>
<P>
The sections of this page are as follows:</P>
<UL>
<LI>
<A HREF="#_cch3_930957465">Nonbond Coulomb</A>
<LI>
<A HREF="#_cch3_930957471">Nonbond Lennard-Jones</A>
<LI>
<A HREF="#_cch3_930957478">Mixing Rules for Lennard-Jones</A>
<LI>
<A HREF="#_cch3_930957482">Bonds</A>
<LI>
<A HREF="#_cch3_930957488">Angles</A>
<LI>
<A HREF="#_cch3_930957509">Dihedrals</A>
<LI>
<A HREF="#_cch3_930957513">Impropers</A>
<LI>
<A HREF="#_cch3_930957527">Class 2 Force Field</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_930957465">Nonbond Coulomb</A></H3>
<P>
Whatever Coulomb style is specified in the input command file, the
short-range Coulombic interactions are computed by this formula,
modified by an appropriate smoother for the smooth, Ewald, PPPM,
charmm, and debye styles.</P>
<PRE>
E = C q1 q2 / (epsilon * r)
r = distance (computed by LAMMPS)
C = hardwired constant to convert to energy units
q1,q2 = charge of each atom in electron units (proton = +1),
specified in &quot;Atoms&quot; entry in data file
epsilon = dielectric constant (vacuum = 1.0),
set by user in input command file
</PRE>
For the debye style, the smoother is exp(-kappa*r) where kappa is an
input parameter.
<HR>
<H3>
<A NAME="_cch3_930957471">Nonbond Lennard-Jones </A></H3>
<P>
The style of nonbond potential is specified in the input command file. </P>
<H4>
(1) lj/cutoff </H4>
<PRE>
E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]
standard Lennard Jones potential
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(2) lj/switch </H4>
<PRE>
E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ] for r &lt; r_inner
= spline fit for r_inner &lt; r &lt; cutoff
= 0 for r &gt; cutoff
switching function (spline fit) is applied to standard LJ
within a switching region (from r_inner to cutoff) so that
energy and force go smoothly to zero
spline coefficients are computed by LAMMPS
so that at inner cutoff (r_inner) the potential, force,
and 1st-derivative of force are all continuous,
and at outer cutoff (cutoff) the potential and force
both go to zero
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
2 cutoffs (r_inner and cutoff) are set in input script
</PRE>
<H4>
(3) lj/shift </H4>
<PRE>
E = 4 epsilon [ (sigma/(r - delta))^12 - (sigma/(r - delta))^6 ]
same as lj/cutoff except that r is shifted by delta
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
coeff3 = delta (distance)
3 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(4) soft </H4>
<PRE>
E = A * [ 1 + cos( pi * r / cutoff ) ]
useful for pushing apart overlapping atoms by ramping A over time
r = distance (computed by LAMMPS)
coeff1 = prefactor A at start of run (energy)
coeff2 = prefactor A at end of run (energy)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(5) class2/cutoff </H4>
<PRE>
E = epsilon [ 2 (sigma/r)^9 - 3 (sigma/r)^6 ]
used with class2 bonded force field
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
6) lj/charmm </H4>
<PRE>
E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ] for r &lt; r_inner
= switch * E for r_inner &lt; r &lt; cutoff
= 0 for r &gt; cutoff
where
switch = [(cutoff^2 - r^2)^2 * (cutoff^2 + 2*r^2 - 3*r_inner)] /
[(cutoff^2 - r_inner^2)^3]
switching function is applied to standard LJ
within a switching region (from r_inner to cutoff) so that
energy and force go smoothly to zero
switching function causes that at inner cutoff (r_inner)
the potential and force are continuous,
and at outer cutoff (cutoff) the potential and force
both go to zero
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
coeff3 = epsilon for 1-4 interactions (energy)
coeff4 = sigma for 1-4 interactions (distance)
4 coeffs are listed in data file or set in input script
2 cutoffs (r_inner and cutoff) are set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957478">Mixing Rules for Lennard-Jones</A></H3>
<P>
The coefficients for each nonbond style are input in either the data
file by the &quot;read data&quot; command or in the input script using
the &quot;nonbond coeff&quot; command. In the former case, only one set
of coefficients is input for each atom type. The cross-type coeffs are
computed using one of three possible mixing rules: </P>
<PRE>
geometric: epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = sqrt(sigma_i * sigma_j)
arithmetic: epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = (sigma_i + sigma_j) / 2
sixthpower: epsilon_ij =
(2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</PRE>
<P>
The default mixing rule for nonbond styles lj/cutoff, lj/switch,
lj/shift, and soft is &quot;geometric&quot;. The default for nonbond
style class2/cutoff is &quot;sixthpower&quot;. </P>
<P>
The default can be overridden using the &quot;mixing style&quot;
command. Two exceptions to this are for the nonbond style soft, for
which only an epsilon prefactor is input. This is always mixed
geometrically. Also, for nonbond style lj/shift, the delta
coefficient is always mixed using the rule </P>
<UL>
<LI>
delta_ij = (delta_i + delta_j) / 2
</UL>
<HR>
<H3>
<A NAME="_cch3_930957482">Bonds</A></H3>
<P>
The style of bond potential is specified in the input command file.</P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (r - r0)^2
standard harmonic spring
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2) (the usual 1/2 is included in the K)
coeff2 = r0 (distance)
2 coeffs are listed in data file or set in input script
</PRE>
<H4>
(2) FENE/standard </H4>
<PRE>
E = -0.5 K R0^2 * ln[1 - (r/R0)^2] +
4 epsilon [(sigma/r)^12 - (sigma/r)^6] + epsilon
finite extensible nonlinear elastic (FENE) potential for
polymer bead-spring models
see Kremer, Grest, J Chem Phys, 92, p 5057 (1990)
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = R0 (distance)
coeff3 = epsilon (energy)
coeff4 = sigma (distance)
1st term is attraction, 2nd term is repulsion (shifted LJ)
1st term extends to R0
2nd term only extends to the minimum of the LJ potential,
a cutoff distance computed by LAMMPS (2^(1/6) * sigma)
4 coeffs are listed in data file or set in input script
</PRE>
<H4>
(3) FENE/shift </H4>
<PRE>
E = -0.5 K R0^2 * ln[1 - ((r - delta)/R0)^2] +
4 epsilon [(sigma/(r - delta))^12 - (sigma/(r - delta))^6] + epsilon
same as FENE/standard expect that r is shifted by delta
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = R0 (distance)
coeff3 = epsilon (energy)
coeff4 = sigma (distance)
coeff5 = delta (distance)
1st term is attraction, 2nd term is repulsion (shifted LJ)
1st term extends to R0
2nd term only extends to the minimum of the LJ potential,
a cutoff distance computed by LAMMPS (2^(1/6) * sigma + delta)
5 coeffs are listed in data file or set in input script
</PRE>
<H4>
(4) nonlinear </H4>
<PRE>
E = epsilon (r - r0)^2 / [ lamda^2 - (r - r0)^2 ]
non-harmonic spring of equilibrium length r0
with finite extension of lamda
see Rector, Van Swol, Henderson, Molecular Physics, 82, p 1009 (1994)
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = r0 (distance)
coeff3 = lamda (distance)
3 coeffs are listed in data file or set in input script
</PRE>
<H4>
(5) class2 </H4>
<PRE>
E = K2 (r - r0)^2 + K3 (r - r0)^3 + K4 (r - r0)^4
r = distance (computed by LAMMPS)
coeff1 = r0 (distance)
coeff2 = K2 (energy/distance^2)
coeff3 = K3 (energy/distance^3)
coeff4 = K4 (energy/distance^4)
4 coeffs are listed in data file - cannot be set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957488">Angles </A></H3>
<P>
The style of angle potential is specified in the input command file. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (theta - theta0)^2
theta = radians (computed by LAMMPS)
coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
2 coeffs are listed in data file or set in input script
</PRE>
<H4>
(2) class2 </H4>
<PRE>
E = K2 (theta - theta0)^2 + K3 (theta - theta0)^3 +
K4 (theta - theta0)^4
theta = radians (computed by LAMMPS)
coeff1 = theta0 (degrees) (converted to radians within LAMMPS)
coeff2 = K2 (energy/radian^2)
coeff3 = K3 (energy/radian^3)
coeff4 = K4 (energy/radian^4)
4 coeffs are listed in data file - cannot be set in input script
</PRE>
<H4>
(3) charmm </H4>
<PRE>
(harmonic + Urey-Bradley)
E = K (theta - theta0)^2 + K_UB (r_13 - r_UB)^2
theta = radians (computed by LAMMPS)
r_13 = distance (computed by LAMMPS)
coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
coeff3 = K_UB (energy/distance^2)
coeff4 = r_UB (distance)
4 coeffs are listed in data file or set in input script
</PRE>
<H4>
(4) cosine </H4>
<PRE>
E = K (1 + cos(theta))
theta = radians (computed by LAMMPS)
coeff1 = K (energy)
1 coeff is listed in data file or set in input script
</PRE>
<H3>
<A NAME="_cch3_930957509">Dihedrals </A></H3>
<P>
The style of dihedral potential is specified in the input command
file. IMPORTANT NOTE for all these dihedral styles: in the LAMMPS
force field the trans position = 180 degrees, while in some force
fields trans = 0 degrees. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K [1 + d * cos (n*phi) ]
phi = radians (computed by LAMMPS)
coeff1 = K (energy)
coeff2 = d (+1 or -1)
coeff3 = n (1,2,3,4,6)
Additional cautions when comparing to other force fields:
some force fields reverse the sign convention on d so that
E = K [1 - d * cos(n*phi)]
some force fields divide/multiply K by the number of multiple
torsions that contain the j-k bond in an i-j-k-l torsion
some force fields let n be positive or negative which
corresponds to d = 1,-1
3 coeffs are listed in data file or set in input script
</PRE>
<H4>
(2) class2 </H4>
<PRE>
E = SUM(n=1,3) { K_n [ 1 - cos( n*Phi - Phi0_n ) ] }
phi = radians (computed by LAMMPS)
coeff1 = K_1 (energy)
coeff2 = Phi0_1 (degrees) (converted to radians within LAMMPS)
coeff3 = K_2 (energy)
coeff4 = Phi0_2 (degrees) (converted to radians within LAMMPS)
coeff5 = K_3 (energy)
coeff6 = Phi0_3 (degrees) (converted to radians within LAMMPS)
6 coeffs are listed in data file - cannot be set in input script
</PRE>
<H4>
(3) multiharmonic </H4>
<PRE>
E = SUM(n=1,5) { A_n * cos(Phi)^(n-1) }
phi = radians (computed by LAMMPS)
coeff1 = A_1
coeff2 = A_2
coeff3 = A_3
coeff4 = A_4
coeff5 = A_5
5 coeffs are listed in data file or set in input script
</PRE>
<H4>
(4) charmm </H4>
<PRE>
(harmonic + 1-4 interactions)
E = K [1 + cos (n*phi + d) ]
phi = radians (computed by LAMMPS)
coeff1 = K (energy)
coeff2 = n (1,2,3,4,6)
coeff3 = d (0 or 180 degrees) (converted to radians within LAMMPS)
coeff4 = weighting factor to turn on/off 1-4 neighbor nonbond interactions
coeff4 weight values are from 0.0 to 1.0 and are used to multiply the
energy and force interaction (both Coulombic and LJ) between the 2 atoms
weight of 0.0 means no interaction
weight of 1.0 means full interaction
must be used with the special bonds charmm command
"special bonds 0 0 0") which shuts off the uniform special bonds and
allows pair-specific special bonds for the 1-4 interactions to be
defined in the data file
LAMMPS assumes that all 1-4 interaction distances, which are
generally less than 6 Angstroms, are less than the smallest of the
inner LJ and Coulombic cutoffs, which are generally at least 8
Angstroms.
4 coeffs are listed in data file or set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957513">Impropers</A></H3>
<P>
The style of improper potential is specified in the input command file. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (chi - chi0)^2
chi = radians (computed by LAMMPS)
coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
coeff2 = chi0 (degrees) (converted to radians within LAMMPS)
2 coeffs are listed in data file or set in input script
</PRE>
<H4>
(2) cvff </H4>
<PRE>
E = K [1 + d * cos (n*chi) ]
chi = radians (computed by LAMMPS)
coeff1 = K (energy)
coeff2 = d (+1 or -1)
coeff3 = n (0,1,2,3,4,6)
3 coeffs are listed in data file or set in input script
</PRE>
<H4>
(3) class2 </H4>
<PRE>
same formula, coeffs, and meaning as &quot;harmonic&quot; except that LAMMPS
averages all 3 angle-contributions to chi
in class 2 this is called a Wilson out-of-plane interaction
2 coeffs are listed in data file - cannot be set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957527">Class 2 Force Field</A></H3>
<P>
If class 2 force fields are selected in the input command file,
additional cross terms are computed as part of the force field. All
class 2 coefficients must be set in the data file; they cannot be set
in the input script.</P>
<H4>
Bond-Bond (computed within class 2 angles) </H4>
<PRE>
E = K (r - r0) * (r' - r0')
r,r' = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = r0 (distance)
coeff3 = r0' (distance)
3 coeffs are input in data file
</PRE>
<H4>
Bond-Angle (computed within class 2 angles for each of 2 bonds) </H4>
<PRE>
E = K_n (r - r0_n) * (theta - theta0)
r = distance (computed by LAMMPS)
theta = radians (computed by LAMMPS)
coeff1 = K_1 (energy/distance-radians)
coeff2 = K_2 (energy/distance-radians)
coeff3 = r0_1 (distance)
coeff4 = r0_2 (distance)
Note: theta0 is known from angle coeffs so don't need it specified here
4 coeffs are listed in data file
</PRE>
<H4>
Middle-Bond-Torsion (computed within class 2 dihedral) </H4>
<PRE>
E = (r - r0) * [ F1*cos(phi) + F2*cos(2*phi) + F3*cos(3*phi) ]
r = distance (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1 (energy/distance)
coeff2 = F2 (energy/distance)
coeff3 = F3 (energy/distance)
coeff4 = r0 (distance)
4 coeffs are listed in data file
</PRE>
<H4>
End-Bond-Torsion (computed within class 2 dihedral for each of 2 bonds) </H4>
<PRE>
E = (r - r0_n) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
r = distance (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1_1 (energy/distance)
coeff2 = F2_1 (energy/distance)
coeff3 = F3_1 (energy/distance)
coeff4 = F1_2 (energy/distance)
coeff5 = F2_3 (energy/distance)
coeff6 = F3_3 (energy/distance)
coeff7 = r0_1 (distance)
coeff8 = r0_2 (distance)
8 coeffs are listed in data file
</PRE>
<H4>
Angle-Torsion (computed within class 2 dihedral for each of 2 angles) </H4>
<PRE>
E = (theta - theta0) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
theta = radians (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1_1 (energy/radians)
coeff2 = F2_1 (energy/radians)
coeff3 = F3_1 (energy/radians)
coeff4 = F1_2 (energy/radians)
coeff5 = F2_3 (energy/radians)
coeff6 = F3_3 (energy/radians)
coeff7 = theta0_1 (degrees) (converted to radians within LAMMPS)
coeff8 = theta0_2 (degrees) (converted to radians within LAMMPS)
8 coeffs are listed in data file
</PRE>
<H4>
Angle-Angle-Torsion (computed within class 2 dihedral) </H4>
<PRE>
E = K (theta - theta0) * (theta' - theta0') * (phi - phi0)
theta,theta' = radians (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = K (energy/radians^3)
coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
coeff3 = theta0' (degrees) (converted to radians within LAMMPS)
Note: phi0 is known from dihedral coeffs so don't need it specified here
3 coeffs are listed in data file
</PRE>
<H4>
Bond-Bond-13-Torsion (computed within class 2 dihedral) </H4>
<PRE>
E = K * (r1 - r10)*(r3 - r30)
r1,r3 = bond lengths of bonds 1 and 3 (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = r10 (distance) = equilibrium bond length for bond 1
coeff3 = r30 (distance) = equilibrium bond length for bond 3
K is only non-zero for aromatic rings
3 coeffs are listed in data file
</PRE>
<H4>
Angle-Angle (computed within class 2 improper for each of 3 pairs of
angles) </H4>
<PRE>
E = K_n (theta - theta0_n) * (theta' - theta0_n')
theta,theta' = radians (computed by LAMMPS)
coeff1 = K_1 (energy/radians^2)
coeff2 = K_2 (energy/radians^2)
coeff3 = K_3 (energy/radians^2)
coeff4 = theta0_1 (degrees) (converted to radians within LAMMPS)
coeff5 = theta0_2 (degrees) (converted to radians within LAMMPS)
coeff6 = theta0_3 (degrees) (converted to radians within LAMMPS)
6 coeffs are listed in data file
</PRE>
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<H2>
History of LAMMPS</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<P>
This is a brief history of features added to each version of LAMMPS.</P>
<HR>
<H3>
LAMMPS 2001 - November 2001</H3>
<UL>
<LI>
F90 + MPI version of code
<LI>
dynamic memory, no param.h file settings to twiddle, see "extra memory"
command
<LI>
changed required ordering of some input script commands (see discussion in
<A HREF="input_commands.html">input_commands</A>) file
<LI>
new commands: "extra memory", "maximum cutoff", "restart version",
"angle coeff", "dihedral coeff", "improper coeff",
"volume control", "slab volume", "rotation zero"
<LI>
changed meaning or syntax of commands:
"special bonds", "fix style rescale", "fix style hoover/drag",
"temp control rescale", "press control", "restart"
<LI>
deleted commands: "log file", "press_x control" (and y,z)
<LI>
better match to CHARMM force fields via "nonbond style lj/charmm",
"coulomb style charmm/switch", "angle style charmm", dihedral style charmm"
(due to Mark Stevens and Paul Crozier)
<LI>
changed "special bonds" default to 0.0 weighting on 1-4 interactions for
CHARMM compatibility, added "special bonds amber" option for AMBER
compatibility
<LI>
ghost atoms and new treatment of periodic boundary conditions,
this allows for cutoffs &gt; box-size and faster neighbor binning,
binned neighbor list construction is now the default as it is almost
always faster
<LI>
perform blocked-input from data and restart files, faster for many MPI
implementations (due to Mathias Puetz)
<LI>
added Velocities option to data file to initialize each atom's
velocity (see <A HREF="data_format.html">data_format</A> file)
<LI>
pressure control was decoupled from temperature control, so that
constant NPH simulations can be run (not just NPT), temperature
controls such as rescale or Langevin can now be used with constant P
simulations (due to Mark Stevens)
<LI>
temperature rescaling (either in "temp control" or "fix style rescale")
has an added fractional parameter which allows it to be applied
in a lightweight or heavy-handed way to induce the desired temperature
<LI>
got rid of crib.html file, see global.f for documentation of all
variables
<LI>
2-d slab Ewald and PPPM option, (see "slab volume" in
<A HREF="input_commands.html">input commands</A>) (due to Paul Crozier)
<LI>
new multiharmonic dihedral and cvff improper force-field options
(due to Mathias Puetz)
<LI>
SHAKE constraint for small clusters of atoms, see "fix style shake"
and "assign fix bondtype" commands
<LI>
added option to output restart files with timestep stamp or to toggle
between 2 files, see "restart" command
<LI>
tools for converting to/from other MD program formats:
msi2lmp (updated by John Carpenter),
lmp2arc (due to John Carpenter),
amber2lammps & dump2trj (Python scripts due to Keir Novik)
<LI>
tools for creating and massaging LAMMPS data and restart files:
setup_lj, setup_flow_2d, setup_chain, peek_restart, restart2data,
replicate
</UL>
<HR>
<H3>
LAMMPS 99 - June 99 </H3>
<UL>
<LI>
all-MPI version of code (F77 + C + MPI) for maximum portablility
<LI>
only one PPPM choice now, the better of the two earlier ones
<LI>
PPPM uses portable FFTs and data remapping routines, written in C w/
MPI, can now use non-power-of-2 processors and grid sizes
<LI>
auto-mapping of simulation box to processors
<LI>
removed a few unused/unneeded commands (bdump, log file, id string,
limit)
<LI>
changed syntax of some commands for simplicity &amp; consistency (see <A
HREF="input_commands.html">input commands</A>)
<LI>
changed method of calling/writing user diagnostic routines to be
simpler
<LI>
documentation in HTML format
</UL>
<HR>
<H3>
Version 5.0 - Oct 1997 </H3>
<UL>
<LI>
final version of class II force fields (due to Eric Simon)
<LI>
new formulation of NVE, NVT, NPT and rRESPA integrators (due to
Mark Stevens)
<LI>
new version of msi2lmp pre-processing tool, does not require DISCOVER
to run, only DISCOVER force field files (due to Steve Lustig)
<LI>
energy minimizer, Hessian-free truncated Newton method
(due to Todd Plantenga)
<LI>
new pressure controllers and constraints (due to Mark Stevens)
<LI>
replicate tool for generating new data files from old ones
</UL>
<HR ALIGN="LEFT">
<H3>
Version 4.0 - March 1997 </H3>
<UL>
<LI>
1st version of class II force fields (due to Eric Simon)
<LI>
new, faster PPPM solver (newpppm, due to Roy Pollock)
<LI>
rRESPA (due to Mark Stevens)
<LI>
new data file format
<LI>
new constraints, diagnostics
<LI>
msi2lmp pre-processing tool (due to Steve Lustig)
</UL>
<HR>
<H3>
Version 3.0 - March 1996 </H3>
<UL>
<LI>
more general force-field formulation
<LI>
atom/group constraints
<LI>
LJ units and bond potentials
<LI>
smoothed LJ potential option
<LI>
Langevin thermostat
<LI>
Newton's 3rd law option
<LI>
hook for user-supplied diagnostic routines
</UL>
<HR>
<H3>
Version 2.0 - October 1995 </H3>
<UL>
<LI>
bug fix of velocity initialization which caused drift
<LI>
PPPM for long-range Coulombic (due to Roy Pollock)
<LI>
constant NPT (due to Mark Stevens)
</UL>
<HR>
<H3>
Version 1.1 - February 1995 </H3>
<UL>
<LI>
Ewald for long-range Coulombic (due to Roy Pollock)
<LI>
full Newton's 3rd law (doubled communication)
<LI>
dumping of atom positions and velocities
<LI>
restart files
</UL>
<HR>
<H3>
Version 1.0 - January 1995 </H3>
<UL>
<LI>
short-range bonded and non-bonded forces
<LI>
partial Newton's 3rd law
<LI>
velocity-Verlet integrator
</UL>
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<H2>
LAMMPS Units</H2>
<P>
<A HREF="README.html">Return</A> to top-level LAMMPS documentation.</P>
<P>
This file describes the units associated with many of the key variables
and equations used inside the LAMMPS code. Units used for input command
parameters are described in the input_commands file. The input command
&quot;units&quot; selects between conventional and Lennard-Jones units.
See the force_fields file for more information on units for the force
field parameters that are input from data files or input scripts. </P>
<P>
Conventional units: </P>
<UL>
<LI>
distance = Angstroms
<LI>
time = femtoseconds
<LI>
mass = grams/mole
<LI>
temperature = degrees K
<LI>
pressure = atmospheres
<LI>
energy = Kcal/mole
<LI>
velocity = Angstroms/femtosecond
<LI>
force = grams/mole * Angstroms/femtosecond^2
<LI>
charge = +/- 1.0 is proton/electron
</UL>
<P>
LJ reduced units: </P>
<UL>
<LI>
distance = sigmas
<LI>
time = reduced LJ tau
<LI>
mass = ratio to unitless 1.0
<LI>
temperature = reduced LJ temp
<LI>
pressure = reduced LJ pressure
<LI>
energy = epsilons
<LI>
velocity = sigmas/tau
<LI>
force = reduced LJ force (sigmas/tau^2)
<LI>
charge = ratio to unitless 1.0
</UL>
<HR>
<P>
This listing of variables assumes conventional units; to convert to LJ
reduced units, simply substitute the appropriate term from the list
above. E.g. x is in sigmas in LJ units. Per-mole in any of the units
simply means for 6.023 x 10^23 atoms.</P>
<P>
</P>
<PRE>
Meaning Variable Units
positions x Angstroms
velocities v Angstroms / click (see below)
forces f Kcal / (mole - Angstrom)
masses mass gram / mole
charges q electron units (-1 for an electron)
(1 e.u. = 1.602 x 10^-19 coul)
time --- clicks (1 click = 48.88821 fmsec)
timestep dt clicks
input timestep dt_in fmsec
time convert dtfactor 48.88821 fmsec / click
temperature t_current degrees K
t_start
t_stop
input damping t_freq_in inverse fmsec
internal temp t_freq inverse clicks
damping
dielec const dielectric 1.0 (unitless)
Boltmann const boltz 0.001987191 Kcal / (mole - degree K)
virial virial[xyz] Kcal/mole = r dot F
pressure factor pfactor 68589.796 (convert internal to atmospheres)
internal p_current Kcal / (mole - Angs^3)
pressure p_start
p_stop
input press p_start_in atmospheres
p_stop_in
output press log file atmospheres
input damping p_freq_in inverse time
internal press p_freq inverse clicks
damping
pot eng e_potential Kcal/mole
kin eng e_kinetic Kcal/mole
eng convert efactor 332.0636 (Kcal - Ang) / (q^2 - mole)
(convert Coulomb eng to Kcal/mole)
LJ coeffs lja,ljb Kcal-Angs^(6,12)/mole
bond various see force_fields file
parameters 2,3,4-body
terms
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<H2>
LAMMPS</H2>
<P>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 99 version, written in F77,
which has been superceded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>
LAMMPS is a classical molecular dynamics code designed for simulating
molecular and atomic systems on parallel computers using
spatial-decomposition techniques. It runs on any parallel platform that
supports the MPI message-passing library or on single-processor
workstations.</P>
<P>
LAMMPS 99 is copyrighted code that is distributed freely as
open-source software under the GNU Public License (GPL). See the
LICENSE file or <A HREF="http://www.gnu.org">www.gnu.org</A> for more
details. Basically the GPL allows you as a user to use, modify, or
distribute LAMMPS however you wish, so long as any software you
distribute remains under the GPL.
<P>
Features of LAMMPS 99 include:</P>
<UL>
<LI>
short-range pairwise Lennard-Jones and Coulombic interactions
<LI>
long-range Coulombic interactions via Ewald or PPPM (particle-mesh
Ewald)
<LI>
short-range harmonic bond potentials (bond, angle, torsion, improper)
<LI>
short-range class II (cross-term) molecular potentials
<LI>
NVE, NVT, NPT dynamics
<LI>
constraints on atoms or groups of atoms
<LI>
rRESPA long-timescale integrator
<LI>
energy minimizer (Hessian-free truncated Newton method)
</UL>
<P>
More details about the code can be found <A HREF="#_cch3_930958294">here</A>,
in the HTML-based documentation. There is also a conference paper
describing the parallel algorithms used in the code:</P>
<P>
S. J. Plimpton, R. Pollock, M. Stevens, &quot;Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations&quot;, in Proc of
the Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN, March 1997.</P>
<P>
LAMMPS was originally developed as part of a 5-way CRADA collaboration
between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and
Dupont) and 2 DoE laboratories (Sandia National Laboratories and
Lawrence Livermore National Laboratories).</P>
<P>
The primary author of LAMMPS is Steve Plimpton, but others have written
or worked on significant portions of the code:</P>
<UL>
<LI>
Roy Pollock (LLNL): Ewald, PPPM solvers
<LI>
Mark Stevens (Sandia): rRESPA, NPT integrators
<LI>
Eric Simon (Cray Research): class II force fields
<LI>
Todd Plantenga (Sandia): energy minimizer
<LI>
Steve Lustig (Dupont): msi2lmp tool
<LI>
Mike Peachey (Cray Research): msi2lmp tool
</UL>
<P>
Other CRADA partners involved in the design and testing of LAMMPS are </P>
<UL>
<LI>
John Carpenter (Cray Research)
<LI>
Terry Stouch (Bristol-Myers Squibb)
<LI>
Jim Belak (LLNL)
</UL>
<P>
LAMMPS is copyrighted code that is distributed freely as open-source
software under the GNU Public License (GPL). See the LICENSE file or
<A HREF="http://www.gnu.org">www.gnu.org</A> for more details.
Basically the GPL allows you as a user to use, modify, or distribute
LAMMPS however you wish, so long as any software you distribute
remains under the GPL.
<P>
If you have questions about LAMMPS, please contact me:
</P>
<DL>
<DT>
Steve Plimpton
<DD>
sjplimp@sandia.gov
<DD>
www.cs.sandia.gov/~sjplimp
<DD>
Sandia National Labs
<DD>
Albuquerque, NM 87185
</DL>
<HR>
<H3>
<A NAME="_cch3_930958294">More Information about LAMMPS</A></H3>
<DIR>
<LI>
<A HREF="basics.html">Basics</A>
<DIR>
<LI>
how to make, run, and test LAMMPS with the example problems
</DIR>
<LI>
<A HREF="input_commands.html">Input Commands</A>
<DIR>
<LI>
a complete listing of input commands used by LAMMPS
</DIR>
<LI>
<A HREF="data_format.html">Data Format</A>
<DIR>
<LI>
the data file format used by LAMMPS
</DIR>
<LI>
<A HREF="force_fields.html">Force Fields</A>
<DIR>
<LI>
the equations LAMMPS uses to compute force-fields
</DIR>
<LI>
<A HREF="units.html">Units</A>
<DIR>
<LI>
the input/output and internal units for LAMMPS variables
</DIR>
<LI>
<A HREF="crib.html">Crib</A>
<DIR>
<LI>
a one-line description of the variables used in LAMMPS
</DIR>
<LI>
<A HREF="history.html">History</A>
<DIR>
<LI>
a brief timeline of features added to LAMMPS
</DIR>
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<H2>
Basics of Using LAMMPS</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<UL>
<LI>
<A HREF="#_cch3_931273040">Distribution</A>
<LI>
<A HREF="#_cch3_930327142">Making LAMMPS</A>
<LI>
<A HREF="#_cch3_930327155">Running LAMMPS</A>
<LI>
<A HREF="#_cch3_930759879">Examples</A>
<LI>
<A HREF="#_cch3_931282515">Other Tools</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_931273040">Distribution</A></H3>
<P>
When you unzip/untar the LAMMPS distribution you should have 5
directories: </P>
<UL>
<LI>
src = source files for LAMMPS
<LI>
doc = HTML documentation
<LI>
examples = sample problems with inputs and outputs
<LI>
msi2lmp = tool for converting files from DISCOVER to LAMMPS format
(this requires that you have DISCOVER force field files)
<LI>
tools = serial program for replicating data files
</UL>
<HR>
<H3>
<A NAME="_cch3_930327142">Making LAMMPS</A></H3>
<P>
The src directory contains the F77 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
<P>
make machine</P>
<P>
from within the src directoy. E.g. &quot;make sgi&quot; or &quot;make
t3e&quot;. This should create an executable named lmp_sgi or lmp_t3e.</P>
<P>
In the src directory, there is one top-level Makefile and several
low-level machine-specific files named Makefile.xxx where xxx = the
machine name. If a low-level Makefile exists for your platform, you do
not need to edit the top-level Makefile. However you should check the
system-specific section of the low-level Makefile to make sure the
various paths are correct for your environment. If a low-level Makefile
does not exist for your platform, you will need to add a suitable
target to the top-level Makefile. You will also need to create a new
low-level Makefile using one of the existing ones as a template. If you
wish to make LAMMPS for a single-processor workstation that doesn't
have an installed MPI library, you can specify the serial target which
uses a directory of MPI stubs to link against - e.g. &quot;make
serial&quot;. You will need to make the stub library (see STUBS
directory) on your workstation before doing this.</P>
<P>
Note that the two-level Makefile system allows you to make LAMMPS for
multiple platforms. Each target creates its own object directory for
separate storage of its *.o files.</P>
<P>
There are a couple compiler switches of interest which can be specified
in the low-level Makefiles. If you use a F77FLAGS switch of -DSYNC then
synchronization calls will be made before the timing routines in
integrate.f. This may slow down the code slightly, but will make the
reported timings at the end of a run more accurate. The CCFLAGS setting
in the low-level Makefiles requires a FFT setting, for example
-DFFT_SGI or -DFFT_T3E. This is for inclusion of the appropriate
machine-specific native 1-d FFT libraries on various platforms.
Currently, the supported machines and switches (used in fft_3d.c) are
FFT_SGI, FFT_DEC, FFT_INTEL, FFT_T3E, and FFT_FFTW. The latter is a
publicly available portable FFT library, <A HREF="http://www.fftw.org">FFTW</A>,
which you can install on any machine. If none of these options is
suitable for your machine, please contact me, and we'll discuss how to
add the capability to call your machine's native FFT library.</P>
<HR>
<H3>
<A NAME="_cch3_930327155">Running LAMMPS</A></H3>
<P>
LAMMPS is run by redirecting a file of input commands into it.</P>
<P>
lmp_sgi &lt; in.lj</P>
<P>
lmp_t3e &lt; in.lj</P>
<P>
The input file contains commands that specify the parameters for the
simulation as well as read other necessary files such as a data file
that describes the initial atom positions, molecular topology, and
force-field parameters. The <A HREF="input_commands.html">input_commands</A>
page describes all the possible commands that can be used. The <A
HREF="data_format.html">data_format</A> page describes the format of
the data file. </P>
<P>
LAMMPS can be run on any number of processors, including a single
processor. In principle you should get identical answers on any number
of processors and on any machine. In practice, numerical round-off can
cause slight differences and eventual divergence of dynamical
trajectories. </P>
<P>
When LAMMPS runs, if you get an error message to the screen about
&quot;boosting&quot; something, it means one (or more) data arrays are
not allocated large enough. Some of these errors are detected at setup,
others like neighbor list overflow may not occur until the middle of a
run. When the latter happens the program will either gracefully stop
(if all processors incurred the same error) or hang (with an error
message). Unfortunately in the current version of LAMMPS which uses
static memory allocation, changing the array size(s) requires you to
edit the appropriate line(s) in the param.h file and recompile the code.</P>
<P>
I've tried to be careful about detecting memory-overflow errors in
LAMMPS. If the code ever crashes or hangs without spitting out an error
message first, it's probably a bug, so let me know about it. Of course
this applies to problems due to algorithmic or parallelism issues, not
to physics mistkaes, like specifying too big a timestep or putting 2
atoms on top of each other! One exception is that different MPI
implementations handle buffering of messages differently. If the code
hangs without an error message, it may be that you need to specify an
MPI setting or two (usually via an environment variable) to enable
buffering or boost the sizes of messages that can be buffered. </P>
<HR>
<H3>
<A NAME="_cch3_930759879">Examples</A></H3>
<P>
There are several sample problems in the examples directory. All of
them use an input file (in.*) of commands and a data file (data.*) of
initial atomic coordinates and produce one or more output files. The
*.xxx.P files are outputs on P processors on a particular machine which
you can compare your answers to.</P>
<P>
(1) lj</P>
<P>
Simple atomic simulations of Lennard-Jones atoms of 1 or 3 species with
various ensembles -- NVE, NVT, NPT.</P>
<P>
(2) charge</P>
<P>
A few timestep simulation of a box of charged atoms for testing the
Coulombic options -- cutoff, Ewald, particle-mesh Ewald (PPPM).</P>
<P>
(3) class2</P>
<P>
A simple test run of phenyalanine using DISCOVER cff95 class II force
fields.</P>
<P>
(4) min</P>
<P>
An energy minimization of a transcription protein.</P>
<P>
(5) lc</P>
<P>
Small (250 atom) and large (6750 atom) simulations of liquid crystal
molecules with various Coulombic options and periodicity settings. The
large-system date file was created by using the &quot;replicate&quot;
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
options.</P>
<P>
(7) polymer</P>
<P>
Simulations of bead-spring polymer models with one chain type and two
chain types (different size monomers). The two-chain system also has
freely diffusing monomers. This illustrates use of the setup_chain
program in the tools directory and also how to use soft potentials to
untangle the initial configurations.</P>
<HR>
<H3>
<A NAME="_cch3_931282515">Other Tools</A></H3>
<P>
The msi2lmp directory has source code for a tool that converts MSI
Discover files to LAMMPS input data files. This tool requires you to
have the Discover force-field description files in order to convert
those parameters to LAMMPS parameters. See the README file in the
msi2lmp directory for additional information.</P>
<P>
The tools directory has a C file called replicate.c which is useful for
generating new LAMMPS data files from existing ones - e.g. scaling the
atom coordinates, replicating the system to make a larger one, etc. See
the comments at the top of replicate.c for instructions on how to use
it.</P>
<P>
The tools directory has a F77 program called setup_lj (compile and link
with print.c) which can be used to generate a 3-d box of Lennard Jones
atoms (one or more atom types) like those used in examples/lj.</P>
<P>
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
chains of what length, a random number seed, etc.</P>
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<H2>
Crib File</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<P>
This file contains one-line descriptions of the key variables and
parameters used in LAMMPS. The variables are listed by their data type:</P>
<UL>
<LI>
<A HREF="#_cch3_930764945">Parameters</A>
<LI>
<A HREF="#_cch3_930764951">Arrays (real</A>)
<LI>
<A HREF="#_cch3_930764957">Arrays (integer)</A>
<LI>
<A HREF="#_cch3_930764964">Variables (real)</A>
<LI>
<A HREF="#_cch3_930764969">Variables (integer)</A>
<LI>
<A HREF="#_cch3_930764974">Variables (character)</A>
</UL>
<P>
Note: this file is somewhat out-of-date for LAMMPS 99.</P>
<HR>
<H3>
<A NAME="_cch3_930764945">Parameters: </A></H3>
<UL>
<LI>
maxown = max # of local owned atoms
<LI>
maxother = max # of local nearby atoms
<LI>
maxtotal = max # of total atoms in simulation
<LI>
maxtype = max # of atom types
<LI>
maxbond = max # of bonds to compute on one procesor
<LI>
maxangle = max # of angles to compute on one processor
<LI>
maxdihed = max # of dihedrals to compute on one processor
<LI>
maximpro = max # of impropers to compute on one processor
<LI>
maxbondper = max # of bonds of one atom
<LI>
maxangleper = max # of angles of one atom
<LI>
maxdihedper = max # of dihedrals of one atom
<LI>
maximproper = max # of impropers of one atom
<LI>
maxbondtype = max # of bond types
<LI>
maxangletype = max # of angle types
<LI>
maxdihedtype = max # of dihedral types
<LI>
maximprotype = max # of improper types
<LI>
maxexch = max # of atoms in exchange buffer
<LI>
maxsend = max # of atoms to send to all neighbors in all swaps
<LI>
maxsendone = max # of atoms to send in one swap
<LI>
maxswap = max # of swaps to do at each timestep
<LI>
maxneigh = max # of neighbors per owned atom
<LI>
maxsneigh = max # of special neighbors of one atom
<LI>
maxbin = max # of local neighbor bins
<LI>
maxfix = max # of defined constraints + 1
<LI>
maxdiag = max # of diagnostic routines
<LI>
maxgrid = max size of PPPM grid with ghosts on one processor
<LI>
maxfft = max size of PPPM FFT grid on one processor
<LI>
maxperatom = max # of data items stored/comm/output per atom
<LI>
maxatom = maxown + maxother = total # of own and nearby atoms
<LI>
maxexchtot = maxexch * (maxperatom + maxsneigh + 3*maxbondper +
4*maxangleper + 5*maxdihedper + 5*maximproper) = total data volume for
all exchanged atoms
<LI>
maxrestot = maxown * (maxperatom - 3 + 3*maxbondper + 4*maxangleper +
5*maxdihedper + 5*maximproper)+1 = total data volume for all buffered
restart atoms
<LI>
maxsendspec = 2 * maxsneigh * maxown total data volume for sending
special requests
<LI>
maxrecvspec = maxsneigh + 1 total data volume for receiving a list of
specials
</UL>
<HR>
<H3>
<A NAME="_cch3_930764951">Arrays (real): </A></H3>
<UL>
<LI>
anglecoeff(2,maxangletype) = angle coeffs for each angle type
<LI>
bondcoeff(5,maxbondtype) = bond coeffs for each bond type
<LI>
boundhi(maxswap) = hi slab boundary on atom positions for each swap
send
<LI>
boundlo(maxswap) = lo slab boundary on atom positions for each swap
send
<LI>
buf1(maxexchtot) = comm buffer for sending exchange atoms
<LI>
buf2(2*maxexchtot) = comm buffer for 2 recv of exchange atoms
<LI>
buf3(3*maxsendone) = comm buffer for sending one set of swap atom
positions
<LI>
buf4(8*maxown) = comm buffer for output
<LI>
buf5(maxrestot) = comm buffer for restart atoms
<LI>
buf6(maxsendone) = comm buffer for sending one set of swap charges
<LI>
cutforcesq(maxtype,maxtype) = force cutoff squared for atom pair
(LJ/Coul)
<LI>
cutljsq(maxtype,maxtype) = LJ cutoff squared for atom pairs
<LI>
cutljinner(maxtype,maxtype) = inner LJ cutoff for switched LJ
<LI>
cutljinnersq(maxtype,maxtype) = inner LJ cutoff squared for switched LJ
<LI>
cutneighsq(maxtype,maxtype) = neigh cutoff squared for atom pair
(LJ/Coul + skin)
<LI>
diagparams(6,maxdiag) = parameters to pass into a diagnostic routine
<LI>
dihedcoeff(3,maxdihedtype) = dihedral coeffs for each dihedral type
<LI>
f(3,maxown) = forces on own atoms
<LI>
fixcoeff(8,maxfix) = constraint coeffs for each constraint
<LI>
fixstore(5*maxfix) = accumulated quantities for each constraint
<LI>
improcoeff(2,maximprotype) = improper coeffs for each improper type
<LI>
lj12345(maxtype,maxtype) = pre-computed LJ coeffs for use in energy and
force
<LI>
ljsw01234(maxtype,maxtype) = pre-computed switched LJ coeffs for eng
and force
<LI>
mass(maxtype) = mass of each atom type
<LI>
noncoeff1234(maxtype,maxtype) = nonbond coeffs input for atom pairs
<LI>
offset(maxtype,maxtype) = LJ potential offsets at cutoff for energy
calc
<LI>
q(maxatom) = charge of own and nearby atoms (electron units)
<LI>
v(3,maxown) = velocity of owned atoms
<LI>
x(3,maxatom) = positions of own and nearby atoms
<LI>
xhold(3,maxown) = positions of own atoms at last reneighboring
</UL>
<HR>
<H3>
<A NAME="_cch3_930764957">Arrays (integer): </A></H3>
<UL>
<LI>
angleatom123(maxangleper,maxown) = angle atoms for angles of owned
atoms
<LI>
anglelist(4,maxangle) = atoms and type of each angle to compute locally
<LI>
angletype(maxangleper,maxown) = angle type for angles of owned atoms
<LI>
bin(maxatom) = linked list pointers from one atom to next in bin
<LI>
binpnt(maxbin) = pointer to 1st atom in each bin
<LI>
bondatom12(maxbondper,maxown) = bond atoms for bonds of owned atoms
<LI>
bondlist(3,maxbond) = atoms and type of each bond to compute locally
<LI>
bondtype(maxbondper,maxown) = bond type for bonds of owned atoms
<LI>
bondtypeflag(maxbondtype) = flag for whether bond coeffs are set
<LI>
diagfileflag(maxdiag) = whether a file has been specified for a diag
routine
<LI>
diagfreq(maxdiag) = call a diagnostic routine every this many steps
<LI>
diagnparams(maxdiag) = # of parameters specified for a diagnostic
routine
<LI>
diagstyle(maxdiag) = whether a diagnostic has been set 0/1
<LI>
dihedatom1234(maxdihedper,maxown) = dihed atoms for diheds of owned
atoms
<LI>
dihedlist(5,maxdihed) = atoms and type of each dihedral to compute
locally
<LI>
dihedtype(maxdihedper,maxown) = dihed type for diheds of owned atoms
<LI>
fix(maxown) = constraint assignments for each owned atom
<LI>
fixflag(3,maxfix) = 0/1 flags for various fix styles
<LI>
fixptr(maxfix) = how many values are accumulated for each constraint
<LI>
fixstyle(maxfix) = style of each constraint
<LI>
ibuf1(maxsendone) = comm buffer for sending one set of swap atom tags
<LI>
ibuf2(maxsendone) = comm buffer for sending one set of swap atom types
<LI>
ibuf3(maxspec) = comm buffer for sending special requests
<LI>
ibuf4(maxspec) = comm buffer for receiving special lists
<LI>
improatom1234(maximproper,maxown) = impro atoms for impros of owned
atoms
<LI>
improlist(5,maximpro) = atoms and type of each improper to compute
locally
<LI>
improtype(maximproper,maxown) = impro type for impros of owned atoms
<LI>
list(maxown) = linked list of local atoms (last one -&gt; maxown+1)
<LI>
localptr(0:maxtotal) = ptr from global atom to local array (0 if don't
have)
<LI>
molecule(maxown) = molecule id # each owned atom is in
<LI>
nlist(maxown*maxneigh+maxneigh) = neighbor lists of own atoms
<LI>
nliststart(maxown) = pointer to where neighbor list for this atom
starts
<LI>
nliststop(maxown) = pointer to where neighbor list for this atom stops
<LI>
nontypeflag(maxtype,maxtype) = flag for whether nonbond coeffs are set
<LI>
nrlist(maxswap+1) = prt to where received other atoms start for each
swap
<LI>
nslist(maxswap+1) = pointer to where swap list starts for each swap
<LI>
numangle(maxown) = # of angles of each owned atom
<LI>
numbond(maxown) = # of 1st neighbors bonded to each owned atom
<LI>
num2bond(maxown) = # of 2nd neighbors for each owned atom
<LI>
num3bond(maxown) = # of 3rd neighbors for each owned atom
<LI>
numdihed(maxown) = # of dihedrals of each owned atom
<LI>
numimpro(maxown) = # of impropers of each owned atom
<LI>
rpart(maxswap) = node # of who to recv from for each swap
<LI>
slist(maxsend) = send list of atoms to send out in all swaps
<LI>
spart(maxswap) = node # of who to send to for each swap
<LI>
specbond(maxsneigh,maxown) = special bond neighbors of each owned atom
<LI>
tag(maxatom) = global id # of own and nearby atoms
<LI>
true(maxown) = which periodic box atom is truly in for all 3 dims
<LI>
type(maxatom) = type # of own and nearby atoms
<LI>
typecheck(maxtype) = consistency check for all existing atom types
<LI>
typechecktmp(maxtype) = summing array for atom type consistency check
<LI>
velflag(maxown) = whether velocity for each atom has been created
</UL>
<HR>
<H3>
<A NAME="_cch3_930764964">Variables (real): </A></H3>
<UL>
<LI>
binsize[xyz] = size of global neighbor bins in each dimension
<LI>
boltz = Boltzmann factor
<LI>
border(2,3) = lo/hi boundaries of my sub-box in each dimension
<LI>
coulpre = Coulombic force prefactor
<LI>
createregion(6) = bounding box for atoms to create temperature for
<LI>
createvec(3) = initial velocity for create temp atoms
<LI>
cutcoul = input force cutoff for Coulombic interactions
<LI>
cutcoulsq = Coul cutoff squared for all atom pairs
<LI>
cutforce = max force cutoff for all atom pairs (LJ/Coul)
<LI>
cutlj = input global (default) LJ cutoff for all atom pairs
<LI>
cutljinterior = global inner LJ cutoff for switched LJ
<LI>
cutneigh = max neighbor cutoff for all atom pairs (LJ/Coul + skin)
<LI>
dielectric = dielectric constant
<LI>
dt = timestep
<LI>
dtfactor = timestep conversion factor from input to program units
<LI>
dthalf = timestep / 2
<LI>
efactor = energy conversion factor from Coulombic to Kcals
<LI>
e_angle = energy in angles
<LI>
e_bond = energy in bonds
<LI>
e_coul = energy in nonbond Coulombic
<LI>
e_dihedral = energy in dihedrals
<LI>
e_improper = energy in impropers
<LI>
e_total = total energy
<LI>
e_vdwl = energy in nonbond LJ
<LI>
fixregion(6) = bounding box for atoms to assign to a constraint
<LI>
skin = distance between force and neighbor cutoffs
<LI>
special(3) = weight factors for special neighbors
<LI>
triggersq = squared distance to trigger neighbor list rebuild
<LI>
two16 = 2 ^ (1/6) constant for use in FENE bond potentials
<LI>
t_create = requested initialization temp
<LI>
t_current = current temp returned from temp routine
<LI>
t_nph = default temp for constant NPH
<LI>
t_start = target temp at beginning of run
<LI>
t_stop = target temp at end of run
<LI>
t_window = control temp within this window
<LI>
time_angle = angle time
<LI>
time_bond = bond time
<LI>
time_comm = communication time
<LI>
time_current = current time
<LI>
time_dihedral = dihedral time
<LI>
time_exch = exchange time
<LI>
time_improper = improper time
<LI>
time_io = i/o time
<LI>
time_loop = time for integration loop
<LI>
time_neigh1 = neighboring time in nonbond
<LI>
time_neigh2 = neighboring time in bonds
<LI>
time_nonbond = nonbond force time
<LI>
time_other = other miscellaneous time
<LI>
time_total = total run time of entire simulation
<LI>
x[yz]mc = box size minus force cutoff for PBC checks
<LI>
x[yz]ms box size minus neighbor list cutoff for PBC checks
<LI>
x[yz]boundlo = lower global box boundary in each dimension
<LI>
x[yz]boundhi = upper global box boundary in each dimension
<LI>
x[yz]prd = global box size in each dimension
</UL>
<HR>
<H3>
<A NAME="_cch3_930764969">Variables (integer): </A></H3>
<UL>
<LI>
atompnt = pointer to 1st atom in my list
<LI>
bondstyle = style of bond computation
<LI>
boxflag = flag if box has been remapped (non-PBC)
<LI>
coulstyle = style of Coulomb interaction
<LI>
creategroup = kind of atom group to create temp for
<LI>
createstyle = style of temp creation
<LI>
createtypehi = upper range of atom types to create temp for
<LI>
createtypelo = lower range of atom types to create temp for
<LI>
dumpfileflag = has dump file been opened or not (1/0)
<LI>
dumpflag = dump atoms to file every this many steps (0 = never)
<LI>
dumpforcefileflag = has dump force file been opened or not (1/0)
<LI>
dumpforceflag = dump forces to file every this many steps (0 = never)
<LI>
dumpvelfileflag = has dump velocity file been opened or not (1/0)
<LI>
dumpvelflag = dump vels to file every this many steps (0 = never)
<LI>
fixatom = assign atom/molecule with this tag to a constraint
<LI>
fixgroup = kind of atom group to assign to a constraint
<LI>
fixnum = total # of accumulated values for all constraints
<LI>
fixtype = assign group of atoms of this type to a constraint
<LI>
fixwhich = which constraint a atom group is to be assigned to
<LI>
freepnt = pointer to 1st free space in list (last one -&gt; 0)
<LI>
idimension = dimension of problem (2-d or 3-d)
<LI>
iseed = RNG seed for generating initial velocities
<LI>
itime = current timestep loop counter in integrator
<LI>
iversion = version number of restart files (for backward compat)
<LI>
max_angle = most angles I ever have to compute
<LI>
max_angleper = most angles ever attached to any atom
<LI>
max_bond = most bonds I ever have to compute
<LI>
max_bondper = most bonds ever attached to any atom
<LI>
max_dihed = most diheds I ever have to compute
<LI>
max_dihedper = most diheds ever attached to any atom
<LI>
max_exch = most atoms ever leaving my box (in one dimension)
<LI>
max_impro = most impros I ever have to compute
<LI>
max_improper = most impros ever attached to any atom
<LI>
max_nlocal = most atoms I ever owned
<LI>
max_neigh = most neighbors ever stored in neighbor list
<LI>
max_nother = most nearby atoms I ever stored
<LI>
max_slist = biggest size swap list ever reached
<LI>
max_swap = most atoms ever sent in one swap
<LI>
mbin[xyz] = # of bins in my box with nearby atoms included
<LI>
mbin[xyz]lo = global bin indices (offset) at corner of extended box
<LI>
me(3) = which box I am (0 - pgrid-1) in each dimension
<LI>
mixflag = whether mixing style has been set or not
<LI>
mixstyle = style of mixing for nonbond coeffs (arith,geom,sixth)
<LI>
mpart(2,3)= node # of neighbor processor in each dimension
<LI>
nanglelocal = local # of angless to compute
<LI>
nangles = total # of angles
<LI>
nangletypes = total # of angle types
<LI>
natoms = total # of atoms
<LI>
nbin[xyz] # of global neighbor bins in each dimension
<LI>
nbondlocal = local # of bonds to compute
<LI>
nbonds = total # of bonds
<LI>
nbondtypes = total # of bond types
<LI>
ndanger = # of neighbor rebuilds triggered by 1st check
<LI>
ndiags = # of user-specified diagnostic routines
<LI>
ndihedlocal = local # of dihedrals to compute
<LI>
ndihedrals = total # of diheds
<LI>
ndihedtypes = total # of dihedral types
<LI>
need(3) how many processors I need neighbors from in each dim
<LI>
neighago = how many timesteps ago neighboring was done
<LI>
neighdelay = delay neighbor list build for this many steps
<LI>
neighfreq = build neighbor list every this many steps
<LI>
neighstyle = neighboring by (0) N^2 or (1) binning method
<LI>
neightop = last used position in neighbor list (nlist)
<LI>
neightrigger = always (0) do neighbor list or trigger (1) on atom move
<LI>
newton = flag for kind of Newton's 3rd law used (0,1,2,3)
<LI>
newton_bond = Newton's 3rd is not used (0) or (1) used for bonds
<LI>
newton_nonbond = Newton's 3rd is not used (0) or (1) used for nonbonds
<LI>
nfixes = # of constraints
<LI>
nimprolocal = local # of impropers to compute
<LI>
nimpropers = total # of impros
<LI>
nimprotypes = total # of improper types
<LI>
nlocal = # of atoms I currently own
<LI>
nother = # of nearby atoms I currently store
<LI>
node = my node #
<LI>
nonstyle = style on nonbond computation
<LI>
nprocs = total # of processors
<LI>
nsteps = # of timesteps to simulate
<LI>
nswap = # of swaps at each timestep
<LI>
ntimestep = current global timestep
<LI>
ntypes = total # of atom types
<LI>
numneigh = number of times reneighboring is done
<LI>
offsetflag = whether to include energy offset in LJ energy calc
<LI>
peratom = # of values/atom not including bond info
<LI>
perflagx[yz] = flag for periodic (0) or non-periodic (1) BC
<LI>
pgrid(3) = # of processors in each dimension
<LI>
readflag = whether atom input file has been read or not (1/0)
<LI>
restartfileflag = which restart file to open next (0/1)
<LI>
restartflag = write restart file every this many steps (0=never)
<LI>
t_every = rescale/replace temp every this many steps
<LI>
tempflag = constant temperature style flag
<LI>
thermoflag = print thermo info every this many steps (0 = never)
<LI>
thermostyle = style of thermo output (0 = full, 1 = reduced)
<LI>
trueflag = whether to dump remapped or true atom positions
<LI>
units = flag for real vs reduced LJ units
</UL>
<HR>
<H3>
<A NAME="_cch3_930764974">Variables (character): </A></H3>
<UL>
<LI>
datafile = file to read atom and connectivity info from
<LI>
diagfile(maxdiag) = files to print user-specified diagnostics to
<LI>
diagname(maxdiag) = name of a user-specified diagnostic routine
<LI>
dumpfile = file to dump atom info to
<LI>
dumpforcefile = file to dump force info to
<LI>
dumpvelfile = file to dump velocity info to
<LI>
restart_in = file to read restart info from
<LI>
restart_out[12] = files to write restart info to
</UL>
<P>
</P>
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<BODY>
<H2>
LAMMPS Data Format</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
<P>
This file describes the format of the data file read into LAMMPS with
the &quot;read data&quot; command. The data file contains basic
information about the size of the problem to be run, the initial atomic
coordinates, molecular topology, and (optionally) force-field
coefficients. It will be easiest to understand this file if you read it
while looking at a sample data file from the examples.</P>
<P>
This page has 2 sections:</P>
<UL>
<LI>
<A HREF="#_cch3_930958962">Rules for formatting the Data File</A>
<LI>
<A HREF="#_cch3_930958969">Sample file with Annotations</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
<P>
Blank lines are important. After the header section, new entries are
separated by blank lines. </P>
<P>
Indentation and space between words/numbers on one line is not
important except that entry keywords (e.g. Masses, Bond Coeffs) must be
left-justified and capitalized as shown. </P>
<P>
The header section (thru box bounds) must appear first in the file, the
remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come
in any order. </P>
<P>
These entries must be in the file: header section, Masses, Atoms. </P>
<P>
These entries must be in the file if there are a non-zero number of
them: Bonds, Angles, Dihedrals, Impropers, Bond Coeffs, Angle Coeffs,
Dihedral Coeffs, Improper Coeffs. Cross-term coefficients for a
particular kind of interaction (e.g. BondAngle Coeffs for bonds) must
appear if class II force fields have been turned on in the input
command file via a &quot;style&quot; command. </P>
<P>
The Nonbond Coeffs entry contains one line for each atom type. These
are the coefficients for an interaction between 2 atoms of the same
type. The cross-type coeffs are computed by the appropriate class I or
class II mixing rules, or can be specified explicitly using the
&quot;nonbond coeff&quot; command in the input command script. See the <A
HREF="force_fields.html">force_fields</A> page for more information. </P>
<P>
The Nonbond Coeffs and Bond Coeffs entries are optional since they can
be specified from the input command script. This is not true if bond
style is set to class II since those coeffs can only be specified in
this data file. </P>
<P>
In the Atoms entry, the atoms can be in any order so long as there are
N entries. The 1st number on the line is the atom-tag (number from 1 to
N) which is used to identify the atom throughout the simulation. The
molecule-tag is a second identifier which is attached to the atom; it
can be 0, or a counter for the molecule the atom is part of, or any
other number you wish. The q value is the charge of the atom in
electron units (e.g. +1 for a proton). The xyz values are the initial
position of the atom. For 2-d simulations specify z as 0.0.</P>
<P>
The final 3 nx,ny,nz values on a line of the Atoms entry are optional.
LAMMPS only reads them if the &quot;true flag&quot; command is
specified in the input command script. Otherwise they are initialized
to 0 by LAMMPS. Their meaning, for each dimension, is that
&quot;n&quot; box-lengths are added to xyz to get the atom's
&quot;true&quot; un-remapped position. This can be useful in pre- or
post-processing to enable the unwrapping of long-chained molecules
which wrap thru the periodic box one or more times. The value of
&quot;n&quot; can be positive, negative, or zero. For 2-d simulations
specify nz as 0. </P>
<P>
For simulations with periodic boundary conditions, xyz are remapped
into the periodic box (from as far away as needed), so the initial
coordinates need not be inside the box. The nx,ny,nz values (as read in
or as set to zero by LAMMPS) are appropriately adjusted by this
remapping. </P>
<P>
The number of coefficients specified on each line of coefficient
entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
&quot;style&quot; of interaction. This is specified in the input
command script, unless the default is used. See the <A
HREF="input_commands.html">input_commands</A> page for a description
of the various style options. The <A HREF="input_commands.html">input_commands</A>
and <A HREF="force_fields.html">force_fields</A> pages explain the
meaning and valid ranges for each of the coefficients. </P>
<HR>
<H3>
<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
<P>
Here is a sample file with annotations in parenthesis and lengthy
sections replaced by dots (...). Note that the blank lines are
important in this example.</P>
<PRE>
LAMMPS Description (1st line of file)
100 atoms (this must be the 3rd line, 1st 2 lines are ignored)
95 bonds (# of bonds to be simulated)
50 angles (include these lines even if number = 0)
30 dihedrals
20 impropers
5 atom types (# of nonbond atom types)
10 bond types (# of bond types = sets of bond coefficients)
18 angle types
20 dihedral types (do not include a bond,angle,dihedral,improper type
2 improper types line if number of bonds,angles,etc is 0)
-0.5 0.5 xlo xhi (for periodic systems this is box size,
-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)
-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)
Masses
1 mass
...
N mass (N = # of atom types)
Nonbond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of atom types)
Bond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of bond types)
Angle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
Dihedral Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
Improper Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of improper types)
BondBond Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
BondAngle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of angle types)
MiddleBondTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
EndBondTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleAngleTorsion Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
BondBond13 Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of dihedral types)
AngleAngle Coeffs
1 coeff1 coeff2 ...
...
N coeff1 coeff2 ... (N = # of improper types)
Atoms
1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -
... see &quot;true flag&quot; input command)
...
N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)
Bonds
1 bond-type atom-1 atom-2
...
N bond-type atom-1 atom-2 (N = # of bonds)
Angles
1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)
...
N angle-type atom-1 atom-2 atom-3 (N = # of angles)
Dihedrals
1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)
...
N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)
Impropers
1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-1 is central atom)
...
N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)
</PRE>
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<BODY>
<H2>
LAMMPS Force Fields</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
<P>
This file outlines the force-field formulas used in LAMMPS. Read this
file in conjunction with the <A HREF="data_format.html">data_format</A>
and <A HREF="units.html">units</A> file.</P>
<P>
The sections of this page are as follows:</P>
<UL>
<LI>
<A HREF="#_cch3_930957465">Nonbond Coulomb</A>
<LI>
<A HREF="#_cch3_930957471">Nonbond Lennard-Jones</A>
<LI>
<A HREF="#_cch3_930957478">Mixing Rules for Lennard-Jones</A>
<LI>
<A HREF="#_cch3_930957482">Bonds</A>
<LI>
<A HREF="#_cch3_930957488">Angles</A>
<LI>
<A HREF="#_cch3_930957509">Dihedrals</A>
<LI>
<A HREF="#_cch3_930957513">Impropers</A>
<LI>
<A HREF="#_cch3_930957527">Class II Force Field</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_930957465">Nonbond Coulomb</A></H3>
<P>
Whatever Coulomb style is specified in the input command file, the
short-range Coulombic interactions are computed by this formula,
modified by an appropriate smoother for the smooth, Ewald, and PPPM
styles.</P>
<PRE>
E = C q1 q2 / (epsilon * r)
r = distance (computed by LAMMPS)
C = hardwired constant to convert to energy units
q1,q2 = charge of each atom in electron units (proton = +1),
specified in &quot;Atoms&quot; entry in data file
epsilon = dielectric constant (vacuum = 1.0),
set by user in input command file
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957471">Nonbond Lennard-Jones </A></H3>
<P>
The style of nonbond potential is specified in the input command file. </P>
<H4>
(1) lj/cutoff </H4>
<PRE>
E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ]
standard Lennard Jones potential
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(2) lj/switch </H4>
<PRE>
E = 4 epsilon [ (sigma/r)^12 - (sigma/r)^6 ] for r &lt; r_inner
= spline fit for r_inner &lt; r &lt; cutoff
= 0 for r &gt; cutoff
switching function (spline fit) is applied to standard LJ
within a switching region (from r_inner to cutoff) so that
energy and force go smoothly to zero
spline coefficients are computed by LAMMPS
so that at inner cutoff (r_inner) the potential, force,
and 1st-derivative of force are all continuous,
and at outer cutoff (cutoff) the potential and force
both go to zero
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
2 cutoffs (r_inner and cutoff) are set in input script
</PRE>
<H4>
(3) lj/shift </H4>
<PRE>
E = 4 epsilon [ (sigma/(r - delta))^12 - (sigma/(r - delta))^6 ]
same as lj/cutoff except that r is shifted by delta
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
coeff3 = delta (distance)
3 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(4) soft </H4>
<PRE>
E = A * [ 1 + cos( pi * r / cutoff ) ]
useful for pushing apart overlapping atoms by ramping A over time
r = distance (computed by LAMMPS)
coeff1 = prefactor A at start of run (energy)
coeff2 = prefactor A at end of run (energy)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<H4>
(5) class2/cutoff </H4>
<PRE>
E = epsilon [ 2 (sigma/r)^9 - 3 (sigma/r)^6 ]
used with class2 bonded force field
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = sigma (distance)
2 coeffs are listed in data file or set in input script
1 cutoff is set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957478">Mixing Rules for Lennard-Jones</A></H3>
<P>
The coefficients for each nonbond style are input in either the data
file by the &quot;read data&quot; command or in the input script using
the &quot;nonbond coeff&quot; command. In the former case, only one set
of coefficients is input for each atom type. The cross-type coeffs are
computed using one of three possible mixing rules: </P>
<PRE>
geometric: epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = sqrt(sigma_i * sigma_j)
arithmetic: epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = (sigma_i + sigma_j) / 2
sixthpower: epsilon_ij =
(2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij= ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</PRE>
<P>
The default mixing rule for nonbond styles lj/cutoff, lj/switch,
lj/shift, and soft is &quot;geometric&quot;. The default for nonbond
style class2/cutoff is &quot;sixthpower&quot;. </P>
<P>
The default can be overridden using the &quot;mixing style&quot;
command. The one exception to this is for the nonbond style soft, for
which only an epsilon prefactor is input. This is always mixed
geometrically. </P>
<P>
Also, for nonbond style lj/shift, the delta coefficient is always mixed
using the rule </P>
<UL>
<LI>
delta_ij = (delta_i + delta_j) / 2
</UL>
<HR>
<H3>
<A NAME="_cch3_930957482">Bonds</A></H3>
<P>
The style of bond potential is specified in the input command file.</P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (r - r0)^2
standard harmonic spring
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2) (the usual 1/2 is included in the K)
coeff2 = r0 (distance)
2 coeffs are listed in data file or set in input script
</PRE>
<H4>
(2) FENE/standard </H4>
<PRE>
E = -0.5 K R0^2 * ln[1 - (r/R0)^2] +
4 epsilon [(sigma/r)^12 - (sigma/r)^6] + epsilon
finite extensible nonlinear elastic (FENE) potential for
polymer bead-spring models
see Kremer, Grest, J Chem Phys, 92, p 5057 (1990)
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = R0 (distance)
coeff3 = epsilon (energy)
coeff4 = sigma (distance)
1st term is attraction, 2nd term is repulsion (shifted LJ)
1st term extends to R0
2nd term only extends to the minimum of the LJ potential,
a cutoff distance computed by LAMMPS (2^(1/6) * sigma)
4 coeffs are listed in data file or set in input script
</PRE>
<H4>
(3) FENE/shift </H4>
<PRE>
E = -0.5 K R0^2 * ln[1 - ((r - delta)/R0)^2] +
4 epsilon [(sigma/(r - delta))^12 - (sigma/(r - delta))^6] + epsilon
same as FENE/standard expect that r is shifted by delta
r = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = R0 (distance)
coeff3 = epsilon (energy)
coeff4 = sigma (distance)
coeff5 = delta (distance)
1st term is attraction, 2nd term is repulsion (shifted LJ)
1st term extends to R0
2nd term only extends to the minimum of the LJ potential,
a cutoff distance computed by LAMMPS (2^(1/6) * sigma + delta)
5 coeffs are listed in data file or set in input script
</PRE>
<H4>
(4) nonlinear </H4>
<PRE>
E = epsilon (r - r0)^2 / [ lamda^2 - (r - r0)^2 ]
non-harmonic spring of equilibrium length r0
with finite extension of lamda
see Rector, Van Swol, Henderson, Molecular Physics, 82, p 1009 (1994)
r = distance (computed by LAMMPS)
coeff1 = epsilon (energy)
coeff2 = r0 (distance)
coeff3 = lamda (distance)
3 coeffs are listed in data file or set in input script
</PRE>
<H4>
(5) class2 </H4>
<PRE>
E = K2 (r - r0)^2 + K3 (r - r0)^3 + K4 (r - r0)^4
r = distance (computed by LAMMPS)
coeff1 = r0 (distance)
coeff2 = K2 (energy/distance^2)
coeff3 = K3 (energy/distance^3)
coeff4 = K4 (energy/distance^4)
4 coeffs are listed in data file - cannot be set in input script
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957488">Angles </A></H3>
<P>
The style of angle potential is specified in the input command file. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (theta - theta0)^2
theta = radians (computed by LAMMPS)
coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
2 coeffs are listed in data file
</PRE>
<H4>
(2) class2 </H4>
<PRE>
E = K2 (theta - theta0)^2 + K3 (theta - theta0)^3 +
K4 (theta - theta0)^4
theta = radians (computed by LAMMPS)
coeff1 = theta0 (degrees) (converted to radians within LAMMPS)
coeff2 = K2 (energy/radian^2)
coeff3 = K3 (energy/radian^3)
coeff4 = K4 (energy/radian^4)
4 coeffs are listed in data file
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957509">Dihedrals </A></H3>
<P>
The style of dihedral potential is specified in the input command file. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K [1 + d * cos (n * phi) ]
phi = radians (computed by LAMMPS)
coeff1 = K (energy)
coeff2 = d (always +1 or -1)
coeff3 = n (1,2,3,4,6)
Cautions when comparing to other force fields:
some force fields reverse the sign convention on d so that
E = K [1 - d * cos(n*phi)]
some force fields divide/multiply K by the number of multiple
torsions that contain the j-k bond in an i-j-k-l torsion
some force fields let n be positive or negative which
corresponds to d = 1,-1
in the LAMMPS force field, the trans position = 180 degrees, while
in some force fields trans = 0 degrees
3 coeffs are listed in data file
</PRE>
<H4>
(2) class2 </H4>
<PRE>
E = SUM(n=1,3) { K_n [ 1 - cos( n*Phi - Phi0_n ) ] }
phi = radians (computed by LAMMPS)
coeff1 = K_1 (energy)
coeff2 = Phi0_1 (degrees) (converted to radians within LAMMPS)
coeff3 = K_2 (energy)
coeff4 = Phi0_2 (degrees) (converted to radians within LAMMPS)
coeff5 = K_3 (energy)
coeff6 = Phi0_3 (degrees) (converted to radians within LAMMPS)
6 coeffs are listed in data file
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957513">Impropers</A></H3>
<P>
The style of improper potential is specified in the input command file. </P>
<H4>
(1) harmonic </H4>
<PRE>
E = K (chi - chi0)^2
chi = radians (computed by LAMMPS)
coeff1 = K (energy/radian^2) (the usual 1/2 is included in the K)
coeff2 = chi0 (degrees) (converted to radians within LAMMPS)
in data file, listing of 4 atoms requires atom-1 as central atom
some force fields (AMBER,Discover) have atom-2 as central atom - it is really
an out-of-plane torsion, may need to treat as dihedral in LAMMPS
2 coeffs are listed in data file
</PRE>
<H4>
(2) class2 </H4>
<PRE>
same formula, coeffs, and meaning as &quot;harmonic&quot; except that LAMMPS
averages all 3 angle-contributions to chi
in class II this is called a Wilson out-of-plane interaction
2 coeffs are listed in data file
</PRE>
<HR>
<H3>
<A NAME="_cch3_930957527">Class II Force Field</A></H3>
<P>
If class II force fields are selected in the input command file,
additional cross terms are computed as part of the force field.</P>
<H4>
Bond-Bond (computed within class II angles) </H4>
<PRE>
E = K (r - r0) * (r' - r0')
r,r' = distance (computed by LAMMPS)
coeff1 = K (energy/distance^2)
coeff2 = r0 (distance)
coeff3 = r0' (distance)
3 coeffs are input in data file
</PRE>
<H4>
Bond-Angle (computed within class II angles for each of 2 bonds) </H4>
<PRE>
E = K_n (r - r0_n) * (theta - theta0)
r = distance (computed by LAMMPS)
theta = radians (computed by LAMMPS)
coeff1 = K_1 (energy/distance-radians)
coeff2 = K_2 (energy/distance-radians)
coeff3 = r0_1 (distance)
coeff4 = r0_2 (distance)
Note: theta0 is known from angle coeffs so don't need it specified here
4 coeffs are listed in data file
</PRE>
<H4>
Middle-Bond-Torsion (computed within class II dihedral) </H4>
<PRE>
E = (r - r0) * [ F1*cos(phi) + F2*cos(2*phi) + F3*cos(3*phi) ]
r = distance (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1 (energy/distance)
coeff2 = F2 (energy/distance)
coeff3 = F3 (energy/distance)
coeff4 = r0 (distance)
4 coeffs are listed in data file
</PRE>
<H4>
End-Bond-Torsion (computed within class II dihedral for each of 2
bonds) </H4>
<PRE>
E = (r - r0_n) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
r = distance (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1_1 (energy/distance)
coeff2 = F2_1 (energy/distance)
coeff3 = F3_1 (energy/distance)
coeff4 = F1_2 (energy/distance)
coeff5 = F2_3 (energy/distance)
coeff6 = F3_3 (energy/distance)
coeff7 = r0_1 (distance)
coeff8 = r0_2 (distance)
8 coeffs are listed in data file
</PRE>
<H4>
Angle-Torsion (computed within class II dihedral for each of 2 angles) </H4>
<PRE>
E = (theta - theta0) * [ F1_n*cos(phi) + F2_n*cos(2*phi) + F3_n*cos(3*phi) ]
theta = radians (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = F1_1 (energy/radians)
coeff2 = F2_1 (energy/radians)
coeff3 = F3_1 (energy/radians)
coeff4 = F1_2 (energy/radians)
coeff5 = F2_3 (energy/radians)
coeff6 = F3_3 (energy/radians)
coeff7 = theta0_1 (degrees) (converted to radians within LAMMPS)
coeff8 = theta0_2 (degrees) (converted to radians within LAMMPS)
8 coeffs are listed in data file
</PRE>
<H4>
Angle-Angle-Torsion (computed within class II dihedral) </H4>
<PRE>
E = K (theta - theta0) * (theta' - theta0') * (phi - phi0)
theta,theta' = radians (computed by LAMMPS)
phi = radians (computed by LAMMPS)
coeff1 = K (energy/radians^3)
coeff2 = theta0 (degrees) (converted to radians within LAMMPS)
coeff3 = theta0' (degrees) (converted to radians within LAMMPS)
Note: phi0 is known from dihedral coeffs so don't need it specified here
3 coeffs are listed in data file
</PRE>
<H4>
Bond-Bond-13-Torsion (computed within class II dihedral) </H4>
<PRE>
(undocumented)
</PRE>
<H4>
Angle-Angle (computed within class II improper for each of 3 pairs of
angles) </H4>
<PRE>
E = K_n (theta - theta0_n) * (theta' - theta0_n')
theta,theta' = radians (computed by LAMMPS)
coeff1 = K_1 (energy/radians^2)
coeff2 = K_2 (energy/radians^2)
coeff3 = K_3 (energy/radians^2)
coeff4 = theta0_1 (degrees) (converted to radians within LAMMPS)
coeff5 = theta0_2 (degrees) (converted to radians within LAMMPS)
coeff6 = theta0_3 (degrees) (converted to radians within LAMMPS)
6 coeffs are listed in data file
</PRE>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
</HEAD>
<BODY>
<H2>
History of LAMMPS</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<P>
This is a brief history of features added to each version of LAMMPS.</P>
<HR>
<H3>
LAMMPS 99 - June 99 </H3>
<UL>
<LI>
all-MPI version of code (F77 + C + MPI) for maximum portablility
<LI>
only one PPPM choice now, the better of the two earlier ones
<LI>
PPPM uses portable FFTs and data remapping routines, written in C w/
MPI, can now use non-power-of-2 processors and grid sizes
<LI>
auto-mapping of simulation box to processors
<LI>
removed a few unused/unneeded commands (bdump, log file, id string,
limit)
<LI>
changed syntax of some commands for simplicity &amp; consistency (see <A
HREF="input_commands.html">input commands</A>)
<LI>
changed method of calling/writing user diagnostic routines to be simpler
<LI>
documentation in HTML format
</UL>
<HR>
<H3>
Version 5.0 - Oct 1997 </H3>
<UL>
<LI>
final version of class II force fields
<LI>
new formulation of NVE, NVT, NPT and rRESPA integrators
<LI>
new version of msi2lmp pre-processing tool, does not require DISCOVER
to run, only DISCOVER force field files
<LI>
energy minimizer, Hessian-free truncated Newton method
<LI>
new pressure controllers and constraints
<LI>
replicate tool for generating new data files from old ones
</UL>
<HR ALIGN="LEFT">
<H3>
Version 4.0 - March 1997 </H3>
<UL>
<LI>
1st version of class II force fields
<LI>
new, faster PPPM solver (newpppm)
<LI>
rRESPA
<LI>
new data file format
<LI>
new constraints, diagnostics
<LI>
msi2lmp pre-processing tool
</UL>
<HR>
<H3>
Version 3.0 - March 1996 </H3>
<UL>
<LI>
more general force-field formulation
<LI>
atom/group constraints
<LI>
LJ units and bond potentials
<LI>
smoothed LJ potential option
<LI>
Langevin thermostat
<LI>
Newton's 3rd law option
<LI>
hook for user-supplied diagnostic routines
</UL>
<HR>
<H3>
Version 2.0 - October 1995 </H3>
<UL>
<LI>
bug fix of velocity initialization which caused drift
<LI>
PPPM for long-range Coulombic
<LI>
constant NPT
</UL>
<HR>
<H3>
Version 1.1 - February 1995 </H3>
<UL>
<LI>
Ewald for long-range Coulombic
<LI>
full Newton's 3rd law (doubled communication)
<LI>
dumping of atom positions and velocities
<LI>
restart files
</UL>
<HR>
<H3>
Version 1.0 - January 1995 </H3>
<UL>
<LI>
short-range bonded and non-bonded forces
<LI>
partial Newton's 3rd law
<LI>
velocity-Verlet integrator
</UL>
</BODY>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
</HEAD>
<BODY>
<H2>
LAMMPS Units</H2>
<P>
<A HREF="README.html">Return</A> to top-level LAMMPS documentation.</P>
<P>
This file describes the units associated with many of the key variables
and equations used inside the LAMMPS code. Units used for input command
parameters are described in the input_commands file. The input command
&quot;units&quot; selects between conventional and Lennard-Jones units.
See the force_fields file for more information on units for the force
field parameters that are input from data files. </P>
<P>
Conventional units: </P>
<UL>
<LI>
distance = Angstroms
<LI>
time = femtoseconds
<LI>
mass = grams/mole
<LI>
temperature = degrees K
<LI>
pressure = atmospheres
<LI>
energy = Kcal/mole
<LI>
velocity = Angstroms/femtosecond
<LI>
force = grams/mole * Angstroms/femtosecond^2
<LI>
charge = +/- 1.0 is proton/electron
</UL>
<P>
LJ reduced units: </P>
<UL>
<LI>
distance = sigmas
<LI>
time = reduced LJ tau
<LI>
mass = ratio to unitless 1.0
<LI>
temperature = reduced LJ temp
<LI>
pressure = reduced LJ pressure
<LI>
energy = epsilons
<LI>
velocity = sigmas/tau
<LI>
force = reduced LJ force (sigmas/tau^2)
<LI>
charge = ratio to unitless 1.0
</UL>
<HR>
<P>
This listing of variables assumes conventional units; to convert to LJ
reduced units, simply substitute the appropriate term from the list
above. E.g. x is in sigmas in LJ units. Per-mole in any of the units
simply means for 6.023 x 10^23 atoms.</P>
<P>
</P>
<PRE>
Meaning Variable Units
positions x Angstroms
velocities v Angstroms / click (see below)
forces f Kcal / (mole - Angstrom)
masses mass gram / mole
charges q electron units (-1 for an electron)
(1 e.u. = 1.602 x 10^-19 coul)
time --- clicks (1 click = 48.88821 fmsec)
timestep dt clicks
input timestep dt_in fmsec
time convert dtfactor 48.88821 fmsec / click
temperature t_current degrees K
t_start
t_stop
input damping t_freq_in inverse fmsec
internal temp t_freq inverse clicks
damping
dielec const dielectric 1.0 (unitless)
Boltmann const boltz 0.001987191 Kcal / (mole - degree K)
virial virial[xyz] Kcal/mole = r dot F
pressure factor pfactor 68589.796 (convert internal to atmospheres)
internal p_current Kcal / (mole - Angs^3)
pressure p_start
p_stop
input press p_start_in atmospheres
p_stop_in
output press log file atmospheres
input damping p_freq_in inverse time
internal press p_freq inverse clicks
damping
pot eng e_potential Kcal/mole
kin eng e_kinetic Kcal/mole
eng convert efactor 332.0636 (Kcal - Ang) / (q^2 - mole)
(convert Coulomb eng to Kcal/mole)
LJ coeffs lja,ljb Kcal-Angs^(6,12)/mole
bond various see force_fields file
parameters 2,3,4-body
terms
</PRE>
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#FIG 3.2 Produced by xfig version 3.2.5a
Portrait
Center
Inches
Letter
100.00
Single
-2
1200 2
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2232 1170 3540 1170 3540 1505 2232 1505 2232 1170
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2220 1830 3015 1830 3015 2219 2220 2219 2220 1830
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2226 3285 3300 3285 3300 3665 2226 3665 2226 3285
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2223 5190 3225 5190 3225 5525 2223 5525 2223 5190
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2232 7125 3090 7125 3090 7478 2232 7478 2232 7125
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
2226 10230 3300 10230 3300 10565 2226 10565 2226 10230
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4026 10305 4980 10305 4980 10592 4026 10592 4026 10305
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4029 9900 5205 9900 5205 10250 4029 10250 4029 9900
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4038 9315 5370 9315 5370 9659 4038 9659 4038 9315
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4023 8955 4530 8955 4530 9278 4023 9278 4023 8955
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4029 8475 5190 8475 5190 8762 4029 8762 4029 8475
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4008 8115 5430 8115 5430 8408 4008 8408 4008 8115
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4026 7425 4995 7425 4995 7712 4026 7712 4026 7425
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4035 6720 4650 6720 4650 7025 4035 7025 4035 6720
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4044 7080 4830 7080 4830 7358 4044 7358 4044 7080
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
4032 6105 5205 6105 5205 6419 4032 6419 4032 6105
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3486 6129 3996 6249
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3361 9291 3991 9531
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3345 9129 4005 9099
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3691 4412 4216 4277
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\documentclass{article}
\usepackage{graphicx}
\begin{document}
\centerline{\Large \bf LAMMPS Developer Guide}
\centerline{\bf 23 Aug 2011}
\vspace{0.5in}
This document is a developer guide to the LAMMPS molecular dynamics
package, whose WWW site is at lammps.sandia.gov. It describes the
internal structure and algorithms of the code. Sections will be added
as we have time, and in response to requests from developers and
users.
\tableofcontents
\pagebreak
\section{LAMMPS source files}
LAMMPS source files are in two directories of the distribution
tarball. The src directory has the majority of them, all of which are
C++ files (*.cpp and *.h). Many of these files are in the src
directory itself. There are also dozens of "packages", which can be
included or excluded when LAMMPS is built. See the
doc/Section\_build.html section of the manual for more information
about packages, or type "make" from within the src directory, which
lists package-related commands, such as ``make package-status''. The
source files for each package are in an all-uppercase sub-directory of
src, like src/MOLECULE or src/USER-CUDA. If the package is currently
installed, copies of the package source files will also exist in the
src directory itself. The src/STUBS sub-directory is not a package
but contains a dummy version of the MPI library, used when building a
serial version of the code.
The lib directory also contains source code for external libraries,
used by a few of the packages. Each sub-directory, like meam or gpu,
contains the source files, some of which are in different languages
such as Fortran. The files are compiled into libraries from within
each sub-directory, e.g. performing a "make" in the lib/meam directory
creates a libmeam.a file. These libraries are linked to during a
LAMMPS build, if the corresponding package is installed.
LAMMPS C++ source files almost always come in pairs, such as run.cpp
and run.h. The pair of files defines a C++ class, the Run class in
this case, which contains the code invoked by the "run" command in a
LAMMPS input script. As this example illustrates, source file and
class names often have a one-to-one correspondence with a command used
in a LAMMPS input script. Some source files and classes do not have a
corresponding input script command, e.g. force.cpp and the Force
class. They are discussed in the next section.
\pagebreak
\section{Class hierarchy of LAMMPS}
Though LAMMPS has a lot of source files and classes, its class
hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each
boxed name refers to a class and has a pair of associated source files
in lammps/src, e.g. memory.cpp and memory.h. More details on the
class and its methods and data structures can be found by examining
its *.h file.
LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It
holds an "instance" of LAMMPS and can be instantiated one or more
times by a calling code. For example, the file src/main.cpp simply
instantiates one instance of LAMMPS and passes it the input script.
The file src/library.cpp contains a C-style library interface to the
LAMMPS class. See the lammps/couple and lammps/python directories for
examples of simple programs that use LAMMPS through its library
interface. A driver program can instantiate the LAMMPS class multiple
times, e.g. to embed several atomistic simulation regions within a
mesoscale or continuum simulation domain.
There are a dozen or so top-level classes within the LAMMPS class that
are visible everywhere in the code. They are shaded blue in Fig
\ref{fig:classes}. Thus any class can refer to the y-coordinate of
local atom $I$ as atom$\rightarrow$x[i][1]. This visibility is
enabled by a bit of cleverness in the Pointers class (see
src/pointers.h) which every class inherits from.
There are a handful of virtual parent classes in LAMMPS that define
what LAMMPS calls "styles". They are shaded red in Fig
\ref{fig:classes}. Each of these are parents of a number of child
classes that implement the interface defined by the parent class. For
example, the fix style has around 100 child classes. They are the
possible fixes that can be specified by the fix command in an input
script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding
classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
etc. The source files for these classes are easy to identify in the
src directory, since they begin with the word "fix", e,g,
fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
The one exception is child class files for the "command" style. These
implement specific commands in the input script that can be invoked
before/after/between runs or which launch a simulation. Examples are
the create\_box, minimize, run, and velocity commands which encode the
CreateBox, Minimize, Run, and Velocity classes. The corresponding
files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
The list of command style files can be found by typing "grep
COMMAND\_CLASS *.h" from within the src directory, since that word in
the header file identifies the class as an input script command.
Similar words can be grepped to list files for the other LAMMPS
styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
FIX\_CLASS, COMPUTE\_CLASS, DUMP\_CLASS, etc.
\begin{figure}[htb]
\begin{center}
\includegraphics[height=4in]{classes.pdf}
\end{center}
\caption{Class hierarchy within LAMMPS source code.}
\label{fig:classes}
\end{figure}
More details on individual classes in Fig \ref{fig:classes} are as
follows:
\begin{itemize}
\item The Memory class handles allocation of all large vectors and
arrays.
\item The Error class prints all error and warning messages.
\item The Universe class sets up partitions of processors so that
multiple simulations can be run, each on a subset of the processors
allocated for a run, e.g. by the mpirun command.
\item The Input class reads an input script, stores variables, and
invokes stand-alone commands that are child classes of the Command
class.
\item As discussed above, the Command class is a parent class for
certain input script commands that perform a one-time operation
before/after/between simulations or which invoke a simulation. They
are instantiated from within the Input class, invoked, then
immediately destructed.
\item The Finish class is instantiated to print statistics to the
screen after a simulation is performed, by commands like run and
minimize.
\item The Special class walks the bond topology of a molecular system
to find 1st, 2nd, 3rd neighbors of each atom. It is invoked by
several commands, like read\_data, read\_restart, and replicate.
\item The Atom class stores all per-atom arrays. More precisely, they
are allocated and stored by the AtomVec class, and the Atom class
simply stores a pointer to them. The AtomVec class is a parent
class for atom styles, defined by the atom\_style command.
\item The Update class holds an integrator and a minimizer. The
Integrate class is a parent style for the Verlet and rRESPA time
integrators, as defined by the run\_style input command. The Min
class is a parent style for various energy minimizers.
\item The Neighbor class builds and stores neighbor lists. The
NeighList class stores a single list (for all atoms). The
NeighRequest class is called by pair, fix, or compute styles when
they need a particular kind of neighbor list.
\item The Comm class performs interprocessor communication, typically
of ghost atom information. This usually involves MPI message
exchanges with 6 neighboring processors in the 3d logical grid of
processors mapped to the simulation box. Sometimes the Irregular
class is used, when atoms may migrate to arbitrary processors.
\item The Domain class stores the simulation box geometry, as well as
geometric Regions and any user definition of a Lattice. The latter
are defined by region and lattice commands in an input script.
\item The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
lingo includes many-body forces such as the Tersoff 3-body
potential. The Bond, Angle, Dihedral, Improper parent classes are
styles for bonded interactions within a static molecular topology.
The KSpace parent class is for computing long-range Coulombic
interactions. One of its child classes, PPPM, uses the FFT3D and
Remap classes to communicate grid-based information with neighboring
processors.
\item The Modify class stores lists of Fix and Compute classes, both
of which are parent styles.
\item The Group class manipulates groups that atoms are assigned to
via the group command. It also computes various attributes of
groups of atoms.
\item The Output class is used to generate 3 kinds of output from a
LAMMPS simulation: thermodynamic information printed to the screen
and log file, dump file snapshots, and restart files. These
correspond to the Thermo, Dump, and WriteRestart classes
respectively. The Dump class is a parent style.
\item The Timer class logs MPI timing information, output at the end
of a run.
\end{itemize}
%%\pagebreak
%%\section{Spatial decomposition and parallel operations}
%%distributed memory
%%Ref to JCP paper
%%diagram of 3d grid of procs and spatial decomp
%%6-way comm
%%ghost atoms, PBC added when comm (in atom class)
%%\pagebreak
%%\section{Fixes, computes, variables}
%%fixes intercolate in timestep, store per-atom info
%%computes based on current snapshot
%%equal- and atom-style variables
%%output they produce - see write-up in HowTo
\pagebreak
\section{How a timestep works}
The first and most fundamental operation within LAMMPS to understand
is how a timestep is structured. Timestepping is performed by the
Integrate class within the Update class. Since Integrate is a parent
class, corresponding to the run\_style input script command, it has
child classes. In this section, the timestep implemented by the
Verlet child class is described. A similar timestep is implemented by
the Respa child class, for the rRESPA hierarchical timestepping
method. The Min parent class performs energy minimization, so does
not perform a literal timestep. But it has logic similar to what is
described here, to compute forces and invoke fixes at each iteration
of a minimization. Differences between time integration and
minimization are highlighted at the end of this section.
The Verlet class is encoded in the src/verlet.cpp and verlet.h files.
It implements the velocity-Verlet timestepping algorithm. The
workhorse method is Verlet::run(), but first we highlight several
other methods in the class.
\begin{itemize}
\item The init() method is called at the beginning of each dynamics
run. It simply sets some internal flags, based on user settings in
other parts of the code.
\item The setup() or setup\_minimal() methods are also called before
each run. The velocity-Verlet method requires current forces be
calculated before the first timestep, so these routines compute
forces due to all atomic interactions, using the same logic that
appears in the timestepping described next. A few fixes are also
invoked, using the mechanism described in the next section. Various
counters are also initialized before the run begins. The
setup\_minimal() method is a variant that has a flag for performing
less setup. This is used when runs are continued and information
from the previous run is still valid. For example, if repeated
short LAMMPS runs are being invoked, interleaved by other commands,
via the ``pre no'' and ``every'' options of the run command, the
setup\_minimal() method is used.
\item The force\_clear() method initializes force and other arrays to
zero before each timestep, so that forces (torques, etc) can be
accumulated.
\end{itemize}
Now for the Verlet::run() method. Its structure in hi-level pseudo
code is shown in Fig \ref{fig:verlet}. In the actual code in
src/verlet.cpp some of these operations are conditionally invoked.
\begin{figure}[htb]
\begin{center}
\begin{verbatim}
loop over N timesteps:
ev_set()
fix->initial_integrate()
fix->post_integrate()
nflag = neighbor->decide()
if nflag:
fix->pre_exchange()
domain->pbc()
domain->reset_box()
comm->setup()
neighbor->setup_bins()
comm->exchange()
comm->borders()
fix->pre_neighbor()
neighbor->build()
else
comm->forward_comm()
force_clear()
fix->pre_force()
pair->compute()
bond->compute()
angle->compute()
dihedral->compute()
improper->compute()
kspace->compute()
comm->reverse_comm()
fix->post_force()
fix->final_integrate()
fix->end_of_step()
if any output on this step: output->write()
\end{verbatim}
\end{center}
\caption{Pseudo-code for the Verlet::run() method.}
\label{fig:verlet}
\end{figure}
The ev\_set() method (in the parent Integrate class), sets two flags
({\em eflag} and {\em vflag}) for energy and virial computation. Each
flag encodes whether global and/or per-atom energy and virial should
be calculated on this timestep, because some fix or variable or output
will need it. These flags are passed to the various methods that
compute particle interactions, so that they can skip the extra
calculations if the energy and virial are not needed. See the
comments with the Integrate::ev\_set() method which document the flag
values.
At various points of the timestep, fixes are invoked,
e.g. fix$\rightarrow$initial\_integrate(). In the code, this is
actually done via the Modify class which stores all the Fix objects
and lists of which should be invoked at what point in the timestep.
Fixes are the LAMMPS mechanism for tailoring the operations of a
timestep for a particular simulation. As described elsewhere
(unwritten section), each fix has one or more methods, each of which
is invoked at a specific stage of the timestep, as in Fig
\ref{fig:verlet}. All the fixes defined in an input script with an
initial\_integrate() method are invoked at the beginning of each
timestep. Fix nve, nvt, npt are examples, since they perform the
start-of-timestep velocity-Verlet integration to update velocities by
a half-step, and coordinates by a full step. The post\_integrate()
method is next. Only a few fixes use this, e.g. to reflect particles
off box boundaries in the FixWallReflect class.
The decide() method in the Neighbor class determines whether neighbor
lists need to be rebuilt on the current timestep. If not, coordinates
of ghost atoms are acquired by each processor via the forward\_comm()
method of the Comm class. If neighbor lists need to be built, several
operations within the inner if clause of Fig \ref{fig:verlet} are
first invoked. The pre\_exchange() method of any defined fixes is
invoked first. Typically this inserts or deletes particles from the
system.
Periodic boundary conditions are then applied by the Domain class via
its pbc() method to remap particles that have moved outside the
simulation box back into the box. Note that this is not done every
timestep. but only when neighbor lists are rebuilt. This is so that
each processor's sub-domain will have consistent (nearby) atom
coordinates for its owned and ghost atoms. It is also why dumped atom
coordinates can be slightly outside the simulation box.
The box boundaries are then reset (if needed) via the reset\_box()
method of the Domain class, e.g. if box boundaries are shrink-wrapped
to current particle coordinates. A change in the box size or shape
requires internal information for communicating ghost atoms (Comm
class) and neighbor list bins (Neighbor class) be updated. The
setup() method of the Comm class and setup\_bins() method of the
Neighbor class perform the update.
The code is now ready to migrate atoms that have left a processor's
geometric sub-domain to new processors. The exchange() method of the
Comm class performs this operation. The borders() method of the Comm
class then identifies ghost atoms surrounding each processor's
sub-domain and communicates ghost atom information to neighboring
processors. It does this by looping over all the atoms owned by a
processor to make lists of those to send to each neighbor processor.
On subsequent timesteps, the lists are used by the
Comm::forward\_comm() method.
Fixes with a pre\_neighbor() method are then called. These typically
re-build some data structure stored by the fix that depends on the
current atoms owned by each processor.
Now that each processor has a current list of its owned and ghost
atoms, LAMMPS is ready to rebuild neighbor lists via the build()
method of the Neighbor class. This is typically done by binning all
owned and ghost atoms, and scanning a stencil of bins around each
owned atom's bin to make a Verlet list of neighboring atoms within the
force cutoff plus neighbor skin distance.
In the next portion of the timestep, all interaction forces between
particles are computed, after zeroing the per-atom force vector via
the force\_clear() method. If the newton flag is set to ``on'' by the
newton command, forces on both owned and ghost atoms are calculated.
Pairwise forces are calculated first, which enables the global virial
(if requested) to be calculated cheaply (at the end of the
Pair::compute() method), by a dot product of atom coordinates and
forces. By including owned and ghost atoms in the dot product, the
effect of periodic boundary conditions is correctly accounted for.
Molecular topology interactions (bonds, angles, dihedrals, impropers)
are calculated next. The final contribution is from long-range
Coulombic interactions, invoked by the KSpace class.
If the newton flag is on, forces on ghost atoms are communicated and
summed back to their corresponding owned atoms. The reverse\_comm()
method of the Comm class performs this operation, which is essentially
the inverse operation of sending copies of owned atom coordinates to
other processor's ghost atoms.
At this point in the timestep, the total force on each atom is known.
Additional force constraints (external forces, SHAKE, etc) are applied
by Fixes that have a post\_force() method. The second half of the
velocity-Verlet integration is then performed (another half-step
update of the velocities) via fixes like nve, nvt, npt.
At the end of the timestep, fixes that define an end\_of\_step()
method are invoked. These typically perform a diagnostic calculation,
e.g. the ave/time and ave/spatial fixes. The final operation of the
timestep is to perform any requested output, via the write() method of
the Output class. There are 3 kinds of LAMMPS output: thermodynamic
output to the screen and log file, snapshots of atom data to a dump
file, and restart files. See the thermo\_style, dump, and restart
commands for more details.
The iteration performed by an energy minimization is similar to the
dynamics timestep of Fig \ref{fig:verlet}. Forces are computed,
neighbor lists are built as needed, atoms migrate to new processors,
and atom coordinates and forces are communicated to neighboring
processors. The only difference is what Fix class operations are
invoked when. Only a subset of LAMMPS fixes are useful during energy
minimization, as explained in their individual doc pages. The
relevant Fix class methods are min\_pre\_exchange(),
min\_pre\_force(), and min\_post\_force(). Each is invoked at the
appropriate place within the minimization iteration. For example, the
min\_post\_force() method is analogous to the post\_force() method for
dynamics; it is used to alter or constrain forces on each atom, which
affects the minimization procedure.
\pagebreak
\section{Extending LAMMPS}
The Section\_modify.html file in the doc directory of
the LAMMPS distribution gives an overview of how LAMMPS can
be extended by writing new classes that derive from existing
parent classes in LAMMPS. Here, some specific coding
details are provided for writing a new fix.
\subsection{New fixes}
(this section provided by Kirill Lykov)
\vspace{0.25cm}
Writing fixes is a flexible way of extending LAMMPS. Users can
implement many things using fixes:
\begin{itemize}
\item changing particles attributes (positions, velocities, forces, etc.).
Example: FixFreeze.
\item reading/writing data. Example: FixRestart.
\item implementing boundary conditions. Example: FixWall.
\item saving information about particles for future use (previous positions,
for instance). Example: FixStoreState.
\end{itemize}
All fixes are derived from class Fix and must have constructor with the
signature: FixMine(class LAMMPS *, int, char **).
Every fix must be registered in LAMMPS by writing the following lines
of code in the header before include guards:
\begin{center}
\begin{verbatim}
#ifdef FIX_CLASS
FixStyle(your/fix/name,FixMine)
#else
\end{verbatim}
\end{center}
Where "your/fix/name" is a name of your fix in the script and FixMine
is the name of the class. This code allows LAMMPS to find your fix
when it parses input script. In addition, your fix header must be
included in the file "style\_fix.h". In case if you use LAMMPS make,
this file is generated automatically - all files starting with prefix
fix\_ are included, so call your header the same way. Otherwise, donÕt
forget to add your include into "style\_fix.h".
Let's write a simple fix which will print average velocity at the end
of each timestep. First of all, implement a constructor:
\begin{center}
\begin{verbatim}
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg)
{
if (narg < 4)
error->all(FLERR,"Illegal fix print command");
nevery = atoi(arg[3]);
if (nevery <= 0)
error->all(FLERR,"Illegal fix print command");
}
\end{verbatim}
\end{center}
In the constructor you should parse your fix arguments which are
specified in the script. All fixes have pretty the same syntax: fix
[fix\_identifier] [group\_name] [fix\_name] [fix\_arguments]. The
first 3 parameters are parsed by Fix class constructor, while
[fix\_arguments] should be parsed by you. In our case, we need to
specify how often we want to print an average velocity. For instance,
once in 50 timesteps: fix 1 print/vel 50. There is a special variable
in Fix class called nevery which specifies how often method
end\_of\_step() is called. Thus all we need to do is just set it up.
The next method we need to implement is setmask():
\begin{center}
\begin{verbatim}
int FixPrintVel::setmask()
{
int mask = 0;
mask |= FixConst::END_OF_STEP;
return mask;
}
\end{verbatim}
\end{center}
Here user specifies which methods of your fix should be called during
the execution. For instance, END\_OF\_STEP corresponds to the
end\_of\_step() method. Overall, there are 8 most important methods,
methods are called in predefined order during the execution of the
verlet algorithm as was mentioned in the Section 3:
\begin{itemize}
\item initial\_integrate()
\item post\_integrate()
\item pre\_exchange()
\item pre\_neighbor()
\item pre\_force()
\item post\_force()
\item final\_integrate()
\item end\_of\_step()
\end{itemize}
Fix developer must understand when he wants to execute his code. In
case if we want to write FixPrintVel, we need only end\_of\_step():
\begin{center}
\begin{verbatim}
void FixPrintVel::end_of_step()
{
// for add3, scale3
using namespace MathExtra;
double** v = atom->v;
int nlocal = atom->nlocal;
double localAvgVel[4]; // 4th element for particles count
memset(localAvgVel, 0, 4 * sizeof(double));
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
add3(localAvgVel, v[particleInd], localAvgVel);
}
localAvgVel[3] = nlocal;
double globalAvgVel[4];
memset(globalAvgVel, 0, 4 * sizeof(double));
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
scale3(1.0 / globalAvgVel[3], globalAvgVel);
if (comm->me == 0) {
printf("\%e, \%e, \%e\n",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
}
}
\end{verbatim}
\end{center}
In the code above, we use MathExtra routines defined in
"math\_extra.h". There are bunch of math functions to work with
arrays of doubles as with math vectors.
In this code we use an instance of Atom class. This object is stored
in the Pointers class (see "pointers.h"). This object contains all
global information about the simulation system. Data from Pointers
class available to all classes inherited from it using protected
inheritance. Hence when you write you own class, which is going to use
LAMMPS data, don't forget to inherit from Pointers. When writing
fixes we inherit from class Fix which is inherited from Pointers so
there is no need to inherit from it directly.
The code above computes average velocity for all particles in the
simulation. Yet you have one unused parameter in fix call from the
script - [group\_name]. This parameter specifies the group of atoms
used in the fix. So we should compute average for all particles in the
simulation if group\_name == all, but it can be any group. The group
information is specified by groupbit which is defined in class Fix:
\begin{center}
\begin{verbatim}
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
if (atom->mask[particleInd] & groupbit) {
//Do all job here
}
}
\end{verbatim}
\end{center}
Class Atom encapsulates atoms positions, velocities, forces, etc. User
can access them using particle index. Note, that particle indexes are
usually changed every timestep because of sorting.
Lets consider another Fix example. We want to have a fix which stores
atoms position from previous time step in your fix. The local atoms
indexes will not be valid on the next iteration. In order to handle
this situation there are several methods which should be implemented:
\begin{itemize}
\item \verb|double memory_usage| - return how much memory fix uses
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
in your fix
\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information
to j-th. Used when atoms sorting is performed
\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
\end{itemize}
Note, that if your class implements these methods, it must call add calls of
add\_callback and delete\_callback to constructor and destructor:
\begin{center}
\begin{verbatim}
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg) {
//...
atom->add_callback(0);
}
FixSavePos::~FixSavePos() {
atom->delete_callback(id, 0);
}
\end{verbatim}
\end{center}
Since we want to store positions of atoms from previous timestep, we
need to add double** x to the header file. Than add allocation code to
constructor:
\verb|memory->create(this->x, atom->nmax, 3, "FixSavePos:x");|. Free memory
at destructor: \verb|memory->destroy(x);|
Finally, implement mentioned methods:
\begin{center}
\begin{verbatim}
double FixSavePos::memory_usage()
{
int nmax = atom->nmax;
double bytes = 0.0;
bytes += nmax * 3 * sizeof(double);
return bytes;
}
void FixSavePos::grow_arrays(int nmax)
{
memory->grow(this->x, nmax, 3, "FixSavePos:x");
}
void FixSavePos::copy_arrays(int i, int j)
{
memcpy(this->x[j], this->x[i], sizeof(double) * 3);
}
void FixSavePos::set_arrays(int i)
{
memset(this->x[i], 0, sizeof(double) * 3);
}
int FixSavePos::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
return m;
}
int FixSavePos::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
return m;
}
\end{verbatim}
\end{center}
Now, a little bit about memory allocation. We used Memory class which
is just a bunch of template functions for allocating 1D and 2D
arrays. So you need to add include "memory.h" to have access to them.
Finally, if you need to write/read some global information used in
your fix to the restart file, you might do it by setting flag
restart\_global = 1 in the constructor and implementing methods void
write\_restart(FILE *fp) and void restart(char *buf).
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
\begin{center}
\large{Additional documentation for the Gay-Berne ellipsoidal potential \\
as implemented in LAMMPS}
\end{center}
\centerline{Mike Brown, Sandia National Labs, April 2007}
\vspace{0.3in}
The Gay-Berne anisotropic LJ interaction between pairs of dissimilar
ellipsoidal particles is given by
$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
where $\mathbf{A}_1$ and $\mathbf{A}_2$ are the transformation
matrices from the simulation box frame to the body frame and
$\mathbf{r}_{12}$ is the center to center vector between the
particles. $U_r$ controls the shifted distance dependent interaction
based on the distance of closest approach of the two particles
($h_{12}$) and the user-specified shift parameter gamma:
$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be
given by the ellipsoid radii. The $\eta$ orientation-dependent energy
based on the user-specified exponent $\upsilon$ is given by
$$ \eta_{12} = [ \frac{ 2 s_1 s_2 }{\det ( \mathbf{G}_{12} )}]^{
\upsilon / 2 } , $$
$$ s_i = [a_i b_i + c_i c_i][a_i b_i]^{ 1 / 2 }, $$
and
$$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 = \mathbf{G}_1 +
\mathbf{G}_2. $$
Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by
the relative well depths (dimensionless energy scales
inversely proportional to the well-depths of the respective
orthogonal configurations of the interacting molecules). The
$\chi$ orientation-dependent energy based on the user-specified
exponent $\mu$ is given by
$$ \chi_{12} = [2 \hat{\mathbf{r}}_{12}^T \mathbf{B}_{12}^{-1}
\hat{\mathbf{r}}_{12}]^\mu, $$
$$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
and
$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
\mathbf{B}_2. $$
Here, we use the distance of closest approach approximation given by the
Perram reference, namely
$$ h_{12} = r - \sigma_{12} ( \mathbf{A}_1, \mathbf{A}_2,
\mathbf{r}_{12} ), $$
$$ r = |\mathbf{r}_{12}|, $$
and
$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}_{12}^T
\mathbf{G}_{12}^{-1} \hat{\mathbf{r}}_{12}.]^{ -1/2 } $$
Forces and Torques: Because the analytic forces and torques have not
been published for this potential, we list them here:
$$ \mathbf{f} = - \eta_{12} ( U_r \cdot { \frac{\partial \chi_{12}
}{\partial r} } + \chi_{12} \cdot { \frac{\partial U_r }{\partial r} }
) $$
where the derivative of $U_r$ is given by (see Allen reference)
$$ \frac{\partial U_r }{\partial r} = \frac{ \partial U_{SLJ} }{
\partial r } \hat{\mathbf{r}}_{12} + r^{-2} \frac{ \partial U_{SLJ} }{
\partial \varphi } [ \mathbf{\kappa} - ( \mathbf{\kappa}^T \cdot
\hat{\mathbf{r}}_{12}) \hat{\mathbf{r}}_{12} ], $$
$$ \frac{ \partial U_{SLJ} }{ \partial \varphi } = 24 \epsilon ( 2
\varrho^{13} - \varrho^7 ) \sigma_{12}^3 / 2 \sigma, $$
$$ \frac{ \partial U_{SLJ} }{ \partial r } = 24 \epsilon ( 2
\varrho^{13} - \varrho^7 ) / \sigma, $$
and
$$ \mathbf{\kappa} = \mathbf{G}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
The derivate of the $\chi$ term is given by
$$ \frac{\partial \chi_{12} }{\partial r} = - r^{-2} \cdot 4.0 \cdot [
\mathbf{\iota} - ( \mathbf{\iota}^T \cdot \hat{\mathbf{r}}_{12} )
\hat{\mathbf{r}}_{12} ] \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu
}, $$
and
$$ \mathbf{\iota} = \mathbf{B}_{12}^{-1} \cdot \mathbf{r}_{12}. $$
The torque is given by:
$$ \mathbf{\tau}_i = U_r \eta_{12} \frac{ \partial \chi_{12} }{
\partial \mathbf{q}_i } + \chi_{12} ( U_r \frac{ \partial \eta_{12} }{
\partial \mathbf{q}_i } + \eta_{12} \frac{ \partial U_r }{ \partial
\mathbf{q}_i } ), $$
$$ \frac{ \partial U_r }{ \partial \mathbf{q}_i } = \mathbf{A}_i \cdot
(- \mathbf{\kappa}^T \cdot \mathbf{G}_i \times \mathbf{f}_k ), $$
$$ \mathbf{f}_k = - r^{-2} \frac{ \delta U_{SLJ} }{ \delta \varphi }
\mathbf{\kappa}, $$
and
$$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
\times \mathbf{\iota} ). $$
For the derivative of the $\eta$ term, we were unable to find a matrix
expression due to the determinant. Let $a_{mi}$ be the mth row of the
rotation matrix $A_i$. Then,
$$ \frac{ \partial \eta_{12} }{ \partial \mathbf{q}_i } = \mathbf{A}_i
\cdot \sum_m \mathbf{a}_{mi} \times \frac{ \partial \eta_{12} }{
\partial \mathbf{a}_{mi} } = \mathbf{A}_i \cdot \sum_m \mathbf{a}_{mi}
\times \mathbf{d}_{mi}, $$
where $d_mi$ represents the mth row of a derivative matrix $D_i$,
$$ \mathbf{D}_i = - \frac{1}{2} \cdot ( \frac{2s1s2}{\det (
\mathbf{G}_{12} ) } )^{ \upsilon / 2 } \cdot {\frac{\upsilon}{\det (
\mathbf{G}_{12} ) }} \cdot \mathbf{E}, $$
where the matrix $E$ gives the derivate with respect to the rotation
matrix,
$$ \mathbf{E} = [ e_{my} ] = \frac{ \partial \eta_{12} }{ \partial
\mathbf{A}_i }, $$
and
$$ e_{my} = \det ( \mathbf{G}_{12} ) \cdot \mbox{trace} [
\mathbf{G}_{12}^{-1} \cdot ( \hat{\mathbf{p}}_y \otimes \mathbf{a}_m +
\mathbf{a}_m \otimes \hat{\mathbf{p}}_y ) \cdot s_{mm}^2 ]. $$
Here, $p_v$ is the unit vector for the axes in the lab frame $(p1=[1, 0,
0], p2=[0, 1, 0], and p3=[0, 0, 1])$ and $s_{mm}$ gives the mth radius of
the ellipsoid $i$.
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\documentstyle[12pt]{article}
\begin{document}
\begin{center}
\large{Additional documentation for the RE-squared ellipsoidal potential \\
as implemented in LAMMPS}
\end{center}
\centerline{Mike Brown, Sandia National Labs, October 2007}
\vspace{0.3in}
Let the shape matrices $\mathbf{S}_i=\mbox{diag}(a_i, b_i, c_i)$ be
given by the ellipsoid radii. Let the relative energy matrices
$\mathbf{E}_i = \mbox{diag} (\epsilon_{ia}, \epsilon_{ib},
\epsilon_{ic})$ be given by the relative well depths
(dimensionless energy scales inversely proportional to the well-depths
of the respective orthogonal configurations of the interacting molecules).
Let $\mathbf{A}_1$ and $\mathbf{A}_2$ be the transformation matrices
from the simulation box frame to the body frame and $\mathbf{r}$
be the center to center vector between the particles. Let $A_{12}$ be
the Hamaker constant for the interaction given in LJ units by
$A_{12}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2$.
\vspace{0.3in}
The RE-squared anisotropic interaction between pairs of
ellipsoidal particles is given by
$$ U=U_A+U_R, $$
$$ U_\alpha=\frac{A_{12}}{m_\alpha}(\frac\sigma{h})^{n_\alpha}
(1+o_\alpha\eta\chi\frac\sigma{h}) \times \prod_i{
\frac{a_ib_ic_i}{(a_i+h/p_\alpha)(b_i+h/p_\alpha)(c_i+h/p_\alpha)}}, $$
$$ m_A=-36, n_A=0, o_A=3, p_A=2, $$
$$ m_R=2025, n_R=6, o_R=45/56, p_R=60^{1/3}, $$
$$ \chi = 2 \hat{\mathbf{r}}^T \mathbf{B}^{-1}
\hat{\mathbf{r}}, $$
$$ \hat{\mathbf{r}} = { \mathbf{r} } / |\mathbf{r}|, $$
$$ \mathbf{B} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 $$
$$ \eta = \frac{ \det[\mathbf{S}_1]/\sigma_1^2+
det[\mathbf{S}_2]/\sigma_2^2}{[\det[\mathbf{H}]/
(\sigma_1+\sigma_2)]^{1/2}}, $$
$$ \sigma_i = (\hat{\mathbf{r}}^T\mathbf{A}_i^T\mathbf{S}_i^{-2}
\mathbf{A}_i\hat{\mathbf{r}})^{-1/2}, $$
$$ \mathbf{H} = \frac{1}{\sigma_1}\mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
\frac{1}{\sigma_2}\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
Here, we use the distance of closest approach approximation given by the
Perram reference, namely
$$ h = |r| - \sigma_{12}, $$
$$ \sigma_{12} = [ \frac{1}{2} \hat{\mathbf{r}}^T
\mathbf{G}^{-1} \hat{\mathbf{r}}]^{ -1/2 }, $$
and
$$ \mathbf{G} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
\mathbf{A}_2^T \mathbf{S}_2^2 \mathbf{A}_2 $$
\vspace{0.3in}
The RE-squared anisotropic interaction between a
ellipsoidal particle and a Lennard-Jones sphere is defined
as the $\lim_{a_2->0}U$ under the constraints that
$a_2=b_2=c_2$ and $\frac{4}{3}\pi a_2^3\rho=1$:
$$ U_{\mathrm{elj}}=U_{A_{\mathrm{elj}}}+U_{R_{\mathrm{elj}}}, $$
$$ U_{\alpha_{\mathrm{elj}}}=(\frac{3\sigma^3c_\alpha^3}
{4\pi h_{\mathrm{elj}}^3})\frac{A_{12_{\mathrm{elj}}}}
{m_\alpha}(\frac\sigma{h_{\mathrm{elj}}})^{n_\alpha}
(1+o_\alpha\chi_{\mathrm{elj}}\frac\sigma{h_{\mathrm{elj}}}) \times
\frac{a_1b_1c_1}{(a_1+h_{\mathrm{elj}}/p_\alpha)
(b_1+h_{\mathrm{elj}}/p_\alpha)(c_1+h_{\mathrm{elj}}/p_\alpha)}, $$
$$ A_{12_{\mathrm{elj}}}=4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3), $$
with $h_{\mathrm{elj}}$ and $\chi_{\mathrm{elj}}$ calculated as above
by replacing $B$ with $B_{\mathrm{elj}}$ and $G$ with $G_{\mathrm{elj}}$:
$$ \mathbf{B}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + I, $$
$$ \mathbf{G}_{\mathrm{elj}} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1.$$
\vspace{0.3in}
The interaction between two LJ spheres is calculated as:
$$
U_{\mathrm{lj}} = 4 \epsilon \left[ \left(\frac{\sigma}{|\mathbf{r}|}\right)^{12} -
\left(\frac{\sigma}{|\mathbf{r}|}\right)^6 \right]
$$
\vspace{0.3in}
The analytic derivatives are used for all force and torque calculation.
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<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
</p>
<ul>
<li>small|large = can be small if molecule size &lt; cutoff radius, must be large otherwise <br/>
</li>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> group WATERGROUP type 1 2 </code> <br/>
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all molecules corresponding to a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
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<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>group|type = LAMMPS defined group or type of atoms <br/>
</li>
<li>&lt;ID&gt; = name of group or type number <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
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<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Cannot change map type after initialization. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>lagrangian </p>
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<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
<ul>
<li>&lt;method&gt; = <br/>
value: atoms in specified group assigned constant value given <br/>
lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>
element: element volume divided among atoms within element <br/>
region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions. <br/>
group: volume per atom determined based on the atom count in a group and its volume<br/>
read_in: list of values for atoms are read-in from specified file <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>lattice </p>
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<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
<ul>
<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc compute include atomic_charge </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC tracks the total charge as a finite element field </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Required for: electrostatics </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>if the atom charge is defined, default is on, otherwise default is off </p>
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<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
<ul>
<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>prescribed on </p>
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<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC boundary_faceset is obndy </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>This is only valid when fe_md_boundary is set to faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
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>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
<ul>
<li>field (string) : name of hardy field</li>
<li>name (string) : name of faceset</li>
<li>axis (string) : x or y or z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
<p><br/>
</p>
<ul>
<li>physics_type (string) = thermal | momentum<br/>
</li>
<li>solution_parameter (string) = max_iterations | tolerance<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control max_iterations &lt;max_iterations&gt;<br/>
</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control tolerance &lt;tolerance&gt; <br/>
</p>
<ul>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p>
</div>
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<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control momentum none <br/>
</p>
<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control momentum glc_displacement <br/>
</p>
<p>fix_modify AtC control momentum glc_velocity <br/>
</p>
<p>fix_modify AtC control momentum hoover <br/>
</p>
<p>fix_modify AtC control momentum flux [faceset face_set_id, interpolate]</p>
<ul>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br/>
</li>
</ul>
<p>fix_modify AtC control thermal rescale &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control thermal hoover <br/>
</p>
<p>fix_modify AtC control thermal flux &lt;boundary_integration_type(optional)&gt; &lt;face_set_id(optional)&gt;<br/>
</p>
<ul>
<li>boundary_integration_type (string) = faceset | interpolate<br/>
</li>
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none<br/>
rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p>
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<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for use with thermal physics using the fractional step method. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>correction_max_iterations is 20 </p>
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<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC decomposition &lt;type&gt;</p>
<ul>
<li>&lt;type&gt; = <br/>
replicated_memory: nodal information replicated on each processor <br/>
distributed_memory: only owned nodal information on processor <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>replicated_memory </p>
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<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
</p>
<ul>
<li>integration_type (string) = explicit | implicit | steady <br/>
</li>
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
</p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>implicit<br/>
subcycle_steps = 1 </p>
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<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc equilibrium_start on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only needed before filtering is begun</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Switches energy exchange between the MD system and electron system on and off</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only valid for use with two_temperature type of AtC fix.</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see for how to specify the faceset name. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Interpolate. </p>
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<h1><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
description</a></h2>
Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
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<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC filter scale &lt;scale&gt; <br/>
</p>
<ul>
<li>scale (real) = characteristic time scale of the filter <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC filter scale 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>0. </p>
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<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC filter type exponential </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Specifies the type of time filter used. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
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default</a></h2>
<p>No default. </p>
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<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p>
<ul>
<li>fixID = name of fix</li>
<li>group = name of group fix is to be applied</li>
<li>type<br/>
= thermal : thermal coupling with fields: temperature <br/>
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br/>
= hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) <br/>
= field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) <br/>
</li>
<li>parameter_file = name of the file with material parameters. <br/>
note: Neither hardy nor field requires a parameter file </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
<code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
<code> fix AtC internal atc hardy </code> <br/>
<code> fix AtC internal atc field </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
<p>The following coupling example is typical, but non-exhaustive:<br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate coupling type and group to apply it to <br/>
# tag group physics material_file <br/>
fix AtC internal atc thermal Ar_thermal.mat<br/>
<br/>
# create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/>
# nx ny nz region periodicity <br/>
fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/>
<br/>
# specify the control method for the type of coupling <br/>
# physics control_type <br/>
fix_modify AtC thermal control flux <br/>
<br/>
# specify the initial values for the empirical field "temperature" <br/>
# field node_group value <br/>
fix_modify AtC initial temperature all 30.<br/>
<br/>
# create an output stream for nodal fields <br/>
# filename output_frequency <br/>
fix_modify AtC output atc_fe_output 100<br/>
<br/>
</code></p>
<p><code> run 1000 <br/>
</code></p>
<p>likewise for this post-processing example: <br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate post-processing and the group to apply it to <br/>
# no material file is allowed nor required <br/>
fix AtC internal atc hardy <br/>
<br/>
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/>
fix AtC kernel quartic_sphere 10.0 <br/>
<br/>
# create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/>
# with periodicity this effectively creats a system average <br/>
fix_modify AtC mesh create 1 1 1 box p p p <br/>
<br/>
# change from default lagrangian map to eulerian <br/>
# refreshed every 100 steps <br/>
fix_modify AtC atom_element_map eulerian 100 <br/>
<br/>
# start with no field defined <br/>
# add mass density, potential energy density, stress and temperature <br/>
fix_modify AtC fields add density energy stress temperature <br/>
<br/>
# create an output stream for nodal fields <br/>
# filename output_frequency <br/>
fix_modify AtC output nvtFE 100 text <br/>
</code></p>
<p><code> run 1000 <br/>
</code></p>
<p>the mesh's linear interpolation functions can be used as the localization function <br/>
by using the field option: <br/>
</p>
<p><code> fix AtC internal atc field <br/>
<br/>
fix_modify AtC mesh create 1 1 1 box p p p <br/>
<br/>
... <br/>
<br/>
</code></p>
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/>
For detailed exposition of the theory and algorithms please see:<br/>
</p>
<ul>
<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
</li>
<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
</li>
<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
</li>
<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
</li>
<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
</li>
<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
</li>
<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
</li>
</ul>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
<p>Currently,</p>
<ul>
<li>the coupling is restricted to thermal physics</li>
<li>the FE computations are done in serial on each processor.</li>
</ul>
<h2><a class="anchor" id="related">
related</a></h2>
<p>fix_modify commands for setup: <br/>
</p>
<ul>
<li><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a></li>
<li><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
<li><a class="el" href="man_mesh_read.html">fix_modify AtC mesh read</a></li>
<li><a class="el" href="man_mesh_write.html">fix_modify AtC mesh write</a></li>
<li><a class="el" href="man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
<li><a class="el" href="man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
<li><a class="el" href="man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
<li><a class="el" href="man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
<li><a class="el" href="man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
<li><a class="el" href="man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
<li><a class="el" href="man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
<li><a class="el" href="man_boundary.html">fix_modify AtC boundary</a></li>
<li><a class="el" href="man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
<li><a class="el" href="man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
<li><a class="el" href="man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
<li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
<li><a class="el" href="man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
<li><a class="el" href="man_decomposition.html">fix_modify AtC decomposition</a></li>
</ul>
<p>fix_modify commands for boundary and initial conditions:<br/>
</p>
<ul>
<li><a class="el" href="man_initial.html">fix_modify AtC initial</a></li>
<li><a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a></li>
<li><a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a></li>
<li><a class="el" href="man_fix_flux.html">fix_modify AtC fix_flux</a></li>
<li><a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
<li><a class="el" href="man_source.html">fix_modify AtC source</a></li>
<li><a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a></li>
</ul>
<p>fix_modify commands for control and filtering: <br/>
</p>
<ul>
<li><a class="el" href="man_control.html">fix_modify AtC control</a></li>
<li><a class="el" href="man_control_thermal.html">fix_modify AtC control thermal</a></li>
<li><a class="el" href="man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
<li><a class="el" href="man_control_momentum.html">fix_modify AtC control momentum</a></li>
<li><a class="el" href="man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
<li><a class="el" href="man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
<li><a class="el" href="man_mask_direction.html">fix_modify AtC control mask_direction</a></li>
<li><a class="el" href="man_time_filter.html">fix_modify AtC filter</a></li>
<li><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></li>
<li><a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></li>
<li><a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
<li><a class="el" href="man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
<li><a class="el" href="man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
</ul>
<p>fix_modify commands for output: <br/>
</p>
<ul>
<li><a class="el" href="man_output.html">fix_modify AtC output</a></li>
<li><a class="el" href="man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
<li><a class="el" href="man_output_elementset.html">fix_modify AtC output elementset</a></li>
<li><a class="el" href="man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
<li><a class="el" href="man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
<li><a class="el" href="man_mesh_output.html">fix_modify AtC mesh output</a></li>
<li><a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a></li>
<li><a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a></li>
</ul>
<p>fix_modify commands for post-processing: <br/>
</p>
<ul>
<li><a class="el" href="man_hardy_kernel.html">fix_modify AtC kernel</a></li>
<li><a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
<li><a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a></li>
<li><a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a></li>
<li><a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a></li>
<li><a class="el" href="man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
<li><a class="el" href="man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
<li><a class="el" href="man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
<li><a class="el" href="man_set.html">fix_modify AtC set</a></li>
</ul>
<p>miscellaneous fix_modify commands: <br/>
</p>
<ul>
<li><a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
<li><a class="el" href="man_atom_weight.html">fix_modify AtC atom_weight</a></li>
<li><a class="el" href="man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
<li><a class="el" href="man_reset_time.html">fix_modify AtC reset_time</a></li>
<li><a class="el" href="man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
<li><a class="el" href="man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
<li><a class="el" href="man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
<li><a class="el" href="man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
<li><a class="el" href="man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
<li><a class="el" href="man_material.html">fix_modify AtC material</a></li>
<li><a class="el" href="man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
<li><a class="el" href="man_source_integration.html">fix_modify AtC source_integration</a></li>
<li><a class="el" href="man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
<li><a class="el" href="man_track_displacement.html">fix_modify AtC track_displacement</a></li>
<li><a class="el" href="man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
<li><a class="el" href="man_add_species.html">fix_modify AtC add_species</a></li>
<li><a class="el" href="man_add_molecule.html">fix_modify AtC add_molecule</a></li>
<li><a class="el" href="man_remove_species.html">fix_modify AtC remove_species</a></li>
<li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
</ul>
<p>Note: a set of example input files with the attendant material files are included with this package </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;face_set&gt; = name of set of element faces </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only normal fluxes (Neumann data) can be prescribed. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
<code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a constraint on the values of the specified field at specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br/>
</li>
<li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br/>
</li>
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> compute virial all stress/atom </code> <br/>
<code> fix_modify AtC computes add virial volume </code> <br/>
<code> fix_modify AtC computes delete virial </code> <br/>
<br/>
<code> compute centrosymmetry all centro/atom </code> <br/>
<code> fix_modify AtC computes add centrosymmetry number </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
Per-atom compute must be specified before corresponding continuum field can be requested <br/>
</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>See manual page for compute </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults exist for this command </p>
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<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fields &lt;all | none&gt; <br/>
fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>all | none (keyword) = output all or no fields <br/>
</li>
<li>add | delete (keyword) = add or delete the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
density : mass per unit volume <br/>
displacement : displacement vector <br/>
momentum : momentum per unit volume <br/>
velocity : defined by momentum divided by density <br/>
projected_velocity : simple kernel estimation of atomic velocities <br/>
temperature : temperature derived from the relative atomic kinetic energy (as done by ) <br/>
kinetic_temperature : temperature derived from the full kinetic energy <br/>
number_density : simple kernel estimation of number of atoms per unit volume <br/>
stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br/>
transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br/>
heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br/>
potential_energy : potential energy per unit volume <br/>
kinetic_energy : kinetic energy per unit volume <br/>
thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume <br/>
internal_energy : total internal energy (potential + thermal) per unit volume <br/>
energy : total energy (potential + kinetic) per unit volume <br/>
number_density : number of atoms per unit volume <br/>
eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] <br/>
vacancy_concentration: volume fraction of vacancy content <br/>
type_concentration: volume fraction of a specific atom type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC fields add velocity temperature </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
<code> fix_modify AtC fields none </code> <br/>
followed by <br/>
<code> fix_modify AtC fields add velocity temperature </code> <br/>
will only output the velocity and temperature fields. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>By default, no fields are output </p>
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<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of gradients for the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
<code> fix_modify AtC gradients delete velocity </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No gradients are calculated by default </p>
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<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
</li>
<li>parameters :<br/>
step = radius (double) <br/>
cell = hx, hy, hz (double) or h (double) <br/>
cubic_bar = half-width (double) <br/>
cubic_cylinder = radius (double) <br/>
cubic_sphere = radius (double) <br/>
quartic_bar = half-width (double) <br/>
quartic_cylinder = radius (double) <br/>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
<code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No default </p>
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<h1><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/>
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
</p>
<ul>
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC on_the_fly bond on </code> <br/>
<code> fix_modify AtC on_the_fly kernel </code> <br/>
<code> fix_modify AtC on_the_fly kernel off </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
</p>
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<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
</p>
<ul>
<li>add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields <br/>
</li>
<li>fields (keyword) = <br/>
rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
<code> fix_modify AtC rates delete stress </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No rates are calculated by default </p>
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<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
<li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li>
<li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the initial values for the specified field at the specified nodes. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in nodeset name </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on for coupling methods, off for post-processors off </p>
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<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
<ul>
<li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see atom_element_map_type and boundary </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>off </p>
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<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc internal_quadrature off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
<h2><a class="anchor" id="optional">
optional</a></h2>
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
</li>
<li>parameters :<br/>
step = radius (double) <br/>
cell = hx, hy, hz (double) or h (double) <br/>
cubic_bar = half-width (double) <br/>
cubic_cylinder = radius (double) <br/>
cubic_sphere = radius (double) <br/>
quartic_bar = half-width (double) <br/>
quartic_cylinder = radius (double) <br/>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No default </p>
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<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control localized_lambda on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off. </p>
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<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to use or not use lumped matrix for lambda solve </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
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default</a></h2>
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<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to mask out certain dimensions from the atomic regulator </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
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default</a></h2>
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<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
<ul>
<li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc mass_matrix fe </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC material gap_region 2</code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the material model in elementset_name to be of type material_id. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>All elements default to the first material in the material file. </p>
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<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id of FE nodeset to be added to</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to add nodes to an already existing FE nodeset. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
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<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE element</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that is coincident with the desired FE faces</li>
<li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default options are units = lattice and the use of outer faces </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
<li>&lt;x|y|z&gt; = coordinate directions that define plane on which faceset lies</li>
<li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default option is units = lattice. </p>
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<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE nodes</li>
<li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p>
<ul>
<li>&lt;element_set&gt; = name of an element set </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC delete_elements gap </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Deletes a group of elements from the mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p>
<ul>
<li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li>
<li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li>
<li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>None. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Unless specified, the maximal element set is created </p>
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<h1><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh output &lt;file_prefix&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh output meshData </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>none </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh quadrature &lt;quad&gt;</p>
<ul>
<li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh quadrature face </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>(Re-)assigns the quadrature style for the existing mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>filename = name of file containing mesh to be read</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>periodicity flags are false by default </p>
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<h1><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh write &lt;filename&gt;</p>
<ul>
<li>filename = name of file to write mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Writes a mesh to a text file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p>
<ul>
<li>descriptor (string) = time integration type <br/>
</li>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc time_integration verlet </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
<ul>
<li>filename_prefix (string) = prefix for data files</li>
<li>frequency (integer) = frequency of output in time-steps</li>
<li>options (keyword/s): <br/>
text = creates text output of index, step and nodal variable values for unique nodes <br/>
full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes <br/>
binary = creates binary Ensight output <br/>
vector_components = outputs vectors as scalar components <br/>
tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output heatFE 100 </code> <br/>
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
<code> fix_modify AtC output index step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>no default format output indexed by time </p>
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<h1><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p>
<ul>
<li>set_name (string) = name of elementset to be integrated over</li>
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output eset1 mass_density </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
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default</a></h2>
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<h1><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p>
<ul>
<li>nodeset_name (string) = name of nodeset to be operated on</li>
<li>operation (keyword/s): <br/>
sum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/>
fix_modify AtC bond_interactions &lt;on|off&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC bond_interactions on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>include bonds and/or pairs in the stress and heat flux computations </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>pair interactions: on, bond interactions: off </p>
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<h1><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = perioidicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC read_restart [file_name] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC read_restart ATC_state </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Reads the current state of the fields from a named text-based restart file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a molecule type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC remove_molecule water </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Removes tag designated for tracking a specified set of molecules. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC remove_source &lt;field&gt; &lt;element_set&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Remove a domain source. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC delete_species &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC remove_species gold </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Removes tag designated for tracking a specified species. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
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<h1><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC reset_atomic_reference_positions </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_atomic_reference_positions </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p><code> Default is off </code></p>
</div>
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<h1><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC reset_time </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_time 0.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Resets the simulation time counter. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel_bandwidth </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_time 8 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only is used if kernel functions are being used. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Number of sample locations. </p>
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<h1><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC sample_frequency [freq]</p>
<ul>
<li>freq (int) : frequency to sample field in number of steps </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC sample_frequency 10 </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p><code> none </code></p>
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<h1><a class="anchor" id="man_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p>
<ul>
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
</li>
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC set reference_potential_energy </code> <br/>
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Defaults to lammps zero point i.e. isolated atoms </p>
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<h1><a class="anchor" id="man_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC source &lt;field&gt; &lt;element_set&gt; &lt;value | function&gt;</p>
<ul>
<li>&lt;field&gt; = field name valid for type of physics</li>
<li>&lt;element_set&gt; = name of set of elements </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>keyword 'all' reserved in element_set name </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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