jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/doc/Section_howto.html

1474 lines
70 KiB
HTML
Raw Blame History

<HTML>
<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_example.html">Next Section</A>
</CENTER>
<HR>
<H3>4. How-to discussions
</H3>
<P>The following sections describe what commands can be used to perform
certain kinds of LAMMPS simulations.
</P>
4.1 <A HREF = "#4_1">Restarting a simulation</A><BR>
4.2 <A HREF = "#4_2">2d simulations</A><BR>
4.3 <A HREF = "#4_3">CHARMM and AMBER force fields</A><BR>
4.4 <A HREF = "#4_4">Running multiple simulations from one input script</A><BR>
4.5 <A HREF = "#4_5">Parallel tempering</A><BR>
4.6 <A HREF = "#4_6">Granular models</A><BR>
4.7 <A HREF = "#4_7">TIP3P water model</A><BR>
4.8 <A HREF = "#4_8">TIP4P water model</A><BR>
4.9 <A HREF = "#4_9">SPC water model</A><BR>
4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A><BR>
4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
4.14 <A HREF = "#4_14">Extended spherical and aspherical particles</A><BR>
4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
4.17 <A HREF = "#4_17">Walls</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
setup and run various kinds of problems.
</P>
<HR>
<A NAME = "4_1"></A><H4>4.1 Restarting a simulation
</H4>
<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
<A HREF = "run.html">run</A> commands can be used in the same input script. Each
run will continue from where the previous run left off. Or binary
restart files can be saved to disk using the <A HREF = "restart.html">restart</A>
command. At a later time, these binary files can be read via a
<A HREF = "read_restart.html">read_restart</A> command in a new script. Or they can
be converted to text data files and read by a
<A HREF = "read_data.html">read_data</A> command in a new script. <A HREF = "Section_tools.html">This
section</A> discusses the <I>restart2data</I> tool that is
used to perform the conversion.
</P>
<P>Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
continue where the previous run left off. They illustrate what
settings must be made in the new script. Details are discussed in the
documentation for the <A HREF = "read_restart.html">read_restart</A> and
<A HREF = "read_data.html">read_data</A> commands.
</P>
<P>Look at the <I>in.chain</I> input script provided in the <I>bench</I> directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
</P>
<PRE>restart 50 tmp.restart
</PRE>
<P>added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
</P>
<P>This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
</P>
<PRE>read_restart tmp.restart.50
</PRE>
<PRE>neighbor 0.4 bin
neigh_modify every 1 delay 1
</PRE>
<PRE>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</PRE>
<PRE>timestep 0.012
</PRE>
<PRE>run 50
</PRE>
<P>Note that the following commands do not need to be repeated because
their settings are included in the restart file: <I>units, atom_style,
special_bonds, pair_style, bond_style</I>. However these commands do
need to be used, since their settings are not in the restart file:
<I>neighbor, fix, timestep</I>.
</P>
<P>If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
100. This is because the <A HREF = "fix_langevin.html">fix langevin</A> command
uses random numbers in a way that does not allow for perfect restarts.
</P>
<P>As an alternate approach, the restart file could be converted to a data
file using this tool:
</P>
<PRE>restart2data tmp.restart.50 tmp.restart.data
</PRE>
<P>Then, this script could be used to re-run the last 50 steps:
</P>
<PRE>units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0
</PRE>
<PRE>read_data tmp.restart.data
</PRE>
<PRE>neighbor 0.4 bin
neigh_modify every 1 delay 1
</PRE>
<PRE>fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
</PRE>
<PRE>timestep 0.012
</PRE>
<PRE>reset_timestep 50
run 50
</PRE>
<P>Note that nearly all the settings specified in the original <I>in.chain</I>
script must be repeated, except the <I>pair_coeff</I> and <I>bond_coeff</I>
commands since the new data file lists the force field coefficients.
Also, the <A HREF = "reset_timestep.html">reset_timestep</A> command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.
</P>
<HR>
<A NAME = "4_2"></A><H4>4.2 2d simulations
</H4>
<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
</P>
<P>Make the simulation box periodic in z via the <A HREF = "boundary.html">boundary</A>
command. This is the default.
</P>
<P>If using the <A HREF = "create_box.html">create box</A> command to define a
simulation box, set the z dimensions narrow, but finite, so that the
create_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
</P>
<PRE><A HREF = "create_box.html">create box</A> 1 -10 10 -10 10 -0.25 0.25
</PRE>
<P>If using the <A HREF = "read_data.html">read data</A> command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
</P>
<P>Use the <A HREF = "fix_enforce2d.html">fix enforce2d</A> command as the last
defined fix to insure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
</P>
<P>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
</P>
<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
</P>
<HR>
<A NAME = "4_3"></A><H4>4.3 CHARMM and AMBER force fields
</H4>
<P>There are many different ways to compute forces in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
and <A HREF = "http://amber.scripps.edu">AMBER</A> molecular dynamics codes, only some of which are
available as options in LAMMPS. A force field has 2 parts: the
formulas that define it and the coefficients used for a particular
system. Here we only discuss formulas implemented in LAMMPS. Setting
coefficients is done in the input data file via the
<A HREF = "read_data.html">read_data</A> command or in the input script with
commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A> for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
field.
</P>
<P>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command's
documentation for the formula it computes.
</P>
<UL><LI><A HREF = "bond_style.html">bond_style</A> harmonic
<LI><A HREF = "angle_style.html">angle_style</A> charmm
<LI><A HREF = "dihedral_style.html">dihedral_style</A> charmm
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm/implicit
<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long
</UL>
<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
<LI><A HREF = "special_bonds.html">special_bonds</A> amber
</UL>
<HR>
<A NAME = "4_4"></A><H4>4.4 Running multiple simulations from one input script
</H4>
<P>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
</P>
<P>If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the <A HREF = "run.html">run</A> command
multiple times. For example, this script
</P>
<PRE>units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000
</PRE>
<P>would run 5 successive simulations of the same system for a total of
50,000 timesteps.
</P>
<P>If you wish to run totally different simulations, one after the other,
the <A HREF = "clear.html">clear</A> command can be used in between them to
re-initialize LAMMPS. For example, this script
</P>
<PRE>units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000
</PRE>
<P>would run 2 independent simulations, one after the other.
</P>
<P>For large numbers of independent simulations, you can use
<A HREF = "variable.html">variables</A> and the <A HREF = "next.html">next</A> and
<A HREF = "jump.html">jump</A> commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
</P>
<PRE>variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
shell cd ..
clear
next d
jump in.polymer
</PRE>
<P>would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
</P>
<PRE>variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
next t
next a
jump in.polymer
</PRE>
<P>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in <A HREF = "Section_start.html#2_6">this
section</A> of the manual.
</P>
<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
replaced with <I>universe</I>-style variables, as described in the
<A HREF = "variable.html">variable</A> command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
</P>
<HR>
<A NAME = "4_5"></A><H4>4.5 Parallel tempering
</H4>
<P>The <A HREF = "temper.html">temper</A> command can be used to perform a parallel
tempering or replica-exchange simulation where multiple copies of a
simulation are run at different temperatures on different sets of
processors, and Monte Carlo temperature swaps are performed between
pairs of copies.
</P>
<P>Use the -procs and -in <A HREF = "Section_start.html#2_6">command-line switches</A>
to launch LAMMPS on multiple partitions.
</P>
<P>In your input script, define a set of temperatures, one for each
processor partition, using the <A HREF = "variable.html">variable</A> command:
</P>
<PRE>variable t world 300.0 310.0 320.0 330.0
</PRE>
<P>Define a fix of style <A HREF = "fix_nh.html">nvt</A> or <A HREF = "fix_langevin.html">langevin</A>
to control the temperature of each simulation:
</P>
<PRE>fix myfix all nvt $t $t 100.0
</PRE>
<P>Use the <A HREF = "temper.html">temper</A> command in place of a <A HREF = "run.html">run</A>
command to perform a simulation where tempering exchanges will take
place:
</P>
<PRE>temper 100000 100 $t myfix 3847 58382
</PRE>
<HR>
<A NAME = "4_6"></A><H4>4.6 Granular models
</H4>
<P>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
velocity and torque can be imparted to them to cause them to rotate.
</P>
<P>To run a simulation of a granular model, you will want to use
the following commands:
</P>
<UL><LI><A HREF = "atom_style.html">atom_style</A> granular
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_gravity.html">fix gravity</A>
</UL>
<P>This compute
</P>
<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</UL>
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#4_15">output with
thermodynamic info</A>.
</P>
<P>Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
</P>
<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history
<LI><A HREF = "pair_style.html">pair_style</A> gran/no_history
<LI><A HREF = "pair_style.html">pair_style</A> gran/hertzian
</UL>
<P>These commands implement fix options specific to granular systems:
</P>
<UL><LI><A HREF = "fix_freeze.html">fix freeze</A>
<LI><A HREF = "fix_pour.html">fix pour</A>
<LI><A HREF = "fix_viscous.html">fix viscous</A>
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A>
</UL>
<P>The fix style <I>freeze</I> zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
<I>setforce</I>.
</P>
<P>For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
</P>
<UL><LI><A HREF = "neigh_modify.html">neigh_modify</A> exclude
</UL>
<HR>
<A NAME = "4_7"></A><H4>4.7 TIP3P water model
</H4>
<P>The TIP3P water model as implemented in CHARMM
<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
used.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model
<A HREF = "#Jorgensen">(Jorgensen)</A>.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
</P>
<P>O charge = -0.834<BR>
H charge = 0.417 <BR>
</P>
<P>LJ epsilon of OO = 0.1521<BR>
LJ sigma of OO = 3.1507<BR>
LJ epsilon of HH = 0.0460<BR>
LJ sigma of HH = 0.4000<BR>
LJ epsilon of OH = 0.0836<BR>
LJ sigma of OH = 1.7753 <BR>
</P>
<P>K of OH bond = 450<BR>
r0 of OH bond = 0.9572 <BR>
</P>
<P>K of HOH angle = 55<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>These are the parameters to use for TIP3P with a long-range Coulombic
solver (Ewald or PPPM in LAMMPS), see <A HREF = "#Price">(Price)</A> for details:
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
</P>
<P>O charge = -0.830<BR>
H charge = 0.415 <BR>
</P>
<P>LJ epsilon of OO = 0.102<BR>
LJ sigma of OO = 3.188<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<P>K of OH bond = 450<BR>
r0 of OH bond = 0.9572 <BR>
</P>
<P>K of HOH angle = 55<BR>
theta of HOH angle = 104.52 <BR>
</P>
<HR>
<A NAME = "4_8"></A><H4>4.8 TIP4P water model
</H4>
<P>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
massless, where the charge associated with the oxygen atom is placed.
This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of <I>harmonic</I> and an
angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
</P>
<P>Currently, only a four-point model for long-range Coulombics is
implemented via the LAMMPS <A HREF = "pair_lj.html">pair style
lj/cut/coul/long/tip4p</A>. A cutoff version may be added
the future. For both models, the bond lengths and bond angles should
be held fixed using the <A HREF = "fix_shake.html">fix shake</A> command.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
<A HREF = "#Jorgensen">(Jorgensen)</A>. Note that the OM distance is specified in
the <A HREF = "pair_style.html">pair_style</A> command, not as part of the pair
coefficients.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
</P>
<P>O charge = -1.040<BR>
H charge = 0.520 <BR>
</P>
<P>r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>OM distance = 0.15 <BR>
</P>
<P>LJ epsilon of O-O = 0.1550<BR>
LJ sigma of O-O = 3.1536<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<P>These are the parameters to use for TIP4P with a long-range Coulombic
solver (Ewald or PPPM in LAMMPS):
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
</P>
<P>O charge = -1.0484<BR>
H charge = 0.5242 <BR>
</P>
<P>r0 of OH bond = 0.9572<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>OM distance = 0.1250 <BR>
</P>
<P>LJ epsilon of O-O = 0.16275<BR>
LJ sigma of O-O = 3.16435<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<HR>
<A NAME = "4_9"></A><H4>4.9 SPC water model
</H4>
<P>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
used.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model with long-range
Coulombics (Ewald or PPPM in LAMMPS).
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
</P>
<P>O charge = -0.820<BR>
H charge = 0.410 <BR>
</P>
<P>LJ epsilon of OO = 0.1553<BR>
LJ sigma of OO = 3.166<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<P>r0 of OH bond = 1.0<BR>
theta of HOH angle = 109.47 <BR>
</P>
<P>To use SPC with a long-range Coulombic solver (Ewald or PPPM in
LAMMPS), the only parameters that change are the partial charge
assignments:
</P>
<P>O charge = -0.8476<BR>
H charge = 0.4238 <BR>
</P>
<HR>
<A NAME = "4_10"></A><H4>4.10 Coupling LAMMPS to other codes
</H4>
<P>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
atoms and pass those forces to LAMMPS. Or a continuum finite element
(FE) simulation might use atom positions as boundary conditions on FE
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
</P>
<P>LAMMPS can be coupled to other codes in at least 3 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
</P>
<P>(1) Define a new <A HREF = "fix.html">fix</A> command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
<A HREF = "http://www.rpi.edu/~anderk5/lab">POEMS</A> package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
<A HREF = "fix_poems.html">fix_poems</A> command for more details. See <A HREF = "Section_modify.html">this
section</A> of the documentation for info on how to add
a new fix to LAMMPS.
</P>
<P>(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
<A HREF = "run.html">run</A> command facilitates this with its <I>every</I> option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
</P>
<P>In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> of the documentation for how to
add a new command to LAMMPS.
</P>
<P>(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
Again, the <A HREF = "run.html">run</A> command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
</P>
<P><A HREF = "Section_start.html#2_4">This section</A> of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, or Fortran (or any other
language that supports a vanilla C-like interface, e.g. a scripting
language). For example, from C++ you could create one (or more)
"instances" of LAMMPS, pass it an input script to process, or execute
individual commands, all by invoking the correct class methods in
LAMMPS. From C or Fortran you can make function calls to do the same
things. Library.cpp and library.h contain such a C interface with the
functions:
</P>
<PRE>void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(void *, char *);
</PRE>
<P>The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are
defined within a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application.
</P>
<P>Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called multiple times, to
create multiple instances of LAMMPS.
</P>
<P>LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically.
</P>
<P>Library.cpp contains a lammps_command() function to which the caller
passes a single LAMMPS command (a string). Thus the calling code can
read or generate a series of LAMMPS commands (e.g. an input script)
one line at a time and pass it thru the library interface to setup a
problem and then run it.
</P>
<P>A few other sample functions are included in library.cpp, but the key
idea is that you can write any functions you wish to define an
interface for how your code talks to LAMMPS and add them to
library.cpp and library.h. The routines you add can access any LAMMPS
data. The examples/couple directory has example C++ and C codes which
show how a stand-alone code can link LAMMPS as a library, run LAMMPS
on a subset of processors, grab data from LAMMPS, change it, and put
it back into LAMMPS.
</P>
<HR>
<A NAME = "4_11"></A><H4>4.11 Visualizing LAMMPS snapshots
</H4>
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
</P>
<P>LAMMPS snapshots are created by the <A HREF = "dump.html">dump</A> command which can
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories.
</P>
<P>Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
<A HREF = "Section_tools.html">Section_tools</A> doc page for details. The first is
the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
LAMMPS dump files into CFG files which can be read into the
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
</P>
<P>A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
WWW site</A> for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
</P>
<P>LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
</P>
<P>LAMMPS can create DCD files directly (via "dump dcd") which can be
read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the <A HREF = "dump.html">dump</A> command for more information on DCD
files.
</P>
<P>LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> for visualization.
See the <A HREF = "dump.html">dump</A> command for more information on XTC files.
</P>
<HR>
<A NAME = "4_12"></A><H4>4.12 Non-orthogonal simulation boxes
</H4>
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
conditions of the box (periodic, non-periodic, etc). If the box size
is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
= (0,0,zprd).
</P>
<P>LAMMPS also allows non-orthogonal simulation boxes (triclinic
symmetry) to be defined with 3 additional "tilt" parameters which
change the edge vectors of the simulation box to be a = (xprd,0,0), b
= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
can be positive or negative. The simulation box must be periodic in
both dimensions associated with a tilt factor. For example, if xz !=
0.0, then the x and z dimensions must be periodic.
</P>
<P>To avoid extremely tilted boxes (which would be computationally
inefficient), no tilt factor can skew the box more than half the
distance of the parallel box length, which is the 1st dimension in the
tilt factor (x for xz). For example, if xlo = 2 and xhi = 12, then
the x box length is 10 and the xy tilt factor must be between -5 and
5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
</P>
<P>You tell LAMMPS to use a non-orthogonal box when the simulation box is
defined. This happens in one of 3 ways. If the
<A HREF = "create_box.html">create_box</A> command is used with a region of style
<I>prism</I>, then a non-orthogonal domain is setup. See the
<A HREF = "region.html">region</A> command for details. If the
<A HREF = "read_data.html">read_data</A> command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a non-orthogonal domain is setup. See the
<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
was written from a simulation using a triclinic box, then a
non-orthogonal box will be enabled for the restarted simulation.
</P>
<P>Note that you can define a non-orthogonal box with all 3 tilt factors
= 0.0, so that it is initially orthogonal. This is necessary if the
box will become non-orthogonal. Alternatively, you can use the
<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
orthogonal to non-orthogonal and vice versa.
</P>
<P>One use of non-orthogonal boxes is to model solid-state crystals with
triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be used
with non-orthogonal basis vectors to define a lattice that will tile a
non-orthogonal simulation box via the <A HREF = "create_atoms.html">create_atoms</A>
command. Note that while the box edge vectors a,b,c cannot be
arbitrary vectors (e.g. a must be aligned with the x axis), it is
possible to rotate any crystal's basis vectors so that they meet these
restrictions.
</P>
<P>A second use of non-orthogonal boxes is to shear a bulk solid to study
the response of the material. The <A HREF = "fix_deform.html">fix deform</A>
command can be used for this purpose. It allows dynamic control of
the xy, xz, and yz tilt factors as a simulation runs.
</P>
<P>Another use of non-orthogonal boxes is to perform non-equilibrium MD
(NEMD) simulations, as discussed in the next section.
</P>
<HR>
<A NAME = "4_13"></A><H4>4.13 NEMD simulations
</H4>
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceding Howto section).
</P>
<P>A shear strain can be applied to the simulation box at a desired
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses <A HREF = "compute_temp_deform.html">compute
temp/deform</A> to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
</P>
<P>As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
deform</A> command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of periodic space. The strain rate can then continue to change
as before. In a long NEMD simulation these box re-shaping events may
occur many times.
</P>
<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
deform</A> should be set to "remap v", since that is what
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
profile consistent with the applied shear strain rate.
</P>
<P>An alternative method for calculating viscosities is provided via the
<A HREF = "fix_viscosity.html">fix viscosity</A> command.
</P>
<HR>
<A NAME = "4_14"></A><H4>4.14 Extended spherical and aspherical particles
</H4>
<P>Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size
particles such as spherioids or aspherical ellipsoids. The difference
is that such particles have a moment of inertia, rotational energy,
and angular momentum. Rotation is induced by torque from interactions
with other particles.
</P>
<P>LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn:
</P>
<UL><LI>atom styles
<LI>pair potentials
<LI>time integration
<LI>computes, thermodynamics, and dump output
<LI>rigid bodies composed of extended particles
</UL>
<H5>Atom styles
</H5>
<P>There are 3 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
finite-size particles: granular, dipole, ellipsoid.
</P>
<P>Granular particles are spheriods and each particle can have a unique
diameter and mass (or density). These particles store an angular
velocity (omega) and can be acted upon by torque.
</P>
<P>Dipolar particles are typically spheriods with a point dipole and each
particle type has a diamater and mass, set by the <A HREF = "shape.html">shape</A>
and <A HREF = "mass.html">mass</A> commands. These particles store an angular
velocity (omega) and can be acted upon by torque. They also store an
orientation for the point dipole (mu) which has a length set by the
<A HREF = "dipole.html">dipole</A> command. The <A HREF = "set.html">set</A> command can be used
to initialize the orientation of dipole moments.
</P>
<P>Ellipsoid particles are aspherical. Each particle type has an
ellipsoidal shape and mass, defined by the <A HREF = "shape.html">shape</A> and
<A HREF = "mass.html">mass</A> commands. These particles store an angular momentum
and their orientation (quaternion), and can be acted upon by torque.
They do not store an angular velocity (omega), which can be in a
different direction than angular momentum, rather they compute it as
needed. Ellipsoidal particles can also store a dipole moment if an
<A HREF = "atom_style.html">atom_style hybrid ellipsoid dipole</A> is used. The
<A HREF = "set.html">set</A> command can be used to initialize the orientation of
ellipsoidal particles and has a brief explanation of quaternions.
</P>
<P>Note that if one of these atom styles is used (or multiple styles via
the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
the system are required to be finite-size or aspherical. For example,
if the 3 shape parameters are set to the same value, the particle will
be a spheroid rather than an ellipsoid. If the 3 shape parameters are
all set to 0.0 or if the diameter is set to 0.0, it will be a point
particle. If the dipole moment is set to zero, the particle will not
have a point dipole associated with it. The pair styles used to
compute pairwise interactions will typically compute the correct
interaction in these simplified (cheaper) cases. <A HREF = "pair_hybrid.html">Pair_style
hybrid</A> can be used to insure the correct
interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoid versus
spheroid versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details.
</P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
spheroids and ellipsoids are still treated as 3d particles, rather
than as disks or ellipses. This means they have the same moment of
inertia for a 3d extended object. When their temperature is
coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system.
</P>
<H5>Pair potentials
</H5>
<P>When a system with extended particles is defined, the particles will
only rotate and experience torque if the force field computes such
interactions. These are the various <A HREF = "pair_style.html">pair styles</A>
that generate torque:
</P>
<UL><LI><A HREF = "pair_gran.html">pair_style gran/history</A>
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A>
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
</UL>
<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style
granular</A>. The <A HREF = "pair_dipole.html">dipole pair style</A>
is used with <A HREF = "atom_style.html">atom_style dipole</A>. The
<A HREF = "pair_gayberne.html">GayBerne</A> and <A HREF = "pair_resquared.html">REsquared</A>
potentials require particles have a <A HREF = "shape.html">shape</A> and are
designed for <A HREF = "atom_style.html">ellipsoidal particles</A>. The
<A HREF = "pair_lubricate.html">lubrication potential</A> requires that particles
have a <A HREF = "shape.html">shape</A>. It can currently only be used with
extended spherical particles.
</P>
<H5>Time integration
</H5>
<P>There are 3 fixes that perform time integration on extended spherical
particles, meaning the integrators update the rotational orientation
and angular velocity or angular momentum of the particles:
</P>
<UL><LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
</UL>
<P>Likewise, there are 3 fixes that perform time integration on extended
aspherical particles:
</P>
<UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
</UL>
<P>The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. Other thermostats can be used with
fix nve/sphere or fix nve/asphere, such as fix langevin or fix
temp/berendsen, but those thermostats only operate on the
translational kinetic energy of the extended particles.
</P>
<P>Note that for mixtures of point and extended particles, you should
only use these integration fixes on <A HREF = "group.html">groups</A> which contain
extended particles.
</P>
<H5>Computes, thermodynamics, and dump output
</H5>
<P>There are 4 computes that calculate the temperature or rotational energy
of extended spherical or aspherical particles:
</P>
<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
<LI><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
</UL>
<P>These include rotational degrees of freedom in their computation. If
you wish the thermodynamic output of temperature or pressure to use
one of these computes (e.g. for a system entirely composed of extended
particles), then the compute can be defined and the
<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by
default thermodynamic quantities will be calculated with a temperature
that only includes translational degrees of freedom. See the
<A HREF = "thermo_style.html">thermo_style</A> command for details.
</P>
<P>The <A HREF = "dump.html">dump custom</A> command can output various attributes of
extended particles, including the dipole moment (mu), the angular
velocity (omega), the angular momentum (angmom), the quaternion
(quat), and the torque (tq) on the particle.
</P>
<H5>Rigid bodies composed of extended particles
</H5>
<P>The <A HREF = "fix_rigid.html">fix rigid</A> command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body.
</P>
<P>(NOTE: the feature described in the following paragraph has not yet
been released. It will be soon.)
</P>
<P>If any of the constituent particles of a rigid body are extended
particles (spheroids or ellipsoids), then their contribution to the
inertia tensor of the body is different than if they were point
particles. This means the rotational dynamics of the rigid body will
be different. Thus a model of a dimer is different if the dimer
consists of two point masses versus two extended sphereoids, even if
the two particles have the same mass. Extended particles that
experience torque due to their interaction with other particles will
also impart that torque to a rigid body they are part of.
</P>
<P>See the "fix rigid" command for example of complex rigid-body models
it is possible to define in LAMMPS.
</P>
<P>Note that the <A HREF = "fix_shake.html">fix shake</A> command can also be used to
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
particles are point masses.
</P>
<HR>
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
</H4>
<P>There are four basic kinds of LAMMPS output:
</P>
<UL><LI><A HREF = "thermo_style.html">Thermodynamic output</A>, which is a list
of quantities printed every few timesteps to the screen and logfile.
<LI><A HREF = "dump.html">Dump files</A>, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency.
<LI>Certain fixes can output user-specified quantities to files: <A HREF = "fix_ave_time.html">fix
ave/time</A> for time averaging, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> for spatial averaging, and <A HREF = "fix_print.html">fix
print</A> for single-line output of
<A HREF = "variable.html">variables</A>. Fix print can also output to the
screen.
<LI><A HREF = "restart.html">Restart files</A>.
</UL>
<P>A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what <A HREF = "dump.html">dump</A> and <A HREF = "fix.html">fix</A>
commands you specify.
</P>
<P>As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also <A HREF = "Section_modify.html">add their own computes and fixes
to LAMMPS</A> which can then generate values that can
then be output with these commands.
</P>
<P>The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:
</P>
<UL><LI><A HREF = "#global">Global/per-atom/local data</A>
<LI><A HREF = "#scalar">Scalar/vector/array data</A>
<LI><A HREF = "#thermo">Thermodynamic output</A>
<LI><A HREF = "#dump">Dump file output</A>
<LI><A HREF = "#fixoutput">Fixes that write output files</A>
<LI><A HREF = "#computeoutput">Computes that process output quantities</A>
<LI><A HREF = "#fixoutput">Fixes that process output quantities</A>
<LI><A HREF = "#compute">Computes that generate values to output</A>
<LI><A HREF = "#fix">Fixes that generate values to output</A>
<LI><A HREF = "#variable">Variables that generate values to output</A>
<LI><A HREF = "#table">Summary table of output options and data flow between commands</A>
</UL>
<H5><A NAME = "global"></A>Global/per-atom/local data
</H5>
<P>Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
</P>
<H5><A NAME = "scalar"></A>Scalar/vector/array data
</H5>
<P>Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a "compute" or "fix" or "variable" that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.
</P>
<P>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
<TR><TD >c_ID[I][J] </TD><TD > one element of array
</TD></TR></TABLE></DIV>
<P>In other words, using one bracket reduces the dimension of the data
once (vector -> scalar, array -> vector). Using two brackets reduces
the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
</P>
<H5><A NAME = "thermo"></A>Thermodynamic output
</H5>
<P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A>
or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the <A HREF = "dump.html">thermo_style custom</A>
command.
</P>
<H5><A NAME = "dump"></A>Dump file output
</H5>
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
pre-defined formats (dump atom, dump xtc, etc).
</P>
<P>There is also a <A HREF = "dump.html">dump custom</A> format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>There is also a <A HREF = "dump.html">dump local</A> format where the user specifies
what local values to output. A pre-defined index keyword can be
specified to enumuerate the local values. Two additional kinds of
keywords can also be specified (c_ID, f_ID), where a
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
provides the values to be output. In each case, the compute or fix
must generate local values for input to the <A HREF = "dump.html">dump local</A>
command.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that write output files
</H5>
<P>Three fixes take various quantities as input and can write output
files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, and <A HREF = "fix_print.html">fix print</A>.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
<A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or
<A HREF = "variable.html">variables</A> of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables direct
output to a file of spatial-averaged per-atom quantities like those
output in dump files, within 1d layers of the simulation box. The
per-atom quantities can be atom density (mass or number) or atom
attributes such as position, velocity, force. They can also be
per-atom quantities calculated by a <A HREF = "compute.html">compute</A>, by a
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
spatial-averaged output of this fix can also be used as input to other
output commands.
</P>
<P>The <A HREF = "fix_ave_histo.html">fix ave/histo</A> command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
</P>
<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
<A HREF = "variable.html">variable</A> values for any style variable except the atom
style). As explained above, variables themselves can contain
references to global values generated by <A HREF = "thermo_style.html">thermodynamic
keywords</A>, <A HREF = "compute.html">computes</A>,
<A HREF = "fix.html">fixes</A>, or other <A HREF = "variable.html">variables</A>, or to per-atom
values for a specific atom. Thus the <A HREF = "fix_print.html">fix print</A>
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
</P>
<H5><A NAME = "computeoutput"></A>Computes that process output quantities
</H5>
<P>The <A HREF = "compute_reduce.html">compute reduce</A> and <A HREF = "compute_reduce.html">compute
reduce/region</A> commands take one or more vector
quantities as inputs and "reduce" them (sum, min, max, ave) to scalar
quantities. These are produced as output values which can be used as
input to other output commands.
</P>
<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>The <A HREF = "compute_property_local.html">compute property/local</A> command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
</H5>
<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a <A HREF = "compute.html">compute</A>, by a
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
time-averaged per-atom output of this fix can be used as input to
other output commands.
</P>
<H5><A NAME = "compute"></A>Computes that generate values to output
</H5>
<P>Every <A HREF = "compute.html">compute</A> in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The doc page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
</P>
<H5><A NAME = "fix"></A>Fixes that generate values to output
</H5>
<P>Some <A HREF = "fix.html">fixes</A> in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.
</P>
<H5><A NAME = "variable"></A>Variables that generate values to output
</H5>
<P>Every <A HREF = "variable.html">variables</A> defined in an input script generates
either a global scalar value or a per-atom vector (only atom-style
variables) when it is accessed. The formulas used to define equal-
and atom-style variables can contain references to the thermodynamic
keywords and to global and per-atom data generated by computes, fixes,
and other variables. The values generated by variables can be output
using the other commands described in this section.
</P>
<H5><A NAME = "table"></A>Summary table of output options and data flow between commands
</H5>
<P>This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
some kind and/or writes data to a file. Most of the commands can take
data from other commands as input. Thus you can link many of these
commands together in pipeline form, where data produced by one command
is used as input to another command and eventually written to the
screen or to a file. Note that to hook two commands together the
output and input data types must match, e.g. global/per-atom/local
data and scalar/vector/array data.
</P>
<P>Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "dump.html">dump local</A></TD><TD > local vectors</TD><TD > dump file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_print.html">fix print</A></TD><TD > global scalar from variable</TD><TD > screen, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "print.html">print</A></TD><TD > global scalar from variable</TD><TD > screen</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > global/per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_histo.html">fix ave/histo</A></TD><TD > global/per-atom/local scalars and vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD >
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
</H4>
<P>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
pressure includes a kinetic component due to particle velocities, both
these operations require calculation of the temperature. Typically a
target temperature (T) and/or pressure (P) is specified by the user,
and the thermostat or barostat attempts to equilibrate the system to
the requested T and/or P.
</P>
<P>Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
</P>
<P>LAMMPS has several options for computing temperatures, any of which
can be used in thermostatting and barostatting. These <A HREF = "compute.html">compute
commands</A> calculate temperature, and the <A HREF = "compute_pressure.html">compute
pressure</A> command calculates pressure.
</P>
<UL><LI><A HREF = "compute_temp.html">compute temp</A>
<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
<P>All but the first 3 calculate velocity biases (i.e. advection
velocities) that are removed when computing the thermal temperature.
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
case by a pair style. Four thermostatting fixes are currently
available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
rescaling (temp/rescale). Dissipative particle dynamics (DPD)
thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
</P>
<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "fix_langevin.html">fix langevin</A>
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
</UL>
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <A HREF = "#4_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
nvt/asphere</A> thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
</P>
<P>DPD thermostatting alters pairwise interactions in a manner analagous
to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>Any of the thermostatting fixes can use temperature computes that
remove bias for two purposes: (a) computing the current temperature to
compare to the requested target temperature, and (b) adjusting only
the thermal temperature component of the particle's velocities. See
the doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with <A HREF = "compute_temp_partial.html">compute
temp/partial</A>.
</P>
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:
</P>
<UL><LI><A HREF = "fix_nve.html">fix nve</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
</UL>
<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
barosttating methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
</P>
<UL><LI><A HREF = "fix_nh.html">fix npt</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
<LI><A HREF = "fix_nh.html">fix nph</A>
<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
</UL>
<P>The <A HREF = "fix_nh.html">fix npt</A> commands include a Nose-Hoover thermostat
and barostat. <A HREF = "fix_nh.html">Fix nph</A> is just a Nose/Hoover barostat;
it does no thermostatting. Both <A HREF = "fix_nh.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
press/bernendsen</A> can be used in conjunction
with any of the thermostatting fixes.
</P>
<P>As with the thermostats, <A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_nh.html">fix
nph</A> only use translational motion of the particles in
computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
npt/asphere</A> thermo/barostat using not only
translation velocities but also rotational velocities for spherical
and aspherical particles.
</P>
<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
pressure</A> compute to calculate a current
pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
pressure</A> command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet which contributes to the current
pressure. See the doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.
</P>
<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_nh.html">fix
npt</A> and <A HREF = "fix_nh.html">fix nph</A>) perform time
integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.
</P>
<P>Finally, thermodynamic output, which can be setup via the
<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
and pressure values. As explained on the doc page for the
<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
setup by the thermo command itself. They are NOT the ones associated
with any thermostatting or barostatting fix you have defined or with
any compute that calculates a temperature or pressure. Thus if you
want to view these values of T and P, you need to specify them
explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
re-define what temperature or pressure compute is used for default
thermodynamic output.
</P>
<HR>
<A NAME = "4_17"></A><H4>4.16 Walls
</H4>
<P>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
</P>
<P>Walls in LAMMPS can be of rough (made of particles) or idealized
surfaces. Ideal walls can be smooth, generating forces only in the
normal direction, or frictional, generating forces also in the
tangential direction.
</P>
<P>Rough walls, built of particles, can be created in various ways. The
particles themselves can be generated like any other particle, via the
<A HREF = "lattice.html">lattice</A> and <A HREF = "create_atoms.html">create_atoms</A> commands,
or read in via the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>Their motion can be constrained by many different commands, so that
they do not move at all, move together as a group at constant velocity
or in response to a net force acting on them, move in a prescribed
fashion (e.g. rotate around a point), etc. Note that if a time
integration fix like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nvt</A>
is not used with the group that contains wall particles, their
positions and velocities will not be updated.
</P>
<UL><LI><A HREF = "fix_aveforce.html">fix aveforce</A> - set force on particles to average value, so they move together
<LI><A HREF = "fix_setforce.html">fix setforce</A> - set force on particles to a value, e.g. 0.0
<LI><A HREF = "fix_freeze.html">fix freeze</A> - freeze particles for use as granular walls
<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - advect particles by their velocity, but without force
<LI><A HREF = "fix_move.html">fix move</A> - prescribe motion of particles by a linear velocity, oscillation, rotation, variable
</UL>
<P>The <A HREF = "fix_move.html">fix move</A> command offers the most generality, since
the motion of individual particles can be specified with
<A HREF = "variable.html">variable</A> formula which depends on time and/or the
particle position.
</P>
<P>For rough walls, it may be useful to turn off pairwise interactions
between wall particles via the <A HREF = "neigh_modify.html">neigh_modify
exclude</A> command.
</P>
<P>Rough walls can also be created by specifying frozen particles that do
not move and do not interact with mobile particles, and then tethering
other particles to the fixed particles, via a <A HREF = "bond_style.html">bond</A>.
The bonded particles do interact with other mobile particles.
</P>
<P>Idealized walls can be specified via several fix commands. <A HREF = "fix_wall_gran.html">Fix
wall/gran</A> creates frictional walls for use with
granular particles; all the other commands create smooth walls.
</P>
<UL><LI><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> - reflective flat walls
<LI><A HREF = "fix_wall.html">fix wall/lj93</A> - flat walls, with Lennard-Jones 9/3 potential
<LI><A HREF = "fix_wall.html">fix wall/lj126</A> - flat walls, with Lennard-Jones 12/6 potential
<LI><A HREF = "fix_wall.html">fix wall/colloid</A> - flat walls, with <A HREF = "pair_colloid.html">pair_style colloid</A> potential
<LI><A HREF = "fix_wall.html">fix wall/harmonic</A> - flat walls, with repulsive harmonic spring potential
<LI><A HREF = "fix_wall_region.html">fix wall/region</A> - use region surface as wall
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - flat or curved walls with <A HREF = "pair_gran.html">pair_style granular</A> potential
</UL>
<P>The <I>lj93</I>, <I>lj126</I>, <I>colloid</I>, and <I>harmonic</I> styles all allow the
flat walls to move with a constant velocity, or oscillate in time.
The <A HREF = "fix_wall_region.html">fix wall/region</A> command offers the most
generality, since the region surface is treated as a wall, and the
geometry of the region can be a simple primitive volume (e.g. a
sphere, or cube, or plane), or a complex volume made from the union
and intersection of primitive volumes. <A HREF = "region.html">Regions</A> can also
specify a volume "interior" or "exterior" to the specified primitive
shape or <I>union</I> or <I>intersection</I>. <A HREF = "region.html">Regions</A> can also be
"dynamic" meaning they move with constant velocity, oscillate, or
rotate.
</P>
<P>The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the <A HREF = "fix_wall_gran.html">fix wall/gran</A>
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.
</P>
<HR>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "Horn"></A>
<P><B>(Horn)</B> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
<A NAME = "Jorgensen"></A>
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
</P>
<A NAME = "Price"></A>
<P><B>(Price)</B> Price and Brooks, J Chem Phys, 121, 10096 (2004).
</P>
</HTML>
Reference in New Issue View Git Blame Copy Permalink