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"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
4. How-to discussions :h3
The following sections describe what commands can be used to perform
certain kinds of LAMMPS simulations.
4.1 "Restarting a simulation"_#4_1
4.2 "2d simulations"_#4_2
4.3 "CHARMM and AMBER force fields"_#4_3
4.4 "Running multiple simulations from one input script"_#4_4
4.5 "Parallel tempering"_#4_5
4.6 "Granular models"_#4_6
4.7 "TIP3P water model"_#4_7
4.8 "TIP4P water model"_#4_8
4.9 "SPC water model"_#4_9
4.10 "Coupling LAMMPS to other codes"_#4_10
4.11 "Visualizing LAMMPS snapshots"_#4_11 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
setup and run various kinds of problems.
:line
4.1 Restarting a simulation :link(4_1),h4
There are 3 ways to continue a long LAMMPS simulation. Multiple
"run"_run.html 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 "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files and read by a
"read_data"_read_data.html command in a new script. "This
section"_Section_tools.html discusses the {restart2data} tool that is
used to perform the conversion.
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 "read_restart"_read_restart.html and
"read_data"_read_data.html commands.
Look at the {in.chain} input script provided in the {bench} directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
restart 50 tmp.restart :pre
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
read_restart tmp.restart.50 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
run 50 :pre
Note that the following commands do not need to be repeated because
their settings are included in the restart file: {units, atom_style,
special_bonds, pair_style, bond_style}. However these commands do
need to be used, since their settings are not in the restart file:
{neighbor, fix, timestep}.
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 "fix langevin"_fix_langevin.html command
uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file using this tool:
restart2data tmp.restart.50 tmp.restart.data :pre
Then, this script could be used to re-run the last 50 steps:
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
read_data tmp.restart.data :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
reset_timestep 50
run 50 :pre
Note that nearly all the settings specified in the original {in.chain}
script must be repeated, except the {pair_coeff} and {bond_coeff}
commands since the new data file lists the force field coefficients.
Also, the "reset_timestep"_reset_timestep.html command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.
:line
4.2 2d simulations :link(4_2),h4
Use the "dimension"_dimension.html command to specify a 2d simulation.
Make the simulation box periodic in z via the "boundary"_boundary.html
command. This is the default.
If using the "create box"_create_box.html 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.
"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
If using the "read data"_read_data.html 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.
Use the "fix enforce2d"_fix_enforce2d.html 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.
Many of the example input scripts included in the LAMMPS distribution
are for 2d models.
:line
4.3 CHARMM and AMBER force fields :link(4_3),h4
There are many different ways to compute forces in the "CHARMM"_charmm
and "AMBER"_amber 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
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html for
additional tools that can use CHARMM or AMBER to assign force field
coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#Cornell for a description of the AMBER force
field.
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
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.
"bond_style"_bond_style.html harmonic
"angle_style"_angle_style.html charmm
"dihedral_style"_dihedral_style.html charmm
"pair_style"_pair_style.html lj/charmm/coul/charmm
"pair_style"_pair_style.html lj/charmm/coul/charmm/implicit
"pair_style"_pair_style.html lj/charmm/coul/long :ul
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
:line
4.4 Running multiple simulations from one input script :link(4_4),h4
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the "run"_run.html command
multiple times. For example, this script
units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000 :pre
would run 5 successive simulations of the same system for a total of
50,000 timesteps.
If you wish to run totally different simulations, one after the other,
the "clear"_clear.html command can be used in between them to
re-initialize LAMMPS. For example, this script
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
would run 2 independent simulations, one after the other.
For large numbers of independent simulations, you can use
"variables"_variable.html and the "next"_next.html and
"jump"_jump.html commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
variable d index run1 run2 run3 run4 run5 run6 run7 run8
cd $d
read_data data.polymer
run 10000
cd ..
clear
next d
jump in.polymer :pre
would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$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
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 "this
section"_Section_start.html#2_6 of the manual.
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 {universe}-style variables, as described in the
"variable"_variable.html 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.
:line
4.5 Parallel tempering :link(4_5),h4
The "temper"_temper.html 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.
Use the -procs and -in "command-line switches"_Section_start.html#2_6
to launch LAMMPS on multiple partitions.
In your input script, define a set of temperatures, one for each
processor partition, using the "variable"_variable.html command:
variable t proc 300.0 310.0 320.0 330.0 :pre
Define a fix of style "nvt"_fix_nvt.html or "langevin"_fix_langevin.html
to control the temperature of each simulation:
fix myfix all nvt $t $t 100.0 :pre
Use the "temper"_temper.html command in place of a "run"_run.html
command to perform a simulation where tempering exchanges will take
place:
temper 100000 100 $t myfix 3847 58382 :pre
:line
4.6 Granular models :link(4_6),h4
To run a simulation of a granular model, you will want to use
the following commands:
"atom_style"_atom_style.html granular
"fix nve/gran"_fix_nve_gran.html
"fix gravity"_fix_gravity.html
"thermo_style"_thermo_style.html gran :ul
Use one of these 3 pair potentials:
"pair_style"_pair_style.html gran/history
"pair_style"_pair_style.html gran/no_history
"pair_style"_pair_style.html gran/hertzian :ul
These commands implement fix options specific to granular systems:
"fix freeze"_fix_freeze.html
"fix gran/diag"_fix_gran_diag.html
"fix pour"_fix_pour.html
"fix viscous"_fix_viscous.html
"fix wall/gran"_fix_wall_gran.html :ul
The fix style {freeze} zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
{setforce}.
For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
"neigh_modify"_neigh_modify.html exclude :ul
:line
4.7 TIP3P water model :link(4_7),h4
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
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
"(Jorgensen)"_#Jorgensen.
O mass = 15.9994
H mass = 1.008 :all(b),p
O charge = -0.834
H charge = 0.417 :all(b),p
LJ epsilon of OO = 0.1521
LJ sigma of OO = 3.188
LJ epsilon of HH = 0.0460
LJ sigma of HH = 0.4000
LJ epsilon of OH = 0.0836
LJ sigma of OH = 1.7753 :all(b),p
K of OH bond = 450
r0 of OH bond = 0.9572 :all(b),p
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
These are the parameters to use for TIP3P with a long-range Coulombic
solver (Ewald or PPPM in LAMMPS):
O mass = 15.9994
H mass = 1.008 :all(b),p
O charge = -0.830
H charge = 0.415 :all(b),p
LJ epsilon of OO = 0.102
LJ sigma of OO = 3.1507
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
K of OH bond = 450
r0 of OH bond = 0.9572 :all(b),p
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
:line
4.8 TIP4P water model :link(4_8),h4
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 {harmonic} and an
angle style of {harmonic} or {charmm} should also be used.
Currently, only a four-point model for long-range Coulombics is
implemented via the LAMMPS "pair style
lj/cut/coul/long/tip4p"_pair_lj.html. We plan to add a cutoff
version in the future. For both models, the bond lengths and bond
angles should be held fixed using the "fix shake"_fix_shake.html
command.
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
"(Jorgensen)"_#Jorgensen. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
O mass = 15.9994
H mass = 1.008 :all(b),p
O charge = -1.040
H charge = 0.520 :all(b),p
r0 of OH bond = 0.9572
theta of HOH angle = 104.52 :all(b),p
OM distance = 0.15 :all(b),p
LJ epsilon of O-O = 0.1550
LJ sigma of O-O = 3.1536
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
These are the parameters to use for TIP4P with a long-range Coulombic
solver (Ewald or PPPM in LAMMPS):
O mass = 15.9994
H mass = 1.008 :all(b),p
O charge = -1.0484
H charge = 0.5242 :all(b),p
r0 of OH bond = 0.9572
theta of HOH angle = 104.52 :all(b),p
OM distance = 0.1250 :all(b),p
LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
:line
4.9 SPC water model :link(4_9),h4
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 "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
{harmonic} and an angle style of {harmonic} or {charmm} should also be
used.
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).
O mass = 15.9994
H mass = 1.008 :all(b),p
O charge = -0.820
H charge = 0.410 :all(b),p
LJ epsilon of OO = 0.1553
LJ sigma of OO = 3.166
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
:line
4.10 Coupling LAMMPS to other codes :link(4_10),h4
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.
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.
(1) Define a new "fix"_fix.html 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
"POEMS"_poems package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
"fix_poems"_fix_poems.html command for more details. See "this
section"_Section_modify.html of the documentation for info on how to add
a new fix to LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
(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
"run"_run.html command facilitates this with its {every} option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
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.
See "this section"_Section_modify.html of the documentation for how to
add a new command to LAMMPS.
(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 "run"_run.html 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.
"This section"_Section_start.html#2_4 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:
void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(doivd *, char *); :pre
The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application.
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 mutliple times, to
create multiple instances of LAMMPS.
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.
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.
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.
:line
4.11 Visualizing LAMMPS snapshots :link(4_11),h4
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
LAMMPS snapshots are created by the "dump"_dump.html 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 "xmovie"_Section_tools.html#xmovie program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geoemtry
and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
"Section_tools"_Section_tools.html doc page for details. The first is
the "ch2lmp tool"_Section_tools.html#charmm, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the "lmp2arc tool"_Section_tools.html#arc which
converts LAMMPS dump files into Accelrys's Insight MD program files.
The thrid is the "lmp2cfg tool"_Section_tools.html#cfg which converts
LAMMPS dump files into CFG files which can be read into the
"AtomEye"_atomeye visualizer.
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 "Pizza.py
WWW site"_pizza for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, 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.
LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including "VMD"_vmd.
LAMMPS can create DCD files directly (via "dump dcd") which can be
read by "VMD"_vmd in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the "dump"_dump.html command for more information on DCD
files.
LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by "VMD"_vmd for visualization.
See the "dump"_dump.html command for more information on XTC files.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://164.107.79.177/Archive/Graphics/A)
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(Horn)
[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
J Chem Phys, 120, 9665 (2004).
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
:link(Jorgensen)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
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