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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META
NAME=
"Generator"
CONTENT=
"Cosmo Create 1.0.3"
>
</HEAD>
<BODY>
<H2>
LAMMPS Input Commands
</H2>
<P>
<A
HREF=
"README.html"
>
Return
</A>
to top-level of LAMMPS documentation.
</P>
<P>
This page contains a complete list of valid LAMMPS commands which are
read-in from an input script. It will be easiest to understand if you
read it while looking at sample input scripts in the examples
directory.
</P>
<P>
The script of input commands is read by LAMMPS, one line at a time.
Each command causes LAMMPS to take some action. Usually it simply
causes some internal variable(s) to be set. Or it may cause a data file
to be read in or a simulation to be run. Note that most commands have
default settings, which means you only need use a particular command if
you do not want the default setting.
</P>
<P>
Each LAMMPS input script contains exactly one
"
read data
"
(or
"
read restart
"
) command which defines the problem to be
simulated. All other commands can be split into three categories: (a)
commands that (if used) must appear before the
"
read data
"
command because they define settings needed to correctly read-in the
problem and allocate memory for it, (b) commands that must appear after
the
"
read data
"
command because they act on the specified
problem, and (c) commands that can appear either before or after the
"
read data
"
command. Commands in category (c) are used before
the
"
read data
"
command if a default setting needs to be
changed before the problem description is read-in. They can be used
after the
"
read data
"
command if the user wishes to change a
setting before the next
"
run
"
or
"
minimize
"
command
is used. Other than these restrictions, commands can generally appear
in any order in the input script, although some commands require others
to have been previously specified.
</P>
<P>
Each LAMMPS input script also contains one or more
"
run
"
or
"
minimize
"
commands. These trigger an actual dynamics or
minimization computation to be done. Following a run, new commands from
categories (b) and (c) can be used to change various settings, and
additional
"
run
"
commands can then be used to continue the
previous simulation. LAMMPS continues to read successive lines from the
input script until the end-of-file is reached, which causes LAMMPS to
terminate.
</P>
<P>
This page gives examples of each command, some of which can be
specified in multiple styles. Typically the commands take one or more
parameters. The keyword for each command should begin in the leftmost
column and all characters in the command and its parameters should be
in lower-case (except the word NULL or characters in filenames).
Parameters can be separated by arbitrary numbers of spaces and/or tabs,
so long as the command fits on one line. The remainder of the line
after the last parameter is ignored.
</P>
<P>
The next section outlines the structure of a LAMMPS input script. The
final section gives a detailed description of the commands in
alphabetic order, each with its associated parameters and default
settings.
</P>
<UL>
<LI>
<A
HREF=
"#_cch3_951156975"
>
Structure of a LAMMPS input script
</A>
<LI>
<A
HREF=
"#_cch3_931277455"
>
Alphabetic Listing of Commands
</A>
</UL>
<HR>
<H3>
<A
NAME=
"_cch3_951156975"
>
Structure of a LAMMPS input script
</A></H3>
<P>
Any line starting with a # is a
<A
HREF=
"#_cch3_931276588"
>
comment
</A>
.
Comments can appear anywhere in the input script.
</P>
<P>
(1)
<A
HREF=
"#_cch3_930960479"
>
Initialization settings
</A>
(must appear
before
"
read data
"
or
"
read restart
"
)
</P>
<P>
(2)
<A
HREF=
"#_cch3_951435622"
>
Optional Settings
</A>
(can appear before
and/or after
"
read data
"
or
"
read restart
"
)
</P>
<P>
(3)
<A
HREF=
"#_cch3_951435906"
>
Read in a Problem
</A>
via a
"
<A
HREF=
"#_cch3_931277059"
>
read data
</A>
"
or
"
<A
HREF=
"#_cch3_931277070"
>
read restart
</A>
"
command
</P>
<P>
(4)
<A
HREF=
"#_cch3_951435622"
>
Optional Settings
</A>
(same as (2))
</P>
<P>
(5) Problem Settings (must appear after
"
read data
"
or
"
read restart
"
)
</P>
<UL>
<LI>
<A
HREF=
"#_cch3_930960510"
>
Velocity Creation
</A>
<LI>
<A
HREF=
"#_cch3_951435663"
>
Force Field Parameters
</A>
<LI>
<A
HREF=
"#_cch3_930960516"
>
Constraints
</A>
<LI>
<A
HREF=
"#_cch3_930960490"
>
Ensemble Control
</A>
<LI>
<A
HREF=
"#_cch3_930960485"
>
Output Control
</A>
<LI>
<A
HREF=
"#_cch3_951435640"
>
Integrator Settings
</A>
<LI>
<A
HREF=
"#_cch3_951435646"
>
Minimizer Settings
</A>
</UL>
<P>
(6)
<A
HREF=
"#_cch3_951435914"
>
Perform a Simulation
</A>
via a
"
<A
HREF=
"#_cch3_931277194"
>
run
</A>
"
or
"
<A
HREF=
"#_cch3_931277212"
>
minimize
</A>
"
command
</P>
<P>
Repeat (4), (5), and (6) as desired ...
</P>
<HR>
<H3>
<A
NAME=
"_cch3_930960479"
>
Initialization Settings
</A></H3>
<P>
(if used, must appear before
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276596"
>
units
</A>
real
<A
HREF=
"#_cch3_951437269"
>
extra memory
</A>
2.0 1.5 2.0 2.5
<A
HREF=
"#_cch3_931276604"
>
dimension
</A>
3
<A
HREF=
"#_cch3_931276624"
>
processor grid
</A>
10 10 10
<A
HREF=
"#_cch3_999182956"
>
periodicity
</A>
0 0 0
<A
HREF=
"#_cch3_999182965"
>
slab volume
</A>
3.0
<A
HREF=
"#_cch3_931276632"
>
newton flag
</A>
3
<A
HREF=
"#_cch3_931276687"
>
true flag
</A>
0
<A
HREF=
"#_cch3_951437278"
>
maximum cutoff
</A>
10.0
<A
HREF=
"#_cch3_931276900"
>
mixing style
</A>
geometric
<A
HREF=
"#_cch3_951437286"
>
restart version
</A>
5
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435622"
>
Optional Settings
</A></H3>
<P>
(if used, can appear before and/or after
"
read data
"
or
"
read restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276654"
>
neighbor
</A>
2.0 1 1 10 1
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
none
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
lj/cutoff 10.0 0
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
lj/smooth 8.0 10.0
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
lj/shift 10.0 0
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
soft 2.5
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
class2/cutoff 10.0 0
<A
HREF=
"#_cch3_931276833"
>
nonbond style
</A>
lj/charmm 15.0 15.1
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
none
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
cutoff 10.0
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
smooth 8.0 10.0
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
ewald 10.0 1.0E-4
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
pppm 10.0 1.0E-4
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
charmm/switch 15.0 15.1
<A
HREF=
"#_cch3_931276910"
>
coulomb style
</A>
debye 10.0 0.5
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
none
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
harmonic
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
fene/standard
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
fene/shift
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
nonlinear
<A
HREF=
"#_cch3_931276958"
>
bond style
</A>
class2
<A
HREF=
"#_cch3_931277007"
>
angle style
</A>
none
<A
HREF=
"#_cch3_931277007"
>
angle style
</A>
harmonic
<A
HREF=
"#_cch3_931277007"
>
angle style
</A>
class2
<A
HREF=
"#_cch3_931277007"
>
angle style
</A>
charmm
<A
HREF=
"#_cch3_931277007"
>
angle style
</A>
cosine
<A
HREF=
"#_cch3_931277020"
>
dihedral style
</A>
none
<A
HREF=
"#_cch3_931277020"
>
dihedral style
</A>
harmonic
<A
HREF=
"#_cch3_931277020"
>
dihedral style
</A>
mutliharmonic
<A
HREF=
"#_cch3_931277020"
>
dihedral style
</A>
class2
<A
HREF=
"#_cch3_931277020"
>
dihedral style
</A>
charmm
<A
HREF=
"#_cch3_931277042"
>
improper style
</A>
none
<A
HREF=
"#_cch3_931277042"
>
improper style
</A>
harmonic
<A
HREF=
"#_cch3_931277042"
>
improper style
</A>
cvff
<A
HREF=
"#_cch3_931277042"
>
improper style
</A>
class2
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435906"
>
Read in a Problem
</A></H3>
<PRE>
<A
HREF=
"#_cch3_931277059"
>
read data
</A>
data.lj
<A
HREF=
"#_cch3_931277070"
>
read restart
</A>
restart.100000
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_930960510"
>
Velocity Creation
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931277080"
>
create group
</A>
types 1 3
<A
HREF=
"#_cch3_931277080"
>
create group
</A>
molecules 200 300
<A
HREF=
"#_cch3_931277080"
>
create group
</A>
region 0.0 1.0 0.0 1.0 INF 1.0
<A
HREF=
"#_cch3_931277080"
>
create group
</A>
remainder
<A
HREF=
"#_cch3_931299999"
>
rotation zero
</A>
1
<A
HREF=
"#_cch3_931277097"
>
create temp
</A>
uniform 300.0 12345678
<A
HREF=
"#_cch3_931277097"
>
create temp
</A>
gaussian 300.0 12345678
<A
HREF=
"#_cch3_931277097"
>
create temp
</A>
velocity 0.0 0.0 0.0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435663"
>
Force Field Parameters
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 3.45 10.0 (nonbond style lj/cutoff)
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 3.45 8.0 10.0 (nonbond style lj/smooth)
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 3.45 2.0 10.0 (nonbond style lj/shift)
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 30.0 2.5 (nonbond style soft)
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 3.45 10.0 (nonbond style class2/cutoff)
<A
HREF=
"#_cch3_931276848"
>
nonbond coeff
</A>
1 2 1.0 3.45 1.0 3.45 (nonbond style lj/charmm)
<A
HREF=
"#_cch3_931276666"
>
special bonds
</A>
amber
<A
HREF=
"#_cch3_931276666"
>
special bonds
</A>
0.0 0.0 0.5
<A
HREF=
"#_cch3_931276941"
>
pppm mesh
</A>
32 32 64
<A
HREF=
"#_cch3_931276947"
>
pppm order
</A>
5
<A
HREF=
"#_cch3_931276953"
>
dielectric
</A>
1.0
<A
HREF=
"#_cch3_931276970"
>
bond coeff
</A>
1 100.0 3.45 (bond style harmonic)
<A
HREF=
"#_cch3_931276970"
>
bond coeff
</A>
1 30.0 1.5 1.0 1.0 (bond style fene/standard )
<A
HREF=
"#_cch3_931276970"
>
bond coeff
</A>
1 30.0 1.5 1.0 1.0 0.2 (bond style fene/shift)
<A
HREF=
"#_cch3_931276970"
>
bond coeff
</A>
1 28.0 0.748308 0.166667 (bond style nonlinear)
<A
HREF=
"#_cch3_999724447"
>
angle coeff
</A>
1 30.0 108.0 (angle style harmonic)
<A
HREF=
"#_cch3_999724447"
>
angle coeff
</A>
1 30.0 108.0 30.0 2.5 (angle style charmm)
<A
HREF=
"#_cch3_999724447"
>
angle coeff
</A>
1 30.0 (angle style cosine)
<A
HREF=
"#_cch3_999724456"
>
dihedral coeff
</A>
1 10.0 1 3 (dihedral style harmonic)
<A
HREF=
"#_cch3_999724456"
>
dihedral coeff
</A>
1 2.0 2.0 2.0 2.0 2.0 (dihedral style multiharmonic)
<A
HREF=
"#_cch3_999724456"
>
dihedral coeff
</A>
1 2.0 5 180.0 0.5 (dihedral style charmm)
<A
HREF=
"#_cch3_999724473"
>
improper coeff
</A>
1 20.0 0.0 (improper style harmonic)
<A
HREF=
"#_cch3_999724473"
>
improper coeff
</A>
1 20.0 10.0 (improper style cvff)
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_930960516"
>
Constraints
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
none
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 setforce 0.0 NULL 0.0
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 addforce 1.0 0.0 0.0
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 aveforce 1.0 0.0 0.0
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 rescale 300.0 300.0 100 20.0 0.5
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 hoover/drag 50.0 50.0 0.001
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 langevin 50.0 50.0 0.01 12345 1 1 1
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 springforce 10.0 NULL NULL 1.0
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 dragforce 10.0 -5.0 NULL 2.0 1.0
<A
HREF=
"#_cch3_931277114"
>
fix style
</A>
1 shake 3 0.001 100
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 atom 200
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 molecule 50
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 type 2
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 region 0.0 1.0 INF INF 0.0 1.0
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 bondtype 4
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 angletype 18 10
<A
HREF=
"#_cch3_931277163"
>
assign fix
</A>
1 remainder
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_930960490"
>
Ensemble Control
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276742"
>
temp control
</A>
none
<A
HREF=
"#_cch3_931276742"
>
temp control
</A>
rescale 300.0 300.0 100 20.0 0.5
<A
HREF=
"#_cch3_931276742"
>
temp control
</A>
replace 300.0 300.0 50 12345678
<A
HREF=
"#_cch3_931276742"
>
temp control
</A>
langevin 50.0 50.0 0.01 123456
<A
HREF=
"#_cch3_931276742"
>
temp control
</A>
nose/hoover 300.0 300.0 0.01
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
none
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
nose/hoover xyz 0.0 0.0 0.001
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
nose/hoover xz 0.0 10.0 5.0 5.0 0.0 10.0 0.001
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
nose/hoover yz NULL NULL 5.0 5.0 0.0 10.0 0.001
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
nose/hoover aniso 0.0 0.0 0.0 0.0 1.0 10.0 0.001
<A
HREF=
"#_cch3_931276784"
>
press control
</A>
nose/hoover aniso 0.0 0.0 0.0 0.0 NULL NULL 0.001
<A
HREF=
"#_cch3_999724492"
>
volume control
</A>
none
<A
HREF=
"#_cch3_999724492"
>
volume control
</A>
linear x 0.0 10.0
<A
HREF=
"#_cch3_999724492"
>
volume control
</A>
linear y -1.0 15.0
<A
HREF=
"#_cch3_999724492"
>
volume control
</A>
linear z -10.0 10.0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_930960485"
>
Output Control
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276675"
>
thermo flag
</A>
50
<A
HREF=
"#_cch3_931276681"
>
thermo style
</A>
0
<A
HREF=
"#_cch3_931276696"
>
dump atoms
</A>
100 filename
<A
HREF=
"#_cch3_931276703"
>
dump velocities
</A>
100 filename
<A
HREF=
"#_cch3_931276712"
>
dump forces
</A>
100 filename
<A
HREF=
"#_cch3_931276719"
>
restart
</A>
1000 1 filename
<A
HREF=
"#_cch3_931276719"
>
restart
</A>
1000 2 file1 file2
<A
HREF=
"#_cch3_931276727"
>
diagnostic
</A>
diffusion 100 filename 3 1.0 -1.0 2.5
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435640"
>
Integrator Settings
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931276638"
>
timestep
</A>
1.0
<A
HREF=
"#_cch3_931276645"
>
respa
</A>
2 2 4
<A
HREF=
"#_cch3_931277185"
>
reset timestep
</A>
0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435646"
>
Minimizer Settings
</A></H3>
<P>
(if used, must appear after
"
read data
"
or
"
read
restart
"
command)
</P>
<PRE>
<A
HREF=
"#_cch3_931277200"
>
min style
</A>
hftn
<A
HREF=
"#_cch3_1001972012"
>
min flag
</A>
10
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951435914"
>
Perform a Simulation
</A></H3>
<PRE>
<A
HREF=
"#_cch3_931277194"
>
run
</A>
10000
<A
HREF=
"#_cch3_931277212"
>
minimize
</A>
0.0001 9999 50000
</PRE>
<HR>
<HR>
<H3>
<A
NAME=
"_cch3_931277455"
>
Alphabetic Listing of Commands:
</A></H3>
<HR>
<H3>
<A
NAME=
"_cch3_999724447"
>
angle coeff
</A></H3>
<UL>
<LI>
1st parameter = angle type #
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
coeffs: harmonic
(1) K (energy units)
(2) theta (degrees)
class2
currently not enabled for
"
angle coeff
"
command
must be specified in data file (see
"
read data
"
command)
charmm
(1) K (energy units)
(2) theta (degrees)
(3) K_UB (energy/distance^2)
(4) r_UB (distance)
cosine
(1) K (energy units)
define (or override) angle coefficients for an individual angle type
use appropriate number of coeffs for a particular style
see force_fields.html for meaning of coefficients for each style
these coefficients can also be set in data file
by a
"
Angle Coeffs
"
entry, the most recently defined
coefficients are used
cannot use this command before a
"
read data
"
or
"
read restart
"
is performed,
because memory is not yet allocated for the necessary arrays
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277007"
>
angle style
</A></H3>
<UL>
<LI>
none = compute no angles
<LI>
harmonic = harmonic angles (class 1)
<LI>
class2 = class 2 angles (and associated cross terms)
<LI>
charmm = harmonic + Urey-Bradley
<LI>
cosine = (1 + cos(theta))
</UL>
<PRE>
define style of angle interactions to use for all 3-body terms
must be used before the
"
read data
"
command (if not using the
default) to tell the program how to read the
"
Angle Coeffs
"
entry
in the data file
can be used after the
"
read data
"
command to change the style to none
coefficients for all angle types must be defined in the data (or restart)
file by a
"
Angle Coeffs
"
entry or by
"
angle coeff
"
commands before a run is performed
Default = harmonic
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277163"
>
assign fix
</A></H3>
<UL>
<LI>
1st parameter = constraint #
<LI>
2nd parameter = style of group of atoms or bondtype
<LI>
3rd-Nth parameters = coeffs 1 to N-2
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
atom = single atom
<LI>
molecule = all atoms in a particular molecule
<LI>
type = single atom type
<LI>
region = geometric region of atoms
<LI>
bondtype = bondtype (only for assigning to fix style SHAKE)
<LI>
angletype = angletype (only for assigning to fix style SHAKE)
<LI>
remainder = rest of unconstrained atoms
</UL>
<PRE>
coeffs: atom
(1) global atom #
molecule
(1) molecule #
type
(1) atom type
region
(1) lower x bound of region
(2) upper x bound of region
(3) lower y bound of region
(4) upper y bound of region
(5) lower z bound of region
(6) upper z bound of region
bondtype
(1) bond type
angletype
(1) angle type
(2) bond type used within that angle
remainder
no other parameters required
assign a group of atoms or a bond type to a particular constraint
use appropriate number of coeffs for a particular style
the constraint itself must first be defined by a
"
fix style
"
command
multiple groups of atoms or bond types can be assigned to the same constraint
the bondtype option can only be assigned to a "fix style" of "shake",
multiple bondtypes can be SHAKEn, so long as the size of clusters of
atoms does not exceed the limit described in the "fix style" command
the angletype option can only be assigned to a "fix style" of "shake",
only a single angletype can be SHAKEn, it is designed to be used
in conjunction with "fix style bondtype" to make clusters of size 3
entirely rigid (e.g. water)
the angletype option enables an additional check when SHAKE constraints
are computed: if a cluster is of size 3 and both bonds in
the cluster are of a bondtype specified by the 2nd paramter of
angletype, then the cluster is SHAKEn with an additional angle
constraint that makes it rigid, using the equilibrium angle appropriate
to the specified angletype
IMPORTANT NOTE: the angletype option has one additional affect, namely
that no angle forces for any angle of type angletype are computed
(since it is assumed those angles will be frozen by being SHAKEn), thus
it will likely cause unintended behavior if the bonds in some atom pairs
within angles of type angletype do not have the appropriate bondtype,
since they will not be SHAKEn but neither will the angle force by computed
for style region, a coeff of INF means + or - infinity (all the way
to the boundary)
an atom can be assigned to multiple constraints, the contraints will be
applied in the reverse order they are assigned to that atom
(e.g. each timestep, the last fix assigned to an atom will be applied
to it first, then the next-to-last applied second, etc)
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276970"
>
bond coeff
</A></H3>
<UL>
<LI>
1st parameter = bond type #
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
coeffs: harmonic
(1) K (energy units)
(2) r0 (distance units)
fene/standard
(1) k for FENE portion (energy/distance^2 units)
(2) r0 for FENE portion (distance units)
(3) epsilon for LJ portion (energy units)
(4) sigma for LJ portion (distance units)
fene/shift
(1) k for FENE (energy/distance^2 units)
(2) r0 for FENE after shift is performed (distance units)
(3) epsilon for LJ (energy units)
(4) sigma for LJ after shift is performed (distance units)
(5) delta shift distance (distance units)
nonlinear
(1) epsilon (energy units)
(2) r0 (distance units)
(3) lamda (distance units)
class2
currently not enabled for
"
bond coeff
"
command
must be specified in data file (see
"
read data
"
command)
define (or override) bond coefficients for an individual bond type
use appropriate number of coeffs for a particular style
see force_fields.html for meaning of coefficients for each style
these coefficients can also be set in data file
by a
"
Bond Coeffs
"
entry, the most recently defined
coefficients are used
cannot use this command before a
"
read data
"
or
"
read restart
"
is performed,
because memory is not yet allocated for the necessary arrays
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276958"
>
bond style
</A></H3>
<UL>
<LI>
none = compute no bonds
<LI>
harmonic = harmonic springs
<LI>
fene/standard = attractive logarithmic term, repulsive LJ
<LI>
fene/shift = same as fene/standard with shift of bond distance
<LI>
nonlinear = non-linear finite-extension spring (van Swol)
<LI>
class2 = class 2 bonds
</UL>
<PRE>
define style of bond interactions to use between all bonded atoms
must be used before the
"
read data
"
command (if not using the
default) to tell the program how to read the
"
Bond
Coeffs
"
entry in the data file (if one exists)
can be used after the
"
read data
"
command to change the style,
in this case
"
bond coeff
"
commands must also be used to set new
coefficients for each bond type (unless the new style is
"
none
"
)
coefficients for all bond types must be defined in the data (or restart)
file by a
"
Bond Coeffs
"
entry or by
"
bond coeff
"
commands before a run is performed
Default = harmonic
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276588"
>
comments
</A></H3>
<PRE>
blank lines are ignored
lines starting with a # are echoed into the log file
for commands, everything on a line after the last parameter is ignored
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276910"
>
coulomb style
</A></H3>
<UL>
<LI>
1st parameter = style of pairwise Coulomb interactions
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no Coulomb interactions are computed
<LI>
cutoff = use a simple cutoff
<LI>
smooth = use a switch region that goes smoothly to zero
<LI>
ewald = use Ewald summations for long-range effects
<LI>
pppm = use particle-mesh Ewald for long-range effects
<LI>
charmm/switch = use the charmm switch to go smoothly to zero
<LI>
debye = add a Debye/Huckel screening exponential
</UL>
<PRE>
coeffs: none
no other parameters required
cutoff
(1) cutoff distance (distance units)
smooth
(1) inner cutoff (distance units)
(2) outer cutoff (distance units)
ewald
(1) cutoff distance for near-field portion (distance units)
(2) accuracy criterion
pppm
(1) cutoff distance for near-field portion (distance units)
(2) accuracy criterion
charmm/switch
(1) inner cutoff (distance units)
(2) outer cutoff (distance units)
debye
(1) cutoff distance (distance units)
(2) kappa (inverse distance units)
use appropriate number of coeffs for a particular style
normally this command should be used before
"
read data
"
or
"
read restart
"
(if simulating a charged system) to tell LAMMPS how big a force cutoff
is being used, the
"
maximum cutoff
"
command can also serve this
purpose
restart files do not store
"
coulomb style
"
choice or cutoff, so
this should be specified in the input script when running from a restart
file
this command can also be used after
"
read data
"
or
"
read restart
"
to
change the style of Coulomb interactions or the cutoff
if simulated system has no charges, should set
"
coulomb style none
"
to
prevent LAMMPS from doing useless nonbond work, LAMMPS will set
this for you and issue a warning
cutoff distance can be smaller or larger than simulation box dimensions
accuracy criterion means
"
one part in value
"
- e.g. 1.0E-4
Ewald and PPPM accuracy criterion are used in conjunction with cutoff
to partition work between short-range and long-range routines
accuracy criterion effectively determines how many k-space vectors are used
to approximate the energy and forces
for PPPM, accuracy criterion determines mesh spacing (see
"
particle mesh
"
command)
3-d periodic boundary conditions are normally used in conjunction with
Ewald and PPPM, see
"
slab volume
"
command for 2-d Ewald/PPPM
cannot use any Coulomb styles other than none with nonbond style = lj/shift or
nonbond style = soft
Coulomb style = smooth should be used with nonbond style = lj/smooth,
and both should use same inner and outer cutoffs
nonbond style = lj/charmm should be used with coulomb style = charmm/switch
for smooth and charmm/switch styles, outer cutoff must be
>
inner cutoff
for smooth and charmm/switch styles, atom pairs less than the inner cutoff
distance use usual Coulomb, pairs between inner and outer are smoothed,
and the potential goes to 0.0 at the outer cutoff
for smooth style, force is continuously differentiable everywhere
for debye style, an exp(-kappa*r) screening is added to the Coulombic
interaction
Default = cutoff 10.0 for real units
cutoff 2.5 for lj units
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277080"
>
create group
</A></H3>
<UL>
<LI>
1st parameter = style of group of atoms
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
types = range of atom types
<LI>
molecules = range of molecule IDs
<LI>
region = geometric region of atoms
<LI>
remainder = rest of uninitialized atoms
</UL>
<PRE>
coeffs: types
(1) lowest atom type
(2) highest atom type
molecules
(1) lowest molecule ID
(2) highest molecule ID
region
(1) lower x bound of region
(2) upper x bound of region
(3) lower y bound of region
(4) upper y bound of region
(5) lower z bound of region
(6) upper z bound of region
remainder
no other parameters required
used with
"
create temp
"
commmand to initialize velocities of atoms
by default, the
"
create temp
"
command initializes the velocities of all atoms,
this command limits the initialization to a group of atoms
this command is only in force for the next
"
create temp
"
command, any
subsequent
"
create temp
"
command is applied to all atoms (unless the
"
create group
"
command is used again)
for style types, only atoms with a type such that lo-type
<
= type
<
= hi-type
will be initialized by "create temp"
for style types, lo-type can equal hi-type if just want to specify one type
for style molecules, only atoms belonging to molecules with an ID # such
that lo-ID
<
= type
<
= hi-ID will be initialized by "create temp"
for style molecules, lo-ID can equal hi-ID if just want to specify one molecule
for style region, only atoms within the specified spatial region
will be initialized by "create temp"
for style region, a coeff of INF means + or - infinity (all the way
to the boundary)
for style remainder, only previously uninitialized atoms
will be initialized by "create temp"
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277097"
>
create temp
</A></H3>
<UL>
<LI>
1st parameter = style of temperature creation
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
uniform = uniform distribution of velocities
<LI>
gaussian = gaussian distribution of velocities
<LI>
velocity = assign specific initial velocity to each atom
</UL>
<PRE>
coeffs: uniform
(1) target T (temperature units)
(2) random # seed (0
< seed
<=
8
digits
)
gaussian
(
1
)
target
T
(
temperature
units
)
(
2
)
random
#
seed
(
0
<
seed
<=
8
digits
)
velocity
(
1
)
x
velocity
component
(
velocity
units
)
(
2
)
y
velocity
component
(
velocity
units
)
(
3
)
z
velocity
component
(
velocity
units
)
initialize
velocities
of
atoms
to
a
specified
temperature
use
appropriate
number
of
coeffs
for
a
particular
style
cannot
be
done
before
a
data
or
restart
file
is
read
by
default
,
velocities
are
created
for
all
atoms
-
this
can
be
overridden
by
first
using
a
"
create
group
"
command
for
uniform
and
Gaussian
styles
velocities
are
created
in
processor-independent
fashion
-
is
slower
but
gives
the
same
initial
state
independent
of
#
of
processors
for
uniform
and
Gaussian
styles
the
momentum
of
the
initialized
atoms
is
also
zeroed
,
but
only
if
all
atoms
are
being
initialized
for
uniform
and
Gaussian
styles
,
RN
are
generated
with
Park
/
Miller
RNG
for
velocity
style
in
2-d
simulations
,
still
specify
z
velocity
component
,
even
though
it
is
ignored
</
PRE
>
<HR>
<H3>
<A
NAME=
"_cch3_931276727"
>
diagnostic
</A></H3>
<UL>
<LI>
1st parameter = nametag of a user routine added to diagnostic.f file
<LI>
2nd parameter = call this user routine every this # of timesteps
<LI>
3rd parameter = file name for this routine's diagnostic output
<LI>
4th parameter = # of remaining parameters (0 to 5)
<LI>
5th-9th parameters = optional parameters to pass to user routine
</UL>
<PRE>
call a user-defined diagnostic routine every this many timesteps
this command can be used multiple times to call different routines
at different frequencies, that use different parameters, and that
send output to different files
value of 0 for 2nd parameter means never call this particular routine
this command causes any previous file associated with this user routine
to be closed
new filename can exist, will be overwritten
if the file name specified is
"
none
"
, then no file is opened
each routine that is added to diagnostic.f and enabled with a
"
diagnostic
"
command will be called at the beginning and end of
each
"
run
"
and every so many timesteps during the run
see *** comments in diagnostic.f for changes that must be made in
that file to enable user diagnostics, LAMMPS must then be re-compiled
and re-linked
see the diagnostic.f file for further information on how to create
routines that operate on internal LAMMPS data, do their own file output,
perform different operations (e.g. setup and clean-up) depending
on when they are called, etc
the optional 5th-9th parameters are stored as internal LAMMPS variables
which can be accessed by the diagnostic routine
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276953"
>
dielectric
</A></H3>
<PRE>
set dielectric constant to this value
Default = 1.0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_999724456"
>
dihedral coeff
</A></H3>
<UL>
<LI>
1st parameter = dihedral type #
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
coeffs: harmonic
(1) K (energy units)
(2) d (+1 or -1)
(3) n (1,2,3,4,6)
multiharmonic
(1) A_1 (energy units)
(2) A_2 (energy units)
(3) A_3 (energy units)
(4) A_4 (energy units)
(5) A_5 (energy units)
class2
currently not enabled for
"
dihedral coeff
"
command
must be specified in data file (see
"
read data
"
command)
charmm
(1) K (energy units)
(2) n (1,2,3,4,6)
(3) d (0 or 180 degrees) (converted to radians within LAMMPS)
(4) weighting factor to turn on/off 1-4 neighbor nonbond interactions
define (or override) dihedral coefficients for an individual dihedral type
use appropriate number of coeffs for a particular style
see force_fields.html for meaning of coefficients for each style
these coefficients can also be set in data file
by a
"
Dihedral Coeffs
"
entry, the most recently defined
coefficients are used
cannot use this command before a
"
read data
"
or
"
read restart
"
is performed,
because memory is not yet allocated for the necessary arrays
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277020"
>
dihedral style
</A></H3>
<UL>
<LI>
none = compute no dihedrals
<LI>
harmonic = simple harmonic dihedrals (class 1)
<LI>
multiharmonic = multiple simple harmonic dihedrals (class 1)
<LI>
class2 = class 2 dihedrals (and associated cross terms)
<LI>
charmm= simple harmonic dihedrals + charmm 1-4 interactions
</UL>
<PRE>
define style of dihedral interactions to use for all 4-body terms
must be used before the
"
read data
"
command (if not using the
default) to tell the program how to read the
"
Dihedral
Coeffs
"
entry in the data file
can be used after the
"
read data
"
command to change the style to none
coefficients for all dihedral types must be defined in the data (or restart)
file by a
"
Dihedral Coeffs
"
entry or by
"
dihedral coeff
"
commands before a run is performed
Default = harmonic
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276604"
>
dimension
</A></H3>
<UL>
<LI>
specify 3 for 3-d or 2 for 2-d run
</UL>
<PRE>
for a 2-d run, assumes all z-coords are set to 0.0 in
"
read data
"
or
"
read restart
"
files and program creates no z velocities
this command sets the processor grid to default values for 2-d or 3-d
so must be used before
"
processor grid
"
command
must be set before data or restart file is read
Default = 3
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276696"
>
dump atoms
</A></H3>
<UL>
<LI>
1st parameter = # of timesteps
<LI>
2nd parameter = file name
</UL>
<PRE>
dump all atom positions to a file every this many timesteps
(every this many iteration when the minimizer is invoked)
when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
positions are also dumped at the start and end of each run
when dumped during minimization, all dumps will have the same timestamp
since the timestep does not change during minimization
value of 0 means never dump
any previous file is closed
new filename can exist, will be overwritten
atom positions in dump file are in
"
box
"
units (0.0 to 1.0) in each dimension
IMPORTANT NOTE: due to the way periodic boundary conditions are enforced
(only when neighbor lists are rebuilt), atom coords appearing in the dump
file can be slightly outside the specified box
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276712"
>
dump forces
</A></H3>
<UL>
<LI>
1st parameter = # of timesteps
<LI>
2nd parameter = file name
</UL>
<PRE>
dump all atom forces to a file every this many timesteps
(every this many iteration when the minimizer is invoked)
when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
forces are also dumped at the start and end of each run
when dumped during minimization, all dumps will have the same timestamp
since the timestep does not change during minimization
any previous file is closed
new filename can exist, will be overwritten
value of 0 means never dump
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276703"
>
dump velocities
</A></H3>
<UL>
<LI>
1st parameter = # of timesteps
<LI>
2nd parameter = file name
</UL>
<PRE>
dump all atom velocities to a file every this many timesteps
when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
velocities are also dumped at the start and end of every run
any previous file is closed
new filename can exist, will be overwritten
value of 0 means never dump
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951437269"
>
extra memory
</A></H3>
<UL>
<LI>
1st parameter = extra_own = padding factor on allocation of owned atom
arrays
<LI>
2nd parameter = extra_ghost = padding factor on allocation of ghost
atom arrays
<LI>
3rd parameter = extra_neigh = padding factor on allocation of neighbor
lists
<LI>
4th parameter = extra_buf = padding factor on allocation of
communication buffers
</UL>
<PRE>
factors that affect how much extra memory is allocated when a problem is setup
factor of 1.0 means no padding (use exactly what LAMMPS estimates is
needed), factor of 2.0 means 2x longer arrays, etc
typically don't need to change default settings unless LAMMPS tells you
to
"
boost
"
some factor at run-time
final section of log file lists optimal settings for these parameters,
i.e. the job could have been run with those
"
extra memory
"
settings
and would have used minimal memory
must be set before data or restart file is read
Default = 1.5 for all 4 parameters
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277114"
>
fix style
</A></H3>
<UL>
<LI>
1st parameter = constraint # (except for none)
<LI>
2nd parameter = style of that constraint
<LI>
3rd-Nth parameters = coeffs 1 to N-2
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = erase all constraints and all atom and bond assignments
<LI>
setforce = set force on each atom in group
<LI>
addforce = add a force to each atom in group
<LI>
aveforce = apply an external force to group of atoms such that every
atom is accelerated the same
<LI>
rescale = thermostat a group of atoms by rescaling their velocities
<LI>
hoover/drag = thermostat a group of atoms by the Hoover method
<LI>
langevin = thermostat a group of atoms by the Langevin method
<LI>
springforce = apply a spring force to each atom in group
<LI>
dragforce = drag each atom in group to a specified position
<LI>
shake = apply bond length constraints to certain bonds, enabling longer
timesteps
</UL>
<PRE>
coeffs: none
no other parameters required (use
"
none
"
as 1st parameter)
setforce
(1) x component of set force (in force units)
(2) y component of set force (in force units)
(3) z component of set force (in force units)
addforce
(1) x component of added force (in force units)
(2) y component of added force (in force units)
(3) z component of added force (in force units)
aveforce
(1) x comp of added average force per atom (in force units)
(2) y comp of added average force per atom (in force units)
(3) z comp of added average force per atom (in force units)
rescale
(1) desired T at beginning of run
(2) desired T at end of run
(3) check for rescaling every this many timesteps
(4) T window outside of which velocities will be rescaled
(5) fractional amount (0.0 to 1.0) of rescaling to perform
hoover/drag
(1) desired T at beginning of run
(2) desired T at end of run
(3) damping constant for drag (roughly inverse time units)
langevin
(1) desired T at beginning of run
(2) desired T at end of run
(3) Langevin damping parameter (inverse time units)
(4) random seed to use for white noise (0
< seed
<=
8
digits
)
(
5
)
0
/
1 =
off/on
x
dimension
(
6
)
0
/
1 =
off/on
y
dimension
(
7
)
0
/
1 =
off/on
z
dimension
springforce
(
1
)
x
position
of
spring
origin
(
2
)
y
position
(
3
)
z
position
(
4
)
force
constant
k
(
so
that
k
*
distance =
force
units
)
dragforce
(
1
)
x
position
to
drag
atom
towards
(
2
)
y
position
(
3
)
z
position
(
4
)
force
magnitude
f
(
in
force
units
)
(
5
)
delta
outside
of
which
to
apply
force
(
in
distance
units
)
shake
(
1
)
max
#
of
SHAKE
iterations
within
each
atom
cluster
(
2
)
SHAKE
tolerance
(
accuracy
of
one
part
in
tolerance
)
(
3
)
print
bond
statistics
every
this
many
steps
(
0 =
never)
define
a
constraint
cannot
skip
a
constraint
number
,
all
must
be
used
before
a
run
is
performed
use
appropriate
number
of
coeffs
for
a
particular
style
which
atoms
or
bonds
the
constraint
will
affect
is
set
by
the
"
assign
fix
"
command
all
of
the
constraints
(
except
for
rescale
)
are
applied
every
timestep
all
specified
temperatures
are
in
temperature
units
for
style
setforce
,
a
coeff
of
NULL
means
do
not
alter
that
force
component
for
style
aveforce
,
average
force
on
the
group
of
fixed
atoms
is
computed
,
then
new
average
force
is
added
in
and
actual
force
on
each
atom
is
set
to
new
total
value
-
>
has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used in
conjuction with global
"
temp control
"
, since they conflict and will
cause atom velocities to be reset twice
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used
when performing a minimization
if multiple Langevin constraints are specified the Marsaglia RNG will
only use the last RNG seed specified for initialization
meaning of rescale and Langevin thermostatting coefficients is same as in
"
temp control
"
command
for rescale style, it can be used as a coarse temperature rescaler,
for example
"
rescale 200.0 300.0 100 10.0 1.0
"
will ramp the temperature
up during the simulation, resetting it to the target temperatue as needed
for rescale style, it can be used to create an instantaneous
drag force that slowly rescales the temperature without oscillation,
for example
"
rescale 300.0 300.0 1 0.0 0.0001
"
will force (or keep)
the temperature to be 300.0, the time frame over which this occurs
will become longer as the last parameter is made smaller
for hoover/drag style, the drag force accumulates over time so some
oscillation in temperature can occur, for example
"
rescale 300.0 300.0 1 0.0 0.0001
"
will force (or keep)
the temperature to be 300.0, the time frame over which the oscillations
occur will become longer as the last parameter is made smaller
style springforce is designed to be applied to an entire group of atoms
en masse (e.g. an umbrella force on an entire molecule)
for springforce style, the center of mass r0 of the group of atoms is computed,
then a restoring force = -k*(r-r0)*mass/masstotal is applied to each
atom in the group where mass = mass of the atom and masstotal = mass of
all the atoms in the group - thus
"
k
"
should represent the total
force on the group of atoms (not per atom)
for springforce style, a xyz position of NULL means do not include that
dimension in the distance or force computation
for dragforce style, apply a drag force of magnitude f to each atom in the
group in the direction (r-r0) where r0 = (x,y,z) - do not apply the force if
the atom is within a distance delta of r0
for dragforce style, a xyz position of NULL means do not include that
dimension in the distance or force computation
for shake style, certain bonds in the system are constrained every timestep
to be at their equilibrium length, this is done by applying a SHAKE-like
constraint to the forces on the atoms so that their position at the next
timestep will preserve the atom separations
for shake style, only atoms in small clusters can be constrained -
e.g. water molecules, CH3 groups, but not the C backbone of a
long polymer chain - a cluster is defined as a central atom
connected to others in the cluster by constrained bonds connected
together by constrained bonds - the max size of such a cluster is
4 atoms to enable easier parallelization
for shake style, the max iteration count need not be large (e.g. 3) since
iterations are only done within a cluster and converge quickly
see the
"
minimize
"
command for what constraints are allowed for use
with the minimizer
see the
"
respa
"
command for how constraints are applied when rRESPA
timestepping is enabled
Default = none
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_999724473"
>
improper coeff
</A></H3>
<UL>
<LI>
1st parameter = improper type #
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
coeffs: harmonic
(1) K (energy units)
(2) chi (degrees)
cvff
(1) K (energy units)
(2) d (+1 or -1)
(3) n (0,1,2,3,4,6)
class2
currently not enabled for
"
improper coeff
"
command
must be specified in data file (see
"
read data
"
command)
define (or override) improper coefficients for an individual improper type
use appropriate number of coeffs for a particular style
see force_fields.html for meaning of coefficients for each style
these coefficients can also be set in data file
by a
"
Improper Coeffs
"
entry, the most recently defined
coefficients are used
cannot use this command before a
"
read data
"
or
"
read restart
"
is performed,
because memory is not yet allocated for the necessary arrays
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277042"
>
improper style
</A></H3>
<UL>
<LI>
none = compute no impropers
<LI>
harmonic = harmonic impropers
<LI>
cvff = cvff improper (class 1 variant)
<LI>
class2 = class 2 Wilson out-of-plane
</UL>
<PRE>
define style of improper interactions to use for all trigonal centers
in class2 case, dictates that angle-angle terms be included for all
trigonal and tetrahedral centers
angle for harmonic is improper torsion, angle for class2 is Wilson out-of-plane
must be used before the
"
read data
"
command (if not using the
default) to tell the program how to read the
"
Improper
Coeffs
"
entry in the data file
can be used after the
"
read data
"
command to change the style to none
coefficients for all improper types must be defined in the data (or restart)
file by a
"
Improper Coeffs
"
entry or by
"
improper coeff
"
commands before a run is performed
Default = harmonic
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951437278"
>
maximum cutoff
</A></H3>
<PRE>
specifies the longest force cutoff that will be used in any runs
this value is used by LAMMPS to accurately allocate memory
for neighbor arrays
if the value is inaccurate (e.g. the command is not used), it is not an
error, but LAMMPS may allocate insufficient memory for neighbor lists
this command is not typically needed if the
"
nonbond style
"
and
"
coulomb style
"
commands are used before the
"
read data
"
or
"
read restart
"
command, since
they specify the appropriate cutoffs
an exception to this is if a short cutoff is used initially,
but a longer cutoff will be used for a subsequent run (in the same
input script), in this case the
"
maximum cutoff
"
command should be
used to insure enough memory is allocated for the later run
note that a restart file contains nonbond cutoffs (so it is not necessary
to use a
"
nonbond style
"
command before
"
read restart
"
), but LAMMPS
still needs to know what the maximum cutoff will be before the
restart file is read
must be set before data or restart file is read
Default = cutoffs for nonbond and Coulomb styles
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_1001972012"
>
min flag
</A></H3>
<PRE>
write out minimization info every this many iterations
value of 0 means never write
Default = 1
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277200"
>
min style
</A></H3>
<UL>
<LI>
hftn = Hessian-free truncated Newton method
</UL>
<PRE>
choose minimization algorithm to use when
"
minimize
"
command is performed
currently, the hftn style is the only option available
Default = hftn
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277212"
>
minimize
</A></H3>
<UL>
<LI>
1st parameter = stopping tolerance (in force units)
<LI>
2nd parameter = max iterations of minimizer
<LI>
3rd parameter = max number of force or energy evaluations
</UL>
<PRE>
perform an energy minimization of the atomic coordinates of the system
uses algorithm selected with
"
min style
"
command
minimize commands can be interspersed with
"
run
"
commands
to alternate between dynamics and relaxation of the system
minimization stops if any of 3 criteria are met:
(1) largest force component
< stopping
tolerance
(
2
)
#
of
iterations
>
max iterations
(3) # of force and energy evaluations
>
max evaluations
output from the minimizer is specified by the
"
dump atoms
"
,
"
dump forces
"
,
and
"
restart
"
commands
when using constraints with the minimizer, fixes are
applied when atoms move except for the following
fixes associated with temperature control are not allowed
(rescale, hoover/drag, langevin)
the minimizer does not invoke the
"
fix style shake
"
contraints on
bond lengths
the minimizer does not invoke pressure control or volume control settings
for good convergence, should specify use of smooth nonbond force fields
that have continuous second derivatives, e.g. set
"
coulomb style
"
to
"
smooth
"
or
"
pppm
"
, set
"
nonbond style
"
to
"
lj/smooth
"
or
use a long cutoff
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276900"
>
mixing style
</A></H3>
<UL>
<LI>
1st parameter = style of mixing used to generate i-j nonbond
interactions
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
geometric = sqrt(i*j) for both epsilon and sigma
<LI>
arithmetic = sqrt(i*j) for epsilon, (i+j)/2 for sigma
<LI>
sixthpower = see force_fields file for details
</UL>
<PRE>
determine the kind of mixing rule that is applied to generate nonbond
coefficients for interactions between type i and type j atoms
mixing rules are applied only when nonbond coeffs are input in a
"
read data
"
file
for nonbond style "soft", only epsilons (prefactor A) are input - they are
always mixed geometrically, regardless of mixing style setting
for nonbond style "lj/charmm", mixing style is always arithmetic,
regardless of mixing style setting
must be set before data file is read
Default = geometric for all nonbond styles except
arithmetic for nonbond style lj/charmm
sixthpower for nonbond style class2/cutoff
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276654"
>
neighbor
</A></H3>
<UL>
<LI>
1st parameter = skin distance in distance units
<LI>
2nd parameter = neighboring style: 0 = N^2, 1 = binning
<LI>
3rd parameter = build neighbor list every this many steps (see next
param)
<LI>
4th parameter = delay building until after this many steps since last
build
<LI>
5th parameter = build criteria: 0 = always build, 1 = only build if
some atom has moved 1/2 or more of the skin thickness
</UL>
<PRE>
factors that affect how and when neighbor lists are constructed
the binning style is almost always faster than the N^2 style
skin must be large enough that all atoms needed for bond
interactions are also acquired by interprocessor communication
last parameter incurs extra checking and communication to test against
skin thickness, but may mean neighbor list is created less often
when rRESPA is run, the 3rd and 4th parameters refer to the
nonbond (short-range) timestepping
normally this command should be used before the data or restart file is read,
since the skin distance is used to estimate memory needed for
neighbor lists
this command can also be used after the
"
read data
"
or
"
read restart
"
command
to change the style of neighbor list construction, but if the
skin distance is changed it can cause LAMMPS to run out of neighbor
list memory, the
"
maximum cutoff
"
command can be used to avoid this
problem
Default = 2.0 1 1 10 1 for real units
0.3 1 1 10 1 for lj units
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276632"
>
newton flag
</A></H3>
<PRE>
turn off or on Newton's 3rd law for bond and non-bond force computation
</PRE>
<UL>
<LI>
value = 0 = no Newton's 3rd law for either
<LI>
value = 1 = Newton's 3rd law only for bonded computations
<LI>
value = 2 = Newton's 3rd law only for non-bonded computations
<LI>
value = 3 = Newton's 3rd law for both bonded and non-bonded
computations
</UL>
<PRE>
no Newton's 3rd law means more force computation and less communication
yes Newton's 3rd law means less force computation and more communication
which choice is faster is problem dependent on N, # of processors,
and cutoff length(s)
expect for round-off errors, setting this flag should not affect answers,
only run time
must be set before data or restart file is read
Default = 3
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276848"
>
nonbond coeff
</A></H3>
<UL>
<LI>
1st parameter = 1st atom type
<LI>
2nd parameter = 2nd atom type
<LI>
3rd-Nth parameters = coeffs 1 to N-2
</UL>
<PRE>
coeffs: lj/cutoff
(1) epsilon (energy units)
(2) sigma (distance units)
(3) cutoff (distance units)
lj/smooth
(1) epsilon (energy units)
(2) sigma (distance units)
(3) inner cutoff (distance units)
(4) outer cutoff (distance units)
lj/shift
(1) epsilon (energy units)
(2) sigma (distance units)
(3) delta shift distance (distance units)
(4) cutoff (distance units)
soft
(1) prefactor A at start of run (energy units)
(2) prefactor A at end of run (energy units)
(3) cutoff (distance units)
class2/cutoff
(1) epsilon (energy units)
(2) sigma (distance units)
(3) cutoff (distance units)
lj/charmm
(1) epsilon (energy units)
(2) sigma (distance units)
(3) epsilon for 1-4 interactions (energy units)
(4) sigma for 1-4 interactions (distance units)
define (or override) nonbond coefficients for an individual atom type pair
use appropriate number of coeffs for a particular style
1st atom type must be
<
= 2nd atom type
all cutoffs are in global units, not local sigma units
(e.g. in reduced units a setting of "lj/cutoff 1.0 1.2 2.5" means a
cutoff of 2.5, not 1.2*2.5)
turn off a particular type pair interaction by setting the
cutoff to 0.0 (both cutoffs to zero for lj/smooth option)
for soft style, prefactor A is ramped from starting value to
ending value during run
these coefficients (except the cutoffs) can also be set in data file
by a "Nonbond Coeffs" entry and associated mixing rules, the cutoffs can
be set (globally) via the "nonbond style" command, the most
recently defined coefficients/cutoffs are used
cannot use this command before a "read data" or "read restart" is performed,
because memory is not yet allocated for the necessary arrays
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276833"
>
nonbond style
</A></H3>
<UL>
<LI>
1st parameter = style of pairwise nonbond interactions (other than
Coulombic)
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no nonbond interactions are computed
<LI>
lj/cutoff = LJ with a cutoff
<LI>
lj/smooth = LJ with a switched region that goes smoothly to zero
<LI>
lj/shift = same as lj/cutoff with shift of interparticle distance
<LI>
soft = cosine potential with time-varying prefactor
<LI>
class2/cutoff
<LI>
lj/charmm = LJ with charmm switched region that goes smoothly to zero
</UL>
<PRE>
coeffs: none
no other parameters required
lj/cutoff
(1) cutoff (distance units)
(2) offset flag (0 or 1)
lj/smooth
(1) inner cutoff (distance units)
(2) outer cutoff (distance units)
lj/shift
(1) cutoff (distance units)
(2) offset flag (0 or 1)
soft
(1) cutoff (distance units)
class2/cutoff
(1) cutoff (distance units)
(2) offset flag (0 or 1)
lj/charmm
(1) inner cutoff (distance units)
(2) outer cutoff (distance units)
define style of pairwise nonbond interactions to use between all atom types
use appropriate number of coeffs for a particular style
this is separate from charge interactions (see
"
coulomb style
"
command)
normally this command should be used before
"
read data
"
to tell LAMMPS how big a force cutoff is being used, the
"
maximum cutoff
"
command can also serve this purpose
when running from a restart file, the restart file contains the nonbond
style and nonbond cutoffs (but not the offset flag), so it is often
not necessary to use a
"
nonbond style
"
command before
"
read restart
"
,
however LAMMPS still needs to know what the maximum cutoff will be
before the restart file is read, see
"
maximum cutoff
"
command
for more details
this command can also be used after
"
read data
"
or
"
read restart
"
to
change the style of nonbond interactions and/or the cutoff
cutoff distance can be smaller or larger than simulation box dimensions
nonbond style determines how many nonbond coefficients the program expects to
find in a
"
Nonbond Coeffs
"
entry in the data file or when using the
"
nonbond coeff
"
command, thus the style must be set (if not using default)
before using the
"
read data
"
command (if the data file contains a
"
Nonbond Coeffs
"
entry) or a
"
nonbond coeff
"
command
coefficients for all atom type pairs must be defined in data (or restart)
file by a
"
Nonbond Coeffs
"
entry or by
"
nonbond coeffs
"
commands before
a run is performed
this command sets the cutoff(s) for all type pair interactions, thus
overriding any previous settings by a
"
nonbond coeff
"
command or
that were read in from a data or restart file
for lj/cutoff, lj/shift, class2/cutoff styles,
offset flag only affects printout of thermodynamic energy
(not forces or dynamics), determines whether offset energy
is added in to LJ potential to make value at cutoff = 0.0,
flag = 0 -
>
do not add in offset energy,
flag = 1 -
>
add in offset energy
for lj/smooth and lj/charmm styles, outer cutoff must be
>
inner cutoff
for lj/smooth and lj/charmm styles, atom pairs less than the inner cutoff
distance use straight LJ, pairs between inner and outer use a smoothed LJ,
and the potential goes to 0.0 at the outer cutoff
for lj/smooth and lj/charmm styles, energy and forces are continuous at inner
cutoff and go smoothly to zero at outer cutoff
for lj/shift and soft styles, must set
"
coulomb style
"
to
"
none
"
for lj/charmm style, must set
"
coulomb style
"
to
"
charmm/switch
"
,
"
pppm
"
,
or
"
ewald
"
for lj/shift style, delta shift distances for each atom pair are set by
"
Nonbond Coeffs
"
entry in data file or by
"
nonbond coeffs
"
command
for soft style, values of the prefactor
"
A
"
, which is ramped from one
value to another during the run, are set by
"
Nonbond Coeffs
"
entry
in data file or by
"
nonbond coeffs
"
command
Default = lj/cutoff 10.0 0 for real units
lj/cutoff 2.5 0 for lj units
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_999182956"
>
periodicity
</A></H3>
<UL>
<LI>
1st parameter = periodic BC in x direction (0) yes, (1) no
<LI>
2nd parameter = periodic BC in y direction (0) yes, (1) no
<LI>
3rd parameter = periodic BC in z direction (0) yes, (1) no
</UL>
<PRE>
turn on/off periodicity in any of three dimensions
used in inter-particle distance computation and when particles move
to map (or not map) them back into periodic box
for a 2-d run (see
"
dimension
"
command), 3rd parameter must be
specified, but doesn't matter if it is 0 or 1
must be set before data or restart file is read
Default = 0 0 0 (periodic in all dimensions)
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276941"
>
pppm mesh
</A></H3>
<UL>
<LI>
1st parameter = # of mesh points in x direction
<LI>
2nd parameter = # of mesh points in y direction
<LI>
3rd parameter = # of mesh points in z direction
</UL>
<PRE>
specify the mesh size used by
"
coulomb style pppm
"
mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
specifed mesh size will override the default
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276947"
>
pppm order
</A></H3>
<PRE>
specify the order of the interpolation function that is used by
"
coulomb
style pppm
"
to map particle charge to the particle mesh
order is roughly equivalent to how many mesh points a point charge
overlaps onto in each dimension
Default = 5
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276784"
>
press control
</A></H3>
<UL>
<LI>
1st parameter = style of pressure control
<LI>
2nd parameter = pressure coupling
<LI>
3rd-9th parameters = coeffs 1 to 7
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no control (constant volume)
<LI>
nose/hoover = Nose-Hoover constant P
</UL>
<PRE>
coupling:
</PRE>
<UL>
<LI>
xyz = couple all 3 dimensions together (isotropic)
<LI>
xy or yz or xz = couple 2 dimensions together, other is independent
<LI>
aniso = all 3 dimensions are independent (anisotropic)
</UL>
<PRE>
coeffs: none
no other parameters required
nose/hoover xyz
(1) desired P at beginning of run
(2) desired P at end of run
nose/hoover xy or yz or xz or aniso
(1) desired Px at beginning of run (or NULL, see below)
(2) desired Px at end of run
(3) desired Py at beginning of run
(4) desired Py at end of run
(5) desired Pz at beginning of run
(6) desired Pz at end of run
(7) frequency constant for volume adjust (inverse time units)
enable constant pressure simulations
all specified pressures are in pressure units
any dimension being varied by pressure control must be periodic
for xyz coupling, all 3 dimensions expand/contract together uniformly
using total scalar pressure as the driving force
for xy/yz/xz coupling, the 2 specified dimensions expand/contract together
uniformly using pressure components averaged over those 2 dimensions
as the driving force, the non-specified dimension will expand/contract
independently using its pressure component as the driving force
for anisotropic, all 3 dimensions expand/contract independently using
individual pressure components as the 3 driving forces
in all cases, the simulation box stays rectilinear (not Parinello-Rahman)
for dimensions coupled together, their specified P values should be the same
a non-coupled dimension (e.g. dimension z for xy option or any dimension
for aniso option) can have 2 NULL values as specified pressures,
which means apply no pressure control in that dimension (constant volume)
target pressure at intermediate points during a run is a ramped value
between the beginning and ending pressure(s)
for nose/hoover style, frequency constant is like an inverse
"
piston
"
mass which determines how rapidly the pressure fluctuates in response to a
restoring force, large frequency -
>
small mass -
>
rapid fluctations
for nose/hoover style, units of frequency/damping constant are
inverse time, so a value of 0.001 means relax in a timespan on the
order of 1000 fmsec (real units) or 1000 tau (LJ units)
IMPORTANT NOTE: the computation of P in LAMMPS does not include
a long-range Van der Waals correction, this introduces a known
error when performing constant P simulations since the correction
factor changes as the box size varies
Default = none
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276624"
>
processor grid
</A></H3>
<UL>
<LI>
1st parameter = # of processors in x dimension
<LI>
2nd parameter = # of processors in y dimension
<LI>
3rd parameter = # of processors in z dimension
</UL>
<PRE>
specify 3-d grid of processors to map to physical simulation domain
for 2-d problem, specify N by M by 1 grid
program will choose these values to best map processor grid to physical
simulation box, only use this command if wish to override program choice
product of 3 parameters must equal total # of processors
must be set before data or restart file is read
Default = none
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277059"
>
read data
</A></H3>
<PRE>
read the initial atom positions and bond info from the specified file
the format for the data file is specified in the file data_format
if a
"
Velocities
"
entry is not in data file, all atom velocities
are set to 0.0
if a
"
Coeffs
"
entry is in data file, the appropriate
"
style
"
command
command must be used first (unless default setting is used) to tell
LAMMPS how many coefficients to expect
a
"
Nonbond Coeffs
"
entry only contains one set of coefficients for each
atom type, after being read-in mixing rules are applied to
compute the cross-type coefficients, see the
"
mixing style
"
command
and data_format file for more information
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277070"
>
read restart
</A></H3>
<PRE>
read atom and force-field information from specified file
allows continuation of a previous run
file is binary to enable exact restarts
do not have to restart on same # of processors, but can only do exact
restarts on same # of processors due to roundoff
when restart file is read, warnings are issued if certain parameters
in the restart file do not match current settings (e.g. newton flag,
dimension, periodicity, units) - this usually indicates an error
the restart file stores the
"
nonbond style
"
and many-body styles and
coefficients and cutoffs, so these do not have to be re-specified in the
input script, unless you want to change them
the restart file does not store
"
coulomb style
"
choice or cutoff, so
this should be re-specified in the input script
the restart file stores the constraint assignments for each atom generated
by using the "assign fix" command, it does NOT store the constraint
parameters themselves, so they must be re-specified with "fix style"
commands after the restart file is read - one exception to this is that
SHAKE constraints (bondtype or angletype) are not stored with the
atoms, so they must be re-specified when performing a restart with both
the "fix style" and "assign fix" commands
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277185"
>
reset timestep
</A></H3>
<PRE>
explicitly reset the timestep to this value
the
"
read data
"
and
"
read restart
"
commands set the timestep to zero
and the file value respectively, so this should be done after those commands
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276645"
>
respa
</A></H3>
<UL>
<LI>
1st parameter = compute bond forces this many times for every one
3/4-body force call
<LI>
2nd parameter = compute 3/4-body forces this many times for every one
nonbond (short-range) force call
<LI>
3rd parameter = compute nonbond (short-range) forces this many times
for every one long-range force call
</UL>
<PRE>
factors that affect sub-cycling of force calculations within rRESPA hierarchy
bonded intramolecular forces are calculated every innermost sub-timestep
bonded 3- and 4-body forces are computed every 1st parameter sub-timesteps
short-range nonbond pairwise forces (LJ, Coulombic) are computed every
(2nd parameter * 1st parameter) sub-timesteps
long-range (Ewald, PPPM) forces are computed every
(3rd parameter * 2nd parameter * 1st parameter) sub-timesteps
the timestepping for all 3 inner loops (bond, 3/4-body, nonbond) is performed
as sub-cycling within the long-range timestepping loop
the fastest (innermost) timestep size is set by the
"
timestep
"
command
when running rRESPA, all input commands that specify numbers of timesteps
(e.g. run, thermo flag, restart, etc) refer to the outermost loop
of long-range timestepping
the only exception to this rule is the
"
neighbor
"
command, where the timestep
parameters refer to the short-range (nonbond) timestepping
when using constraints (via the
"
fix style
"
and
"
assign fix
"
commands)
with rRESPA, the setforce and aveforce constraints are applied at every
level of the hierarchy (whenever forces are computed), the other
constraints are applied only at the short-range (nonbond) level
when using
"
temp control langevin
"
with rRESPA, thermostatting is applied
at the short-range (nonbond) level
rRESPA cannot be used with
"
fix style shake
"
setting all 3 parameters to 1 turns off rRESPA
Default = 1 1 1 (no rRESPA)
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276719"
>
restart
</A></H3>
<UL>
<LI>
1st parameter = # of timesteps
<LI>
2nd parameter = 1 or 2 = naming convention for restart files
<LI>
3rd (and 4th) parameters = file name(s)
</UL>
<PRE>
create a restart file every this many timesteps
value of 0 means never create one
if the style is 1, restart information will be written to files
named filename.timestep and no 4th parameter is needed
if the style is 2, restart information will be written alternately to files
given by the 3rd and 4th parameters, so only 2 restart files ever exist
when the minimizer is invoked this command means create a restart file
at the end of the minimization with the filename filename.timestep.min
a restart file stores atom and force-field information in binary form
allows program to restart from where it left off (see
"
read restart
"
commmand)
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_951437286"
>
restart version
</A></H3>
<PRE>
tell LAMMPS that a restart file from an older version of LAMMPS will be read-in
via a
"
read restart
"
command
this command is necessary because older restart files have a different format
valid settings are 2001 (LAMMPS 2001), 2000 (LAMMPS 2000),
6 (LAMMPS 99) or 5 (LAMMPS 5.0)
restart files from earlier versions of LAMMPS are not readable without
some source code modifications
restart files are always written out in the current-version format
regardless of this setting
this must be set before the
"
read restart
"
command is executed
Default = current version of code = 2001
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931299999"
>
rotation zero
</A></H3>
<PRE>
zero out angular momentum when creating velocities for a group of atoms
value of 0 means don't zero out, value of 1 means zero it
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931277194"
>
run
</A></H3>
<PRE>
run or continue dynamics for specified # of timesteps
when rRESPA is enabled, this is steps of outermost loop (longest timesteps)
must have performed
"
read data
"
or
"
read restart
"
command first
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_999182965"
>
slab volume
</A></H3>
<PRE>
invoke 2-d slab Ewald/PPPM and set extended slab volume via this ratio
2-d slab Ewald/PPPM can be used for a system that is periodic in x-y,
but not in z
this ratio dampens inter-slab interactions in the z dimension
by providing empty volume between slabs and removing
dipole inter-slab interactions
ratio value is the size of the extended dimension in z divided by
the actual dimension in z
recommended ratio value is 3.0: larger is inefficient, smaller
risks unwanted inter-slab interactions
when 2-d slab Ewald/PPPM is used, z-direction periodicity must be
turned off - e.g. periodicity 0 0 1
when 2-d slab Ewald/PPPM is used, user must prevent particle migration
beyond initial z-bounds, typically by providing walls
2-d slab Ewald/PPPM can only be used only with electrostatically
neutral systems
2-d slab Ewald/PPPM can only be used (for the moment) with constant
volume simulations (no pressure control) - the pressure computation
(printed as thermodynamic data) does not include any slab correction
factor or a volume correction for the extended z direction
must be set before data or restart file is read
Default = none (normal 3-D Ewald/PPPM)
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276666"
>
special bonds
</A></H3>
<UL>
<LI>
charmm (0.0 0.0 0.0)
<LI>
amber (0.0 0.0 0.5/0.8333)
<LI>
1st parameter = nonbond weight applied to 1-2 neighbors
<LI>
2nd parameter = nonbond weight applied to 1-3 neighbors
<LI>
3rd parameter = nonbond weight applied to 1-4 neighbors
</UL>
<PRE>
weighting factors to turn on/off nonbond interactions of atom pairs that
are
"
close
"
in the molecular topology
1-2 neighbors are a pair of atoms connected by a bond
1-3 neighbors are a pair of atoms 2 hops away, etc.
weight values are from 0.0 to 1.0 and are used to multiply the
energy and force interaction (both Coulombic and LJ) between the 2 atoms
weight of 0.0 means no interaction
weight of 1.0 means full interaction
can either specify a single keyword (charmm, amber) or can give
3 numeric values
using the charmm keyword means use the CHARMM force field
settings of 0.0 0.0 0.0, requiring that pair-specific 1-4 interactions
be read in individually (see
"
dihedral style charmm
"
command)
using the amber keyword means use the AMBER force field
settings of 0.0 0.0 N, where N = 0.5 for Van der Waals 1-4 interactions
and 1.0/1.2 for Coulombic 1-4 interactions
Default = CHARMM force field values of 0.0 0.0 0.0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276742"
>
temp control
</A></H3>
<UL>
<LI>
1st parameter = style of temperature control
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no control
<LI>
rescale = instantaneous rescaling
<LI>
replace = Gaussian replacement
<LI>
langevin = Langevin white noise
<LI>
nose/hoover = Nose-Hoover constant T
</UL>
<PRE>
coeffs: none
no other parameters required
rescale
(1) desired T at beginning of run
(2) desired T at end of run
(3) check for rescaling every this many timesteps
(4) T window outside of which velocities will be rescaled
(5) fractional amount (0.0 to 1.0) of rescaling to perform
replace
(1) desired T at beginning of run
(2) desired T at end of run
(3) do Gaussian replacement every this many timesteps
(4) random # seed to use for replacement (0
< seed
<=
8
digits
)
langevin
(
1
)
desired
T
at
beginning
of
run
(
2
)
desired
T
at
end
of
run
(
3
)
Langevin
damping
parameter
(
inverse
time
units
)
(
4
)
random
seed
to
use
for
white
noise
(
0
<
seed
<=
8
digits
)
nose
/
hoover
(
1
)
desired
T
at
beginning
of
run
(
2
)
desired
T
at
end
of
run
(
3
)
frequency
constant
for
friction
force
(
inverse
time
units
)
enable
constant
temperature
simulations
use
appropriate
number
of
coeffs
for
a
particular
style
all
specified
temperatures
are
in
temperature
units
target
temperature
at
intermediate
points
during
run
is
a
ramped
value
between
the
beginning
and
ending
temperatures
for
rescale
style
,
temperature
is
controlled
by
explicitly
rescaling
velocities
towards
the
target
temperature
for
rescale
style
,
rescaling
is
only
done
if
current
temperature
is
beyond
the
target
temperature
plus
or
minus
the
window
value
for
rescale
style
,
the
amount
of
rescaling
is
contfolled
by
the
fractional
amount
(
0
.
0
to
1
.
0
),
e
.
g
.
a
value
of
0
.
5
means
set
the
velocities
to
halfway
between
the
current
and
target
temperature
for
rescale
style
,
it
can
be
used
as
a
coarse
temperature
rescaler
,
for
example
"
rescale
200
.
0
300
.
0
100
10
.
0
1
.
0
"
will
ramp
the
temperature
up
during
the
simulation
,
resetting
it
to
the
target
temperatue
as
needed
for
rescale
style
,
it
can
be
used
to
create
an
instantaneous
drag
force
that
slowly
rescales
the
temperature
without
oscillation
,
for
example
"
rescale
300
.
0
300
.
0
1
0
.
0
0
.
0001
"
will
force
(
or
keep
)
the
temperature
to
be
300
.
0
,
the
time
frame
over
which
this
occurs
will
become
longer
as
the
last
parameter
is
made
smaller
for
replace
style
,
Gaussian
RNs
from
the
Marsaglia
RNG
are
used
for
langevin
style
,
uniform
RNs
from
the
Marsaglia
RNG
are
used
for
replace
and
langevin
styles
,
the
seed
is
used
to
initialize
the
Marsaglia
RNG
,
on
successive
runs
the
RNG
will
just
continue
on
for
replace
and
langevin
styles
,
generated
RNs
depend
on
#
of
processors
so
will
not
get
same
answers
independent
of
#
of
processors
for
replace
and
langevin
styles
,
RNG
states
are
not
saved
in
restart
file
,
so
cannot
do
an
exact
restart
for
langevin
style
,
damping
parameter
means
small
value
-
>
less damping
for nose/hoover style, frequency constant is like an inverse
"
piston
"
mass which determines how rapidly the temperature
fluctuates in response to a restoring force, large frequency -
>
small mass -
>
rapid fluctations
for nose/hoover style, cannot use a end-of-run T of 0.0, must be finite
for langevin and nose/hoover styles, units of frequency/damping constant are
inverse time, so a value of 0.01 means relax in a timespan on the
order of 100 fmsec (real units) or 100 tau (LJ units)
Default = none
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276675"
>
thermo flag
</A></H3>
<PRE>
print thermodynamic info to screen and log file every this many timesteps
value of 0 means never print
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276681"
>
thermo style
</A></H3>
<PRE>
determines format of thermodynamic output to screen and log file
</PRE>
<UL>
<LI>
style = 0 -
>
standard output - about 5 lines per entry
<LI>
style = 1 -
>
reduced output - 1 line per entry
<LI>
style = 2 -
>
output with class 2 terms - about 8 lines per entry
</UL>
<PRE>
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276638"
>
timestep
</A></H3>
<PRE>
timestep size for MD run (time units)
when rRESPA is enabled, the timestep size is for the innermost (bond) loop
Default = 1.0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276687"
>
true flag
</A></H3>
<PRE>
read atom positions (see
"
read data
"
command) and dump atom positions
(see
"
dump atoms
"
command) in one of 2 formats
</PRE>
<UL>
<LI>
flag = 0 -
>
read/dump only atom positions (remapped to periodic box)
<LI>
flag = 1 -
>
dump atom positions plus integer box counts
<LI>
flag = 2 -
>
read atom positions plus integer box counts
<LI>
flag = 3 -
>
read/dump atom positions plus integer box counts
</UL>
<PRE>
for each dimension, box count of
"
n
"
means add that many box lengths
to get
"
true
"
un-remapped position,
"
n
"
can be positive, negative, or zero
must be set before data or restart file is read
Default = 0
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_931276596"
>
units
</A></H3>
<UL>
<LI>
real or lj
</UL>
<PRE>
set units to one of two options for all subsequent input parameters
option real = conventional units:
</PRE>
<UL>
<LI>
distance = Angstroms
<LI>
time = femtoseconds
<LI>
mass = grams/mole
<LI>
temperature = degrees K
<LI>
pressure = atmospheres
<LI>
energy = Kcal/mole
<LI>
velocity = Angstroms/femtosecond
<LI>
force = grams/mole * Angstroms/femtosecond^2
</UL>
<PRE>
option lj = LJ reduced units:
</PRE>
<UL>
<LI>
distance = sigmas
<LI>
time = reduced LJ tau
<LI>
temperature = reduced LJ temp
<LI>
pressure = reduced LJ pressure
<LI>
energy = epsilons
<LI>
velocity = sigmas/tau
<LI>
force = reduced LJ force (sigmas/tau^2)
</UL>
<PRE>
for LJ units, LAMMPS sets global epsilon,sigma,mass all equal to 1.0
subsequent input numbers in data and command file must be in these units
output numbers to screen and log and dump files will be in these units
this command (if it appears) must be the first command (aside from
comments) in the input script
must be set before data or restart file is read
Default = real
</PRE>
<HR>
<H3>
<A
NAME=
"_cch3_999724492"
>
volume control
</A></H3>
<UL>
<LI>
1st parameter = style of volume control
<LI>
2nd parameter = dimension to control (x,y,z)
<LI>
3rd-4th parameters = lo/hi simulation box boundaries in this dimension
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no variation in any dimension (constant volume)
<LI>
linear = uniform expansion or contraction
</UL>
<PRE>
enable volume changes (density changes) during a simulation
specified box boundaries are in distance units
each dimension is controlled separately
dimensions not specified by a
"
volume control
"
command can be left
alone (constant volume or nonperiodic) or controlled by
a
"
press control
"
command
any dimension being varied by volume control must be periodic
the lo/hi values are the desired global simulation box boundaries at
the end of the simulation run
at each timestep, the box is expanded/contracted uniformly from its initial
lo/hi values to the specified ending lo/hi values
initial lo/hi values are specified in the data or restart file or
inherited from the end of the previous run
at each timestep, all atom coordinates are also scaled to the new box
Default = none
</PRE>
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