Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/src/99/input_commands.html
3b8ecd5c0634lammm-devel

Last Change
Raw File

input_commands.html
View Options

<!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 inputs. It will be
easiest to understand if you read it while looking at sample input
files such as those in the examples directory. </P>
<P>
The input file of 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 file to be read
in or a simulation to be run. In general, commands can be listed in any
order, although some commands require others to have been executed
previously. </P>
<P>
LAMMPS continues to read successive lines from the input command file
until the end-of-file is reached which causes LAMMPS to terminate. Thus
new simulations can be run or current simulations continued by simply
specifying additional commands in the input command file. </P>
<P>
The next section of this page gives an example 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. 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 final section of this page gives a more detailed description of
each command with its associated parameters. It also lists the default
parameters associated with each command. When performing a simulation,
you only need specify a particular command if you do not want to use
the default settings.</P>
<UL>
<LI>
<A HREF="#_cch3_931277449">Categories of Commands with Examples</A>
<LI>
<A HREF="#_cch3_931277455">Alphabetic Listing of Commands</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_931277449">Categories of Commands withExamples</A></H3>
<UL>
<LI>
<A HREF="#_cch3_930960479">Basic Settings</A>
<LI>
<A HREF="#_cch3_930960485">Output Control</A>
<LI>
<A HREF="#_cch3_930960490">Ensemble Control</A>
<LI>
<A HREF="#_cch3_930960495">Nonbond Force Field</A>
<LI>
<A HREF="#_cch3_930960501">Bonded Force Field</A>
<LI>
<A HREF="#_cch3_930960506">Atom Creation</A>
<LI>
<A HREF="#_cch3_930960510">Velocity Creation</A>
<LI>
<A HREF="#_cch3_930960516">Constraint Creation</A>
<LI>
<A HREF="#_cch3_930960521">Dynamics or Minimization</A>
</UL>
<HR>
<H3>
<A NAME="_cch3_930960479">Basic Settings </A></H3>
<PRE>
<A HREF="#_cch3_931276588">comments</A>
<A HREF="#_cch3_931276596">units</A> real
<A HREF="#_cch3_931276604">dimension</A> 3
<A HREF="#_cch3_931276612">periodicity</A> 0 0 0
<A HREF="#_cch3_931276624">processor grid</A> 10 10 10
<A HREF="#_cch3_931276632">newton flag</A> 3
<A HREF="#_cch3_931276638">timestep</A> 1.0
<A HREF="#_cch3_931276645">respa</A> 2 2 4
<A HREF="#_cch3_931276654">neighbor</A> 2.0 0 1 10 1
<A HREF="#_cch3_931276666">special bonds</A> 0.0 0.0 0.4
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960485">Output Control</A></H3>
<PRE>
<A HREF="#_cch3_931276675">thermo flag</A> 50
<A HREF="#_cch3_931276681">thermo style</A> 0
<A HREF="#_cch3_931276687">true flag</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 file1 file2
<A HREF="#_cch3_931276727">diagnostic</A> diffusion 100 filename 3 1.0 -1.0 2.5
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960490">Ensemble Control</A></H3>
<PRE>
<A HREF="#_cch3_931276742">temp control</A> none
<A HREF="#_cch3_931276742">temp control</A> rescale 300.0 300.0 100 20.0
<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 1.0 1.0 0.001
<A HREF="#_cch3_931276810">press_x control</A> nose/hoover 1.0 1.0 0.001
<A HREF="#_cch3_931276810">press_y control</A> nose/hoover 1.0 1.0 0.001
<A HREF="#_cch3_931276810">press_z control</A> nose/hoover 1.0 1.0 0.001
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960495">Nonbond Force Field</A></H3>
<PRE>
<A HREF="#_cch3_931276833">nonbond style</A> none
<A HREF="#_cch3_931276833">nonbond style</A> lj/cutoff 10.0 0
<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0
<A HREF="#_cch3_931276833">nonbond style</A> lj/smooth 8.0 10.0
<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 8.0 10.0
<A HREF="#_cch3_931276833">nonbond style</A> lj/shift 10.0 0
<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 2.0 10.0
<A HREF="#_cch3_931276833">nonbond style</A> soft 2.5
<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 30.0 2.5
<A HREF="#_cch3_931276833">nonbond style</A> class2/cutoff 10.0 0
<A HREF="#_cch3_931276848">nonbond coeff</A> 1 2 1.0 3.45 10.0
<A HREF="#_cch3_931276900">mixing style</A> geometric
<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_931276941">pppm mesh</A> 32 32 64
<A HREF="#_cch3_931276947">pppm order</A> 5
<A HREF="#_cch3_931276953">dielectric</A> 1.0
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960501">Bonded Force Field</A></H3>
<PRE>
<A HREF="#_cch3_931276958">bond style</A> none
<A HREF="#_cch3_931276958">bond style</A> harmonic
<A HREF="#_cch3_931276970">bond coeff</A> 1 100.0 3.45
<A HREF="#_cch3_931276958">bond style</A> fene/standard
<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0
<A HREF="#_cch3_931276958">bond style</A> fene/shift
<A HREF="#_cch3_931276970">bond coeff</A> 1 30.0 1.5 1.0 1.0 0.2
<A HREF="#_cch3_931276958">bond style</A> nonlinear
<A HREF="#_cch3_931276970">bond coeff</A> 1 28.0 0.748308 0.166667
<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_931277020">dihedral style</A> none
<A HREF="#_cch3_931277020">dihedral style</A> harmonic
<A HREF="#_cch3_931277020">dihedral style</A> class2
<A HREF="#_cch3_931277042">improper style</A> none
<A HREF="#_cch3_931277042">improper style</A> harmonic
<A HREF="#_cch3_931277042">improper style</A> class2
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960506">Atom Creation</A></H3>
<PRE>
<A HREF="#_cch3_931277059">read data</A> filename
<A HREF="#_cch3_931277070">read restart</A> filename
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960510">Velocity Creation</A></H3>
<PRE>
<A HREF="#_cch3_931277080">create group</A> types 1 3
<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_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_930960516">Constraint Creation</A></H3>
<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
<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 nose/hoover 50.0 50.0 0.01
<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_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 remainder
</PRE>
<HR>
<H3>
<A NAME="_cch3_930960521">Dynamics or Minimization</A></H3>
<PRE>
<A HREF="#_cch3_931277185">reset timestep</A> 0
<A HREF="#_cch3_931277194">run</A> 1000
<A HREF="#_cch3_931277200">min style</A> hftn
<A HREF="#_cch3_931277206">min file</A> filename
<A HREF="#_cch3_931277212">minimize</A> 0.0001 9999 50000
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277455">Alphabetic Listing of Commands:</A></H3>
<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)
</UL>
<PRE>
define style of angle interactions to use for all 3-body terms
angle style determines how many angle coefficients the program expects to
find in a &quot;Angle Coeffs&quot; entry in the data file,
thus the style must be set (if not using default)
before using the &quot;read data&quot; command (if the data file contains a
&quot;Angle Coeffs&quot; entry)
coefficients for all angle types must be defined in data (or restart)
file by &quot;Angle Coeffs&quot; entry before a run is performed
style of &quot;none&quot; erases all previously defined angle coefficients, must
reset style to something else before defining new coefficients
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
<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>
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
remainder
no other parameters required
assign a group of atoms to a particular constraint
use appropriate number of coeffs for a particular style
the constraint itself is defined by the &quot;fix style&quot; command
multiple groups of atoms can be assigned to the same constraint
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)
for style region, a coeff of INF means + or - infinity (all the way
to the boundary)
</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)
class 2
currently not enabled for &quot;bond coeff&quot; command
must be specified in data file (see &quot;read data&quot; command)
define (or override) bond coefficients for an individual bond type
use appropriate number of coeffs for a particular style
these coefficients can also be set in data file
by &quot;Bond Coeffs&quot; entry, the most recently defined coefficients are used
Default = no settings
</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 cosine, 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
bond style determines how many bond coefficients the program expects to
find in a &quot;Bond Coeffs&quot; entry in the data file or when using the
&quot;bond coeff&quot; command, thus the style must be set (if not using default)
before using the &quot;read data&quot; command (if the data file contains a
&quot;Bond Coeffs&quot; entry)
coefficients for all bond types must be defined in data (or restart)
file by &quot;Bond Coeffs&quot; entry or by &quot;bond coeffs&quot; commands before a run
is performed
style of &quot;none&quot; erases all previously defined bond coefficients, must
reset style to something else before defining new coefficients
Default = harmonic
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276588">comments </A></H3>
<PRE>
blank lines are ignored
everything on a line after the last parameter is ignored
lines starting with a # are echoed into the log file
</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
</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
use appropriate number of coeffs for a particular style
if simulated system has no charges, must set &quot;coulomb style none&quot; to
prevent LAMMPS from doing useless nonbond work
accuracy criterion means &quot;one part in value&quot; - 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 &quot;particle mesh&quot;
command)
for PPPM, must be running on power-of-2 number of processors for FFTs
must use periodic boundary conditions in conjuction with Ewald and PPPM
cannot use any styles other than none with nonbond style = lj/shift or
nonbond style = soft
Coulomb style = smooth should be used with nonbond style = lj/switch,
and both should use same inner and outer cutoffs
for smooth style, outer cutoff must be &gt; inner cutoff
for smooth style, 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
Default = cutoff 10.0
</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>
region = geometric region of atoms
<LI>
remainder = rest of uninitialized atoms
</UL>
<PRE>
coeffs: types
(1) lowest atom type
(2) highest 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
remainder
no other parameters required
used with &quot;create temp&quot; commmand to initialize velocities of atoms
by default, the &quot;create temp&quot; 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 &quot;create temp&quot; command, any
subsequent &quot;create temp&quot; command is applied to all atoms (unless the
&quot;create group&quot; command is used again)
for style types, only atoms with a type such that lo-type &lt;= type &lt;= hi-type
will be initialized by &quot;create temp&quot;
for style types, lo-type can equal hi-type if just want to specify one type
for style region, only atoms within the specified spatial region
will be initialized by &quot;create temp&quot;
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 &quot;create temp&quot;
</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 &lt; seed &lt;= 8 digits)
gaussian
(1) target T (temperature units)
(2) random # seed (0 &lt; seed &lt;= 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 &quot;create group&quot; 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 &quot;none&quot;, then no file is opened
each routine that is added to diagnostic.f and enabled with a
&quot;diagnostic&quot; command will be called at the beginning and end of
each "run" and every so many timesteps during the run
the diagnostic.f file has 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 user routines must be compiled and linked into LAMMPS
the optional 5th-9th parameters are stored in program variables which
can be accessed by the diagnostic routine
Default = none
</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_931277020">dihedral style </A></H3>
<UL>
<LI>
none = compute no dihedrals
<LI>
harmonic = harmonic dihedrals (class 1)
<LI>
class2 = class 2 dihedrals (and associated cross terms)
</UL>
<PRE>
define style of dihedral interactions to use for all 4-body terms
dihedral style determines how many dihedral coefficients the program expects to
find in a &quot;Dihedral Coeffs&quot; entry in the data file,
thus the style must be set (if not using default)
before using the &quot;read data&quot; command (if the data file contains a
&quot;Dihedral Coeffs&quot; entry)
coefficients for all dihedral types must be defined in data (or restart)
file by &quot;Dihedral Coeffs&quot; entry before a run is performed
style of &quot;none&quot; erases all previously defined dihedral coefficients, must
reset style to something else before defining new coefficients
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 &quot;read data&quot; or
&quot;read restart&quot; 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 &quot;processor grid&quot; 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
positions are also dumped at the start and end of every run
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 &quot;box&quot; units (0.0 to 1.0) in each dimension
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
forces 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_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
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_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 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>
langevin = thermostat a group of atoms by the Langevin method
<LI>
nose/hoover = thermostat a group of atoms by the Nose/Hoover method
<LI>
springforce = apply a spring force to each atom in group
<LI>
dragforce = drag each atom in group to a specified position
</UL>
<PRE>
coeffs: none
no other parameters required (use &quot;none&quot; 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
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 &lt; seed &lt;= 8 digits)
(5) 0/1 = off/on x dimension
(6) 0/1 = off/on y dimension
(7) 0/1 = off/on z dimension
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)
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)
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 the constraint will affect is set by the &quot;assign fix&quot; 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 -&gt; has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
conjuction with global &quot;temp control&quot;, since they conflict and will
cause atom velocities to be reset twice
if multiple Langevin constraints are specified the Marsaglia RNG will
only use the last RNG seed specified for initialization
meaning of thermostatting coefficients is same as in &quot;temp control&quot; command
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 style springforce, 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 &quot;k&quot; should represent the total
force on the group of atoms (not per atom)
for style springforce, a xyz position of NULL means do not include that
dimension in the distance or force computation
for style dragforce, 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 style dragforce, a xyz position of NULL means do not include that
dimension in the distance or force computation
Default = none
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277042">improper style </A></H3>
<UL>
<LI>
none = compute no impropers
<LI>
harmonic = harmonic impropers (class 1) (V = k*phi*phi)
<LI>
cvff = cvff improper (class 1 variant) (V = K*(1 +/- cos(n*phi))
<LI>
class2 = class 2 Wilson out-of-plane (V = K*chi*chi)
</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
in above formulas, phi = improper torsion, chi = Wilson out-of-plane
improper style determines how many improper coefficients the program
expects to find in a &quot;Improper Coeffs&quot; entry in the data file,
thus the style must be set (if not using default)
before using the &quot;read data&quot; command (if the data file contains a
&quot;Improper Coeffs&quot; entry)
coefficients for all improper types must be defined in data (or restart)
file by &quot;Improper Coeffs&quot; entry before a run is performed
style of &quot;none&quot; erases all previously defined improper coefficients, must
reset style to something else before defining new coefficients
Default = harmonic
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277206">min file </A></H3>
<PRE>
name of file to write minimization iteration info to
filename can exist, will be overwritten when minimization occurs
if no file is specified, no minimization output will be written to a file
Default = none
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277200">min style </A></H3>
<UL>
<LI>
htfn = Hessian-free truncated Newton method
</UL>
<PRE>
choose minimization algorithm to use when &quot;minimize&quot; command is performed
currently, only htfn style is available
Default = htfn
</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 &quot;min style&quot; command
minimization stops if any of 3 criteria are met:
(1) largest force component &lt; stopping tolerance
(2) # of iterations &gt; max iterations
(3) # of force and energy evaluations &gt; max evaluations
for good convergence, should specify use of smooth nonbond force fields
that have continuous second derivatives, set &quot;coulomb style&quot; to &quot;smooth&quot;,
set nonbond style to &quot;lj/smooth&quot; 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.txt 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 used only when nonbond coeffs are input in a &quot;read data&quot; file
for nonbond style &quot;soft&quot;, only epsilons (prefactor A) are input - they are
always mixed geometrically, regardless of mixing style setting
Default = geometric for all nonbond styles except class2/cutoff
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
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 RESPA is run, the 3rd and 4th parameters refer to the
nonbond (short-range) timestepping
defaults = 2.0 0 1 10 1
</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 -&gt; no Newton's 3rd law for either
<LI>
value = 1 -&gt; Newton's 3rd law only for bonded computations
<LI>
value = 2 -&gt; Newton's 3rd law only for non-bonded computations
<LI>
value = 3 -&gt; 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)
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 &lt;= 2nd atom type
all cutoffs are in global units, not local sigma units
(e.g. in reduced units a setting of &quot;lj/cutoff 1.0 1.2 2.5&quot; 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 &quot;Nonbond Coeffs&quot; entry and associated mixing rules, the cutoffs can
be set (globally) via the &quot;nonbond style&quot; command, the most
recently defined coefficients/cutoffs are used
Default = no settings
</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
</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)
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 &quot;coulomb style&quot; command)
nonbond style determines how many nonbond coefficients the program expects to
find in a &quot;Nonbond Coeffs&quot; entry in the data file or when using the
&quot;nonbond coeff&quot; command, thus the style must be set (if not using default)
before using the &quot;read data&quot; command (if the data file contains a
&quot;Nonbond Coeffs&quot; entry)
coefficients for all atom type pairs must be defined in data (or restart)
file by &quot;Nonbond Coeffs&quot; entry or by &quot;nonbond coeffs&quot; commands before a run
is performed
style of &quot;none&quot; erases all previously defined nonbond coefficients, must
reset style to something else before defining new coefficients
for all styles (except none), this command sets the cutoff(s) for all type
pair interactions, thus overriding any previous settings by a &quot;nonbond
coeff&quot; command or that were read in from a 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 -&gt; do not add in offset energy,
flag = 1 -&gt; add in offset energy
for lj/smooth style, outer cutoff must be &gt; inner cutoff
for lj/smooth style, 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 style, energy and forces are continuous at inner cutoff and go
smoothly to zero at outer cutoff
for lj/shift and soft styles, must set &quot;coulomb style&quot; to &quot;none&quot;
for lj/shift style, delta shift distances for each atom pair are set by
&quot;Nonbond Coeffs&quot; entry in data file or by &quot;nonbond coeffs&quot; command
for soft style, values of the prefactor &quot;A&quot;, which is ramped from one
value to another during the run, are set by &quot;Nonbond Coeffs&quot; entry
in data file or by &quot;nonbond coeffs&quot; command
Default = lj/cutoff 10.0 0
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276612">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 &quot;dimension&quot; 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 size
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
Default = none
</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
Default = 5
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276784">press control </A></H3>
<UL>
<LI>
1st parameter = style of pressure control
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no control
<LI>
nose/hoover = Nose-Hoover constant P
</UL>
<PRE>
coeffs: none
no other parameters required
nose/hoover
(1) desired P at beginning of run
(2) desired P at end of run
(3) frequency constant for volume adjust (inverse time units)
use appropriate number of coeffs for a particular style
all specified pressures are in pressure units
target pressure at intermediate points during run is a ramped value
between the beginning and ending pressure
for nose/hoover style, frequency constant is like an inverse &quot;piston&quot;
mass which determines how rapidly the pressure fluctuates in response to a
restoring force, large frequency -&gt; small mass -&gt; 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)
Default = none
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276810">press_x control </A></H3>
<H3>
press_y control </H3>
<H3>
press_z control </H3>
<UL>
<LI>
1st parameter = style of pressure control
<LI>
2nd-Nth parameters = coeffs 1 to N-1
</UL>
<PRE>
styles:
</PRE>
<UL>
<LI>
none = no control
<LI>
nose/hoover = Nose-Hoover constant P
</UL>
<PRE>
coeffs: none
no other parameters required
nose/hoover
(1) desired P at beginning of run
(2) desired P at end of run
(3) frequency constant for volume adjust (inverse time units)
commands for anisotropic pressure control, any combination is allowed
for a component with style = none, the cell dimension in that direction
is held constant (constant volume)
use appropriate number of coeffs for a particular style
all specified pressures are in pressure units
target pressure at intermediate points during run is a ramped value
between the beginning and ending pressure
cannot be used with isotropic &quot;press control&quot; command
for nose/hoover style, frequency constant is like an inverse &quot;piston&quot;
mass which determines how rapidly the pressure fluctuates in response to a
restoring force, large frequency -&gt; small mass -&gt; 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)
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 &quot;Coeffs&quot; entry is in data file, the appropriate &quot;style&quot; command
command must be used first (unless default setting is used) to tell
LAMMPS how many coefficients to expect
most &quot;Coeffs&quot; entries must be present in this file if a particular &quot;style&quot;
is desired, an exception are the &quot;Nonbond Coeffs&quot; and &quot;Bond Coeffs&quot; entries
which can be omitted if all the settings are made via &quot;nonbond coeff&quot;
and &quot;bond coeff&quot; commands
a &quot;Nonbond Coeffs&quot; entry only contains one set of coefficients for each
atom type, after being read-in the appropriate class I or class II mixing
rules are applied to compute the cross-type coefficients (see the file
data_format for more information)
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277070">read restart </A></H3>
<PRE>
read atom positions and velocities and nonbond and bond coefficients
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
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 all nonbond and many-body styles and coefficients,
so reading the file will overwrite any current settings
the restart file stores the constraint assignments for each atom, but
not the constraints themselves, so they must still be specified with
the &quot;fix style&quot; command
for a restart do not use the &quot;read data&quot; and &quot;create temp&quot; commands
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277185">reset timestep </A></H3>
<PRE>
explicitly reset the timestep to this value
the &quot;read data&quot; and &quot;read restart&quot; commands set the timestep to zero
and 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 RESPA 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 &quot;timestep&quot; command
when running RESPA, all input commands that specify numbers of timesteps
(e.g. run, thermo flag, restart flag, etc) refer to the outermost loop
of long-range timestepping
the only exception to this rule is the &quot;neighbor&quot; command, where the timestep
parameters refer to the nonbond (short-range) timestepping
setting all 3 parameters to 1 turns off RESPA
Default = 1 1 1 (no RESPA)
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276719">restart </A></H3>
<UL>
<LI>
1st parameter = # of timesteps
<LI>
2nd parameter = 1st file name
<LI>
3rd parameter = 2nd file name
</UL>
<PRE>
create a restart file every this many timesteps
value of 0 means never create one
program will toggle between 2 filenames as the run progresses
so always have at least one good file even if the program dies in mid-write
restart file stores atom positions and velocities in binary form
allows program to restart from where it left off (see &quot;read restart&quot; commmand)
Default = 0
</PRE>
<HR>
<H3>
<A NAME="_cch3_931277194">run </A></H3>
<PRE>
run or continue dynamics for specified # of timesteps
must have performed &quot;read data&quot;/&quot;create temp&quot; or &quot;read restart&quot;
commands first
</PRE>
<HR>
<H3>
<A NAME="_cch3_931276666">special bonds </A></H3>
<UL>
<LI>
1st parameter = nonbond weight applied to 1st nearest neighbors
<LI>
2nd parameter = nonbond weight applied to 2nd nearest neighbors
<LI>
3rd parameter = nonbond weight applied to 3rd nearest neighbors
</UL>
<PRE>
weighting factors to turn on/off nonbond interactions of atom pairs that
are &quot;close&quot; in the molecular topology
1st nearest neighbors are a pair of atoms connected by a bond
2nd nearest 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
Default = 0.0 0.0 0.4 (CHARMM standard)
</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>
nose/hoover = Nose-Hoover constant T
<LI>
langevin = Langevin white noise
</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
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 &lt; seed &lt;= 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 &lt; seed &lt;= 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)
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 to exactly 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 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 -&gt; less damping
for nose/hoover style, frequency constant is like an inverse &quot;piston&quot;
mass which determines how rapidly the temperature fluctuates in response to a
restoring force, large frequency -&gt; small mass -&gt; rapid fluctations
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 -&gt; standard output - about 5 lines per entry
<LI>
style = 1 -&gt; reduced output - 1 line per entry
<LI>
style = 2 -&gt; 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 RESPA is run, 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 &quot;read data&quot; command) and dump atom positions
(see &quot;dump flag&quot; command) in one of 2 formats
</PRE>
<UL>
<LI>
flag = 0 -&gt; read/dump only atom positions (remapped to periodic box)
<LI>
flag = 1 -&gt; dump atom positions plus integer box counts
<LI>
flag = 2 -&gt; read atom positions plus integer box counts
<LI>
flag = 3 -&gt; read/dump atom positions plus integer box counts
</UL>
<PRE>
for each dimension, box count of &quot;n&quot; means add that many box lengths
to get &quot;true&quot; un-remapped position, &quot;n&quot; can be positive, negative, or zero
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
must be set before data or restart file is read
Default = real
</PRE>
</BODY>
</HTML>
c4science · Help