-<LI>If you find a bug, <A HREF = "Section_errors.html#10_2">this section</A> describes
+<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
how to report it.
<LI>If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,
Pictures, and Movies pages of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>, with links
and attributions back to you.
<LI>Create a new Makefile.machine that can be added to the src/MAKE
directory.
<LI>The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in <A HREF = "Section_tools.html">this section</A>. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution.
<LI>LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
<A HREF = "Section_modify.html">This section</A> gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution.
<LI>The Benchmark page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> lists LAMMPS
performance on various platforms. The files needed to run the
benchmarks are part of the LAMMPS distribution. If your machine is
sufficiently different from those listed, your timing data can be
added to the page.
<LI>You can send feedback for the User Comments page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
Site</A>. It might be added to the page. No promises.
<LI>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged.
</UL>
<HR>
-<H4><A NAME = "1_5"></A>1.5 Acknowledgments and citations
+<H4><A NAME = "intro_5"></A>1.5 Acknowledgments and citations
</H4>
<P>LAMMPS development has been funded by the <A HREF = "http://www.doe.gov">US Department of
Energy</A> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and <A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices.
</P>
<P>Specifically, work on the latest version was funded in part by the US
Department of Energy's Genomics:GTL program
(<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the <A HREF = "http://www.genomes2life.org">project</A>, "Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling".
</P>
<P>The following papers describe the parallel algorithms used in LAMMPS.
</P>
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
</P>
<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov).
</P>
<P>If you send is information about your publication, we'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs. They
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
</P>
<P>Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >pppm GPU single and double </TD><TD > Mike Brown (ORNL)</TD></TR>
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)</TD></TR>
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson and Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >region prism </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (Sandia)</TD></TR>
-<LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
+10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
extract_fix(), and extract_variable() methods return values or
pointers to data structures internal to LAMMPS.
</P>
<P>For extract_global() see the src/library.cpp file for the list of
valid names. New names could easily be added. A double or integer is
returned. You need to specify the appropriate data type via the type
argument.
</P>
<P>For extract_atom(), a pointer to internal LAMMPS atom-based data is
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double **)
is returned. You need to specify the appropriate data type via the
type argument.
</P>
<P>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
returned depends on whether the compute or fix calculates a scalar or
vector or array. For a scalar, a single double value is returned. If
the compute or fix calculates a vector or array, a pointer to the
internal LAMMPS data is returned, which you can use via normal Python
subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
-See <A HREF = "Section_howto.html#4_15">this section</A> of the manual for a
+See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
they calculate and store.
</P>
<P>For extract_variable(), an <A HREF = "variable.html">equal-style or atom-style
variable</A> is evaluated and its result returned.
</P>
<P>For equal-style variables a single double value is returned and the
group argument is ignored. For atom-style variables, a vector of
doubles is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
</P>
<P>The get_natoms() method returns the total number of atoms in the
simulation, as an int. Note that extract_global("natoms") returns the
same value, but as a double, which is the way LAMMPS stores it to
allow for systems with more atoms than can be stored in an int (> 2
billion).
</P>
<P>The get_coords() method returns an ctypes vector of doubles of length
3*natoms, for the coordinates of all the atoms in the simulation,
ordered by x,y,z and then by atom ID (see code for put_coords()
below). The array can be used via normal Python subscripting. If
atom IDs are not consecutively ordered within LAMMPS, a None is
returned as indication of an error.
</P>
<P>Note that the data structure get_coords() returns is different from
the data structure returned by extract_atom("x") in four ways. (1)
Get_coords() returns a vector which you index as x[i];
extract_atom() returns an array which you index as x[i][j]. (2)
Get_coords() orders the atoms by atom ID while extract_atom() does
not. (3) Get_coords() returns a list of all atoms in the simulation;
extract_atoms() returns just the atoms local to each processor. (4)
Finally, the get_coords() data structure is a copy of the atom coords
stored internally in LAMMPS, whereas extract_atom returns an array
that points directly to the internal data. This means you can change
values inside LAMMPS from Python by assigning a new values to the
extract_atom() array. To do this with the get_atoms() vector, you
need to change values in the vector, then invoke the put_coords()
method.
</P>
<P>The put_coords() method takes a vector of coordinates for all atoms in
the simulation, assumed to be ordered by x,y,z and then by atom ID,
and uses the values to overwrite the corresponding coordinates for
each atom inside LAMMPS. This requires LAMMPS to have its "map"
option enabled; see the <A HREF = "atom_modify.html">atom_modify</A> command for
details. If it is not or if atom IDs are not consecutively ordered,
no coordinates are reset,
</P>
<P>The array of coordinates passed to put_coords() must be a ctypes
vector of doubles, allocated and initialized something like this:
</P>
<PRE>from ctypes import *
natoms = lmp.get_atoms()
n3 = 3*natoms
x = (c_double*n3)()
x<B>0</B> = x coord of atom with ID 1
x<B>1</B> = y coord of atom with ID 1
x<B>2</B> = z coord of atom with ID 1
x<B>3</B> = x coord of atom with ID 2
...
x<B>n3-1</B> = z coord of atom with ID natoms
lmp.put_coords(x)
</PRE>
<P>Alternatively, you can just change values in the vector returned by
get_coords(), since it is a ctypes vector of doubles.
</P>
<HR>
<P>As noted above, these Python class methods correspond one-to-one with
the functions in the LAMMPS library interface in src/library.cpp and
library.h. This means you can extend the Python wrapper via the
following steps:
</P>
<UL><LI>Add a new interface function to src/library.cpp and
src/library.h.
<LI>Verify the new function is syntactically correct by building LAMMPS as
-a library - see <A HREF = "Section_start.html#2_4">this section</A> of the
+a library - see <A HREF = "Section_start.html#start_4">this section</A> of the
manual.
<LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py
for this interface function.
<LI>Rebuild the Python wrapper via python/setup_serial.py or
python/setup.py.
<LI>You should now be able to invoke the new interface function from a
Python script. Isn't ctypes amazing?
</UL>
<HR>
<HR>
-<A NAME = "9_7"></A><H4>Example Python scripts that use LAMMPS
+<A NAME = "py_7"></A><H4>11.7 Example Python scripts that use LAMMPS
</H4>
<P>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of
things that are possible when Python wraps LAMMPS. If you create your
own scripts, send them to us and we can include them in the LAMMPS
distribution.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script thru Python</TD></TR>
<TR><TD >demo.py</TD><TD > invoke various LAMMPS library interface routines</TD></TR>
<TR><TD >simple.py</TD><TD > mimic operation of couple/simple/simple.cpp in Python</TD></TR>
<TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz_tool.py and plot.py and gui.py
</TD></TR></TABLE></DIV>
<HR>
<P>For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
visualization package you have installed.
</P>
<P>Note that for GL, you need to be able to run the Pizza.py GL tool,
which is included in the pizza sub-directory. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
pages</A> for more info:
</P>
<P>Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>atom_style atomic
atom_style bond
atom_style full
atom_style hybrid charge bond
</PRE>
<P><B>Description:</B>
</P>
<P>Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
command.
</P>
<P>Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style <I>bond</I>, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
</P>
<P>The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
<A HREF = "set.html">set</A> commands for info on how to set these various
quantities.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>fene</I> or <I>fene/expand</I> or <I>harmonic</I> or <I>morse</I> or <I>nonlinear</I> or <I>quartic</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic
bond_style fene
bond_style hybrid harmonic fene
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the <A HREF = "pair_style.html">pair_style</A>
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
</P>
<P>Hybrid models where bonds are computed using different bond potentials
can be setup using the <I>hybrid</I> bond style.
</P>
<P>The coefficients associated with a bond style can be specified in a
data or restart file or via the <A HREF = "bond_coeff.html">bond_coeff</A> command.
</P>
<P>All bond potentials store their coefficient data in binary restart
files which means bond_style and <A HREF = "bond_coeff.html">bond_coeff</A> commands
do not need to be re-specified in an input script that restarts a
simulation. See the <A HREF = "read_restart.html">read_restart</A> command for
details on how to do this. The one exception is that bond_style
<I>hybrid</I> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
</P>
<P>IMPORTANT NOTE: When both a bond and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.
</P>
<P>In the formulas listed for each bond style, <I>r</I> is the distance
between the 2 atoms in the bond.
</P>
<HR>
<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</P>
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<PRE>compute ID group-ID pressure temp-ID keyword ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pressure = style name of this compute command
<LI>temp-ID = ID of compute that calculates temperature
<LI>zero or more keywords may be appended
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pressure myTemp
compute 1 all pressure thermo_temp pair bond
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all". See the <A HREF = "compute_stress_atom.html">compute
stress/atom</A> command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the <A HREF = "compute_reduce.html">compute reduce</A> command.
</P>
<P>The pressure is computed by the formula
</P>
<CENTER><IMG SRC = "Eqs/pressure.jpg">
</CENTER>
<P>where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
virial term.
</P>
<P>A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
(where I and J = x,y,z) is similar to the above formula, except that
the first term uses components of the kinetic energy tensor and the
second term uses components of the virial tensor:
</P>
<CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
</CENTER>
<P>If no extra keywords are listed, the entire equations above are
calculated which include a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The <I>virial</I> keyword
means include all terms except the kinetic energy <I>ke</I>.
</P>
<P>The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified with the
command. Normally this compute should calculate the temperature of
all atoms for consistency with the virial term, but any compute style
that calculates temperature can be used, e.g. one that excludes frozen
atoms or other degrees of freedom.
</P>
<P>Note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various <A HREF = "compute.html">compute
temperature</A> styles for details.
</P>
<P>A compute of this style with the ID of "thermo_press" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_press all pressure thermo_temp
</PRE>
<P>where "thermo_temp" is the ID of a similarly defined compute of style
"temp". See the "thermo_style" command for more details.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda" package. They
are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
+<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
-switch</A> when you invoke LAMMPS, or you can use
-the <A HREF = "suffix.html">suffix</A> command in your input script.
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
+switch</A> when you invoke LAMMPS, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
+or vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>harmonic</I> or <I>helix</I> or <I>multi/harmonic</I> or <I>opls</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
from a data or restart file.
</P>
<P>Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the <I>hybrid</I> dihedral style.
</P>
<P>The coefficients associated with a dihedral style can be specified in
a data or restart file or via the <A HREF = "dihedral_coeff.html">dihedral_coeff</A>
command.
</P>
<P>All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands do not need to be
re-specified in an input script that restarts a simulation. See the
<A HREF = "read_restart.html">read_restart</A> command for details on how to do
this. The one exception is that dihedral_style <I>hybrid</I> only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
</P>
<P>IMPORTANT NOTE: When both a dihedral and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
</P>
<P>In the formulas listed for each dihedral style, <I>phi</I> is the torsional
angle defined by the quadruplet of atoms.
</P>
<P>Here are some important points to take note of when defining the
LAMMPS dihedral coefficients in the formulas that follow so that they
are compatible with other force fields:
</P>
<UL><LI>The LAMMPS convention is that the trans position = 180 degrees, while
in some force fields trans = 0 degrees.
<LI>Some force fields reverse the sign convention on <I>d</I>.
<LI>Some force fields divide/multiply <I>K</I> by the number of multiple
torsions that contain the j-k bond in an i-j-k-l torsion.
<LI>Some force fields let <I>n</I> be positive or negative which corresponds to
<I>d</I> = 1 or -1 for the harmonic style.
</UL>
<HR>
<P>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command:
</P>
<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
<PRE>dump ID group-ID image N file color diameter keyword value ...
</PRE>
<UL><LI>ID = user-assigned name for the dump
<LI>group-ID = ID of the group of atoms to be imaged
<LI>image = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
<LI>N = dump every this many timesteps
<LI>file = name of file to write image to
<LI>color = atom attribute that determines color of each atom
<LI>diameter = atom attribute that determines size of each atom
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>adiam</I> or <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I>
<PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
<I>atom</I> = yes/no = do or do not draw atoms
<I>bond</I> values = color width = color and width of bonds
color = <I>atom</I> or <I>type</I> or <I>none</I>
width = number or <I>atom</I> or <I>type</I> or <I>none</I>
number = numeric value for bond width (distance units)
<I>size</I> values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
<I>view</I> values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
<I>center</I> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
<I>up</I> values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
<I>zoom</I> value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
<I>persp</I> value = pfactor = amount of "perspective" in image
dump ID group-ID image N file color diameter keyword value ... :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
image = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file = name of file to write image to :l
color = atom attribute that determines color of each atom :l
diameter = atom attribute that determines size of each atom :l
zero or more keyword/value pairs may be appended :l
keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
{adiam} value = number = numeric value for atom diameter (distance units)
{atom} = yes/no = do or do not draw atoms
{bond} values = color width = color and width of bonds
color = {atom} or {type} or {none}
width = number or {atom} or {type} or {none}
number = numeric value for bond width (distance units)
{size} values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
{view} values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
{up} values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
{zoom} value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
{persp} value = pfactor = amount of "perspective" in image
<LI><A HREF = "fix_neb.html">neb</A> - nudged elastic band (NEB) spring forces
<LI><A HREF = "fix_nh.html">nph</A> - constant NPH time integration via Nose/Hoover
<LI><A HREF = "fix_nph_asphere.html">nph/asphere</A> - NPH for aspherical particles
<LI><A HREF = "fix_nph_sphere.html">nph/sphere</A> - NPH for spherical particles
<LI><A HREF = "fix_nh.html">npt</A> - constant NPT time integration via Nose/Hoover
<LI><A HREF = "fix_npt_asphere.html">npt/asphere</A> - NPT for aspherical particles
<LI><A HREF = "fix_npt_sphere.html">npt/sphere</A> - NPT for spherical particles
<LI><A HREF = "fix_nve.html">nve</A> - constant NVE time integration
<LI><A HREF = "fix_nve_asphere.html">nve/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nve_limit.html">nve/limit</A> - NVE with limited step length
<LI><A HREF = "fix_nve_noforce.html">nve/noforce</A> - NVE without forces (v only)
<LI><A HREF = "fix_nve_sphere.html">nve/sphere</A> - NVT for spherical particles
<LI><A HREF = "fix_nh.html">nvt</A> - constant NVT time integration via Nose/Hoover
<LI><A HREF = "fix_nvt_asphere.html">nvt/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nvt_sllod.html">nvt/sllod</A> - NVT for NEMD with SLLOD equations
<LI><A HREF = "fix_nvt_sphere.html">nvt/sphere</A> - NVT for spherical particles
<LI><A HREF = "fix_orient_fcc.html">orient/fcc</A> - add grain boundary migration force
<LI><A HREF = "fix_planeforce.html">planeforce</A> - constrain atoms to move in a plane
<LI><A HREF = "fix_poems.html">poems</A> - constrain clusters of atoms to move as coupled rigid bodies
<LI><A HREF = "fix_pour.html">pour</A> - pour new atoms into a granular simulation domain
<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
<LI><A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
+<LI><A HREF = "fix_restrain.html">restrain</A> - constrain a bond, angle, dihedral
<LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to move as a rigid body with NVE integration
<LI><A HREF = "fix_rigid.html">rigid/nve</A> - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
<LI><A HREF = "fix_rigid.html">rigid/nvt</A> - constrain one or more clusters of atoms to move as a rigid body with NVT integration
<LI><A HREF = "fix_setforce.html">setforce</A> - set the force on each atom
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>box/relax = style name of this fix command
<PRE>one or more keyword value pairs may be appended
keyword = <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>nreset</I> or <I>vmax</I> or <I>dilate</I>
<I>iso</I> or <I>aniso</I> or <I>tri</I> value = Ptarget = desired pressure (pressure units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> value = Ptarget = desired pressure (pressure units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>nreset</I> value = reset reference cell every this many minimizer iterations
<I>vmax</I> value = fraction = max allowed volume change in one iteration
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all box/relax iso 0.0 vmax 0.001
fix 2 water box/relax aniso 0.0 dilate partial
fix 2 ice box/relax tri 0.0 couple xy nreset 100
</PRE>
<P><B>Description:</B>
</P>
<P>Apply an external pressure or stress tensor to the simulation box
during an <A HREF = "minimize.html">energy minimization</A>. This allows the box
size and shape to vary during the iterations of the minimizer so that
the final configuration will be both an energy minimum for the
potential energy of the atoms, and the system pressure tensor will be
close to the specified external tensor. Conceptually, specifying a
positive pressure is like squeezing on the simulation box; a negative
pressure typically allows the box to expand.
</P>
<HR>
<P>The external pressure tensor is specified using one or more of the
<PRE>fix ID group-ID deposit N type M seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>deposit = style name of this fix command
<LI>N = # of atoms to insert
<LI>type = atom type to assign to inserted atoms
<LI>M = insert a single particle every M steps
<LI>seed = random # seed (positive integer)
<LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region to use as insertion volume
<I>global</I> values = lo hi
lo,hi = put new particle a distance lo-hi above all other particles (distance units)
<I>local</I> values = lo hi delta
lo,hi = put new particle a distance lo-hi above any nearby particle beneath it (distance units)
delta = lateral distance within which a neighbor is considered "nearby" (distance units)
<I>near</I> value = R
R = only insert particle if further than R from existing particles (distance units)
<I>attempt</I> value = Q
Q = attempt a single insertion up to Q times
<I>rate</I> value = V
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
<I>vx</I> values = vxlo vxhi
vxlo,vxhi = range of x velocities for inserted particle (velocity units)
<I>vy</I> values = vylo vyhi
vylo,vyhi = range of y velocities for inserted particle (velocity units)
<I>vz</I> values = vzlo vzhi
vzlo,vzhi = range of z velocities for inserted particle (velocity units)
<I>units</I> value = <I>lattice</I> or <I>box</I>
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
</PRE>
<P><B>Description:</B>
</P>
<P>Insert a single particle into the simulation domain every M timesteps
until N particles have been inserted. This is useful for simulating
the deposition of particles onto a surface.
</P>
<P>Inserted particles have the specified atom type and are assigned to
two groups: the default group "all" and the group specified in the fix
deposit command (which can also be "all").
</P>
<P>If you are computing temperature values which include inserted
particles, you will want to use the <A HREF = "compute_modify.html">compute_modify</A>
dynamic option, which insures the current number of atoms is used as a
normalizing factor each time temperature is computed.
</P>
<P>Care must be taken that inserted particles are not too near existing
particles, using the options described below. When inserting
particles above a surface in a non-periodic box (see the
<A HREF = "boundary.html">boundary</A> command), the possibility of a particle
escaping the surface and flying upward should be considered, since the
particle may be lost or the box size may grow infinitely large. A
<A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command can be used to
prevent this behavior. Note that if a shrink-wrap boundary is used,
it is OK to insert the new particle outside the box, however the box
will immediately be expanded to include the new particle.
</P>
<P>This command must use the <I>region</I> keyword to define an insertion
volume. The specified region must have been previously defined with a
<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.
</P>
<P>Each timestep a particle is to be inserted, its coordinates are chosen
as follows. A random position within the insertion volume is
generated. If neither the <I>global</I> or <I>local</I> keyword is used, that
is the trial position. If the <I>global</I> keyword is used, the random
x,y values are used, but the z position of the new particle is set
above the highest current atom in the simulation by a distance
randomly chosen between lo/hi. (For a 2d simulation, this is done for
the y position.) If the <I>local</I> keyword is used, the z position is
set a distance between lo/hi above the highest current atom in the
simulation that is "nearby" the chosen x,y position. In this context,
"nearby" means the lateral distance (in x,y) between the new and old
particles is less than the delta parameter.
</P>
<P>Once a trial x,y,z location has been computed, the insertion is only
performed if no current particle in the simulation is within a
distance R of the new particle. If this test fails, a new random
position within the insertion volume is chosen and another trial is
made. Up to Q attempts are made. If an atom is not successfully
deposited, LAMMPS prints a warning message.
</P>
<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a
successively higher height over time. Note that this parameter is
ignored if the <I>global</I> or <I>local</I> keywords are used, since those
options choose a z-coordinate for insertion independently.
</P>
<P>The vx, vy, and vz components of velocity for the inserted particle
are set using the values specified for the <I>vx</I>, <I>vy</I>, and <I>vz</I>
keywords. Note that normally, new particles should be a assigned a
negative vertical velocity so that they move towards the surface.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for the other deposition parameters. A <I>box</I> value selects standard
distance units as defined by the <A HREF = "units.html">units</A> command,
e.g. Angstroms for units = real or metal. A <I>lattice</I> value means the
distance units are in lattice spacings. The <A HREF = "lattice.html">lattice</A>
command must have been previously used to define the lattice spacing.
Note that the units choice affects all the keyword values that have
units of distance or velocity.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
files</A>. This includes information about how many atoms
have been depositied, the random number generator seed, the next
timestep for deposition, etc. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various <A HREF = "Section_howto.html#4_15">output commands</A>. No
+access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>The specified insertion region cannot be a "dynamic" region, as
defined by the <A HREF = "region.html">region</A> command.
<OL><LI><I>dhugoniot</I> is the departure from the Hugoniot (temperature units).
<LI><I>drayleigh</I> is the departure from the Rayleigh line (pressure units).
<LI><I>lagrangian_speed</I> is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
<LI><I>lagrangian_position</I> is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front.
</OL>
<P>To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
</P>
<PRE>fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
</PRE>
<P>These fixes compute a global scalar and a global vector of 4
-quantities, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
-commands</A>. The scalar values calculated by
-this fix are "extensive"; the vector values are "intensive".
+quantities, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
+commands</A>. The scalar values calculated
+by this fix are "extensive"; the vector values are "intensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix style is part of the "shock" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
all.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_deform.html">fix deform</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
{dhugoniot} is the departure from the Hugoniot (temperature units).
{drayleigh} is the departure from the Rayleigh line (pressure units).
{lagrangian_speed} is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
{lagrangian_position} is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. :ol
To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst\[1\]
variable dray equal f_msst\[2\]
variable lgr_vel equal f_msst\[3\]
variable lgr_pos equal f_msst\[4\]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst :pre
These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various "output
-commands"_Section_howto.html#4_15. The scalar values calculated by
-this fix are "extensive"; the vector values are "intensive".
+commands"_Section_howto.html#howto_15. The scalar values calculated
+by this fix are "extensive"; the vector values are "intensive".
[Restrictions:]
This fix style is part of the "shock" package. It is only enabled if
LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+LAMMPS"_Section_start.html#start_3 section for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
all.
[Related commands:]
"fix deform"_fix_deform.html
[Default:]
The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt</I> or <I>npt</I> or <I>nph</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
<I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
<I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
<I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt} or {npt} or {nph} :l
one or more keyword value pairs may be appended
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tchain} value = length of thermostat chain (1 = single thermostat)
{pchain} values = length of thermostat chain on barostat (0 = no thermostat)
{mtk} value = {yes} or {no} = add in MTK adjustment term or not
{tloop} value = number of sub-cycles to perform on thermostat
{ploop} value = number of sub-cycles to perform on barostat thermostat
{nreset} value = reset reference cell every this many timesteps
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial}
{scaleyz} value = {yes} or {no} = scale yz with lz
{scalexz} value = {yes} or {no} = scale xz with lz
{scalexy} value = {yes} or {no} = scale xy with ly :pre
:ule
[Examples:]
fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>
<P>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the <A HREF = "pair_eff.html">electron force field</A> model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the <I>xy</I>,
<I>xz</I> and <I>yz</I> tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
</P>
<P>The operation of these fixes is exactly like that described by the
<A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A>
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
</P>
<P>IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining the pair_style (see <A HREF = "pair_eff_cut.html">pair
eff/cut</A> to understand these settings), one
(default) that considers electrons do not contribute radial virial
components (i.e. electrons treated as incompressible 'rigid' spheres)
and one that does. The radial electronic contributions to the virials
are only tallied if the flexible pressure option is set, and this will
affect both global and per-atom quantities. In principle, the true
pressure of a system is somewhere in between the rigid and the
flexible eFF pressures, but, for most cases, the difference between
these two pressures will not be significant over long-term averaged
runs (i.e. even though the energy partitioning changes, the total
energy remains similar).
</P>
<P>IMPORTANT NOTE: currently, there is no available option for the user
to set or create temperature distributions that include the radial
electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A>
command, so the the user must allow for these degrees of freedom to
equilibrate (i.e. equi-partitioning of energy) through time
integration.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>See the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands
for details.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "user-eff" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Other restriction discussed on the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and
nph</A> commands also apply.
</P>
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt/eff} or {npt/eff} or {nph/eff} :l
one or more keyword value pairs may be appended
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tchain} value = length of thermostat chain (1 = single thermostat)
{pchain} values = length of thermostat chain on barostat (0 = no thermostat)
{mtk} value = {yes} or {no} = add in MTK adjustment term or not
{tloop} value = number of sub-cycles to perform on thermostat
{ploop} value = number of sub-cycles to perform on barostat thermostat
{nreset} value = reset reference cell every this many timesteps
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
[Description:]
These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the "electron force field"_pair_eff.html model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the {xy},
{xz} and {yz} tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
The operation of these fixes is exactly like that described by the
"fix nvt, npt, and nph"_fix_nh.html commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining the pair_style (see "pair
eff/cut"_pair_eff_cut.html to understand these settings), one
(default) that considers electrons do not contribute radial virial
components (i.e. electrons treated as incompressible 'rigid' spheres)
and one that does. The radial electronic contributions to the virials
are only tallied if the flexible pressure option is set, and this will
affect both global and per-atom quantities. In principle, the true
pressure of a system is somewhere in between the rigid and the
flexible eFF pressures, but, for most cases, the difference between
these two pressures will not be significant over long-term averaged
runs (i.e. even though the energy partitioning changes, the total
energy remains similar).
IMPORTANT NOTE: currently, there is no available option for the user
to set or create temperature distributions that include the radial
electronic degrees of freedom with the "velocity"_velocity.html
command, so the the user must allow for these degrees of freedom to
equilibrate (i.e. equi-partitioning of energy) through time
integration.
[Restart, fix_modify, output, run start/stop, minimize info:]
See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands
for details.
[Restrictions:]
This fix is part of the "user-eff" package. It is only enabled if
LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+LAMMPS"_Section_start.html#start_3 section for more info.
Other restriction discussed on the doc page for the "fix nvt, npt, and
nph"_fix_nh.html commands also apply.
IMPORTANT NOTE: The temperature for systems (regions or groups) with
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.
<PRE>fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>srd = style name of this fix command
<LI>N = reset SRD particle velocities every this many timesteps
<LI>groupbig-ID = ID of group of large particles that SRDs interact with
<LI>Tsrd = temperature of SRD particles (temperature units)
<LI>hgrid = grid spacing for SRD grouping (distance units)
<LI>seed = random # seed (positive integer)
</UL>
<UL><LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>lamda</I> or <I>collision</I> or <I>overlap</I> or <I>inside</I> or <I>exact</I> or <I>radius</I> or <I>bounce</I> or <I>search</I> or <I>cubic</I> or <I>shift</I> or <I>stream</I>
<PRE> <I>lamda</I> value = mean free path of SRD particles (distance units)
<I>collision</I> value = <I>noslip</I> or <I>slip</I> = collision model
<I>overlap</I> value = <I>yes</I> or <I>no</I> = whether big particles may overlap
<I>inside</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I> = how SRD particles which end up inside a big particle are treated
<I>exact</I> value = <I>yes</I> or <I>no</I>
<I>radius</I> value = rfactor = scale collision radius by this factor
<I>bounce</I> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
<I>search</I> value = sgrid = grid spacing for collision partner searching (distance units)
<I>cubic</I> values = style tolerance
style = <I>error</I> or <I>warn</I>
tolerance = fractional difference allowed (0 <= tol <= 1)
<I>shift</I> values = style seed
style = <I>no</I> or <I>yes</I> or <I>possible</I>
seed = random # seed (positive integer)
<I>stream</I> value = <I>yes</I> or <I>no</I> = whether or not streaming velocity is added for shear deformation
<LI>style = <I>delete</I> or <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>plane</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I>
<PRE> <I>delete</I> = no args
<I>block</I> args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
<I>cone</I> args = dim c1 c2 radlo radhi lo hi
dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cone
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
<I>cylinder</I> args = dim c1 c2 radius lo hi
dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
lo,hi = bounds of cylinder in dim (distance units)
<I>plane</I> args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
nx,ny,nz = direction normal to plane (distance units)
<LI>style = <I>delete</I> or <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or <I>uloop</I> or <I>string</I> or <I>equal</I> or <I>atom</I>
<PRE> <I>delete</I> = no args
<I>index</I> args = one or more strings
<I>loop</I> args = N
N = integer size of loop, loop from 1 to N inclusive
<I>loop</I> args = N pad
N = integer size of loop, loop from 1 to N inclusive
pad = all values will be same length, e.g. 001, 002, ..., 100
<I>loop</I> args = N1 N2
N1,N2 = loop from N1 to N2 inclusive
<I>loop</I> args = N1 N2 pad
N1,N2 = loop from N1 to N2 inclusive
pad = all values will be same length, e.g. 050, 051, ..., 100
<I>world</I> args = one string for each partition of processors
<I>universe</I> args = one or more strings
<I>uloop</I> args = N
N = integer size of loop
<I>uloop</I> args = N pad
N = integer size of loop
pad = all values will be same length, e.g. 001, 002, ..., 100
<I>string</I> arg = one string
<I>equal</I> or <I>atom</I> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {equal} or {atom} :l
{delete} = no args
{index} args = one or more strings
{loop} args = N
N = integer size of loop, loop from 1 to N inclusive
{loop} args = N pad
N = integer size of loop, loop from 1 to N inclusive
pad = all values will be same length, e.g. 001, 002, ..., 100
{loop} args = N1 N2
N1,N2 = loop from N1 to N2 inclusive
{loop} args = N1 N2 pad
N1,N2 = loop from N1 to N2 inclusive
pad = all values will be same length, e.g. 050, 051, ..., 100
{world} args = one string for each partition of processors
{universe} args = one or more strings
{uloop} args = N
N = integer size of loop
{uloop} args = N pad
N = integer size of loop
pad = all values will be same length, e.g. 001, 002, ..., 100
{string} arg = one string
{equal} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI
thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html