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12
doc/Section_tools.html
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@ -49,6 +49,7 @@ own sub-directories with their own Makefiles.
<LI><A HREF = "#chain">chain</A>
<LI><A HREF = "#data">data2xmovie</A>
<LI><A HREF = "#eam">eam generate</A>
<LI>"eff_#eff
<LI><A HREF = "#arc">lmp2arc</A>
<LI><A HREF = "#cfg">lmp2cfg</A>
<LI><A HREF = "#traj">lmp2traj</A>
@ -152,6 +153,17 @@ produce are in the potentials directory.
</P>
<HR>
<H4><A NAME = "eff"></A>eff tool
</H4>
<P>The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
electron force field (EFF).
</P>
<P>These tools were provided by Andres Jaramillo-Botero at CalTech
(ajaramil at wag.caltech.edu).
</P>
<HR>
<H4><A NAME = "arc"></A>lmp2arc tool
</H4>
<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output

12
doc/Section_tools.txt
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@ -45,6 +45,7 @@ own sub-directories with their own Makefiles.
"chain"_#chain
"data2xmovie"_#data
"eam generate"_#eam
"eff_#eff
"lmp2arc"_#arc
"lmp2cfg"_#cfg
"lmp2traj"_#traj
@ -148,6 +149,17 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
electron force field (EFF).
These tools were provided by Andres Jaramillo-Botero at CalTech
(ajaramil at wag.caltech.edu).
:line
lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output

31
doc/atom_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</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
@ -59,6 +59,7 @@ quantities.
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>colloid</I> </TD><TD > angular velocity </TD><TD > extended spherical particles </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > atomic system with dipoles </TD></TR>
<TR><TD ><I>electron</I> </TD><TD > spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>granular</I> </TD><TD > diameter, density, angular velocity </TD><TD > granular models </TD></TR>
@ -67,15 +68,18 @@ quantities.
</TD></TR></TABLE></DIV>
<P>All of the styles define point particles, except the <I>colloid</I>,
<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles, which define
finite-size particles. For <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I>
systems, the <A HREF = "shape.html">shape</A> command is used to specify the size
and shape of particles on a per-type basis, which is spherical for
<I>colloid</I> and <I>dipole</I> particles and spherical or aspherical for
<I>ellipsoid</I> particles. For <I>granular</I> systems, the particles are
spherical and each has a per-particle specified diameter. For <I>peri</I>
systems, the particles are spherical and each has a per-particle
specified volume.
<I>dipole</I>, <I>electron</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles,
which define finite-size particles. For <I>colloid</I>, <I>dipole</I>, and
<I>ellipsoid</I> systems, the <A HREF = "shape.html">shape</A> command is used to specify
the size and shape of particles on a per-type basis, which is
spherical for <I>colloid</I> and <I>dipole</I> particles and spherical or
aspherical for <I>ellipsoid</I> particles. For <I>granular</I> systems, the
particles are spherical and each has a per-particle specified
diameter. For <I>peri</I> systems, the particles are spherical and each
has a per-particle specified volume. For <I>electron</I> systems, the
particles are three dimensional Gaussians with a specified position
and bandwidth or uncertainty in position, which is described as the
eradius = electron size.
</P>
<P>All of the styles assign mass to particles on a per-type basis, using
the <A HREF = "mass.html">mass</A> command, except the <I>granular</I> and <I>peri</I> styles
@ -113,9 +117,10 @@ section</A>.
package. The <I>colloid</I> style is part of the "colloid" package. The
<I>dipole</I> style is part of the "dipole" package. The <I>ellipsoid</I> style
is part of the "asphere" package. The <I>peri</I> style is part of the
"peri" package for Peridynamics. 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.
"peri" package for Peridynamics. The <I>electron</I> style is part of the
"user-eff" package for <A HREF = "pair_eff.html">electronic force fields</A>. 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.
</P>
<P><B>Related commands:</B>
</P>

31
doc/atom_style.txt
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@ -13,7 +13,7 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
{ellipsoid} or {full} or {granular} or {molecular} or \
{electron} or {ellipsoid} or {full} or {granular} or {molecular} or \
{peri} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -56,6 +56,7 @@ quantities.
{charge} | charge | atomic system with charges |
{colloid} | angular velocity | extended spherical particles |
{dipole} | charge and dipole moment | atomic system with dipoles |
{electron} | spin and eradius | electronic force field |
{ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{granular} | diameter, density, angular velocity | granular models |
@ -63,15 +64,18 @@ quantities.
{peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|)
All of the styles define point particles, except the {colloid},
{dipole}, {ellipsoid}, {granular}, and {peri} styles, which define
finite-size particles. For {colloid}, {dipole}, and {ellipsoid}
systems, the "shape"_shape.html command is used to specify the size
and shape of particles on a per-type basis, which is spherical for
{colloid} and {dipole} particles and spherical or aspherical for
{ellipsoid} particles. For {granular} systems, the particles are
spherical and each has a per-particle specified diameter. For {peri}
systems, the particles are spherical and each has a per-particle
specified volume.
{dipole}, {electron}, {ellipsoid}, {granular}, and {peri} styles,
which define finite-size particles. For {colloid}, {dipole}, and
{ellipsoid} systems, the "shape"_shape.html command is used to specify
the size and shape of particles on a per-type basis, which is
spherical for {colloid} and {dipole} particles and spherical or
aspherical for {ellipsoid} particles. For {granular} systems, the
particles are spherical and each has a per-particle specified
diameter. For {peri} systems, the particles are spherical and each
has a per-particle specified volume. For {electron} systems, the
particles are three dimensional Gaussians with a specified position
and bandwidth or uncertainty in position, which is described as the
eradius = electron size.
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except the {granular} and {peri} styles
@ -109,9 +113,10 @@ The {angle}, {bond}, {full}, and {molecular} styles are part of the
package. The {colloid} style is part of the "colloid" package. The
{dipole} style is part of the "dipole" package. The {ellipsoid} style
is part of the "asphere" package. The {peri} style is part of the
"peri" package for Peridynamics. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
"peri" package for Peridynamics. The {electron} style is part of the
"user-eff" package for "electronic force fields"_pair_eff.html. They
are only enabled if LAMMPS was built with that package. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

14
doc/dump.html
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@ -49,6 +49,7 @@
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, evel, eforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
</PRE>
<PRE> id = atom ID
@ -68,6 +69,10 @@
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
evel = electron radial velocity
eforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@ -84,7 +89,8 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress<B>2</B>
dump 1 all xtc 1000 file.xtc
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
</PRE>
<P><B>Description:</B>
</P>
@ -374,6 +380,12 @@ particle.
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
</P>
<P>The <I>spin</I>, <I>eradius</I>, <I>evel</I>, and <I>eforce</I> attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See <A HREF = "atom_style.html">atom_style
electron</A> and <A HREF = "pair_eff.html">pair_style eff</A> for more
details.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has

14
doc/dump.txt
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@ -40,6 +40,7 @@ args = list of arguments for a particular style :l
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, evel, eforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
@ -59,6 +60,10 @@ args = list of arguments for a particular style :l
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
evel = electron radial velocity
eforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@ -74,7 +79,8 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc :pre
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre
[Description:]
@ -364,6 +370,12 @@ The {tqx}, {tqy}, {tqz} attributes are for extended spherical or
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
The {spin}, {eradius}, {evel}, and {eforce} attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See "atom_style
electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
details.
The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
calculated by a "compute"_compute.html to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has

15
doc/read_data.html
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@ -280,6 +280,7 @@ of analysis.
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >colloid</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID atom-type spin eradius x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
@ -299,7 +300,9 @@ of analysis.
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = direction of dipole moment of atom
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
<LI>spin = electron spin (+1/-1)
<LI>eradius = electron radius
</UL>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
@ -692,6 +695,7 @@ style dipole or ellipsoid.
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID vx vy vz evel</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz wx wy wz
</TD></TR></TABLE></DIV>
@ -700,16 +704,17 @@ style dipole or ellipsoid.
</P>
<UL><LI>vx,vy,vz = translational velocity of atom
<LI>lx,ly,lz = angular momentum of aspherical atom
<LI>wx,wy,wz = angular velocity of granular atom
<LI>wx,wy,wz = angular velocity of granular atom
<LI>evel = electron radial velocity
</UL>
<P>The velocity lines can appear in any order. This section can only be
used after an <I>Atoms</I> section. This is because the <I>Atoms</I> section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
</P>
<P>Vx,vy,vz are in <A HREF = "units.html">units</A> of velocity. Lx, ly, lz are in
units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
units of angular velocity (radians/time).
<P>Vx, vy, vz, and evel are in <A HREF = "units.html">units</A> of velocity. Lx, ly,
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
Wz are in units of angular velocity (radians/time).
</P>
<P>Translational velocities can also be set by the
<A HREF = "velocity.html">velocity</A> command in the input script.

15
doc/read_data.txt
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@ -260,6 +260,7 @@ bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
colloid: atom-ID atom-type x y z
dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type spin eradius x y z
ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
@ -278,7 +279,9 @@ density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = direction of dipole moment of atom
quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul
quatw,quati,quatj,quatk = quaternion components for orientation of atom
spin = electron spin (+1/-1)
eradius = electron radius :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
@ -605,6 +608,7 @@ line syntax: depends on atom style :ul
all styles except those listed: atom-ID vx vy vz
dipole: atom-ID vx vy vz wx wy wz
electron: atom-ID vx vy vz evel
ellipsoid: atom-ID vx vy vz lx ly lz
granular: atom-ID vx vy vz wx wy wz :tb(s=:)
@ -612,16 +616,17 @@ where the keywords have these meanings:
vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of granular atom :ul
wx,wy,wz = angular velocity of granular atom
evel = electron radial velocity :ul
The velocity lines can appear in any order. This section can only be
used after an {Atoms} section. This is because the {Atoms} section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
Vx,vy,vz are in "units"_units.html of velocity. Lx, ly, lz are in
units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in
units of angular velocity (radians/time).
Vx, vy, vz, and evel are in "units"_units.html of velocity. Lx, ly,
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
Wz are in units of angular velocity (radians/time).
Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.

32
doc/units.html
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@ -15,7 +15,7 @@
</P>
<PRE>units style
</PRE>
<UL><LI>style = <I>lj</I> or <I>real</I> or <I>metal</I> or <I>si</I> or <I>cgs</I>
<UL><LI>style = <I>lj</I> or <I>real</I> or <I>metal</I> or <I>si</I> or <I>cgs</I> or <I>electron</I>
</UL>
<P><B>Examples:</B>
</P>
@ -126,14 +126,30 @@ results from a unitless LJ simulation into physical quantities.
<LI>electric field = statvolt/cm or dyne/esu
<LI>density = grams/cm^dim
</UL>
<P>The units command also sets the timestep size and neighbor skin
distance to default values for each style. For style <I>lj</I> these are
dt = 0.005 tau and skin = 0.3 sigma. For style <I>real</I> these are dt =
1.0 fmsec and skin = 2.0 Angstroms. For style <I>metal</I> these are dt =
0.001 psec and skin = 2.0 Angstroms. For style <I>si</I> these are dt =
1.0e-8 sec and skin = 0.001 meters. For style <I>cgs</I> these are dt =
1.0e-8 sec and skin = 0.1 cm.
<P>For style <I>electron</I>, these are the units:
</P>
<UL><LI>mass = atomic mass units
<LI>distance = Bohr
<LI>time = femtoseconds
<LI>energy = Kcal/mole
<LI>velocity = Bohr/atomic time units <B>1.03275e-15 seconds</B>
<LI>force = Hartrees*Bohr
<LI>temperature = degrees K
<LI>pressure = Pascals
<LI>charge = multiple of electron charge (+1.0 is a proton)
<LI>dipole moment = Debye
<LI>electric field = volts/cm
</UL>
<P>The units command also sets the timestep size and neighbor skin
distance to default values for each style:
</P>
<UL><LI>For style <I>lj</I> these are dt = 0.005 tau and skin = 0.3 sigma.
<LI>For style <I>real</I> these are dt = 1.0 fmsec and skin = 2.0 Angstroms.
<LI>For style <I>metal</I> these are dt = 0.001 psec and skin = 2.0 Angstroms.
<LI>For style <I>si</I> these are dt = 1.0e-8 sec and skin = 0.001 meters.
<LI>For style <I>cgs</I> these are dt = 1.0e-8 sec and skin = 0.1 cm.
<LI>For style <I>electron</I> these are dt = 0.001 fmsec and skin = 2.0 Bohr.
</UL>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a

30
doc/units.txt
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@ -12,7 +12,7 @@ units command :h3
units style :pre
style = {lj} or {real} or {metal} or {si} or {cgs} :ul
style = {lj} or {real} or {metal} or {si} or {cgs} or {electron} :ul
[Examples:]
@ -123,13 +123,29 @@ dipole = statcoul-cm = 10^18 debye
electric field = statvolt/cm or dyne/esu
density = grams/cm^dim :ul
For style {electron}, these are the units:
mass = atomic mass units
distance = Bohr
time = femtoseconds
energy = Kcal/mole
velocity = Bohr/atomic time units [1.03275e-15 seconds]
force = Hartrees*Bohr
temperature = degrees K
pressure = Pascals
charge = multiple of electron charge (+1.0 is a proton)
dipole moment = Debye
electric field = volts/cm :ul
The units command also sets the timestep size and neighbor skin
distance to default values for each style. For style {lj} these are
dt = 0.005 tau and skin = 0.3 sigma. For style {real} these are dt =
1.0 fmsec and skin = 2.0 Angstroms. For style {metal} these are dt =
0.001 psec and skin = 2.0 Angstroms. For style {si} these are dt =
1.0e-8 sec and skin = 0.001 meters. For style {cgs} these are dt =
1.0e-8 sec and skin = 0.1 cm.
distance to default values for each style:
For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma.
For style {real} these are dt = 1.0 fmsec and skin = 2.0 Angstroms.
For style {metal} these are dt = 0.001 psec and skin = 2.0 Angstroms.
For style {si} these are dt = 1.0e-8 sec and skin = 0.001 meters.
For style {cgs} these are dt = 1.0e-8 sec and skin = 0.1 cm.
For style {electron} these are dt = 0.001 fmsec and skin = 2.0 Bohr. :ul
[Restrictions:]