jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6841 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-08-27 20:35:24 +00:00
parent 63a91f7c87
commit 34f129eb03
6 changed files with 68 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
doc/atom_style.html
View File

@ -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>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><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>meso</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
@ -61,6 +61,7 @@ quantities.
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, 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>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
@ -93,6 +94,10 @@ position, which is represented by the eradius = electron size.
<P>For the <I>peri</I> style, the particles are spherical and each stores a
per-particle mass and volume.
</P>
<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
</P>
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
@ -128,11 +133,13 @@ MOLECULAR 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. The
<I>electron</I> style is part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
fields</A>. The <I>wavepacket</I> style is part of the
USER-AWPMD package for the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD
method</A>. They are only enabled if LAMMPS was built
with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
fields</A>. The <I>meso</I> style is part of the USER-SPH
package for <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">smoothed particle
hydrodyanmics</A> (SPH). The
<I>wavepacket</I> style is part of the USER-AWPMD package for the
<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

19
doc/atom_style.txt
View File

@ -13,7 +13,7 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {molecular} or \
{electron} or {ellipsoid} or {full} or {meso} or {molecular} or \
{peri} or {sphere} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -58,6 +58,7 @@ quantities.
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular models |
@ -89,6 +90,10 @@ position, which is represented by the eradius = electron size.
For the {peri} style, the particles are spherical and each stores a
per-particle mass and volume.
The {meso} style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
@ -124,11 +129,13 @@ MOLECULAR 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. The
{electron} style is part of the USER-EFF package for "electronic force
fields"_pair_eff.html. The {wavepacket} style is part of the
USER-AWPMD package for the "antisymmetrized wave packet MD
method"_pair_awpmd.html. They are only enabled if LAMMPS was built
with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
fields"_pair_eff.html. The {meso} style is part of the USER-SPH
package for "smoothed particle
hydrodyanmics"_USER/sph/SPH_LAMMPS_userguide.pdf (SPH). The
{wavepacket} style is part of the USER-AWPMD package for the
"antisymmetrized wave packet MD method"_pair_awpmd.html. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

23
doc/fix_gravity.html
View File

@ -113,12 +113,23 @@ instructions on how to use the accelerated styles effectively.
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. 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#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>.
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the gravitational potential energy of the system to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. This scalar is the
gravitational potential energy of the particles in the defined field,
namely mass * (g dot x) for each particles, where x and mass are the
particles position and mass, and g is the gravitational field. The
scalar value calculated by this fix is "extensive".
</P>
<P>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> none
</P>

23
doc/fix_gravity.txt
View File

@ -104,12 +104,23 @@ instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the gravitational potential energy of the system to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. This scalar is the
gravitational potential energy of the particles in the defined field,
namely mass * (g dot x) for each particles, where x and mass are the
particles position and mass, and g is the gravitational field. The
scalar value calculated by this fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none

4
doc/read_data.html
View File

@ -290,6 +290,7 @@ of analysis.
<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type ellipsoidflag density x y z</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
@ -309,6 +310,9 @@ of analysis.
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
<LI>rho = density (need units) for SPH particles
<LI>e = energy (need units) for SPH particles
<LI>cv = heat capacity (need units) for SPH particles
<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
<LI>eradius = electron radius (or fixed-core radius)
<LI>etag = integer ID of electron that each wavepacket belongs to

4
doc/read_data.txt
View File

@ -270,6 +270,7 @@ dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
full: atom-ID molecule-ID atom-type q x y z
meso: atom-ID atom-type rho e cv x y z
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
sphere: atom-ID atom-type diameter density x y z
@ -288,6 +289,9 @@ density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = components of dipole moment of atom (dipole units)
rho = density (need units) for SPH particles
e = energy (need units) for SPH particles
cv = heat capacity (need units) for SPH particles
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius)
etag = integer ID of electron that each wavepacket belongs to