Commit 34f129eb authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6841 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 63a91f7c

doc/atom_style.html

+13 −6
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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>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>

doc/atom_style.txt

+13 −6
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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 {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:]

doc/fix_gravity.html

+17 −6
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@@ -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>

doc/fix_gravity.txt

+17 −6
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@@ -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

doc/read_data.html

+4 −0
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@@ -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

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