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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1293 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-01-04 00:27:56 +00:00
parent 0808bd4c86
commit b06573d3fb
10 changed files with 171 additions and 18 deletions
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20
doc/Section_commands.html
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@ -317,13 +317,13 @@ in the command's documentation.
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
@ -333,9 +333,9 @@ descriptions of each style or click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

2
doc/Section_commands.txt
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@ -381,6 +381,7 @@ of each style or click on the style itself for a full description:
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"com"_fix_com.html,
"coord/original"_fix_coord_original.html,
"deform"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
@ -439,6 +440,7 @@ description:
"centro/atom"_compute_centro_atom.html,
"coord/atom"_compute_coord_atom.html,
"displace/atom"_compute_displace_atom.html,
"ke/atom"_compute_ke_atom.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,

1
doc/compute.html
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@ -111,6 +111,7 @@ available in LAMMPS:
</P>
<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom

1
doc/compute.txt
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@ -108,6 +108,7 @@ available in LAMMPS:
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"displace/atom"_compute_displace_atom.html - displacement of each atom
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"pe"_compute_pe.html - potential energy
"pe/atom"_compute_pe_atom.html - potential energy for each atom

1
doc/fix.html
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@ -109,6 +109,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_ave_spatial.html">ave/spatial</A> - output per-atom quantities by layer
<LI><A HREF = "fix_ave_time.html">ave/time</A> - output time-averaged compute quantities
<LI><A HREF = "fix_com.html">com</A> - compute a center-of-mass
<LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom
<LI><A HREF = "fix_deform.html">deform</A> - change the simulation box size/shape
<LI><A HREF = "fix_deposit.html">deposit</A> - add new atoms above a surface
<LI><A HREF = "fix_drag.html">drag</A> - drag atoms towards a defined coordinate

1
doc/fix.txt
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@ -106,6 +106,7 @@ list of fix styles available in LAMMPS:
"ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
"ave/time"_fix_ave_time.html - output time-averaged compute quantities
"com"_fix_com.html - compute a center-of-mass
"coord/original"_fix_coord_original.html - store original coords of each atom
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"drag"_fix_drag.html - drag atoms towards a defined coordinate

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doc/fix_coord_original.html Normal file
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@ -0,0 +1,77 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix coord/original command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID coord/original
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>coord/original = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all coord/original
</PRE>
<P><B>Description:</B>
</P>
<P>Store the original coordinates of atoms in the group at the time the
fix command is issued. This is useful for computing a displacement of
the atoms at later times, via the <A HREF = "compute_displace_atom.html">compute
displace/atom</A> command. Or the original
coordinates can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A> that use per-atom quantities such as
the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>IMPORTANT NOTE: To enable displacements to be calculated which include
the effects of atoms passing through periodic boundaries, the original
coordinates are stored in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom.
</P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
restart files</A>, so that the values can be restored when a
simulation is restarted. 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.
</P>
<P>This fix produces a per-atom vector which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The length of the vector
for each atom is 3, and the components store the x,y,z coords of each
atom. The per-atom values be accessed on any timestep.
</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>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_msd.html">fix msd</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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doc/fix_coord_original.txt Normal file
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@ -0,0 +1,72 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix coord/original command :h3
[Syntax:]
fix ID group-ID coord/original :pre
ID, group-ID are documented in "fix"_fix.html command
coord/original = style name of this fix command :ul
[Examples:]
fix 1 all coord/original :pre
[Description:]
Store the original coordinates of atoms in the group at the time the
fix command is issued. This is useful for computing a displacement of
the atoms at later times, via the "compute
displace/atom"_compute_displace_atom.html command. Or the original
coordinates can be accessed by other "output
commands"_Section_howto.html#4_15 that use per-atom quantities such as
the "dump custom"_dump.html command.
IMPORTANT NOTE: To enable displacements to be calculated which include
the effects of atoms passing through periodic boundaries, the original
coordinates are stored in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom.
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
"fix rigid"_fix_rigid.html command for details.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the original coordinates of the atoms to "binary
restart files"_restart.html, so that the values can be restored when a
simulation is restarted. See the "read_restart"_read_restart.html
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.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom vector which can be accessed by various
"output commands"_Section_howto.html#4_15. The length of the vector
for each atom is 3, and the components store the x,y,z coords of each
atom. The per-atom values be accessed on any timestep.
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
[Related commands:]
"fix msd"_fix_msd.html
[Default:] none

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doc/fix_msd.html
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@ -60,7 +60,9 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_coord_original.html">fix coord/original</A>
</P>
<P><B>Default:</B> none
</P>

10
doc/fix_msd.txt
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@ -57,12 +57,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:] none
[Related commands:]
"fix coord/original"_fix_coord_original.html
[Default:] none