From b06573d3fb3f4eed57ed5c063861a6c9aee9d09f Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 4 Jan 2008 00:27:56 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1293
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html   | 20 +++++-----
 doc/Section_commands.txt    |  2 +
 doc/compute.html            |  1 +
 doc/compute.txt             |  1 +
 doc/fix.html                |  1 +
 doc/fix.txt                 |  1 +
 doc/fix_coord_original.html | 77 +++++++++++++++++++++++++++++++++++++
 doc/fix_coord_original.txt  | 72 ++++++++++++++++++++++++++++++++++
 doc/fix_msd.html            |  4 +-
 doc/fix_msd.txt             | 10 ++---
 10 files changed, 171 insertions(+), 18 deletions(-)
 create mode 100644 doc/fix_coord_original.html
 create mode 100644 doc/fix_coord_original.txt

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 67ae662f1e..223e391672 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -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
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index aa60e9fb4a..6be399b358 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -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,
diff --git a/doc/compute.html b/doc/compute.html
index ac7382b791..04d1957ab7 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -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
diff --git a/doc/compute.txt b/doc/compute.txt
index 3d5694eef5..23411cd26a 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -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
diff --git a/doc/fix.html b/doc/fix.html
index 9a33878555..cb5db74d7d 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -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
diff --git a/doc/fix.txt b/doc/fix.txt
index 3fac8ecfb2..97c76907e9 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -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
diff --git a/doc/fix_coord_original.html b/doc/fix_coord_original.html
new file mode 100644
index 0000000000..3eceaffa3c
--- /dev/null
+++ b/doc/fix_coord_original.html
@@ -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>
diff --git a/doc/fix_coord_original.txt b/doc/fix_coord_original.txt
new file mode 100644
index 0000000000..11655cdfbc
--- /dev/null
+++ b/doc/fix_coord_original.txt
@@ -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
diff --git a/doc/fix_msd.html b/doc/fix_msd.html
index a80e955bb2..244d8ed136 100644
--- a/doc/fix_msd.html
+++ b/doc/fix_msd.html
@@ -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>
diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt
index 9cbb5c7420..13ae6ba80a 100644
--- a/doc/fix_msd.txt
+++ b/doc/fix_msd.txt
@@ -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
-
-
-
-
-
-