git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12978 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_howto.html

@@ -34,7 +34,8 @@
 6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
 6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
 6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
-6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A> <BR>
+6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
+6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A> <BR>
 
 <P>The example input scripts included in the LAMMPS distribution and
 highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
@@ -2146,6 +2147,160 @@ and thus extract D.
 </P>
 <HR>
 
+<A NAME = "howto_23"></A><H4>6.23 Using chunks to calculate system properties 
+</H4>
+<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command, which assigns each atom
+to a chunk (or to no chunk at all).  The per-atom chunk assignments
+can be used as input to two other kinds of commands, to calculate
+various properties of a system:
+</P>
+<UL><LI><A HREF = "fix_ave_chunk.html">fix ave/chunk</A>
+<LI>a variety of <A HREF = "compute.html">compute */chunk</A> commands 
+</UL>
+<P>Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed, and some examples given of how to compute 
+different properties with chunk commands.
+</P>
+<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command 
+</H5>
+<P>This compute assigns atoms to chunks of various styles.  Only atoms in
+the specified group and optional specified region are assigned to a
+chunk.  Here is a list of possible chunk definitions:
+</P>
+<DIV ALIGN=center><TABLE  BORDER=1 >
+<TR><TD >atoms in same molecule </TD><TD > chunk ID = molecule ID </TD></TR>
+<TR><TD >atoms with same atom type -</TD><TD > chunk ID = atom type </TD></TR>
+<TR><TD >all atoms with same atom property (charge, radius, etc) </TD><TD > chunk ID = output of compute property/atom </TD></TR>
+<TR><TD >atoms in same cluster </TD><TD > chunk ID = output of compute cluster/atom command </TD></TR>
+<TR><TD >atoms in same spatial bin </TD><TD > chunk ID = bin ID </TD></TR>
+<TR><TD >atoms in same rigid body </TD><TD > chunk ID = ID of an atom in the body </TD></TR>
+<TR><TD >all atoms with same local defect structure </TD><TD > chunk ID = output of compute centro/atom or coord/atom command 
+</TD></TR></TABLE></DIV>
+
+<P>Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+</P>
+<P>This compute also calculates the number of chunks <I>Nchunk</I> which is
+used by other commands to tally per-chunk data.  <I>Nchunk</I> can be a
+static value or change over time (e.g. the number of clusters).  The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+</P>
+<P>Note that this compute allows the per-atom output of other
+<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
+<A HREF = "variable.html">variables</A> to be used to define chunk IDs for each
+atom.  This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID; See
+<A HREF = "Section_modify.html">Section_modify</A> of the documentation for how to
+do this.  You can also define a <A HREF = "variable.html">per-atom variable</A> in
+the input script that uses a formula to generate a chunk ID for each
+atom.
+</P>
+<H5><A HREF = "fix_ave_chunk_atom.html">Fix ave/chunk</A> command 
+</H5>
+<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command as input.  For each chunk
+it then sums one or more specified per-atom values over the atoms in
+each chunk.  The per-atom values can be any atom property, such as
+force, charge, potential energy, kinetic energy, stress.  Additional
+keywords are allowed for per-chunk properties like density and
+temperature.  More generally any per-atom value generated by other
+<A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and <A HREF = "variable.html">per-atom
+variables</A>, can be summed over atoms in each chunk.
+</P>
+<P>Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file.  The
+fix produces a global array as output with one row of values per
+chunk.  Global arrays or columns thereof can be used as input for
+other commands, as described in the following section.
+</P>
+<H5>Compute */chunk commands 
+</H5>
+<P>Currently the following computes operate on chunks:
+</P>
+<UL><LI><A HREF = "compute_com_chunk.html">compute com/chunk</A>
+<LI><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</A>
+<LI><A HREF = "compute_inertia_chunk.html">compute inertia/chunk</A>
+<LI><A HREF = "compute_msd_chunk.html">compute msd/chunk</A>
+<LI><A HREF = "compute_property_chunk.html">compute property/chunk</A>
+<LI><A HREF = "compute_vcm_chunk.html">compute vcm/chunk</A> 
+</UL>
+<P>They each take the ID of a <A HREF = "compute_chunk_atom.html">compute
+chunk/atom</A> command as input.  As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, and velocity of
+center-of-mass for each chunk of atoms.  The <A HREF = "compute_property_chunk.html">compute
+property/chunk</A> command can be tally the
+count of atoms in each chunk and extract other per-chunk properties.
+</P>
+<P>The reason these various calculations are not part of the <A HREF = "fix_ave_chunk.html">fix
+ave/chunk command</A>, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk.  Most of them require calculation of a center of
+mass, which requires summing mass*position over the atoms and dividing
+by summed mass.
+</P>
+<P>All of these computes produce a global vector or global array as
+output, wih one or more values per chunk.  Global vectors or arrays
+can be used as input for other commands, e.g. 
+</P>
+<UL><LI>As input to the <A HREF = "fix_ave_time.html">fix ave/time</A> command, so the
+per-chunk values output to a file it creates.  The <A HREF = "fix_ave_time.html">fix
+ave/time</A> command can also average the values for
+each chunk over time if desired. 
+
+<LI>As input to the <A HREF = "fix_ave_histo.html">fix ave/histo</A> command to
+histogram values across chunks.  E.g. a histogram of cluster sizes or
+molecule diffusion rates. 
+
+<LI>As input to special functions of <A HREF = "variable.html">equal-style
+variables</A>, like sum() and max().  E.g. to find the
+largest cluster or fastest diffusing molecule. 
+</UL>
+<H5>Example calculations with chunks 
+</H5>
+<P>Here are chunk commands that can be used to calculate various
+properties:
+</P>
+<P>(1) Mimic the deprecated fix ave/spatial command, to average atom
+velocity in each spatial bin:
+</P>
+<P>Old command:
+</P>
+<P>fix ave/spatial
+</P>
+<P>New commands:
+</P>
+<P>compute chunk/atom
+fix ave/chunk
+</P>
+<P>(2) Mimincing the deprecated compute msd/molecule command
+to compute the mean-squared displacement of each molecule:
+</P>
+<P>Old commands:
+</P>
+<P>compute molecule/msd
+fix ave/time file msd.molecule
+</P>
+<P>New commands:
+</P>
+<P>compute chunk/atom style
+compute molecule/chunk
+fix ave/time file msd.molecule
+</P>
+<P>(3) print or time ave total force per molecule
+   average across molecules (variable special functions)
+</P>
+<P>(4) histogram of cluster sizes (use fix ave/histo)
+</P>
+<P>(5) count of # of atoms with each coord #
+  don't need chunking, just fix ave/histo on coord/atom
+</P>
+<P>(6) ave temperature per bin
+</P>
+<HR>
+
 <HR>
 
 <A NAME = "Berendsen"></A>

doc/Section_howto.txt

@@ -31,7 +31,8 @@ This section describes how to perform common tasks using LAMMPS.
 6.19 "Library interface to LAMMPS"_#howto_19
 6.20 "Calculating thermal conductivity"_#howto_20
 6.21 "Calculating viscosity"_#howto_21
-6.22 "Calculating a diffusion coefficient"_#howto_22 :all(b)
+6.22 "Calculating a diffusion coefficient"_#howto_22
+6.23 "Using chunks to calculate system properties"_#howto_23 :all(b)
 
 The example input scripts included in the LAMMPS distribution and
 highlighted in "Section_example"_Section_example.html also show how to
@@ -2131,6 +2132,158 @@ accumulated in a vector via the "fix vector"_fix_vector.html command,
 and time integrated via the "variable trap"_variable.html function,
 and thus extract D.
 
+:line
+
+6.23 Using chunks to calculate system properties :link(howto_23),h4
+
+In LAMMPS, chunks are collections of atoms defined by a "compute
+chunk/atom"_compute_chunk_atom.html command, which assigns each atom
+to a chunk (or to no chunk at all).  The per-atom chunk assignments
+can be used as input to two other kinds of commands, to calculate
+various properties of a system:
+
+"fix ave/chunk"_fix_ave_chunk.html
+a variety of "compute */chunk"_compute.html commands :ul
+
+Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed, and some examples given of how to compute 
+different properties with chunk commands.
+
+"Compute chunk/atom"_compute_chunk_atom.html command :h5
+
+This compute assigns atoms to chunks of various styles.  Only atoms in
+the specified group and optional specified region are assigned to a
+chunk.  Here is a list of possible chunk definitions:
+
+atoms in same molecule | chunk ID = molecule ID |
+atoms with same atom type -| chunk ID = atom type |
+all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
+atoms in same cluster | chunk ID = output of compute cluster/atom command |
+atoms in same spatial bin | chunk ID = bin ID |
+atoms in same rigid body | chunk ID = ID of an atom in the body |
+all atoms with same local defect structure | chunk ID = output of compute centro/atom or coord/atom command :tb(s=|,c=2)
+
+Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+
+This compute also calculates the number of chunks {Nchunk} which is
+used by other commands to tally per-chunk data.  {Nchunk} can be a
+static value or change over time (e.g. the number of clusters).  The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+
+Note that this compute allows the per-atom output of other
+"computes"_compute.html, "fixes"_fix.html, and
+"variables"_variable.html to be used to define chunk IDs for each
+atom.  This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID; See
+"Section_modify"_Section_modify.html of the documentation for how to
+do this.  You can also define a "per-atom variable"_variable.html in
+the input script that uses a formula to generate a chunk ID for each
+atom.
+
+"Fix ave/chunk"_fix_ave_chunk_atom.html command :h5
+
+This fix takes the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input.  For each chunk
+it then sums one or more specified per-atom values over the atoms in
+each chunk.  The per-atom values can be any atom property, such as
+force, charge, potential energy, kinetic energy, stress.  Additional
+keywords are allowed for per-chunk properties like density and
+temperature.  More generally any per-atom value generated by other
+"computes"_compute.html, "fixes"_fix.html, and "per-atom
+variables"_variable.html, can be summed over atoms in each chunk.
+
+Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file.  The
+fix produces a global array as output with one row of values per
+chunk.  Global arrays or columns thereof can be used as input for
+other commands, as described in the following section.
+
+Compute */chunk commands :h5
+
+Currently the following computes operate on chunks:
+
+"compute com/chunk"_compute_com_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html
+"compute inertia/chunk"_compute_inertia_chunk.html
+"compute msd/chunk"_compute_msd_chunk.html
+"compute property/chunk"_compute_property_chunk.html
+"compute vcm/chunk"_compute_vcm_chunk.html :ul
+
+They each take the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input.  As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, and velocity of
+center-of-mass for each chunk of atoms.  The "compute
+property/chunk"_compute_property_chunk.html command can be tally the
+count of atoms in each chunk and extract other per-chunk properties.
+
+The reason these various calculations are not part of the "fix
+ave/chunk command"_fix_ave_chunk.html, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk.  Most of them require calculation of a center of
+mass, which requires summing mass*position over the atoms and dividing
+by summed mass.
+
+All of these computes produce a global vector or global array as
+output, wih one or more values per chunk.  Global vectors or arrays
+can be used as input for other commands, e.g. 
+
+As input to the "fix ave/time"_fix_ave_time.html command, so the
+per-chunk values output to a file it creates.  The "fix
+ave/time"_fix_ave_time.html command can also average the values for
+each chunk over time if desired. :ulb,l
+
+As input to the "fix ave/histo"_fix_ave_histo.html command to
+histogram values across chunks.  E.g. a histogram of cluster sizes or
+molecule diffusion rates. :l
+
+As input to special functions of "equal-style
+variables"_variable.html, like sum() and max().  E.g. to find the
+largest cluster or fastest diffusing molecule. :l,ule
+
+Example calculations with chunks :h5
+
+Here are chunk commands that can be used to calculate various
+properties:
+
+(1) Mimic the deprecated fix ave/spatial command, to average atom
+velocity in each spatial bin:
+
+Old command:
+
+fix ave/spatial
+
+New commands:
+
+compute chunk/atom
+fix ave/chunk
+
+(2) Mimincing the deprecated compute msd/molecule command
+to compute the mean-squared displacement of each molecule:
+
+Old commands:
+
+compute molecule/msd
+fix ave/time file msd.molecule
+
+New commands:
+
+compute chunk/atom style
+compute molecule/chunk
+fix ave/time file msd.molecule
+
+(3) print or time ave total force per molecule
+   average across molecules (variable special functions)
+
+(4) histogram of cluster sizes (use fix ave/histo)
+
+(5) count of # of atoms with each coord #
+  don't need chunking, just fix ave/histo on coord/atom
+
+(6) ave temperature per bin
+
 :line
 :line
 

doc/compute_temp_asphere.html

@@ -23,7 +23,7 @@
 
 <LI>keyword = <I>bias</I> or <I>dof</I> 
 
-<PRE>  <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
+<PRE>  <I>bias</I> value = bias-ID
     bias-ID = ID of a temperature compute that removes a velocity bias
   <I>dof</I> value = <I>all</I> or <I>rotate</I>
     all = compute temperature of translational and rotational degrees of freedom
@@ -113,10 +113,10 @@ thermostatting.
 compute that removes a "bias" velocity from each atom.  This allows
 compute temp/sphere to compute its thermal temperature after the
 translational kinetic energy components have been altered in a
-prescribed way, e.g. to remove a velocity profile.  Thermostats that
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
-use this compute will work with this bias term.  See the doc pages for
+that use this compute will work with this bias term.  See the doc
-individual computes that calculate a temperature and the doc pages for
+pages for individual computes that calculate a temperature and the doc
-fixes that perform thermostatting for more details.
+pages for fixes that perform thermostatting for more details.
 </P>
 <P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
 that includes both translational and rotational degrees of freedom.  A

doc/compute_temp_asphere.txt

@@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 temp/asphere = style name of this compute command :l
 zero or more keyword/value pairs may be appended :l
 keyword = {bias} or {dof} :l
-  {bias} value = bias-ID{uniform} or {gaussian}
+  {bias} value = bias-ID
     bias-ID = ID of a temperature compute that removes a velocity bias
   {dof} value = {all} or {rotate}
     all = compute temperature of translational and rotational degrees of freedom
@@ -105,10 +105,10 @@ For the {bias} keyword, {bias-ID} refers to the ID of a temperature
 compute that removes a "bias" velocity from each atom.  This allows
 compute temp/sphere to compute its thermal temperature after the
 translational kinetic energy components have been altered in a
-prescribed way, e.g. to remove a velocity profile.  Thermostats that
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
-use this compute will work with this bias term.  See the doc pages for
+that use this compute will work with this bias term.  See the doc
-individual computes that calculate a temperature and the doc pages for
+pages for individual computes that calculate a temperature and the doc
-fixes that perform thermostatting for more details.
+pages for fixes that perform thermostatting for more details.
 
 For the {dof} keyword, a setting of {all} calculates a temperature
 that includes both translational and rotational degrees of freedom.  A

doc/compute_temp_region.html

@@ -74,12 +74,13 @@ compute.
 </P>
 <P>Unlike other compute styles that calculate temperature, this compute
 does not subtract out degrees-of-freedom due to fixes that constrain
-molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
+motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
 rigid</A>.  This is because those degrees of freedom
-(e.g. a constrained bond) can straddle the region boundary, and hence
+(e.g. a constrained bond) could apply to sets of atoms that straddle
-the concept is somewhat ill-defined.  If needed the number of
+the region boundary, and hence the concept is somewhat ill-defined.
-subtracted degrees-of-freedom can be set explicitly using the <I>extra</I>
+If needed the number of subtracted degrees-of-freedom can be set
-option of the <A HREF = "compute_modify.html">compute_modify</A> command.
+explicitly using the <I>extra</I> option of the
+<A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
 <P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
 a discussion of different ways to compute temperature and perform

doc/compute_temp_region.txt

@@ -71,12 +71,13 @@ compute.
 
 Unlike other compute styles that calculate temperature, this compute
 does not subtract out degrees-of-freedom due to fixes that constrain
-molecular motion, such as "fix shake"_fix_shake.html and "fix
+motion, such as "fix shake"_fix_shake.html and "fix
 rigid"_fix_rigid.html.  This is because those degrees of freedom
-(e.g. a constrained bond) can straddle the region boundary, and hence
+(e.g. a constrained bond) could apply to sets of atoms that straddle
-the concept is somewhat ill-defined.  If needed the number of
+the region boundary, and hence the concept is somewhat ill-defined.
-subtracted degrees-of-freedom can be set explicitly using the {extra}
+If needed the number of subtracted degrees-of-freedom can be set
-option of the "compute_modify"_compute_modify.html command.
+explicitly using the {extra} option of the
+"compute_modify"_compute_modify.html command.
 
 See "this howto section"_Section_howto.html#howto_16 of the manual for
 a discussion of different ways to compute temperature and perform

doc/compute_temp_sphere.html

@@ -23,7 +23,7 @@
 
 <LI>keyword = <I>bias</I> or <I>dof</I> 
 
-<PRE>  <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
+<PRE>  <I>bias</I> value = bias-ID
     bias-ID = ID of a temperature compute that removes a velocity bias
   <I>dof</I> value = <I>all</I> or <I>rotate</I>
     all = compute temperature of translational and rotational degrees of freedom
@@ -99,10 +99,10 @@ thermostatting.
 compute that removes a "bias" velocity from each atom.  This allows
 compute temp/sphere to compute its thermal temperature after the
 translational kinetic energy components have been altered in a
-prescribed way, e.g. to remove a velocity profile.  Thermostats that
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
-use this compute will work with this bias term.  See the doc pages for
+that use this compute will work with this bias term.  See the doc
-individual computes that calculate a temperature and the doc pages for
+pages for individual computes that calculate a temperature and the doc
-fixes that perform thermostatting for more details.
+pages for fixes that perform thermostatting for more details.
 </P>
 <P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
 that includes both translational and rotational degrees of freedom.  A

doc/compute_temp_sphere.txt

@@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 temp/sphere = style name of this compute command :l
 zero or more keyword/value pairs may be appended :l
 keyword = {bias} or {dof} :l
-  {bias} value = bias-ID{uniform} or {gaussian}
+  {bias} value = bias-ID
     bias-ID = ID of a temperature compute that removes a velocity bias
   {dof} value = {all} or {rotate}
     all = compute temperature of translational and rotational degrees of freedom
@@ -91,10 +91,10 @@ For the {bias} keyword, {bias-ID} refers to the ID of a temperature
 compute that removes a "bias" velocity from each atom.  This allows
 compute temp/sphere to compute its thermal temperature after the
 translational kinetic energy components have been altered in a
-prescribed way, e.g. to remove a velocity profile.  Thermostats that
+prescribed way, e.g. to remove a flow velocity profile.  Thermostats
-use this compute will work with this bias term.  See the doc pages for
+that use this compute will work with this bias term.  See the doc
-individual computes that calculate a temperature and the doc pages for
+pages for individual computes that calculate a temperature and the doc
-fixes that perform thermostatting for more details.
+pages for fixes that perform thermostatting for more details.
 
 For the {dof} keyword, a setting of {all} calculates a temperature
 that includes both translational and rotational degrees of freedom.  A

doc/dump_modify.html

@@ -44,6 +44,8 @@
   <I>precision</I> arg = power-of-10 value from 10 to 1000000
   <I>region</I> arg = region-ID or "none"
   <I>scale</I> arg = <I>yes</I> or <I>no</I>
+  <I>sfactor</I> arg = coordinate scaling factor (> 0.0)
+  <I>tfactor</I> arg = time scaling factor (> 0.0)
   <I>sort</I> arg = <I>off</I> or <I>id</I> or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
@@ -111,7 +113,7 @@
 <PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
 dump_modify myDump image yes scale no flush yes
 dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000
+dump_modify xtcdump precision 10000 sfactor 0.1
 dump_modify 1 every 1000 nfile 20
 dump_modify 1 every v_myVar
 dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red 
@@ -364,6 +366,21 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
 </P>
 <HR>
 
+<P>The <I>sfactor</I> and <I>tfactor</I> keywords only apply to the dump <I>xtc</I>
+style.  They allow customization of the unit conversion factors used
+when writing to XTC files.  By default they are initialized for
+whatever <A HREF = "units.html">units</A> style is being used, to write out
+coordinates in nanometers and time in picoseconds.  I.e. for <I>real</I>
+units, LAMMPS defines <I>sfactor</I> = 0.1 and <I>tfactor</I> = 0.001, since the
+Angstroms and fmsec used by <I>real</I> units are 0.1 nm and 0.001 psec
+respectively.  If you are using a units system with distance and time
+units far from nm and psec, you may wish to write XTC files with
+different units, since the compression algorithm used in XTC files is
+most effective when the typical magnitude of position data is between
+10.0 and 0.1.
+</P>
+<HR>
+
 <P>The <I>region</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
 <I>image</I>, and <I>movie</I> styles.  If specified, only atoms in the region
 will be written to the dump file or included in the image/movie.  Only

doc/dump_modify.txt

@@ -37,6 +37,8 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
   {precision} arg = power-of-10 value from 10 to 1000000
   {region} arg = region-ID or "none"
   {scale} arg = {yes} or {no}
+  {sfactor} arg = coordinate scaling factor (> 0.0)
+  {tfactor} arg = time scaling factor (> 0.0)
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
@@ -100,7 +102,7 @@ keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or
 dump_modify 1 format "%d %d %20.15g %g %g" scale yes
 dump_modify myDump image yes scale no flush yes
 dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000
+dump_modify xtcdump precision 10000 sfactor 0.1
 dump_modify 1 every 1000 nfile 20
 dump_modify 1 every v_myVar
 dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red :pre
@@ -352,6 +354,21 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
 
 :line
 
+The {sfactor} and {tfactor} keywords only apply to the dump {xtc}
+style.  They allow customization of the unit conversion factors used
+when writing to XTC files.  By default they are initialized for
+whatever "units"_units.html style is being used, to write out
+coordinates in nanometers and time in picoseconds.  I.e. for {real}
+units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the
+Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec
+respectively.  If you are using a units system with distance and time
+units far from nm and psec, you may wish to write XTC files with
+different units, since the compression algorithm used in XTC files is
+most effective when the typical magnitude of position data is between
+10.0 and 0.1.
+
+:line
+
 The {region} keyword only applies to the dump {custom}, {cfg},
 {image}, and {movie} styles.  If specified, only atoms in the region
 will be written to the dump file or included in the image/movie.  Only