git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3509 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_howto.html

@@ -1136,18 +1136,18 @@ frequencies and global vs per-atom attributes are the same.
 <DIV ALIGN=center><TABLE  BORDER=1 >
 <TR><TD >Command</TD><TD > Input</TD><TD > Input Freq</TD><TD > Output</TD><TD > Output Freq</TD></TR>
 <TR><TD >thermo_style custom</TD><TD > thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable</TD><TD > nthermo</TD><TD > screen, log</TD><TD > nthermo</TD></TR>
-<TR><TD >dump custom</TD><TD > keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable</TD><TD > dump freq</TD><TD > file</TD><TD > dump freq</TD></TR>
+<TR><TD >dump custom</TD><TD > keyword, per-atom compute, per-atom fix, atom variable</TD><TD > dump freq</TD><TD > file</TD><TD > dump freq</TD></TR>
 <TR><TD >global fixes</TD><TD > N/A</TD><TD > N/A</TD><TD >	global scalar/vector</TD><TD > 1 or nevery</TD></TR>
-<TR><TD >peratom fixes</TD><TD > N/A</TD><TD > N/A</TD><TD > peratom scalar/vector</TD><TD > 1 or nevery</TD></TR>
+<TR><TD >per-atom fixes</TD><TD > N/A</TD><TD > N/A</TD><TD > per-atom vector/array</TD><TD > 1 or nevery</TD></TR>
 <TR><TD >fix ave/time</TD><TD > global scalar/vector fix, global scalar/vector compute, equal variable</TD><TD > nevery</TD><TD > global scalar/vector, file</TD><TD > nfreq</TD></TR>
-<TR><TD >fix ave/spatial</TD><TD > peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number</TD><TD > nevery</TD><TD > global vector</TD><TD > nfreq, file</TD></TR>
+<TR><TD >fix ave/spatial</TD><TD > per-atom fix, per-atom compute, atom vector, atom variable, density mass/number</TD><TD > nevery</TD><TD > global vector</TD><TD > nfreq, file</TD></TR>
-<TR><TD >fix ave/atom</TD><TD > peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector</TD><TD > nevery</TD><TD > peratom scalar/vector</TD><TD > nfreq</TD></TR>
+<TR><TD >fix ave/atom</TD><TD > per-atom compute, per-atom fix, atom variable, atom vector</TD><TD > nevery</TD><TD > per-atom vector/array</TD><TD > nfreq</TD></TR>
 <TR><TD >fix print</TD><TD > any variable</TD><TD > nevery</TD><TD > screen, file</TD><TD > nevery</TD></TR>
 <TR><TD >global computes</TD><TD > N/A</TD><TD > N/A</TD><TD > global scalar/vector</TD><TD > N/A</TD></TR>
-<TR><TD >peratom computes</TD><TD > N/A</TD><TD > N/A</TD><TD > peratom scalar/vector</TD><TD > N/A</TD></TR>
+<TR><TD >per-atom computes</TD><TD > N/A</TD><TD > N/A</TD><TD > per-atom vector/array</TD><TD > N/A</TD></TR>
-<TR><TD >compute sum</TD><TD > peratom scalar/vector compute, peratom scalar/vector fix, atom variable</TD><TD > N/A</TD><TD > global scalar/vector</TD><TD > N/A</TD></TR>
+<TR><TD >compute sum</TD><TD > per-atom compute, per-atom fix, atom variable</TD><TD > N/A</TD><TD > global scalar/vector</TD><TD > N/A</TD></TR>
 <TR><TD >variable equal</TD><TD > thermo keywords, atom value vx[123], global scalar/vector compute, global scalar/vector fix, non-atom variable</TD><TD > N/A</TD><TD > global scalar</TD><TD > N/A</TD></TR>
-<TR><TD >variable atom</TD><TD > thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable</TD><TD > N/A</TD><TD > peratom scalar</TD><TD > N/A</TD></TR>
+<TR><TD >variable atom</TD><TD > thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, per-atom compute, global fix, per-atom fix, any variable</TD><TD > N/A</TD><TD > per-atom vector</TD><TD > N/A</TD></TR>
 <TR><TD >print</TD><TD > any variable</TD><TD > N/A</TD><TD > screen, log</TD><TD > between runs</TD></TR>
 <TR><TD >run every</TD><TD > any variable</TD><TD > nevery</TD><TD > screen, log</TD><TD > nevery 
 </TD></TR></TABLE></DIV>

doc/Section_howto.txt

@@ -1128,18 +1128,18 @@ frequencies and global vs per-atom attributes are the same.
 
 Command: Input: Input Freq: Output: Output Freq
 thermo_style custom: thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable: nthermo: screen, log: nthermo
-dump custom: keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable: dump freq: file: dump freq
+dump custom: keyword, per-atom compute, per-atom fix, atom variable: dump freq: file: dump freq
 global fixes: N/A: N/A:	global scalar/vector: 1 or nevery
-peratom fixes: N/A: N/A: peratom scalar/vector: 1 or nevery
+per-atom fixes: N/A: N/A: per-atom vector/array: 1 or nevery
 fix ave/time: global scalar/vector fix, global scalar/vector compute, equal variable: nevery: global scalar/vector, file: nfreq
-fix ave/spatial: peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file
+fix ave/spatial: per-atom fix, per-atom compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file
-fix ave/atom: peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector: nevery: peratom scalar/vector: nfreq
+fix ave/atom: per-atom compute, per-atom fix, atom variable, atom vector: nevery: per-atom vector/array: nfreq
 fix print: any variable: nevery: screen, file: nevery
 global computes: N/A: N/A: global scalar/vector: N/A
-peratom computes: N/A: N/A: peratom scalar/vector: N/A
+per-atom computes: N/A: N/A: per-atom vector/array: N/A
-compute sum: peratom scalar/vector compute, peratom scalar/vector fix, atom variable: N/A: global scalar/vector: N/A
+compute sum: per-atom compute, per-atom fix, atom variable: N/A: global scalar/vector: N/A
 variable equal: thermo keywords, atom value vx\[123\], global scalar/vector compute, global scalar/vector fix, non-atom variable: N/A: global scalar: N/A
-variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable: N/A: peratom scalar: N/A
+variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, per-atom compute, global fix, per-atom fix, any variable: N/A: per-atom vector: N/A
 print: any variable: N/A: screen, log: between runs
 run every: any variable: nevery: screen, log: nevery :tb(s=:)
 

doc/compute.html

@@ -46,11 +46,11 @@ calculate a global temperature or pressure can be used by fixes that
 do thermostatting or barostatting and when atom velocities are
 created.
 </P>
-<P>The results of per-atom computes can be output via the <A HREF = "dump.html">dump
+<P>The results of per-atom computes that calculate a per-atom vector or
-custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
+array can be output via the <A HREF = "dump.html">dump custom</A> command or the
-ave/spatial</A> command.  Or the per-atom values can
+<A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.  Or the per-atom
-be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command and
+values can be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A>
-then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
+command and then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
 ave/spatial</A> commands.  Or the per-atom values
 can be referenced in a <A HREF = "variable.html">variable atom</A> command.  Note
 that the value of per-atom computes will be 0.0 for atoms not in the

doc/compute.txt

@@ -43,11 +43,11 @@ calculate a global temperature or pressure can be used by fixes that
 do thermostatting or barostatting and when atom velocities are
 created.
 
-The results of per-atom computes can be output via the "dump
+The results of per-atom computes that calculate a per-atom vector or
-custom"_dump.html command or the "fix
+array can be output via the "dump custom"_dump.html command or the
-ave/spatial"_fix_ave_spatial.html command.  Or the per-atom values can
+"fix ave/spatial"_fix_ave_spatial.html command.  Or the per-atom
-be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
+values can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
-then output via the "dump custom"_dump.html or "fix
+command and then output via the "dump custom"_dump.html or "fix
 ave/spatial"_fix_ave_spatial.html commands.  Or the per-atom values
 can be referenced in a "variable atom"_variable.html command.  Note
 that the value of per-atom computes will be 0.0 for atoms not in the

doc/compute_centro_atom.html

@@ -52,10 +52,10 @@ too frequently or to have multiple compute/dump commands, each with a
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_centro_atom.txt

@@ -49,10 +49,10 @@ too frequently or to have multiple compute/dump commands, each with a
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:] none
 

doc/compute_cna_atom.html

@@ -75,10 +75,10 @@ too frequently or to have multiple compute/dump commands, each with a
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_cna_atom.txt

@@ -72,10 +72,10 @@ too frequently or to have multiple compute/dump commands, each with a
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:] none
 

doc/compute_coord_atom.html

@@ -44,10 +44,10 @@ too frequently or to have multiple compute/dump commands, each of a
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_coord_atom.txt

@@ -41,10 +41,10 @@ too frequently or to have multiple compute/dump commands, each of a
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:] none
 

doc/compute_damage_atom.html

@@ -35,10 +35,10 @@ compute group.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_damage_atom.txt

@@ -32,10 +32,10 @@ compute group.
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:]
 

doc/compute_displace_atom.html

@@ -74,10 +74,10 @@ file.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a vector of length 4 for each atom, which can
+<P>This compute calculates a per-atom array with 4 columns, which can be
-be accessed by indices 1-4 by any command that uses per-atom values
+accessed by indices 1-4 by any command that uses per-atom values from
-from a compute as input.  See <A HREF = "Section_howto.html#4_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an
-for an overview of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_displace_atom.txt

@@ -71,10 +71,10 @@ file.
 
 [Output info:]
 
-This compute calculates a vector of length 4 for each atom, which can
+This compute calculates a per-atom array with 4 columns, which can be
-be accessed by indices 1-4 by any command that uses per-atom values
+accessed by indices 1-4 by any command that uses per-atom values from
-from a compute as input.  See "this section"_Section_howto.html#4_15
+a compute as input.  See "this section"_Section_howto.html#4_15 for an
-for an overview of LAMMPS output options.
+overview of LAMMPS output options.
 
 [Restrictions:] none
 

doc/compute_ke_atom.html

@@ -35,10 +35,10 @@ specified compute group.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_ke_atom.txt

@@ -32,10 +32,10 @@ specified compute group.
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:] none
 

doc/compute_pe_atom.html

@@ -65,10 +65,10 @@ contribution can easily be computed.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a scalar quantity for each atom, which can be
+<P>This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
-LAMMPS output options.
+output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_pe_atom.txt

@@ -62,10 +62,10 @@ contribution can easily be computed.
 
 [Output info:]
 
-This compute calculates a scalar quantity for each atom, which can be
+This compute calculates a per-atom vector, which can be accessed by
-accessed by any command that uses per-atom values from a compute as
+any command that uses per-atom values from a compute as input.  See
-input.  See "this section"_Section_howto.html#4_15 for an overview of
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 [Restrictions:]
 

doc/compute_reduce.html

@@ -32,11 +32,11 @@
 <LI>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name 
 
 <PRE>  x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  v_name = per-atom vector calculated by an atom-style variable with name 
 </PRE>
 
 </UL>

doc/compute_reduce.txt

@@ -22,11 +22,11 @@ mode = {sum} or {min} or {max} :l
 one or more inputs can be listed :l
 input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
   x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name :pre
+  v_name = per-atom vector calculated by an atom-style variable with name :pre
 :ule
 
 [Examples:]

doc/compute_stress_atom.html

@@ -100,10 +100,10 @@ contribution can easily be computed.
 </P>
 <P><B>Output info:</B>
 </P>
-<P>This compute calculates a vector of length 6 for each atom, which can
+<P>This compute calculates a per-atom array with 6 columns, which can be
-be accessed by indices 1-6 by any command that uses per-atom values
+accessed by indices 1-6 by any command that uses per-atom values from
-from a compute as input.  See <A HREF = "Section_howto.html#4_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#4_15">this section</A> for an
-for an overview of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/compute_stress_atom.txt

@@ -97,10 +97,10 @@ contribution can easily be computed.
 
 [Output info:]
 
-This compute calculates a vector of length 6 for each atom, which can
+This compute calculates a per-atom array with 6 columns, which can be
-be accessed by indices 1-6 by any command that uses per-atom values
+accessed by indices 1-6 by any command that uses per-atom values from
-from a compute as input.  See "this section"_Section_howto.html#4_15
+a compute as input.  See "this section"_Section_howto.html#4_15 for an
-for an overview of LAMMPS output options.
+overview of LAMMPS output options.
 
 [Restrictions:] none
 

doc/dump.html

@@ -58,11 +58,11 @@
       angmomx,angmomy,angmomz = angular momentum of extended particle
       quatw,quati,quatj,quatk = quaternion components for aspherical particles
       tqx,tqy,tqz = torque on extended particles
-      c_ID = per-atom scalar value calculated by a compute with ID
+      c_ID = per-atom vector value calculated by a compute with ID
-      c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
+      c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-      f_ID = per-atom scalar value calculated by a fix with ID
+      f_ID = per-atom vector value calculated by a fix with ID
-      f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
+      f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom value calculated by an atom-style variable with name 
+      v_name = per-atom vector calculated by an atom-style variable with name 
 </PRE>
 
 </UL>
@@ -331,8 +331,8 @@ custom</A> command.
 </P>
 <P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
 calculated by the compute is printed.  If <I>c_ID[N]</I> is used, then N
-must be in the range from 1-M, which will print the Nth component of
+must be in the range from 1-M, which will print the Nth column of
-the M-length per-atom vector calculated by the compute.
+the M-length per-atom array calculated by the compute.
 </P>
 <P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
 quantities calculated by a <A HREF = "fix.html">fix</A> to be output.  The ID in the
@@ -346,8 +346,8 @@ be written to a dump file.
 </P>
 <P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
 calculated by the fix is printed.  If <I>f_ID[N]</I> is used, then N must
-be in the range from 1-M, which will print the Nth component of the
+be in the range from 1-M, which will print the Nth column of the
-M-length per-atom vector calculated by the fix.
+M-length per-atom array calculated by the fix.
 </P>
 <P>The <I>v_name</I> keyword allows per-atom quantities calculated by a
 <A HREF = "variable.html">variable</A> to be output.  The name in the keyword should

doc/dump.txt

@@ -49,11 +49,11 @@ args = list of arguments for a particular style :l
       angmomx,angmomy,angmomz = angular momentum of extended particle
       quatw,quati,quatj,quatk = quaternion components for aspherical particles
       tqx,tqy,tqz = torque on extended particles
-      c_ID = per-atom scalar value calculated by a compute with ID
+      c_ID = per-atom vector value calculated by a compute with ID
-      c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID
+      c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
-      f_ID = per-atom scalar value calculated by a fix with ID
+      f_ID = per-atom vector value calculated by a fix with ID
-      f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
+      f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom value calculated by an atom-style variable with name :pre
+      v_name = per-atom vector calculated by an atom-style variable with name :pre
 :ule
 
 [Examples:]
@@ -321,8 +321,8 @@ custom"_thermo_style.html command.
 
 If {c_ID} is used as a keyword, then the scalar per-atom quantity
 calculated by the compute is printed.  If {c_ID\[N\]} is used, then N
-must be in the range from 1-M, which will print the Nth component of
+must be in the range from 1-M, which will print the Nth column of
-the M-length per-atom vector calculated by the compute.
+the M-length per-atom array calculated by the compute.
 
 The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom
 quantities calculated by a "fix"_fix.html to be output.  The ID in the
@@ -336,8 +336,8 @@ be written to a dump file.
 
 If {f_ID} is used as a keyword, then the scalar per-atom quantity
 calculated by the fix is printed.  If {f_ID\[N\]} is used, then N must
-be in the range from 1-M, which will print the Nth component of the
+be in the range from 1-M, which will print the Nth column of the
-M-length per-atom vector calculated by the fix.
+M-length per-atom array calculated by the fix.
 
 The {v_name} keyword allows per-atom quantities calculated by a
 "variable"_variable.html to be output.  The name in the keyword should

doc/fix.html

@@ -71,7 +71,7 @@ accessed by various commands for output, including <A HREF = "variable.html">equ
 atom-style variables</A>, <A HREF = "thermo_style.html">thermo_style
 custom</A>, and <A HREF = "fix_ave_time.html">fix ave/time</A>.
 </P>
-<P>Some fixes calculate a per-atom scalar or vector quantity which can be
+<P>Some fixes calculate a per-atom vector or array quantity which can be
 accessed by various commands for output, including <A HREF = "variable.html">atom-style
 variables</A>, <A HREF = "dump.html">dump_style custom</A>, and <A HREF = "fix_ave_spatial.html">fix
 ave/spatial</A>.

doc/fix.txt

@@ -68,7 +68,7 @@ accessed by various commands for output, including "equal- and
 atom-style variables"_variable.html, "thermo_style
 custom"_thermo_style.html, and "fix ave/time"_fix_ave_time.html.
 
-Some fixes calculate a per-atom scalar or vector quantity which can be
+Some fixes calculate a per-atom vector or array quantity which can be
 accessed by various commands for output, including "atom-style
 variables"_variable.html, "dump_style custom"_dump.html, and "fix
 ave/spatial"_fix_ave_spatial.html.

doc/fix_ave_atom.html

@@ -30,11 +30,11 @@
 <LI>value = x, y, z, xu, yu, zu, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name 
 
 <PRE>  x,y,z,xu,yu,zu,vx,vy,vz,fx,fy,fz = atom attribute (position, unwrapped position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  v_name = per-atom vector calculated by an atom-style variable with name 
 </PRE>
 
 </UL>
@@ -101,19 +101,19 @@ is meant by image flags.
 </P>
 <P>If a value begins with "c_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the compute is used.  If a
+appended, the per-atom vector calculated by the compute is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth columnd of the per-atom array
-by the compute is used.  Users can also write code for their own
+calculated by the compute is used.  Users can also write code for
-compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
 </P>
 <P>If a value begins with "f_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the fix is used.  If a
+appended, the per-atom vector calculated by the fix is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the fix is used.  Note that some fixes only produce their values on
+calculated by the fix is used.  Note that some fixes only produce
-certain timesteps, which must be compatible with <I>Nevery</I>, else an
+their values on certain timesteps, which must be compatible with
-error will results.  Users can also write code for their own fix
+<I>Nevery</I>, else an error will results.  Users can also write code for
-styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+their own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
 </P>
 <P>If a value begins with "v_", a variable name must follow which has
 been previously defined in the input script.  Variables of style
@@ -131,10 +131,10 @@ are relevant to this fix.  No global scalar or vector quantities are
 stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
 commands</A>.
 </P>
-<P>This fix produces a per-atom scalar or vector which can be accessed by
+<P>This fix produces a per-atom vector or array which can be accessed by
-various <A HREF = "Section_howto.html#4_15">output commands</A>.  A scalar is
+various <A HREF = "Section_howto.html#4_15">output commands</A>.  A vector is
 produced if only a single quantity is averaged by this fix.  If two or
-more quantities are averaged, then a vector of values is produced.
+more quantities are averaged, then an array of values is produced.
 The per-atom values can only be accessed on timesteps that are
 multiples of <I>Nfreq</I> since that is when averaging is performed.
 </P>

doc/fix_ave_atom.txt

@@ -20,11 +20,11 @@ Nfreq = timestep frequency at which the average value is calculated :l
 one or more values can be listed :l
 value = x, y, z, xu, yu, zu, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
   x,y,z,xu,yu,zu,vx,vy,vz,fx,fy,fz = atom attribute (position, unwrapped position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name :pre
+  v_name = per-atom vector calculated by an atom-style variable with name :pre
 :ule
 
 [Examples:]
@@ -90,19 +90,19 @@ is meant by image flags.
 
 If a value begins with "c_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the compute is used.  If a
+appended, the per-atom vector calculated by the compute is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth columnd of the per-atom array
-by the compute is used.  Users can also write code for their own
+calculated by the compute is used.  Users can also write code for
-compute styles and "add them to LAMMPS"_Section_modify.html.
+their own compute styles and "add them to LAMMPS"_Section_modify.html.
 
 If a value begins with "f_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the fix is used.  If a
+appended, the per-atom vector calculated by the fix is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the fix is used.  Note that some fixes only produce their values on
+calculated by the fix is used.  Note that some fixes only produce
-certain timesteps, which must be compatible with {Nevery}, else an
+their values on certain timesteps, which must be compatible with
-error will results.  Users can also write code for their own fix
+{Nevery}, else an error will results.  Users can also write code for
-styles and "add them to LAMMPS"_Section_modify.html.
+their own fix styles and "add them to LAMMPS"_Section_modify.html.
 
 If a value begins with "v_", a variable name must follow which has
 been previously defined in the input script.  Variables of style
@@ -120,10 +120,10 @@ are relevant to this fix.  No global scalar or vector quantities are
 stored by this fix for access by various "output
 commands"_Section_howto.html#4_15.
 
-This fix produces a per-atom scalar or vector which can be accessed by
+This fix produces a per-atom vector or array which can be accessed by
-various "output commands"_Section_howto.html#4_15.  A scalar is
+various "output commands"_Section_howto.html#4_15.  A vector is
 produced if only a single quantity is averaged by this fix.  If two or
-more quantities are averaged, then a vector of values is produced.
+more quantities are averaged, then an array of values is produced.
 The per-atom values can only be accessed on timesteps that are
 multiples of {Nfreq} since that is when averaging is performed.
 

doc/fix_ave_spatial.html

@@ -37,11 +37,11 @@
 
 <PRE>  x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
   density/number, density/mass = number or mass density
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  v_name = per-atom vector calculated by an atom-style variable with name 
 </PRE>
 <LI>zero or more keyword/arg pairs may be appended 
 
@@ -156,19 +156,19 @@ output.
 </P>
 <P>If a value begins with "c_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the compute is used.  If a
+appended, the per-atom vector calculated by the compute is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the compute is used.  Users can also write code for their own
+calculated by the compute is used.  Users can also write code for
-compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
+their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
 </P>
 <P>If a value begins with "f_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the fix is used.  If a
+appended, the per-atom vector calculated by the fix is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the fix is used.  Note that some fixes only produce their values on
+calculated by the fix is used.  Note that some fixes only produce
-certain timesteps, which must be compatible with <I>Nevery</I>, else an
+their values on certain timesteps, which must be compatible with
-error results.  Users can also write code for their own fix styles and
+<I>Nevery</I>, else an error results.  Users can also write code for their
-<A HREF = "Section_modify.html">add them to LAMMPS</A>.
+own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
 </P>
 <P>If a value begins with "v_", a variable name must follow which has
 been previously defined in the input script.  Variables of style

doc/fix_ave_spatial.txt

@@ -24,11 +24,11 @@ one or more values can be listed :l
 value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
   x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
   density/number, density/mass = number or mass density
-  c_ID = per-atom scalar value calculated by a compute with ID
+  c_ID = per-atom vector value calculated by a compute with ID
-  c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID
+  c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
+  f_ID = per-atom vector value calculated by a fix with ID
-  f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
+  f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name :pre
+  v_name = per-atom vector calculated by an atom-style variable with name :pre
 
 zero or more keyword/arg pairs may be appended :l
 keyword = {norm} or {units} or {file} or {ave} :l
@@ -140,19 +140,19 @@ output.
 
 If a value begins with "c_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the compute is used.  If a
+appended, the per-atom vector calculated by the compute is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the compute is used.  Users can also write code for their own
+calculated by the compute is used.  Users can also write code for
-compute styles and "add them to LAMMPS"_Section_modify.html.
+their own compute styles and "add them to LAMMPS"_Section_modify.html.
 
 If a value begins with "f_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
-appended, the per-atom scalar calculated by the fix is used.  If a
+appended, the per-atom vector calculated by the fix is used.  If a
-bracketed term is appended, the Nth vector per-atom value calculated
+bracketed term is appended, the Nth column of the per-atom array
-by the fix is used.  Note that some fixes only produce their values on
+calculated by the fix is used.  Note that some fixes only produce
-certain timesteps, which must be compatible with {Nevery}, else an
+their values on certain timesteps, which must be compatible with
-error results.  Users can also write code for their own fix styles and
+{Nevery}, else an error results.  Users can also write code for their
-"add them to LAMMPS"_Section_modify.html.
+own fix styles and "add them to LAMMPS"_Section_modify.html.
 
 If a value begins with "v_", a variable name must follow which has
 been previously defined in the input script.  Variables of style

doc/fix_coord_original.html

@@ -72,9 +72,9 @@ uninterrupted fashion.
 <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
+<P>This fix produces a per-atom array which can be accessed by various
-<A HREF = "Section_howto.html#4_15">output commands</A>.  The length of the vector
+<A HREF = "Section_howto.html#4_15">output commands</A>.  The number of columns
-for each atom is 3, and the components store the original unwrapped
+for each atom is 3, and the columns store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 </P>

doc/fix_coord_original.txt

@@ -64,9 +64,9 @@ 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
+This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#4_15.  The length of the vector
+"output commands"_Section_howto.html#4_15.  The number of columns
-for each atom is 3, and the components store the original unwrapped
+for each atom is 3, and the columns store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 

doc/fix_move.html

@@ -183,9 +183,9 @@ uninterrupted fashion.
 <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
+<P>This fix produces a per-atom array which can be accessed by various
-<A HREF = "Section_howto.html#4_15">output commands</A>.  The length of the vector
+<A HREF = "Section_howto.html#4_15">output commands</A>.  The number of columns
-for each atom is 3, and the components store the original unwrapped
+for each atom is 3, and the columns store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 </P>

doc/fix_move.txt

@@ -174,9 +174,9 @@ 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
+This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#4_15.  The length of the vector
+"output commands"_Section_howto.html#4_15.  The number of columns
-for each atom is 3, and the components store the original unwrapped
+for each atom is 3, and the columns store the original unwrapped
 x,y,z coords of each atom.  The per-atom values be accessed on any
 timestep.
 

doc/variable.html

@@ -342,8 +342,8 @@ compute.  N is a global atom ID (positive integer).
 <TR><TD >c_ID[2]</TD><TD > vector component of a global compute</TD></TR>
 <TR><TD >c_ID[N]</TD><TD > single atom's scalar value of a per-atom compute</TD></TR>
 <TR><TD >c_ID[N][M]</TD><TD > single atom's vector component of a per-atom compute</TD></TR>
-<TR><TD >c_ID[]</TD><TD > per-atom scalar from a per-atom compute</TD></TR>
+<TR><TD >c_ID[]</TD><TD > per-atom vector from a per-atom compute</TD></TR>
-<TR><TD >c_ID[][M]</TD><TD > per-atom vector component from a per-atom compute 
+<TR><TD >c_ID[][M]</TD><TD > column of per-atom array from a per-atom compute 
 </TD></TR></TABLE></DIV>
 
 <P>Fix references access one or more quantities calculated by a

doc/variable.txt

@@ -337,8 +337,8 @@ c_ID: scalar value of a global compute
 c_ID\[2\]: vector component of a global compute
 c_ID\[N\]: single atom's scalar value of a per-atom compute
 c_ID\[N\]\[M\]: single atom's vector component of a per-atom compute
-c_ID\[\]: per-atom scalar from a per-atom compute
+c_ID\[\]: per-atom vector from a per-atom compute
-c_ID\[\]\[M\]: per-atom vector component from a per-atom compute :tb(s=:)
+c_ID\[\]\[M\]: column of per-atom array from a per-atom compute :tb(s=:)
 
 Fix references access one or more quantities calculated by a
 "fix"_fix.html.  The ID in the reference should be replaced by the

lib/atc/ATC_Transfer.cpp

@@ -44,7 +44,7 @@ namespace ATC {
     scalarFlag_(0),
     vectorFlag_(0),
     sizeVector_(0),
-    scalarVectorFreq_(0),
+    globalFreq_(0),
     extScalar_(0),
     extVector_(0),
     extList_(NULL),

lib/atc/ATC_Transfer.h

@@ -201,7 +201,7 @@ namespace ATC {
     int scalar_flag() const {return scalarFlag_;}
     int vector_flag() const {return vectorFlag_;}
     int size_vector() const {return sizeVector_;}
-    int scalar_vector_freq() const {return scalarVectorFreq_;};
+    int global_freq() const {return globalFreq_;};
     int extscalar() const {return extScalar_;};
     int extvector() const {return extVector_;};
     int * extlist() {return extList_;};
@@ -716,7 +716,7 @@ namespace ATC {
     int scalarFlag_;              // 0/1 if compute_scalar() function exists
     int vectorFlag_;              // 0/1 if compute_vector() function exists
     int sizeVector_;              // N = size of global vector
-    int scalarVectorFreq_;        // frequency compute s/v data is available at
+    int globalFreq_;              // frequency global data is available at
     int extScalar_;               // 0/1 if scalar is intensive/extensive
     int extVector_;               // 0/1/-1 if vector is all int/ext/extlist
     int *extList_;                // list of 0/1 int/ext for each vec component

lib/atc/ATC_TransferThermal.cpp

@@ -43,7 +43,7 @@ namespace ATC {
     // output[2] = average temperature
     vectorFlag_ = 1;
     sizeVector_ = 2;
-    scalarVectorFreq_ = 1;
+    globalFreq_ = 1;
     extVector_ = 1;
     if (extrinsicModel != NO_MODEL)
       sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);

lib/atc/LammpsInterface.cpp

@@ -557,7 +557,7 @@ double**  LammpsInterface::compute_vector_data(const char* tag)
     cmpt->compute_peratom();
     cmpt->invoked_flag |= INVOKED_PERATOM;
   }
-  return cmpt->vector_atom;
+  return cmpt->array_atom;
 }
 
 double*  LammpsInterface::compute_scalar_data(const char* tag) 
@@ -567,13 +567,13 @@ double*  LammpsInterface::compute_scalar_data(const char* tag)
     cmpt->compute_peratom();
     cmpt->invoked_flag |= INVOKED_PERATOM;
   }
-  return cmpt->scalar_atom;
+  return cmpt->vector_atom;
 }
 
 int  LammpsInterface::compute_ncols(const char* tag) 
 {
   int icompute = find_compute(tag);
-  int ncols = lammps_->modify->compute[icompute]->size_peratom;
+  int ncols = lammps_->modify->compute[icompute]->size_peratom_cols;
   if (ncols == 0) ncols = 1; // oddity of lammps, used as flag for scalar
   return ncols;
 }
@@ -615,7 +615,7 @@ double * LammpsInterface::atomPE_compute(void)
 {
   if (atomPE_) {
     atomPE_->compute_peratom();
-    return atomPE_->scalar_atom;
+    return atomPE_->vector_atom;
   }
   else {
     return NULL;