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

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2009-12-04 21:04:00 +00:00
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14
doc/Section_howto.html
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@ -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/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/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 > 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 >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 >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 > 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>

14
doc/Section_howto.txt
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@ -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/atom: peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector: nevery: peratom scalar/vector: nfreq
fix ave/spatial: per-atom fix, per-atom compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file
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
compute sum: peratom scalar/vector compute, peratom scalar/vector fix, atom variable: N/A: global scalar/vector: N/A
per-atom computes: N/A: N/A: per-atom vector/array: 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=:)

10
doc/compute.html
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@ -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
custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command. Or the per-atom values can
be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command and
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
<P>The results of per-atom computes that calculate a per-atom vector or
array can be output via the <A HREF = "dump.html">dump custom</A> command or the
<A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command. Or the per-atom
values can be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A>
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

10
doc/compute.txt
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@ -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
custom"_dump.html command or the "fix
ave/spatial"_fix_ave_spatial.html command. Or the per-atom values can
be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
then output via the "dump custom"_dump.html or "fix
The results of per-atom computes that calculate a per-atom vector or
array can be output via the "dump custom"_dump.html command or the
"fix ave/spatial"_fix_ave_spatial.html command. Or the per-atom
values can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
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

8
doc/compute_centro_atom.html
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B> none
</P>

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doc/compute_centro_atom.txt
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:] none

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

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doc/compute_cna_atom.txt
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:] none

8
doc/compute_coord_atom.html
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B> none
</P>

8
doc/compute_coord_atom.txt
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:] none

8
doc/compute_damage_atom.html
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B>
</P>

8
doc/compute_damage_atom.txt
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@ -32,10 +32,10 @@ compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:]

8
doc/compute_displace_atom.html
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@ -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
be accessed by indices 1-4 by any command that uses per-atom values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
<P>This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

8
doc/compute_displace_atom.txt
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@ -71,10 +71,10 @@ file.
[Output info:]
This compute calculates a vector of length 4 for each atom, which can
be accessed by indices 1-4 by any command that uses per-atom values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See "this section"_Section_howto.html#4_15 for an
overview of LAMMPS output options.
[Restrictions:] none

8
doc/compute_ke_atom.html
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B> none
</P>

8
doc/compute_ke_atom.txt
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@ -32,10 +32,10 @@ specified compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:] none

8
doc/compute_pe_atom.html
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@ -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
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P><B>Restrictions:</B>
</P>

8
doc/compute_pe_atom.txt
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@ -62,10 +62,10 @@ contribution can easily be computed.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
output options.
[Restrictions:]

10
doc/compute_reduce.html
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@ -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[N] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name
c_ID = per-atom vector value 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 vector value 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 vector calculated by an atom-style variable with name
</PRE>
</UL>

10
doc/compute_reduce.txt
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@ -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\[N\] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name :pre
c_ID = per-atom vector value 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 vector value 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 vector calculated by an atom-style variable with name :pre
:ule
[Examples:]

8
doc/compute_stress_atom.html
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@ -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
be accessed by indices 1-6 by any command that uses per-atom values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
<P>This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

8
doc/compute_stress_atom.txt
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@ -97,10 +97,10 @@ contribution can easily be computed.
[Output info:]
This compute calculates a vector of length 6 for each atom, which can
be accessed by indices 1-6 by any command that uses per-atom values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See "this section"_Section_howto.html#4_15 for an
overview of LAMMPS output options.
[Restrictions:] none

18
doc/dump.html
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@ -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[N] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name
c_ID = per-atom vector value 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 vector value 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 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
the M-length per-atom vector calculated by the compute.
must be in the range from 1-M, which will print the Nth column of
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
M-length per-atom vector calculated by the fix.
be in the range from 1-M, which will print the Nth column of the
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

18
doc/dump.txt
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@ -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\[N\] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name :pre
c_ID = per-atom vector value 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 vector value 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 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
the M-length per-atom vector calculated by the compute.
must be in the range from 1-M, which will print the Nth column of
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
M-length per-atom vector calculated by the fix.
be in the range from 1-M, which will print the Nth column of the
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

2
doc/fix.html
View File

@ -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>.

2
doc/fix.txt
View File

@ -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.

36
doc/fix_ave_atom.html
View File

@ -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[N] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name
c_ID = per-atom vector value 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 vector value 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 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
bracketed term is appended, the Nth vector per-atom value calculated
by the compute is used. Users can also write code for their own
compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
appended, the per-atom vector calculated by the compute is used. If a
bracketed term is appended, the Nth columnd of the per-atom array
calculated by the compute is used. Users can also write code for
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
bracketed term is appended, the Nth vector per-atom value calculated
by the fix is used. Note that some fixes only produce their values on
certain timesteps, which must be compatible with <I>Nevery</I>, else an
error will results. Users can also write code for their own fix
styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
appended, the per-atom vector calculated by the fix is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
<I>Nevery</I>, else an error will results. Users can also write code for
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
various <A HREF = "Section_howto.html#4_15">output commands</A>. A scalar is
<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 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>

36
doc/fix_ave_atom.txt
View File

@ -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\[N\] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name :pre
c_ID = per-atom vector value 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 vector value 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 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
bracketed term is appended, the Nth vector per-atom value calculated
by the compute is used. Users can also write code for their own
compute styles and "add them to LAMMPS"_Section_modify.html.
appended, the per-atom vector calculated by the compute is used. If a
bracketed term is appended, the Nth columnd of the per-atom array
calculated by the compute is used. Users can also write code for
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
bracketed term is appended, the Nth vector per-atom value calculated
by the fix is used. Note that some fixes only produce their values on
certain timesteps, which must be compatible with {Nevery}, else an
error will results. Users can also write code for their own fix
styles and "add them to LAMMPS"_Section_modify.html.
appended, the per-atom vector calculated by the fix is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
{Nevery}, else an error will results. Users can also write code for
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
various "output commands"_Section_howto.html#4_15. A scalar is
This fix produces a per-atom vector or array which can be accessed by
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.

30
doc/fix_ave_spatial.html
View File

@ -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[N] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name
c_ID = per-atom vector value 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 vector value 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 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
bracketed term is appended, the Nth vector per-atom value calculated
by the compute is used. Users can also write code for their own
compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
appended, the per-atom vector calculated by the compute is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the compute is used. Users can also write code for
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
bracketed term is appended, the Nth vector per-atom value calculated
by the fix is used. Note that some fixes only produce their values on
certain timesteps, which must be compatible with <I>Nevery</I>, else an
error results. Users can also write code for their own fix styles and
<A HREF = "Section_modify.html">add them to LAMMPS</A>.
appended, the per-atom vector calculated by the fix is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
<I>Nevery</I>, else an error results. Users can also write code for 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

30
doc/fix_ave_spatial.txt
View File

@ -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\[N\] = Nth component of per-atom vector calculated by a compute with ID
f_ID = per-atom scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID
v_name = per-atom value calculated by an atom-style variable with name :pre
c_ID = per-atom vector value 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 vector value 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 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
bracketed term is appended, the Nth vector per-atom value calculated
by the compute is used. Users can also write code for their own
compute styles and "add them to LAMMPS"_Section_modify.html.
appended, the per-atom vector calculated by the compute is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the compute is used. Users can also write code for
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
bracketed term is appended, the Nth vector per-atom value calculated
by the fix is used. Note that some fixes only produce their values on
certain timesteps, which must be compatible with {Nevery}, else an
error results. Users can also write code for their own fix styles and
"add them to LAMMPS"_Section_modify.html.
appended, the per-atom vector calculated by the fix is used. If a
bracketed term is appended, the Nth column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
{Nevery}, else an error results. Users can also write code for 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

6
doc/fix_coord_original.html
View File

@ -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
<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 original unwrapped
<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 number of columns
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>

6
doc/fix_coord_original.txt
View File

@ -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
"output commands"_Section_howto.html#4_15. The length of the vector
for each atom is 3, and the components store the original unwrapped
This fix produces a per-atom array which can be accessed by various
"output commands"_Section_howto.html#4_15. The number of columns
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.

6
doc/fix_move.html
View File

@ -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
<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 original unwrapped
<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 number of columns
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>

6
doc/fix_move.txt
View File

@ -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
"output commands"_Section_howto.html#4_15. The length of the vector
for each atom is 3, and the components store the original unwrapped
This fix produces a per-atom array which can be accessed by various
"output commands"_Section_howto.html#4_15. The number of columns
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.

4
doc/variable.html
View File

@ -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[][M]</TD><TD > per-atom vector component from a per-atom compute
<TR><TD >c_ID[]</TD><TD > per-atom vector from a per-atom compute</TD></TR>
<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

4
doc/variable.txt
View File

@ -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\[\]\[M\]: per-atom vector component from a per-atom compute :tb(s=:)
c_ID\[\]: per-atom vector from a per-atom compute
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

2
lib/atc/ATC_Transfer.cpp
View File

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

4
lib/atc/ATC_Transfer.h
View File

@ -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

2
lib/atc/ATC_TransferThermal.cpp
View File

@ -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_);

8
lib/atc/LammpsInterface.cpp
View File

@ -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;