jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1105 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-10-26 20:42:35 +00:00
parent 189ad3f05e
commit 15f0990332
18 changed files with 191 additions and 55 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
doc/Section_commands.html
View File

@ -334,9 +334,9 @@ description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ebond_atom.html">ebond/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

1
doc/Section_commands.txt
View File

@ -448,6 +448,7 @@ description:
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"sum"_compute_sum.html,
"sum/atom"_compute_sum_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,

30
doc/Section_howto.html
View File

@ -827,12 +827,15 @@ these are described in turn.
</P>
<P>In LAMMPS, a <A HREF = "compute.html">compute</A> comes in two flavors: ones that
compute one or more global values (e.g. temperature, kinetic energy
tensor) and ones that compute one or more per-atom values. Only the
former can be used for thermodynamic output. The user-defined ID of
the compute is used along with an optional subscript as part of the
<A HREF = "thermo_style.html">thermo_style</A> command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp[2] would
output the 2nd vector value.
tensor) and ones that compute one or more per-atom values. There is a
<A HREF = "compute_sum.html">compute sum</A> command which sums per-atom quantities
into a global scalar or vector.
</P>
<P>Only global quantities from a compute can be used for thermodynamic
output. The user-defined ID of the compute is used along with an
optional subscript as part of the <A HREF = "thermo_style.html">thermo_style</A>
command. E.g. c_myTemp outputs the single scalar value generated by
the compute; c_myTemp[2] would output the 2nd vector value.
</P>
<P><A HREF = "fix.html">Fixes</A> can also generate global scalar or vector values
which can be output with thermodynamic output, e.g. the energy of an
@ -896,13 +899,14 @@ and <A HREF = "fix_print.html">fix print</A>.
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
compute or fix must generate global scalar or vector quantities. The
time-averaged values generated by <A HREF = "fix_ave_time.html">fix ave/time</A> can
be written directly to a file and/or accessed by any output command
that uses fixes as a source of input, e.g. the <A HREF = "thermo_style.html">thermo_style
custom</A> command. Fix ave/time options allow for
running cummulative averages or moving time-windowed averages to be
output.
compute or fix must generate global scalar or vector quantities. Note
that this includes the "compute sum" command which computes global
values by summing per-atom quantities. The time-averaged values
generated by <A HREF = "fix_ave_time.html">fix ave/time</A> can be written directly
to a file and/or accessed by any output command that uses fixes as a
source of input, e.g. the <A HREF = "thermo_style.html">thermo_style custom</A>
command. Fix ave/time options allow for running cummulative averages
or moving time-windowed averages to be output.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
spatial-averaging of per-atom quantities like per-atom energy or

30
doc/Section_howto.txt
View File

@ -820,12 +820,15 @@ these are described in turn.
In LAMMPS, a "compute"_compute.html comes in two flavors: ones that
compute one or more global values (e.g. temperature, kinetic energy
tensor) and ones that compute one or more per-atom values. Only the
former can be used for thermodynamic output. The user-defined ID of
the compute is used along with an optional subscript as part of the
"thermo_style"_thermo_style.html command. E.g. c_myTemp outputs the
single scalar value generated by the compute; c_myTemp\[2\] would
output the 2nd vector value.
tensor) and ones that compute one or more per-atom values. There is a
"compute sum"_compute_sum.html command which sums per-atom quantities
into a global scalar or vector.
Only global quantities from a compute can be used for thermodynamic
output. The user-defined ID of the compute is used along with an
optional subscript as part of the "thermo_style"_thermo_style.html
command. E.g. c_myTemp outputs the single scalar value generated by
the compute; c_myTemp\[2\] would output the 2nd vector value.
"Fixes"_fix.html can also generate global scalar or vector values
which can be output with thermodynamic output, e.g. the energy of an
@ -889,13 +892,14 @@ and "fix print"_fix_print.html.
The "fix ave/time"_fix_ave_time.html command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a "compute"_compute.html or a "fix"_fix.html. The
compute or fix must generate global scalar or vector quantities. The
time-averaged values generated by "fix ave/time"_fix_ave_time.html can
be written directly to a file and/or accessed by any output command
that uses fixes as a source of input, e.g. the "thermo_style
custom"_thermo_style.html command. Fix ave/time options allow for
running cummulative averages or moving time-windowed averages to be
output.
compute or fix must generate global scalar or vector quantities. Note
that this includes the "compute sum" command which computes global
values by summing per-atom quantities. The time-averaged values
generated by "fix ave/time"_fix_ave_time.html can be written directly
to a file and/or accessed by any output command that uses fixes as a
source of input, e.g. the "thermo_style custom"_thermo_style.html
command. Fix ave/time options allow for running cummulative averages
or moving time-windowed averages to be output.
The "fix ave/spatial"_fix_ave_spatial.html command enables
spatial-averaging of per-atom quantities like per-atom energy or

7
doc/compute.html
View File

@ -96,7 +96,8 @@ defined in LAMMPS:
<LI><A HREF = "compute_rotate_dipole.html">rotate/dipole</A> - rotational energy of dipolar atoms
<LI><A HREF = "compute_rotate_gran.html">rotate/gran</A> - rotational energy of granular atoms
<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
<LI><A HREF = "compute_sum_atom.html">sum/atom</A> - sum 2 or more quantities for each atom
<LI><A HREF = "compute_sum.html">sum</A> - sum per-atom quantities to a global value
<LI><A HREF = "compute_sum_atom.html">sum/atom</A> - sum per-atom quantities to per-atom values
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
@ -116,7 +117,9 @@ page</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>
<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
<A HREF = "fix_ave_time.html">fix ave/time</A>
</P>
<P><B>Default:</B> none
</P>

7
doc/compute.txt
View File

@ -93,7 +93,8 @@ defined in LAMMPS:
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"sum/atom"_compute_sum_atom.html - sum 2 or more quantities for each atom
"sum"_compute_sum.html - sum per-atom quantities to a global value
"sum/atom"_compute_sum_atom.html - sum per-atom quantities to per-atom values
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
@ -113,6 +114,8 @@ page"_Section_commands.html#3_5.
[Related commands:]
"uncompute"_uncompute.html, "compute_modify"_compute_modify.html
"uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix
ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
"fix ave/time"_fix_ave_time.html
[Default:] none

53
doc/compute_sum.html Normal file
View File

@ -0,0 +1,53 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute sum command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID sum compute-ID1 compute-ID2 ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>sum/ = style name of this compute command
<LI>compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all sum c_force
compute 1 all sum atomKE atomEpair atomEbond
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that sums the results of one or more per-atom
computes across all atoms in the group to yield a global scalar or
vector quantity. For example, the forces on a group of atoms could be
summed to yield a net force on the group. The resulting value(s) can
be accessed by any command that uses global computes, e.g. the <A HREF = "therml_style.html">thermo
custom</A> command or <A HREF = "fix_ave_time.html">fix ave/time</A>
command or by a <A HREF = "variable.html">variable</A> command.
</P>
<P>Unlike the "compute sum/atom" command, the result of this is not a
per-atom quantity, but a global scalar or vector. If the other
computes each generate a scalar value per atom, this compute will
generate a single scalar value. If the other computes each generate a
vector of values per atom, this compute will generate a vector of
values. In the latter case, all the other computes must generate
vectors of the same size.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_sum_atom.html">compute sum/atom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

48
doc/compute_sum.txt Normal file
View File

@ -0,0 +1,48 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute sum command :h3
[Syntax:]
compute ID group-ID sum compute-ID1 compute-ID2 ... :pre
ID, group-ID are documented in "compute"_compute.html command
sum/ = style name of this compute command
compute-ID1, 2, ... = IDs of computes that calculate per-atom quantities :ul
[Examples:]
compute 1 all sum c_force
compute 1 all sum atomKE atomEpair atomEbond :pre
[Description:]
Define a computation that sums the results of one or more per-atom
computes across all atoms in the group to yield a global scalar or
vector quantity. For example, the forces on a group of atoms could be
summed to yield a net force on the group. The resulting value(s) can
be accessed by any command that uses global computes, e.g. the "thermo
custom"_therml_style.html command or "fix ave/time"_fix_ave_time.html
command or by a "variable"_variable.html command.
Unlike the "compute sum/atom" command, the result of this is not a
per-atom quantity, but a global scalar or vector. If the other
computes each generate a scalar value per atom, this compute will
generate a single scalar value. If the other computes each generate a
vector of values per atom, this compute will generate a vector of
values. In the latter case, all the other computes must generate
vectors of the same size.
[Restrictions:] none
[Related commands:]
"compute sum/atom"_compute_sum_atom.html
[Default:] none

4
doc/compute_sum_atom.html
View File

@ -42,7 +42,9 @@ vectors of the same size.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_sum.html">compute sum</A>
</P>
<P><B>Default:</B> none
</P>

4
doc/compute_sum_atom.txt
View File

@ -39,6 +39,8 @@ vectors of the same size.
[Restrictions:] none
[Related commands:] none
[Related commands:]
"compute sum"_compute_sum.html
[Default:] none

2
doc/fix.html
View File

@ -97,7 +97,7 @@ for individual fixes for info on which ones can be restarted.
<LI><A HREF = "fix_gran_diag.html">gran/diag</A> - compute granular diagnostics
<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
<LI><A HREF = "fix_gyration.html">gyration</A> - compute radius of gyration
<LI><A HREF = "fix_gyration.html">heat</A> - add/subtract momentum-conserving heat
<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
<LI><A HREF = "fix_indent.html">indent</A> - impose force due to an indenter
<LI><A HREF = "fix_langevin.html">langevin</A> - Langevin temperature control
<LI><A HREF = "fix_lineforce.html">lineforce</A> - constrain atoms to move in a line

2
doc/fix.txt
View File

@ -94,7 +94,7 @@ Here is an alphabetic list of fix styles available in LAMMPS:
"gran/diag"_fix_gran_diag.html - compute granular diagnostics
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"gyration"_fix_gyration.html - compute radius of gyration
"heat"_fix_gyration.html - add/subtract momentum-conserving heat
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"indent"_fix_indent.html - impose force due to an indenter
"langevin"_fix_langevin.html - Langevin temperature control
"lineforce"_fix_lineforce.html - constrain atoms to move in a line

15
doc/fix_ave_time.html
View File

@ -71,12 +71,15 @@ ave/time command is ignored.
<P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which
calculates the desired property. The compute must be a "global"
compute that calculates one or more global properties rather than a
"per-atom" compute. The compute must be previously defined in the
input script. Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. Users
can write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
"per-atom" compute. However, there is a <A HREF = "compute_sum.html">compute
sum</A> command which sums per-atom quantities into a
global scalar or vector which can be accessed by fix ave/time.
</P>
<P>The compute must be previously defined in the input script. Or it can
be a compute defined by <A HREF = "thermo_style.html">thermodynamic output</A> or
other fixes such as <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>. Users can write code for their
own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
</P>
<P>For style <I>fix</I> the <I>ID</I> specifies a <A HREF = "fix.html">fix</A> which calculates
the desired property. The fix must calculate a global scalar or

15
doc/fix_ave_time.txt
View File

@ -59,12 +59,15 @@ ave/time command is ignored.
For style {compute} the {ID} specifies a "compute"_compute.html which
calculates the desired property. The compute must be a "global"
compute that calculates one or more global properties rather than a
"per-atom" compute. The compute must be previously defined in the
input script. Or it can be a compute defined by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users
can write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
"per-atom" compute. However, there is a "compute
sum"_compute_sum.html command which sums per-atom quantities into a
global scalar or vector which can be accessed by fix ave/time.
The compute must be previously defined in the input script. Or it can
be a compute defined by "thermodynamic output"_thermo_style.html or
other fixes such as "fix nvt"_fix_nvt.html or "fix
temp/rescale"_fix_temp_rescale.html. Users can write code for their
own compute styles and "add them to LAMMPS"_Section_modify.html.
For style {fix} the {ID} specifies a "fix"_fix.html which calculates
the desired property. The fix must calculate a global scalar or

7
doc/thermo_style.html
View File

@ -204,9 +204,12 @@ quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
<A HREF = "compute.html">compute</A> command for details. Note that only global
scalar or vector quantites calculated by a compute can be output as
scalar or vector quantities calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the <A HREF = "dump.html">dump custom</A> command.
output by the <A HREF = "dump.html">dump custom</A> command. However, there is a
<A HREF = "compute_sum.html">compute sum</A> command which sums per-atom quantities
into a global scalar or vector which can be output by thermo_style
custom.
</P>
<P>Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like

7
doc/thermo_style.txt
View File

@ -198,9 +198,12 @@ quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
"compute"_compute.html command for details. Note that only global
scalar or vector quantites calculated by a compute can be output as
scalar or vector quantities calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the "dump custom"_dump.html command.
output by the "dump custom"_dump.html command. However, there is a
"compute sum"_compute_sum.html command which sums per-atom quantities
into a global scalar or vector which can be output by thermo_style
custom.
Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like

4
doc/variable.html
View File

@ -251,7 +251,9 @@ variable.
the actual ID of the compute defined elsewhere in the input script.
See the <A HREF = "compute.html">compute</A> command for details. Note that
per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities.
way, but only global scalar or vector quantities. However, there is a
<A HREF = "compute_sum.html">compute sum</A> command which sums per-atom quantities
into a global scalar or vector which can be accessed by a variable.
</P>
<P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity
calculated by the compute is used. If <I>c_ID[N]</I> is used, then one

4
doc/variable.txt
View File

@ -249,7 +249,9 @@ Compute references access scalar or vector quantities calculated by a
the actual ID of the compute defined elsewhere in the input script.
See the "compute"_compute.html command for details. Note that
per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities.
way, but only global scalar or vector quantities. However, there is a
"compute sum"_compute_sum.html command which sums per-atom quantities
into a global scalar or vector which can be accessed by a variable.
If {c_ID\[0\]} is used as a keyword, then the scalar quantity
calculated by the compute is used. If {c_ID\[N\]} is used, then one