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@1111 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-11-01 16:46:50 +00:00
parent 8779ea9807
commit 05ccdfc151
14 changed files with 249 additions and 41 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.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>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><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

@ -444,6 +444,7 @@ description:
"ebond/atom"_compute_ebond_atom.html,
"epair/atom"_compute_epair_atom.html,
"ke/atom"_compute_ke_atom.html,
"pe"_compute_pe.html,
"pressure"_compute_pressure.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,

11
doc/compute.html
View File

@ -53,12 +53,14 @@ ave/spatial</A> commands.
<P>See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
various LAMMPS output options.
</P>
<P>LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
<P>LAMMPS creates its own global computes for thermodynamic output.
Three computes are always created, named "thermo_temp",
"thermo_pressure", and"thermo_pe", as if these commands had been
invoked in the input script:
</P>
<PRE>compute thermo_temp all temp
compute thermo_pressure all pressure thermo_temp
compute thermo_pressure all pressure thermo_temp
compute thermo_pe all pe
</PRE>
<P>Additional computes are created if the thermo style requires it. See
the documentation for the <A HREF = "thermo_style.html">thermo_style</A> command.
@ -92,6 +94,7 @@ defined in LAMMPS:
<LI><A HREF = "compute_ebond_atom.html">ebond/atom</A> - bond energy for each atom
<LI><A HREF = "compute_epair_atom.html">epair/atom</A> - pairwise energy for each atom
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
<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

11
doc/compute.txt
View File

@ -50,12 +50,14 @@ ave/spatial"_fix_ave_spatial.html commands.
See this "howto section"_Section_howto.html#4_15 for a summary of
various LAMMPS output options.
LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
LAMMPS creates its own global computes for thermodynamic output.
Three computes are always created, named "thermo_temp",
"thermo_pressure", and"thermo_pe", as if these commands had been
invoked in the input script:
compute thermo_temp all temp
compute thermo_pressure all pressure thermo_temp :pre
compute thermo_pressure all pressure thermo_temp
compute thermo_pe all pe :pre
Additional computes are created if the thermo style requires it. See
the documentation for the "thermo_style"_thermo_style.html command.
@ -89,6 +91,7 @@ defined in LAMMPS:
"ebond/atom"_compute_ebond_atom.html - bond energy for each atom
"epair/atom"_compute_epair_atom.html - pairwise energy for each atom
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"pe"_compute_pe.html - potential energy
"pressure"_compute_pressure.html - total pressure and pressure tensor
"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms
"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms

14
doc/compute_modify.html
View File

@ -24,7 +24,9 @@
<PRE> <I>extra</I> value = N
N = # of extra degrees of freedom to subtract
<I>dynamic</I> value = <I>yes</I> or <I>no</I>
yes/no = do or do not recompute the number of atoms contributing to the temperature
yes/no = do or do not recompute the number of atoms contributing to the temperature
<I>thermo</I> value = <I>yes</I> or <I>no</I>
yes/no = do or do not add contributions from fixes to the potential energy
</PRE>
</UL>
@ -53,6 +55,12 @@ deposit</A> commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
</P>
<P>The <I>thermo</I> keyword determines whether the potential energy
contribution calculated by some <A HREF = "fix.html">fixes</A> is added to the
potential energy calculated by the compute. Only the compute of style
<I>pe</I> uses this option. See the doc pages for <A HREF = "fix.html">individual
fixes</A> for details.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@ -61,6 +69,8 @@ temperature is correctly normalized.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are extra = 3 and dynamic = no.
<P>The option defaults are extra = 3 and dynamic = no. Thermo is <I>yes</I> if
the compute of style <I>pe</I> was defined with no extra keywords; otherwise
it is <I>no</I>.
</P>
</HTML>

14
doc/compute_modify.txt
View File

@ -18,7 +18,9 @@ keyword = {extra} or {dynamic} :l
{extra} value = N
N = # of extra degrees of freedom to subtract
{dynamic} value = {yes} or {no}
yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
yes/no = do or do not recompute the number of atoms contributing to the temperature
{thermo} value = {yes} or {no}
yes/no = do or do not add contributions from fixes to the potential energy :pre
:ule
[Examples:]
@ -46,6 +48,12 @@ deposit"_fix_deposit.html commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
The {thermo} keyword determines whether the potential energy
contribution calculated by some "fixes"_fix.html is added to the
potential energy calculated by the compute. Only the compute of style
{pe} uses this option. See the doc pages for "individual
fixes"_fix.html for details.
[Restrictions:] none
[Related commands:]
@ -54,4 +62,6 @@ temperature is correctly normalized.
[Default:]
The option defaults are extra = 3 and dynamic = no.
The option defaults are extra = 3 and dynamic = no. Thermo is {yes} if
the compute of style {pe} was defined with no extra keywords; otherwise
it is {no}.

64
doc/compute_pe.html Normal file
View File

@ -0,0 +1,64 @@
<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 pe command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pe keyword ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pe = style name of this compute command
<LI>zero of more keywords may be appended
<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pe
compute molPE all bond angle dihedral improper
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all". See the
<A HREF = "compute_epair_atom.html">compute epair/atom</A> <A HREF = "compute_ebond_atom.html">compute
ebond/atom</A> or commands if you want per-atom
energies. These per-atom values could be summed for a group of atoms
via the <A HREF = "compute_sum.html">compute sum</A> command.
</P>
<P>The energy is calulated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
</P>
<P>Various fixes can contribute to the total potential energy of the
system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
details. The <I>thermo</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command determines whether these
contributions are added into the computed potential energy. If no
keywords are specified the default is <I>yes</I>. If any keywords are
specified, the default is <I>no</I>.
</P>
<P>A compute of this style with the ID of "thermo_pe" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_pe all pe
</PRE>
<P>See the "thermo_style" command for more details.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

59
doc/compute_pe.txt Normal file
View File

@ -0,0 +1,59 @@
"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 pe command :h3
[Syntax:]
compute ID group-ID pe keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
pe = style name of this compute command
zero of more keywords may be appended
keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
[Examples:]
compute 1 all pe
compute molPE all bond angle dihedral improper :pre
[Description:]
Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all". See the
"compute epair/atom"_compute_epair_atom.html "compute
ebond/atom"_compute_ebond_atom.html or commands if you want per-atom
energies. These per-atom values could be summed for a group of atoms
via the "compute sum"_compute_sum.html command.
The energy is calulated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
Various fixes can contribute to the total potential energy of the
system. See the doc pages for "individual fixes"_fix.html for
details. The {thermo} option of the
"compute_modify"_compute_modify.html command determines whether these
contributions are added into the computed potential energy. If no
keywords are specified the default is {yes}. If any keywords are
specified, the default is {no}.
A compute of this style with the ID of "thermo_pe" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_pe all pe :pre
See the "thermo_style" command for more details.
[Restrictions:] none
[Related commands:] none
[Default:] none

20
doc/compute_pressure.html
View File

@ -25,13 +25,13 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the pressure of atoms averaged
over the entire system. The specified group must be "all". See the
<A HREF = "dump.html">dump custom</A> command for how to dump the per-atom stress
tensor if you want more localized information about pressure (stress)
in your system.
<P>Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all". See the <A HREF = "compute_stress_atom.html">compute
stress/atom</A> command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the <A HREF = "compute_sum.html">compute sum</A> command.
</P>
<P>The pressure is computed by the standard formula
<P>The pressure is computed by the formula
</P>
<CENTER><IMG SRC = "Eqs/pressure.jpg">
</CENTER>
@ -62,6 +62,14 @@ excludes frozen atoms or other degrees of freedom.
where the DOF is specified by the temperature compute. See the
various <A HREF = "compute.html">compute temperature</A> styles for details.
</P>
<P>A compute of this style with the ID of "thermo_press" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_press all pressure thermo_temp
</PRE>
<P>where "thermo_temp" is the ID of a similarly defined compute of style
"temp". See the "thermo_style" command for more details.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

20
doc/compute_pressure.txt
View File

@ -22,13 +22,13 @@ compute 1 all pressure myTemp :pre
[Description:]
Define a computation that calculates the pressure of atoms averaged
over the entire system. The specified group must be "all". See the
"dump custom"_dump.html command for how to dump the per-atom stress
tensor if you want more localized information about pressure (stress)
in your system.
Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all". See the "compute
stress/atom"_compute_stress_atom.html command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the "compute sum"_compute_sum.html command.
The pressure is computed by the standard formula
The pressure is computed by the formula
:c,image(Eqs/pressure.jpg)
@ -59,6 +59,14 @@ Note that the N is the above formula is really degrees-of-freedom/d
where the DOF is specified by the temperature compute. See the
various "compute temperature"_compute.html styles for details.
A compute of this style with the ID of "thermo_press" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_press all pressure thermo_temp :pre
where "thermo_temp" is the ID of a similarly defined compute of style
"temp". See the "thermo_style" command for more details.
[Restrictions:] none
[Related commands:]

7
doc/compute_temp.html
View File

@ -51,6 +51,13 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>A compute of this style with the ID of "thermo_temp" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_temp all temp
</PRE>
<P>See the "thermo_style" command for more details.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

7
doc/compute_temp.txt
View File

@ -48,6 +48,13 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
A compute of this style with the ID of "thermo_temp" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_temp all temp :pre
See the "thermo_style" command for more details.
[Restrictions:] none
[Related commands:]

28
doc/thermo_style.html
View File

@ -123,7 +123,7 @@ use the thermo_modify command after it.
<P>Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
default this is done by using the "thermo_temp" compute which is
created by LAMMPS as if this command had been issued:
created when LAMMPS starts up, as if this command had been issued:
</P>
<PRE>compute thermo_temp all temp
</PRE>
@ -137,9 +137,9 @@ calculating any thermodynamic quantity that requires a temperature.
This is done via the <A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". By default this is
done by using the "thermo_pressure" compute which is created by LAMMPS
as if this command had been issued:
computed: "press", "enthalpy", "pxx", etc. By default this is done by
using the "thermo_pressure" compute which is created when LAMMPS
starts up, as if this command had been issued:
</P>
<PRE>compute thermo_pressure all pressure thermo_temp
</PRE>
@ -152,6 +152,18 @@ have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
<A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>Several of the thermodynamic quantities require a potential energy to
be computed: "pe", "etotal", "ebond", etc. This is done by using the
"thermo_pe" compute which is created when LAMMPS starts up, as if this
command had been issued:
</P>
<PRE>compute thermo_pe all pe
</PRE>
<P>See the <A HREF = "compute_pe.html">compute pe</A> command for details. Note that
the ID of this compute is <I>thermo_pe</I> and the group is <I>all</I>. You can
change the attributes of this potential energy via the
<A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>The <I>drot</I> keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
@ -186,9 +198,11 @@ be useful if you wish to exclude frozen particles from the compuation.
<HR>
<P>The potential energy of the system <I>pe</I> will include contributions
from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option was set
for each fix. For example, the <A HREF = "fix_wall_lj93">fix wall/lj93</A> fix will
contribute the energy of atoms interacting with the wall.
from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall_lj93">fix
wall/lj93</A> fix calculates the energy of atoms
interacting with the wall. See the doc pages for "individual fixes"
to see which ones contribute.
</P>
<P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify

28
doc/thermo_style.txt
View File

@ -117,7 +117,7 @@ use the thermo_modify command after it.
Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
default this is done by using the "thermo_temp" compute which is
created by LAMMPS as if this command had been issued:
created when LAMMPS starts up, as if this command had been issued:
compute thermo_temp all temp :pre
@ -131,9 +131,9 @@ calculating any thermodynamic quantity that requires a temperature.
This is done via the "thermo_modify"_thermo_modify.html command.
Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". By default this is
done by using the "thermo_pressure" compute which is created by LAMMPS
as if this command had been issued:
computed: "press", "enthalpy", "pxx", etc. By default this is done by
using the "thermo_pressure" compute which is created when LAMMPS
starts up, as if this command had been issued:
compute thermo_pressure all pressure thermo_temp :pre
@ -146,6 +146,18 @@ have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
"thermo_modify"_thermo_modify.html command.
Several of the thermodynamic quantities require a potential energy to
be computed: "pe", "etotal", "ebond", etc. This is done by using the
"thermo_pe" compute which is created when LAMMPS starts up, as if this
command had been issued:
compute thermo_pe all pe :pre
See the "compute pe"_compute_pe.html command for details. Note that
the ID of this compute is {thermo_pe} and the group is {all}. You can
change the attributes of this potential energy via the
"compute_modify"_compute_modify.html command.
The {drot} keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
@ -180,9 +192,11 @@ be useful if you wish to exclude frozen particles from the compuation.
:line
The potential energy of the system {pe} will include contributions
from fixes if the "fix_modify thermo"_fix_modify.html option was set
for each fix. For example, the "fix wall/lj93"_fix_wall_lj93 fix will
contribute the energy of atoms interacting with the wall.
from fixes if the "fix_modify thermo"_fix_modify.html option is set
for a fix that calculates such a contribution. For example, the "fix
wall/lj93"_fix_wall_lj93 fix calculates the energy of atoms
interacting with the wall. See the doc pages for "individual fixes"
to see which ones contribute.
A long-range tail correction {etail} for the VanderWaal pairwise
energy will be non-zero only if the "pair_modify