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@7781 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-02-14 20:13:00 +00:00
parent 61dac0f38d
commit 860fbe49c1
8 changed files with 54 additions and 48 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
doc/compute_heat_flux.html
View File

@ -68,9 +68,7 @@ for which terms to include in their calculation (pair, bond, etc).
The heat flux calculation will thus include exactly the same terms.
Normally you should use <A HREF = "compute_stress_atom.html">compute stress/atom
virial</A> so as not to include a kinetic energy
term in the heat flux. Note that neither of those computes is able to
include a long-range Coulombic contribution to the per-atom energy or
stress.
term in the heat flux.
</P>
<P>This compute calculates 6 quantities and stores them in a 6-component
vector. The first 3 components are the x, y, z components of the full

4
doc/compute_heat_flux.txt
View File

@ -65,9 +65,7 @@ for which terms to include in their calculation (pair, bond, etc).
The heat flux calculation will thus include exactly the same terms.
Normally you should use "compute stress/atom
virial"_compute_stress_atom.html so as not to include a kinetic energy
term in the heat flux. Note that neither of those computes is able to
include a long-range Coulombic contribution to the per-atom energy or
stress.
term in the heat flux.
This compute calculates 6 quantities and stores them in a 6-component
vector. The first 3 components are the x, y, z components of the full

6
doc/compute_pe.html
View File

@ -41,6 +41,12 @@ 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>The KSpace contribution requires 1 extra FFT each timestep the
per-atom energy is calculated, if using the PPPM solver via the
<A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it can increase
the cost of the PPPM calculation if it is needed on a large fraction
of the simulation timesteps.
</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

6
doc/compute_pe.txt
View File

@ -37,6 +37,12 @@ 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.
The KSpace contribution requires 1 extra FFT each timestep the
per-atom energy is calculated, if using the PPPM solver via the
"kspace_style pppm"_kspace_style.html command. Thus it can increase
the cost of the PPPM calculation if it is needed on a large fraction
of the simulation timesteps.
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

17
doc/compute_pe_atom.html
View File

@ -18,7 +18,7 @@
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pe/atom = style name of this compute command
<LI>zero or 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>
<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>
@ -35,8 +35,9 @@ you want the potential energy of the entire system.
<P>The per-atom energy is calculated 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, and improper energy. If any extra keywords are listed, then
only those components are summed to compute the potential energy.
dihedral,improper, and kspace energy. If any extra keywords are
listed, then only those components are summed to compute the potential
energy.
</P>
<P>Note that the energy of each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.
@ -58,13 +59,9 @@ in the last 2 columns of thermo output:
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe
</PRE>
<P>IMPORTANT NOTE: The per-atom energy does NOT include contributions due
to long-range Coulombic interactions (via the
<A HREF = "kspace_style.html">kspace_style</A> command). It's not clear this
contribution can easily be computed. It also does not include any
Lennard-Jones tail corrections invoked by the <A HREF = "pair_modify.html">pair_modify tail
yes</A> command, since those are global contributions to
the system energy.
<P>IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
corrections invoked by the <A HREF = "pair_modify.html">pair_modify tail yes</A>
command, since those are global contributions to the system energy.
</P>
<P><B>Output info:</B>
</P>

17
doc/compute_pe_atom.txt
View File

@ -15,7 +15,7 @@ compute ID group-ID pe/atom keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
pe/atom = style name of this compute command
zero or more keywords may be appended
keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} :ul
keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
[Examples:]
@ -32,8 +32,9 @@ you want the potential energy of the entire system.
The per-atom energy is calculated 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, and improper energy. If any extra keywords are listed, then
only those components are summed to compute the potential energy.
dihedral,improper, and kspace energy. If any extra keywords are
listed, then only those components are summed to compute the potential
energy.
Note that the energy of each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.
@ -55,13 +56,9 @@ compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe :pre
IMPORTANT NOTE: The per-atom energy does NOT include contributions due
to long-range Coulombic interactions (via the
"kspace_style"_kspace_style.html command). It's not clear this
contribution can easily be computed. It also does not include any
Lennard-Jones tail corrections invoked by the "pair_modify tail
yes"_pair_modify.html command, since those are global contributions to
the system energy.
IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
corrections invoked by the "pair_modify tail yes"_pair_modify.html
command, since those are global contributions to the system energy.
[Output info:]

24
doc/compute_stress_atom.html
View File

@ -18,7 +18,7 @@
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>stress/atom = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>fix</I> or <I>virial</I>
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
</UL>
<P><B>Examples:</B>
</P>
@ -47,11 +47,12 @@ atoms in the pairwise interaction, and <I>F1</I> and <I>F2</I> are the forces on
the 2 atoms resulting from the pairwise interaction. The third term
is a bond contribution of similar form for the <I>Nb</I> bonds which atom
<I>I</I> is part of. There are similar terms for the <I>Na</I> angle, <I>Nd</I>
dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of.
Finally, there is a term for the <I>Nf</I> <A HREF = "fix.html">fixes</A> that apply
internal constraint forces to atom <I>I</I>. Currently, only the <A HREF = "fix_shake.html">fix
shake</A> and <A HREF = "fix_rigid.html">fix rigid</A> commands
contribute to this term.
dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of. There
is also a term for the KSpace contribution from long-range Coulombic
interactions, if defined. Finally, there is a term for the <I>Nf</I>
<A HREF = "fix.html">fixes</A> that apply internal constraint forces to atom <I>I</I>.
Currently, only the <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
rigid</A> commands contribute to this term.
</P>
<P>As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
@ -74,6 +75,12 @@ other atoms in the simulation, not just with other atoms in the group.
pairwise interactions between 1-4 atoms. The virial contribution of
these terms is included in the pair virial, not the dihedral virial.
</P>
<P>The KSpace contribution to the per-atom stress requires 6 extra FFTs
each timestep that per-atom stress is calculated, if using the PPPM
solver via the <A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it
can significantly increase the cost of the PPPM calculation if it is
needed on a large fraction of the simulation timesteps.
</P>
<P>Note that as defined in the formula, per-atom stress is the negative
of the per-atom pressure tensor. It is also really a stress*volume
formulation, meaning the computed quantity is in units of
@ -93,11 +100,6 @@ compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo_style custom step temp etotal press v_press
</PRE>
<P>IMPORTANT NOTE: The per-atom stress does NOT include contributions due
to long-range Coulombic interactions (via the
<A HREF = "kspace_style.html">kspace_style</A> command). It's not clear this
contribution can easily be computed.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom array with 6 columns, which can be

24
doc/compute_stress_atom.txt
View File

@ -15,7 +15,7 @@ compute ID group-ID stress/atom keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
stress/atom = style name of this compute command
zero or more keywords may be appended
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {fix} or {virial} :ul
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
[Examples:]
@ -44,11 +44,12 @@ atoms in the pairwise interaction, and {F1} and {F2} are the forces on
the 2 atoms resulting from the pairwise interaction. The third term
is a bond contribution of similar form for the {Nb} bonds which atom
{I} is part of. There are similar terms for the {Na} angle, {Nd}
dihedral, and {Ni} improper interactions atom {I} is part of.
Finally, there is a term for the {Nf} "fixes"_fix.html that apply
internal constraint forces to atom {I}. Currently, only the "fix
shake"_fix_shake.html and "fix rigid"_fix_rigid.html commands
contribute to this term.
dihedral, and {Ni} improper interactions atom {I} is part of. There
is also a term for the KSpace contribution from long-range Coulombic
interactions, if defined. Finally, there is a term for the {Nf}
"fixes"_fix.html that apply internal constraint forces to atom {I}.
Currently, only the "fix shake"_fix_shake.html and "fix
rigid"_fix_rigid.html commands contribute to this term.
As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
@ -71,6 +72,12 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates
pairwise interactions between 1-4 atoms. The virial contribution of
these terms is included in the pair virial, not the dihedral virial.
The KSpace contribution to the per-atom stress requires 6 extra FFTs
each timestep that per-atom stress is calculated, if using the PPPM
solver via the "kspace_style pppm"_kspace_style.html command. Thus it
can significantly increase the cost of the PPPM calculation if it is
needed on a large fraction of the simulation timesteps.
Note that as defined in the formula, per-atom stress is the negative
of the per-atom pressure tensor. It is also really a stress*volume
formulation, meaning the computed quantity is in units of
@ -90,11 +97,6 @@ compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
thermo_style custom step temp etotal press v_press :pre
IMPORTANT NOTE: The per-atom stress does NOT include contributions due
to long-range Coulombic interactions (via the
"kspace_style"_kspace_style.html command). It's not clear this
contribution can easily be computed.
[Output info:]
This compute calculates a per-atom array with 6 columns, which can be