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27
doc/compute_stress_atom.html
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@ -38,25 +38,26 @@ custom</A> command or <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
command or <A HREF = "fix_ave_atom.html">fix ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview.
</P>
<P>The stress tensor for each atom is given by the following formula.
where the ab component of stress on atom <I>I</I> is as shown where <I>a</I> and
<I>b</I> take on values x,y,z to generate the 6 components of the symmetric
tensor:
<P>The stress tensor for atom <I>I</I> is given by the following formula,
where <I>a</I> and <I>b</I> take on values x,y,z to generate the 6 components of
the symmetric tensor:
</P>
<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
</CENTER>
<P>The first term is a kinetic energy contribution for atom <I>I</I>. The
second term is a pairwise energy contribution where <I>N</I> loops over the
second term is a pairwise energy contribution where <I>n</I> loops over the
<I>Np</I> neighbors of atom <I>I</I>, <I>r1</I> and <I>r2</I> are the positions of the 2
atoms, and <I>F1</I> and <I>F2</I> are the forces on the 2 atoms. The third
term is a bond contribution for the <I>Nb</I> bonds whihc atom <I>I</I> is part
of. And similarly for the <I>Na</I> angle, <I>Nd</I> dihedral, and <I>Ni</I>
improper interactions atom <I>I</I> is part of.
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. The remaining terms are for the <I>Na</I> angle, <I>Nd</I>
dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of.
</P>
<P>As the formula implies, a virial contribution produced by a small set
of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a Tersoff 3-body
interaction) is assigned in equal portions to each atom in the set.
E.g. 1/4 of the dihedral virial to each of the 4 atoms.
<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
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
the 4 atoms.
</P>
<P>If no extra keywords are listed, all of the terms in this formula are
included in the per-atom stress tensor. If any extra keywords are

27
doc/compute_stress_atom.txt
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@ -34,25 +34,26 @@ custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html
command or "fix ave/atom"_fix_ave_atom.html command. See "this
section"_Section_howto.html#4_15 for an overview.
The stress tensor for each atom is given by the following formula.
where the ab component of stress on atom {I} is as shown where {a} and
{b} take on values x,y,z to generate the 6 components of the symmetric
tensor:
The stress tensor for atom {I} is given by the following formula,
where {a} and {b} take on values x,y,z to generate the 6 components of
the symmetric tensor:
:c,image(Eqs/stress_tensor.jpg)
The first term is a kinetic energy contribution for atom {I}. The
second term is a pairwise energy contribution where {N} loops over the
second term is a pairwise energy contribution where {n} loops over the
{Np} neighbors of atom {I}, {r1} and {r2} are the positions of the 2
atoms, and {F1} and {F2} are the forces on the 2 atoms. The third
term is a bond contribution for the {Nb} bonds whihc atom {I} is part
of. And similarly for the {Na} angle, {Nd} dihedral, and {Ni}
improper interactions atom {I} is part of.
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. The remaining terms are for the {Na} angle, {Nd}
dihedral, and {Ni} improper interactions atom {I} is part of.
As the formula implies, a virial contribution produced by a small set
of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a Tersoff 3-body
interaction) is assigned in equal portions to each atom in the set.
E.g. 1/4 of the dihedral virial to each of the 4 atoms.
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
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
the 4 atoms.
If no extra keywords are listed, all of the terms in this formula are
included in the per-atom stress tensor. If any extra keywords are

12
doc/dihedral_charmm.html
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@ -28,8 +28,8 @@ dihedral_coeff 1 120.0 1 60 0.5
</CENTER>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see the comment on weighting factors below). See
<A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force field.
(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
for a description of the AMBER force field.
</P>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
@ -42,9 +42,11 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
<LI>weighting factor (0.0 to 1.0)
</UL>
<P>The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the <A HREF = "special_bonds.html">special
bonds</A> command which applies to all 1-4
1st and 4th atoms in the dihedral, which are computed by a CHARMM
<A HREF = "pair_charmm.html">pair_style</A> with epsilon and sigma values specified
with a <A HREF = "pair_charmm.html">pair_coeff</A> command. Note that this
weighting factor is unrelated to the weighting factor specified by the
<A HREF = "special_bonds.html">special bonds</A> command which applies to all 1-4
interactions in the system.
</P>
<P>For CHARMM force fields, the special_bonds 1-4 weighting factor should

12
doc/dihedral_charmm.txt
View File

@ -25,8 +25,8 @@ The {charmm} dihedral style uses the potential
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see the comment on weighting factors below). See
"(Cornell)"_#Cornell for a description of the AMBER force field.
(see comment on weighting factors below). See "(Cornell)"_#Cornell
for a description of the AMBER force field.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
@ -39,9 +39,11 @@ d (integer value of degrees)
weighting factor (0.0 to 1.0) :ul
The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the "special
bonds"_special_bonds.html command which applies to all 1-4
1st and 4th atoms in the dihedral, which are computed by a CHARMM
"pair_style"_pair_charmm.html with epsilon and sigma values specified
with a "pair_coeff"_pair_charmm.html command. Note that this
weighting factor is unrelated to the weighting factor specified by the
"special bonds"_special_bonds.html command which applies to all 1-4
interactions in the system.
For CHARMM force fields, the special_bonds 1-4 weighting factor should