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parent b93b67bd

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.

</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.

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 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

doc/compute_stress_atom.txt

+15 −14
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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.



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.

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 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

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

doc/dihedral_charmm.txt

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@@ -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

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