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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5248 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-11-17 18:20:48 +00:00
parent 7ccbc7e75b
commit 5c92d3a7ac
6 changed files with 168 additions and 74 deletions
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34
doc/angle_class2.html
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@ -32,8 +32,13 @@ the equilibrium bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>For this style, coefficients for the Ea formula can be specified in
the input script or data file. These are the 4 coefficients:
<P>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <A HREF = "bond_coeff.html">bond_coeff</A> command as in the
example above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 4 coefficients for the Ea formula:
</P>
<UL><LI>theta0 (degrees)
<LI>K2 (energy/radian^2)
@ -43,20 +48,27 @@ the input script or data file. These are the 4 coefficients:
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.
</P>
<P>Coefficients for the Ebb and Eba formulas can only be specified in the
data file.
<P>For the Ebb formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients can be listed under a "BondBond Coeffs" heading and
you must leave out the "bb", i.e. only list 3 coefficients after the
angle type.
</P>
<P>For the Ebb formula, the coefficients are listed under a "BondBond
Coeffs" heading and each line lists 3 coefficients:
</P>
<UL><LI>M (energy/distance^2)
<UL><LI>bb
<LI>M (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)
</UL>
<P>For the Eba formula, the coefficients are listed under a "BondAngle
Coeffs" heading and each line lists 4 coefficients:
<P>For the Eba formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients can be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
</P>
<UL><LI>N1 (energy/distance^2)
<UL><LI>ba
<LI>N1 (energy/distance^2)
<LI>N2 (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)

30
doc/angle_class2.txt
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@ -29,8 +29,13 @@ the equilibrium bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, coefficients for the Ea formula can be specified in
the input script or data file. These are the 4 coefficients:
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the "bond_coeff"_bond_coeff.html command as in the
example above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
These are the 4 coefficients for the Ea formula:
theta0 (degrees)
K2 (energy/radian^2)
@ -40,19 +45,26 @@ K4 (energy/radian^4) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.
Coefficients for the Ebb and Eba formulas can only be specified in the
data file.
For the Ebb formula, the coefficients are listed under a "BondBond
Coeffs" heading and each line lists 3 coefficients:
For the Ebb formula, each line in a "bond_coeff"_bond_coeff.html
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients can be listed under a "BondBond Coeffs" heading and
you must leave out the "bb", i.e. only list 3 coefficients after the
angle type.
bb
M (energy/distance^2)
r1 (distance)
r2 (distance) :ul
For the Eba formula, the coefficients are listed under a "BondAngle
Coeffs" heading and each line lists 4 coefficients:
For the Eba formula, each line in a "bond_coeff"_bond_coeff.html
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients can be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
ba
N1 (energy/distance^2)
N2 (energy/distance^2)
r1 (distance)

71
doc/dihedral_class2.html
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@ -35,8 +35,14 @@ bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>For this style, coefficients for the Ed formula can be specified in
either the input script or data file. These are the 6 coefficients:
<P>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
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 the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 6 coefficients for the Ed formula:
</P>
<UL><LI>K1 (energy)
<LI>phi1 (degrees)
@ -45,21 +51,30 @@ either the input script or data file. These are the 6 coefficients:
<LI>K3 (energy)
<LI>phi3 (degrees)
</UL>
<P>Coefficients for all the other formulas can only be specified in the
data file.
<P>For the Embt formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
5 coefficients, the first of which is "mbt" to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a "MiddleBondTorsion Coeffs" heading and you
must leave out the "mbt", i.e. only list 4 coefficients after the
dihedral type.
</P>
<P>For the Embt formula, the coefficients are listed under a
"MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
</P>
<UL><LI>A1 (energy/distance)
<UL><LI>mbt
<LI>A1 (energy/distance)
<LI>A2 (energy/distance)
<LI>A3 (energy/distance)
<LI>r2 (distance)
</UL>
<P>For the Eebt formula, the coefficients are listed under a
"EndBondTorsion Coeffs" heading and each line lists 8 coefficients:
<P>For the Eebt formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
9 coefficients, the first of which is "ebt" to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a "EndBondTorsion Coeffs" heading and you must
leave out the "ebt", i.e. only list 8 coefficients after the dihedral
type.
</P>
<UL><LI>B1 (energy/distance)
<UL><LI>ebt
<LI>B1 (energy/distance)
<LI>B2 (energy/distance)
<LI>B3 (energy/distance)
<LI>C1 (energy/distance)
@ -68,10 +83,15 @@ data file.
<LI>r1 (distance)
<LI>r3 (distance)
</UL>
<P>For the Eat formula, the coefficients are listed under a "AngleTorsion
Coeffs" heading and each line lists 8 coefficients:
<P>For the Eat formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
9 coefficients, the first of which is "at" to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a "AngleTorsion Coeffs" heading and you must leave out
the "at", i.e. only list 8 coefficients after the dihedral type.
</P>
<UL><LI>D1 (energy/radian)
<UL><LI>at
<LI>D1 (energy/radian)
<LI>D2 (energy/radian)
<LI>D3 (energy/radian)
<LI>E1 (energy/radian)
@ -84,20 +104,31 @@ Coeffs" heading and each line lists 8 coefficients:
to radians internally; hence the units of D and E are in
energy/radian.
</P>
<P>For the Eaat formula, the coefficients are listed under a
"AngleAngleTorsion Coeffs" heading and each line lists 3 coefficients:
<P>For the Eaat formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
4 coefficients, the first of which is "aat" to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a "AngleAngleTorsion Coeffs" heading and you
must leave out the "aat", i.e. only list 3 coefficients after the
dihedral type.
</P>
<UL><LI>M (energy/radian^2)
<UL><LI>aat
<LI>M (energy/radian^2)
<LI>theta1 (degrees)
<LI>theta2 (degrees)
</UL>
<P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.
</P>
<P>For the Ebb13 formula, the coefficients are listed under a "BondBond13
Coeffs" heading and each line lists 3 coefficients:
<P>For the Ebb13 formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
4 coefficients, the first of which is "bb13" to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a "BondBond13 Coeffs" heading and you must leave out the
"bb13", i.e. only list 3 coefficients after the dihedral type.
</P>
<UL><LI>N (energy/distance^2)
<UL><LI>bb13
<LI>N (energy/distance^2)
<LI>r1 (distance)
<LI>r3 (distance)
</UL>

61
doc/dihedral_class2.txt
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@ -32,8 +32,14 @@ bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, coefficients for the Ed formula can be specified in
either the input script or data file. These are the 6 coefficients:
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above,
or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
These are the 6 coefficients for the Ed formula:
K1 (energy)
phi1 (degrees)
@ -42,20 +48,29 @@ phi2 (degrees)
K3 (energy)
phi3 (degrees) :ul
Coefficients for all the other formulas can only be specified in the
data file.
For the Embt formula, the coefficients are listed under a
"MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
For the Embt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
5 coefficients, the first of which is "mbt" to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a "MiddleBondTorsion Coeffs" heading and you
must leave out the "mbt", i.e. only list 4 coefficients after the
dihedral type.
mbt
A1 (energy/distance)
A2 (energy/distance)
A3 (energy/distance)
r2 (distance) :ul
For the Eebt formula, the coefficients are listed under a
"EndBondTorsion Coeffs" heading and each line lists 8 coefficients:
For the Eebt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "ebt" to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a "EndBondTorsion Coeffs" heading and you must
leave out the "ebt", i.e. only list 8 coefficients after the dihedral
type.
ebt
B1 (energy/distance)
B2 (energy/distance)
B3 (energy/distance)
@ -65,9 +80,14 @@ C3 (energy/distance)
r1 (distance)
r3 (distance) :ul
For the Eat formula, the coefficients are listed under a "AngleTorsion
Coeffs" heading and each line lists 8 coefficients:
For the Eat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "at" to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a "AngleTorsion Coeffs" heading and you must leave out
the "at", i.e. only list 8 coefficients after the dihedral type.
at
D1 (energy/radian)
D2 (energy/radian)
D3 (energy/radian)
@ -81,9 +101,15 @@ Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of D and E are in
energy/radian.
For the Eaat formula, the coefficients are listed under a
"AngleAngleTorsion Coeffs" heading and each line lists 3 coefficients:
For the Eaat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "aat" to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a "AngleAngleTorsion Coeffs" heading and you
must leave out the "aat", i.e. only list 3 coefficients after the
dihedral type.
aat
M (energy/radian^2)
theta1 (degrees)
theta2 (degrees) :ul
@ -91,9 +117,14 @@ theta2 (degrees) :ul
Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.
For the Ebb13 formula, the coefficients are listed under a "BondBond13
Coeffs" heading and each line lists 3 coefficients:
For the Ebb13 formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "bb13" to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a "BondBond13 Coeffs" heading and you must leave out the
"bb13", i.e. only list 3 coefficients after the dihedral type.
bb13
N (energy/distance^2)
r1 (distance)
r3 (distance) :ul

24
doc/improper_class2.html
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@ -50,13 +50,13 @@ this is not required.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each improper type via the
<A HREF = "improper_coeff.html">improper_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
<P>Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the <A HREF = "improper_coeff.html">improper_coeff</A> command as
in the example above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>For this style, coefficients for the Ei formula can be specified in
either the input script or data file. These are the 2 coefficients:
<P>These are the 2 coefficients for the Ei formula:
</P>
<UL><LI>K (energy/radian^2)
<LI>X0 (degrees)
@ -64,11 +64,15 @@ either the input script or data file. These are the 2 coefficients:
<P>X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P>Coefficients for the Eaa formula can only be specified in the data
file. For the Eaa formula, the coefficients are listed under a
"AngleAngle Coeffs" heading and each line lists 6 coefficients:
<P>For the Eaa formula, each line in a
<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script lists
7 coefficients, the first of which is "aa" to indicate they are
AngleAngle coefficients. In a data file, these coefficients should be
listed under a "AngleAngle Coeffs" heading and you must leave out the
"aa", i.e. only list 6 coefficients after the improper type.
</P>
<UL><LI>M1 (energy/distance)
<UL><LI>aa
<LI>M1 (energy/distance)
<LI>M2 (energy/distance)
<LI>M3 (energy/distance)
<LI>theta1 (degrees)

22
doc/improper_class2.txt
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@ -47,13 +47,13 @@ this is not required.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each improper type via the
"improper_coeff"_improper_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the "improper_coeff"_improper_coeff.html command as
in the example above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
For this style, coefficients for the Ei formula can be specified in
either the input script or data file. These are the 2 coefficients:
These are the 2 coefficients for the Ei formula:
K (energy/radian^2)
X0 (degrees) :ul
@ -61,10 +61,14 @@ X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
Coefficients for the Eaa formula can only be specified in the data
file. For the Eaa formula, the coefficients are listed under a
"AngleAngle Coeffs" heading and each line lists 6 coefficients:
For the Eaa formula, each line in a
"improper_coeff"_improper_coeff.html command in the input script lists
7 coefficients, the first of which is "aa" to indicate they are
AngleAngle coefficients. In a data file, these coefficients should be
listed under a "AngleAngle Coeffs" heading and you must leave out the
"aa", i.e. only list 6 coefficients after the improper type.
aa
M1 (energy/distance)
M2 (energy/distance)
M3 (energy/distance)