lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9014 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-10-26 23:02:13 +00:00
parent 8bd8b77489
commit b6e5ec143f
14 changed files with 760 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

53
doc/angle_fourier.html Normal file
View File

@ -0,0 +1,53 @@
<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>angle_style fourier command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style fourier
</PRE>
<P><B>Examples:</B>
</P>
<P>angle_style fourier
angle_coeff 75.0 1.0 1.0 1.0
</P>
<P><B>Description:</B>
</P>
<P>The <I>fourier</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_fourier.jpg">
</CENTER>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_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>
<UL><LI>K (energy)
<LI>C0 (real)
<LI>C1 (real)
<LI>C2 (real)
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

48
doc/angle_fourier.txt Normal file
View File

@ -0,0 +1,48 @@
"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
angle_style fourier command :h3
[Syntax:]
angle_style fourier :pre
[Examples:]
angle_style fourier
angle_coeff 75.0 1.0 1.0 1.0
[Description:]
The {fourier} angle style uses the potential
:c,image(Eqs/angle_fourier.jpg)
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_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:
K (energy)
C0 (real)
C1 (real)
C2 (real) :ul
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none

52
doc/angle_fourier_simple.html Normal file
View File

@ -0,0 +1,52 @@
<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>angle_style fourier/simple command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style fourier/simple
</PRE>
<P><B>Examples:</B>
</P>
<P>angle_style fourier/simple
angle_coeff 100.0 -1.0 1.0
</P>
<P><B>Description:</B>
</P>
<P>The <I>fourier/simple</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_fourier_simple.jpg">
</CENTER>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_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>
<UL><LI>K (energy)
<LI>c (real)
<LI>n (real)
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

47
doc/angle_fourier_simple.txt Normal file
View File

@ -0,0 +1,47 @@
"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
angle_style fourier/simple command :h3
[Syntax:]
angle_style fourier/simple :pre
[Examples:]
angle_style fourier/simple
angle_coeff 100.0 -1.0 1.0
[Description:]
The {fourier/simple} angle style uses the potential
:c,image(Eqs/angle_fourier_simple.jpg)
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_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:
K (energy)
c (real)
n (real) :ul
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none

59
doc/angle_quartic.html Normal file
View File

@ -0,0 +1,59 @@
<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>angle_style quartic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style quartic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style quartic
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>quartic</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_quartic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_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>
<UL><LI>theta0 (degrees)
<LI>K2 (energy/radian^2)
<LI>K3 (energy/radian^3)
<LI>K4 (energy/radian^4)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

54
doc/angle_quartic.txt Normal file
View File

@ -0,0 +1,54 @@
"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
angle_style quartic command :h3
[Syntax:]
angle_style quartic :pre
[Examples:]
angle_style quartic
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 :pre
[Description:]
The {quartic} angle style uses the potential
:c,image(Eqs/angle_quartic.jpg)
where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_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:
theta0 (degrees)
K2 (energy/radian^2)
K3 (energy/radian^3)
K4 (energy/radian^4) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none

57
doc/dihedral_fourier.html Normal file
View File

@ -0,0 +1,57 @@
<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>dihedral_style fourier command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style fourier
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style fourier
dihedral_coeff 3 -0.846200 3 0 7.578800 1 0 0.138000 2 -180
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fourier</I> dihedral style uses the potential:
</P>
<CENTER><IMG SRC = "Eqs/dihedral_fourier.jpg">
</CENTER>
<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
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>m (integer >=1)
K1 (energy)
n1 (integer >= 0)
d1 (integer value of degrees)
....
Km (energy)
nm (integer >= 0)
dm (integer value of degrees)
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

53
doc/dihedral_fourier.txt Normal file
View File

@ -0,0 +1,53 @@
"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
dihedral_style fourier command :h3
[Syntax:]
dihedral_style fourier :pre
[Examples:]
dihedral_style fourier
dihedral_coeff 3 -0.846200 3 0 7.578800 1 0 0.138000 2 -180 :pre
[Description:]
The {fourier} dihedral style uses the potential:
:c,image(Eqs/dihedral_fourier.jpg)
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
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
m (integer >=1)
K1 (energy)
n1 (integer >= 0)
d1 (integer value of degrees)
....
Km (energy)
nm (integer >= 0)
dm (integer value of degrees)
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none

54
doc/dihedral_nharmonic.html Normal file
View File

@ -0,0 +1,54 @@
<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>dihedral_style nharmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style nharmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style nharmonic
dihedral_coeff 3 10.0 20.0 30.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>nharmonic</I> dihedral style uses the potential:
</P>
<CENTER><IMG SRC = "Eqs/dihedral_nharmonic.jpg">
</CENTER>
<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
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>
<UL><LI>n (integer >=1)
<LI>A1 (energy)
<LI>A2 (energy)
<LI>...
<LI>An (energy)
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

49
doc/dihedral_nharmonic.txt Normal file
View File

@ -0,0 +1,49 @@
"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
dihedral_style nharmonic command :h3
[Syntax:]
dihedral_style nharmonic :pre
[Examples:]
dihedral_style nharmonic
dihedral_coeff 3 10.0 20.0 30.0 :pre
[Description:]
The {nharmonic} dihedral style uses the potential:
:c,image(Eqs/dihedral_nharmonic.jpg)
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
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
n (integer >=1)
A1 (energy)
A2 (energy)
...
An (energy) :ul
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none

53
doc/dihedral_quadratic.html Normal file
View File

@ -0,0 +1,53 @@
<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>dihedral_style quadratic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style quadratic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style quadratic
dihedral_coeff 100.0 80.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>quadratic</I> dihedral style uses the potential:
</P>
<CENTER><IMG SRC = "Eqs/dihedral_quadratic.jpg">
</CENTER>
<P>This dihedral potential can be used to keep a dihedral in a predefined value.
</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
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>K (energy)
phi0 (degrees)
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

49
doc/dihedral_quadratic.txt Normal file
View File

@ -0,0 +1,49 @@
"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
dihedral_style quadratic command :h3
[Syntax:]
dihedral_style quadratic :pre
[Examples:]
dihedral_style quadratic
dihedral_coeff 100.0 80.0 :pre
[Description:]
The {quadratic} dihedral style uses the potential:
:c,image(Eqs/dihedral_quadratic.jpg)
This dihedral potential can be used to keep a dihedral in a predefined value.
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
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
phi0 (degrees)
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none

69
doc/improper_fourier.html Normal file
View File

@ -0,0 +1,69 @@
<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>improper_style fourier command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style fourier
</PRE>
<P><B>Examples:</B>
</P>
<PRE>improper_style fourier
improper_coeff 1 100.0 180.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fourier</I> improper style uses the following potential:
</P>
<CENTER><IMG SRC = "Eqs/improper_fourier.jpg">
</CENTER>
<P>where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
</P>
<CENTER><IMG SRC = "Eqs/umbrella.jpg">
</CENTER>
<P>If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
</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>
<UL><LI>K (energy)
<LI>C0 (real)
<LI>C1 (real)
<LI>C2 (real)
<LI>all (integer >= 0)
</UL>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),
</P>
</HTML>

63
doc/improper_fourier.txt Normal file
View File

@ -0,0 +1,63 @@
"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
improper_style fourier command :h3
[Syntax:]
improper_style fourier :pre
[Examples:]
improper_style fourier
improper_coeff 1 100.0 180.0 :pre
[Description:]
The {fourier} improper style uses the following potential:
:c,image(Eqs/improper_fourier.jpg)
where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
:c,image(Eqs/umbrella.jpg)
If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
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:
K (energy)
C0 (real)
C1 (real)
C2 (real)
all (integer >= 0) :ul
:line
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
:line
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),