From c676ea4d6d40393f3951fe359cda5c5a4d75476d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 22 May 2012 16:09:28 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8141 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 8 ++++ doc/Section_commands.txt | 7 ++++ doc/improper_cossq.html | 70 +++++++++++++++++++++++++++++++++++ doc/improper_cossq.txt | 65 +++++++++++++++++++++++++++++++++ doc/improper_ring.html | 77 +++++++++++++++++++++++++++++++++++++++ doc/improper_ring.txt | 72 ++++++++++++++++++++++++++++++++++++ doc/improper_style.html | 8 ++-- doc/improper_style.txt | 8 ++-- 8 files changed, 307 insertions(+), 8 deletions(-) create mode 100644 doc/improper_cossq.html create mode 100644 doc/improper_cossq.txt create mode 100644 doc/improper_ring.html create mode 100644 doc/improper_ring.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 48ddf42e0a..0a19860bfb 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -594,6 +594,14 @@ description: harmonicumbrella +

These are improper styles contributed by users, which can be used if +LAMMPS is built with the appropriate +package. +

+
+
cossqring +
+

These are accelerated improper styles, which can be used if LAMMPS is built with the appropriate accelerated package. diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 6a1f142bd5..4680d74fef 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -993,6 +993,13 @@ description: "harmonic"_improper_harmonic.html, "umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100) +These are improper styles contributed by users, which can be used if +"LAMMPS is built with the appropriate +package"_Section_start.html#start_3. + +"cossq"_improper_cossq.html, +"ring"_improper_ring.html :tb(c=4,ea=c) + These are accelerated improper styles, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. diff --git a/doc/improper_cossq.html b/doc/improper_cossq.html new file mode 100644 index 0000000000..01dd2b4bad --- /dev/null +++ b/doc/improper_cossq.html @@ -0,0 +1,70 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

improper_style cossq command +

+

Syntax: +

+
improper_style cossq 
+
+

Examples: +

+
improper_style cossq
+improper_coeff 1 4.0 0.0 
+
+

Description: +

+

The cossq improper style uses the potential +

+
+
+

where x is the improper angle, x0 is its equilibrium value, and K is a +prefactor. +

+

If the 4 atoms in an improper quadruplet (listed in the data file read +by the read_data command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. +

+

Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. +

+

The following coefficients must be defined for each improper type via +the improper_coeff command as in the example +above, or in the data file or restart files read by the +read_data or read_restart +commands: +

+ +

X0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. +

+
+ +

Restrictions: +

+

This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the Making LAMMPS +section for more info on packages. +

+

Related commands: +

+

improper_coeff +

+

Default: none +

+ diff --git a/doc/improper_cossq.txt b/doc/improper_cossq.txt new file mode 100644 index 0000000000..1a8a5c200a --- /dev/null +++ b/doc/improper_cossq.txt @@ -0,0 +1,65 @@ +"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 cossq command :h3 + +[Syntax:] + +improper_style cossq :pre + +[Examples:] + +improper_style cossq +improper_coeff 1 4.0 0.0 :pre + +[Description:] + +The {cossq} improper style uses the potential + +:c,image(Eqs/improper_cossq.jpg) + +where x is the improper angle, x0 is its equilibrium value, and K is a +prefactor. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the "read_data"_read_data.html command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. + +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/radian^2) +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. + +:line + +[Restrictions:] + +This improper 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 diff --git a/doc/improper_ring.html b/doc/improper_ring.html new file mode 100644 index 0000000000..26b6529440 --- /dev/null +++ b/doc/improper_ring.html @@ -0,0 +1,77 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

improper_style ring command +

+

Syntax: +

+
improper_style ring 
+
+

Examples: +

+
improper_style ring
+improper_coeff 1 8000 70.5 
+
+

Description: +

+

The ring improper style uses the potential +

+
+
+

where K is a prefactor, theta is the angle formed by the atoms +specified by (i,j,k,l) indices and theta0 its equilibrium value. +

+

If the 4 atoms in an improper quadruplet (listed in the data file read +by the read_data command) are ordered i,j,k,l then +theta_ijl is the angle between atoms i,j and l, theta_ijk is the +angle between atoms i,j and k, theta_kjl is the angle between atoms +j,k, and l. +

+

The "ring" improper style implements the improper potential introduced +by Destree et al., in Equation (9) of (Destree). This +potential does not affect small amplitude vibrations but is used in an +ad-hoc way to prevent the onset of accidentially large amplitude +fluctuations leading to the occurrence of a planar conformation of the +three bonds i-j, j-k and j-l, an intermediate conformation toward the +chiral inversion of a methine carbon. In the "Impropers" section of +data file four atoms: i, j, k and l are specified with i,j and l lying +on the backbone of the chain and k specifying the chirality of j. +

+

The following coefficients must be defined for each improper type via +the improper_coeff command as in the example +above, or in the data file or restart files read by the +read_data or read_restart +commands: +

+ +

theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. +

+
+ +

Restrictions: +

+

This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the Making LAMMPS +section for more info on packages. +

+

Related commands: +

+

improper_coeff +

+ + +

(Destree) M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, +J Chem Phys, 112, 9632 (2000). +

+ diff --git a/doc/improper_ring.txt b/doc/improper_ring.txt new file mode 100644 index 0000000000..dc493d99b5 --- /dev/null +++ b/doc/improper_ring.txt @@ -0,0 +1,72 @@ +"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 ring command :h3 + +[Syntax:] + +improper_style ring :pre + +[Examples:] + +improper_style ring +improper_coeff 1 8000 70.5 :pre + +[Description:] + +The {ring} improper style uses the potential + +:c,image(Eqs/improper_ring.jpg) + +where K is a prefactor, theta is the angle formed by the atoms +specified by (i,j,k,l) indices and theta0 its equilibrium value. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the "read_data"_read_data.html command) are ordered i,j,k,l then +theta_{ijl} is the angle between atoms i,j and l, theta_{ijk} is the +angle between atoms i,j and k, theta_{kjl} is the angle between atoms +j,k, and l. + +The "ring" improper style implements the improper potential introduced +by Destree et al., in Equation (9) of "(Destree)"_#Destree. This +potential does not affect small amplitude vibrations but is used in an +ad-hoc way to prevent the onset of accidentially large amplitude +fluctuations leading to the occurrence of a planar conformation of the +three bonds i-j, j-k and j-l, an intermediate conformation toward the +chiral inversion of a methine carbon. In the "Impropers" section of +data file four atoms: i, j, k and l are specified with i,j and l lying +on the backbone of the chain and k specifying the chirality of j. + +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/radian^2) +theta0 (degrees) :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 improper 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 + +:link(Destree) +[(Destree)] M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, +J Chem Phys, 112, 9632 (2000). + diff --git a/doc/improper_style.html b/doc/improper_style.html index f2c9ffd1ea..f4b110b693 100644 --- a/doc/improper_style.html +++ b/doc/improper_style.html @@ -62,10 +62,10 @@ Click on the style to display the formula it computes and coefficients specified by the associated improper_coeff command.

-

There are also additional improper styles submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the improper section of this -page. +

Note that there are also additional improper styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the improper section of +this page.