From 11948c4cfbbefe38b83f44b0bccb0f54216cf127 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 27 May 2011 23:59:19 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6242 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 2 +- doc/Manual.txt | 2 +- doc/pair_hbond_dreiding.html | 33 ++++++++++++++++++--------------- doc/pair_hbond_dreiding.txt | 33 ++++++++++++++++++--------------- 4 files changed, 38 insertions(+), 32 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 25359981fd..00ae3b3b78 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -40,7 +40,7 @@ describe the most current version of LAMMPS. describe the version you have.
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want +about once per month. This is because it is large, and we don't want it to be part of very patch.

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel diff --git a/doc/Manual.txt b/doc/Manual.txt index 24e4f17924..03ac2c5a66 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -37,7 +37,7 @@ If you browse the HTML doc pages included in your tarball, they describe the version you have. :l The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want +about once per month. This is because it is large, and we don't want it to be part of very patch. :ule,l LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel diff --git a/doc/pair_hbond_dreiding.html b/doc/pair_hbond_dreiding.html index 06689575d9..8c6358faa7 100644 --- a/doc/pair_hbond_dreiding.html +++ b/doc/pair_hbond_dreiding.html @@ -15,23 +15,24 @@

    Syntax:

    -
    pair_style style distance_cutoff angle_cutof N 
+
    pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof 
 
    
 
    • style = hbond/dreiding/lj or hbond/dreiding/morse 
 
    • n = cosine angle periodicity
-
    • distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
+
    • inner_distance_cutoff = global inner spline cutoff for Donor-Acceptor interactions (distance units)
+
    • outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
 
    • angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
 
    • interactions (degrees) 
 
    
 
    Examples:
 
    
-
    pair_style hbond/dreiding/lj 4 5.0 90
+
    pair_style hbond/dreiding/lj 4 4.5 5.0 90
 pair_coeff * * 3 i 100.0 3.1
-pair_coeff * * 2*5 i 100.0 3.1 2 200.0 
+pair_coeff * * 2*5 i 100.0 3.1 2 15.0 20.0 135.0 
 
    
-
    pair_style hbond/dreiding/morse 2 4.6 75.0 
+
    pair_style hbond/dreiding/morse 2 3.0 4.6 75.0 
 pair_coeff * * 3 j 100.0 1.0 2.0
-pair_coeff * * 2*5 j 100.0 1.0 2.0 4 
+pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0 
 
    
 
    Description:
 
    
@@ -41,8 +42,9 @@ pair_coeff * * 2*5 j 100.0 1.0 2.0 4
 
    
 
    
 
    
-
    where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
-the cosine periodicity.
+
    where Rin is the inner spline distance cutoff, Rout is the outer
+distance cutoff, theta_c is the angle cutoff, and n is the cosine
+periodicity.
 
    
 
    Here, r is the radial distance between the donor (D) and acceptor
 (A) atoms and theta is the bond angle between the acceptor, the
@@ -169,17 +171,18 @@ re-specified in an input script that reads a restart file.
 run_style respa command.  They do not support the
 inner, middle, outer keywords.
 
    
-
    These pair style tally a count of how many hydrogen bonding
-interactions they calculate each timestep.  This quantity can be
-accessed via the compute pair command as a vector
-of values of length 1.
+
    These pair styles tally a count of how many hydrogen bonding
+interactions they calculate each timestep and the hbond energy.  These
+quantities can be accessed via the compute pair
+command as a vector of values of length 2.
 
    
-
    To print this quantity to the log file (with a descriptive column
+
    To print these quantities to the log file (with a descriptive column
 heading) the following commands could be included in an input script:
 
    
 
    compute hb all pair hbond/dreiding/lj
-variable hb equal c_hb[1]
-thermo_style custom step temp epair v_hb 
+variable n_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom step temp epair v_E_hbond 
 
    
 
    
 
diff --git a/doc/pair_hbond_dreiding.txt b/doc/pair_hbond_dreiding.txt
index 77b92ae73a..bcd3c15add 100644
--- a/doc/pair_hbond_dreiding.txt
+++ b/doc/pair_hbond_dreiding.txt
@@ -11,23 +11,24 @@ pair_style hbond/dreiding/morse command :h3
 
 [Syntax:]
 
-pair_style style distance_cutoff angle_cutof N :pre
+pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof :pre
 
 style = {hbond/dreiding/lj} or {hbond/dreiding/morse} 
 n = cosine angle periodicity
-distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
+inner_distance_cutoff = global inner spline cutoff for Donor-Acceptor interactions (distance units)
+outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
 angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
 interactions (degrees) :ul
 
 [Examples:]
 
-pair_style hbond/dreiding/lj 4 5.0 90
+pair_style hbond/dreiding/lj 4 4.5 5.0 90
 pair_coeff * * 3 i 100.0 3.1
-pair_coeff * * 2*5 i 100.0 3.1 2 200.0 :pre
+pair_coeff * * 2*5 i 100.0 3.1 2 15.0 20.0 135.0 :pre
 
-pair_style hbond/dreiding/morse 2 4.6 75.0 
+pair_style hbond/dreiding/morse 2 3.0 4.6 75.0 
 pair_coeff * * 3 j 100.0 1.0 2.0
-pair_coeff * * 2*5 j 100.0 1.0 2.0 4 :pre
+pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0 :pre
 
 [Description:]
 
@@ -37,8 +38,9 @@ The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
 
 :c,image(Eqs/pair_hbond_dreiding.jpg)
 
-where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
-the cosine periodicity.
+where Rin is the inner spline distance cutoff, Rout is the outer
+distance cutoff, theta_c is the angle cutoff, and n is the cosine
+periodicity.
 
 Here, {r} is the radial distance between the donor (D) and acceptor
 (A) atoms and {theta} is the bond angle between the acceptor, the
@@ -165,17 +167,18 @@ These pair styles can only be used via the {pair} keyword of the
 "run_style respa"_run_style.html command.  They do not support the
 {inner}, {middle}, {outer} keywords.
 
-These pair style tally a count of how many hydrogen bonding
-interactions they calculate each timestep.  This quantity can be
-accessed via the "compute pair"_compute_pair.html command as a vector
-of values of length 1.
+These pair styles tally a count of how many hydrogen bonding
+interactions they calculate each timestep and the hbond energy.  These
+quantities can be accessed via the "compute pair"_compute_pair.html
+command as a vector of values of length 2.
 
-To print this quantity to the log file (with a descriptive column
+To print these quantities to the log file (with a descriptive column
 heading) the following commands could be included in an input script:
 
 compute hb all pair hbond/dreiding/lj
-variable hb equal c_hb\[1\]
-thermo_style custom step temp epair v_hb :pre
+variable n_hbond equal c_hb\[1\] #number hbonds
+variable E_hbond equal c_hb\[2\] #hbond energy
+thermo_style custom step temp epair v_E_hbond :pre
 
 :line