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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6242 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -40,7 +40,7 @@ describe the most current version of LAMMPS.
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describe the version you have.
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<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
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about once per month. This is because it is large, and we don't want
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about once per month. This is because it is large, and we don't want
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it to be part of very patch.
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</UL>
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<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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@ -37,7 +37,7 @@ If you browse the HTML doc pages included in your tarball, they
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describe the version you have. :l
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The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
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about once per month. This is because it is large, and we don't want
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about once per month. This is because it is large, and we don't want
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it to be part of very patch. :ule,l
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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@ -15,23 +15,24 @@
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style style distance_cutoff angle_cutof N
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<PRE>pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
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</PRE>
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<UL><LI>style = <I>hbond/dreiding/lj</I> or <I>hbond/dreiding/morse</I>
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<LI>n = cosine angle periodicity
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<LI>distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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<LI>inner_distance_cutoff = global inner spline cutoff for Donor-Acceptor interactions (distance units)
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<LI>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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<LI>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
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<LI>interactions (degrees)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style hbond/dreiding/lj 4 5.0 90
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<PRE>pair_style hbond/dreiding/lj 4 4.5 5.0 90
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pair_coeff * * 3 i 100.0 3.1
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pair_coeff * * 2*5 i 100.0 3.1 2 200.0
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pair_coeff * * 2*5 i 100.0 3.1 2 15.0 20.0 135.0
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</PRE>
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<PRE>pair_style hbond/dreiding/morse 2 4.6 75.0
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<PRE>pair_style hbond/dreiding/morse 2 3.0 4.6 75.0
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pair_coeff * * 3 j 100.0 1.0 2.0
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pair_coeff * * 2*5 j 100.0 1.0 2.0 4
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pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -41,8 +42,9 @@ pair_coeff * * 2*5 j 100.0 1.0 2.0 4
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</P>
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<CENTER><IMG SRC = "Eqs/pair_hbond_dreiding.jpg">
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</CENTER>
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<P>where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
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the cosine periodicity.
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<P>where Rin is the inner spline distance cutoff, Rout is the outer
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distance cutoff, theta_c is the angle cutoff, and n is the cosine
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periodicity.
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</P>
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<P>Here, <I>r</I> is the radial distance between the donor (D) and acceptor
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(A) atoms and <I>theta</I> is the bond angle between the acceptor, the
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@ -169,17 +171,18 @@ re-specified in an input script that reads a restart file.
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<A HREF = "run_style.html">run_style respa</A> command. They do not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<P>These pair style tally a count of how many hydrogen bonding
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interactions they calculate each timestep. This quantity can be
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accessed via the <A HREF = "compute_pair.html">compute pair</A> command as a vector
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of values of length 1.
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<P>These pair styles tally a count of how many hydrogen bonding
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interactions they calculate each timestep and the hbond energy. These
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quantities can be accessed via the <A HREF = "compute_pair.html">compute pair</A>
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command as a vector of values of length 2.
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</P>
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<P>To print this quantity to the log file (with a descriptive column
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<P>To print these quantities to the log file (with a descriptive column
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heading) the following commands could be included in an input script:
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</P>
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<PRE>compute hb all pair hbond/dreiding/lj
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variable hb equal c_hb[1]
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thermo_style custom step temp epair v_hb
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variable n_hbond equal c_hb[1] #number hbonds
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variable E_hbond equal c_hb[2] #hbond energy
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thermo_style custom step temp epair v_E_hbond
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</PRE>
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<HR>
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@ -11,23 +11,24 @@ pair_style hbond/dreiding/morse command :h3
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[Syntax:]
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pair_style style distance_cutoff angle_cutof N :pre
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pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof :pre
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style = {hbond/dreiding/lj} or {hbond/dreiding/morse}
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n = cosine angle periodicity
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distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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inner_distance_cutoff = global inner spline cutoff for Donor-Acceptor interactions (distance units)
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outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
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interactions (degrees) :ul
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[Examples:]
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pair_style hbond/dreiding/lj 4 5.0 90
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pair_style hbond/dreiding/lj 4 4.5 5.0 90
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pair_coeff * * 3 i 100.0 3.1
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pair_coeff * * 2*5 i 100.0 3.1 2 200.0 :pre
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pair_coeff * * 2*5 i 100.0 3.1 2 15.0 20.0 135.0 :pre
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pair_style hbond/dreiding/morse 2 4.6 75.0
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pair_style hbond/dreiding/morse 2 3.0 4.6 75.0
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pair_coeff * * 3 j 100.0 1.0 2.0
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pair_coeff * * 2*5 j 100.0 1.0 2.0 4 :pre
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pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0 :pre
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[Description:]
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@ -37,8 +38,9 @@ The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
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:c,image(Eqs/pair_hbond_dreiding.jpg)
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where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
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the cosine periodicity.
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where Rin is the inner spline distance cutoff, Rout is the outer
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distance cutoff, theta_c is the angle cutoff, and n is the cosine
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periodicity.
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Here, {r} is the radial distance between the donor (D) and acceptor
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(A) atoms and {theta} is the bond angle between the acceptor, the
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@ -165,17 +167,18 @@ These pair styles can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. They do not support the
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{inner}, {middle}, {outer} keywords.
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These pair style tally a count of how many hydrogen bonding
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interactions they calculate each timestep. This quantity can be
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accessed via the "compute pair"_compute_pair.html command as a vector
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of values of length 1.
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These pair styles tally a count of how many hydrogen bonding
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interactions they calculate each timestep and the hbond energy. These
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quantities can be accessed via the "compute pair"_compute_pair.html
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command as a vector of values of length 2.
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To print this quantity to the log file (with a descriptive column
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To print these quantities to the log file (with a descriptive column
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heading) the following commands could be included in an input script:
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compute hb all pair hbond/dreiding/lj
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variable hb equal c_hb\[1\]
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thermo_style custom step temp epair v_hb :pre
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variable n_hbond equal c_hb\[1\] #number hbonds
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variable E_hbond equal c_hb\[2\] #hbond energy
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thermo_style custom step temp epair v_E_hbond :pre
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:line
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