forked from lijiext/lammps
245 lines
9.4 KiB
Plaintext
245 lines
9.4 KiB
Plaintext
"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
|
|
|
|
pair_style hbond/dreiding/lj command :h3
|
|
pair_style hbond/dreiding/lj/omp command :h3
|
|
pair_style hbond/dreiding/morse command :h3
|
|
pair_style hbond/dreiding/morse/omp command :h3
|
|
|
|
[Syntax:]
|
|
|
|
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
|
|
inner_distance_cutoff = global inner 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 hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
|
|
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 :pre
|
|
|
|
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
|
|
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre
|
|
|
|
[Description:]
|
|
|
|
The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
|
|
3-body hydrogen bond interaction for the
|
|
"DREIDING"_Section_howto.html#howto_4 force field, given by:
|
|
|
|
:c,image(Eqs/pair_hbond_dreiding.jpg)
|
|
|
|
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
|
|
hydrogen (H) and the donor atoms:
|
|
|
|
:c,image(Eqs/dreiding_hbond.jpg)
|
|
|
|
These 3-body interactions can be defined for pairs of acceptor and
|
|
donor atoms, based on atom types. For each donor/acceptor atom pair,
|
|
the 3rd atom in the interaction is a hydrogen permanently bonded to
|
|
the donor atom, e.g. in a bond list read in from a data file via the
|
|
"read_data"_read_data.html command. The atom types of possible
|
|
hydrogen atoms for each donor/acceptor type pair are specified by the
|
|
"pair_coeff"_pair_coeff.html command (see below).
|
|
|
|
Style {hbond/dreiding/lj} is the original DREIDING potential of
|
|
"(Mayo)"_#Mayo. It uses a LJ 12/10 functional for the Donor-Acceptor
|
|
interactions. To match the results in the original paper, use n = 4.
|
|
|
|
Style {hbond/dreiding/morse} is an improved version using a Morse
|
|
potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed
|
|
that the Morse form gives improved results for Dendrimer simulations,
|
|
when n = 2.
|
|
|
|
See this "howto section"_Section_howto.html#howto_4 of the manual for
|
|
more information on the DREIDING forcefield.
|
|
|
|
IMPORTANT NOTE: Because the Dreiding hydrogen bond potential is only
|
|
one portion of an overall force field which typically includes other
|
|
pairwise interactions, it is common to use it as a sub-style in a
|
|
"pair_style hybrid/overlay"_pair_hybrid.html command, where another
|
|
pair style provides the repulsive core interaction between pairs of
|
|
atoms, e.g. a 1/r^12 Lennard-Jones repulsion.
|
|
|
|
IMPORTANT NOTE: When using the hbond/dreiding pair styles with
|
|
"pair_style hybrid/overlay"_pair_hybrid.html, you should explicitly
|
|
define pair interactions between the donor atom and acceptor atoms,
|
|
(as well as between these atoms and ALL other atoms in your system).
|
|
Whenever "pair_style hybrid/overlay"_pair_hybrid.html is used,
|
|
ordinary mixing rules are not applied to atoms like the donor and
|
|
acceptor atoms because they are typically referenced in multiple pair
|
|
styles. Neglecting to do this can cause difficult-to-detect physics
|
|
problems.
|
|
|
|
IMPORTANT NOTE: In the original Dreiding force field paper 1-4
|
|
non-bonded interactions ARE allowed. If this is desired for your
|
|
model, use the special_bonds command (e.g. "special_bonds lj 0.0 0.0
|
|
1.0") to turn these interactions on.
|
|
|
|
:line
|
|
|
|
The following coefficients must be defined for pairs of eligible
|
|
donor/acceptor types via the "pair_coeff"_pair_coeff.html command as
|
|
in the examples above.
|
|
|
|
IMPORTANT NOTE: Unlike other pair styles and their associated
|
|
"pair_coeff"_pair_coeff.html commands, you do not need to specify
|
|
pair_coeff settings for all possible I,J type pairs. Only I,J type
|
|
pairs for atoms which act as joint donors/acceptors need to be
|
|
specified; all other type pairs are assumed to be inactive.
|
|
|
|
IMPORTANT NOTE: A "pair_coeff"_pair_coeff.html command can be
|
|
speficied multiple times for the same donor/acceptor type pair. This
|
|
enables multiple hydrogen types to be assigned to the same
|
|
donor/acceptor type pair. For other pair_styles, if the pair_coeff
|
|
command is re-used for the same I.J type pair, the settings for that
|
|
type pair are overwritten. For the hydrogen bond potentials this is
|
|
not the case; the settings are cummulative. This means the only way
|
|
to turn off a previous setting, is to re-use the pair_style command
|
|
and start over.
|
|
|
|
For the {hbond/dreiding/lj} style the list of coefficients is as
|
|
follows:
|
|
|
|
K = hydrogen atom type = 1 to Ntypes
|
|
donor flag = {i} or {j}
|
|
epsilon (energy units)
|
|
sigma (distance units)
|
|
n = exponent in formula above
|
|
distance cutoff Rin (distance units)
|
|
distance cutoff Rout (distance units)
|
|
angle cutoff (degrees) :ul
|
|
|
|
For the {hbond/dreiding/morse} style the list of coefficients is as
|
|
follows:
|
|
|
|
K = hydrogen atom type = 1 to Ntypes
|
|
donor flag = {i} or {j}
|
|
D0 (energy units)
|
|
alpha (1/distance units)
|
|
r0 (distance units)
|
|
n = exponent in formula above
|
|
distance cutoff Rin (distance units)
|
|
distance cutoff Rout (distance units)
|
|
angle cutoff (degrees) :ul
|
|
|
|
A single hydrogen atom type K can be specified, or a wild-card
|
|
asterisk can be used in place of or in conjunction with the K
|
|
arguments to select multiple types as hydrogens. This takes the form
|
|
"*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff command
|
|
doc page for details.
|
|
|
|
If the donor flag is {i}, then the atom of type I in the pair_coeff
|
|
command is treated as the donor, and J is the acceptor. If the donor
|
|
flag is {j}, then the atom of type J in the pair_coeff command is
|
|
treated as the donor and I is the donor. This option is required
|
|
because the "pair_coeff"_pair_coeff.html command requires that I <= J.
|
|
|
|
Epsilon and sigma are settings for the hydrogen bond potential based
|
|
on a Lennard-Jones functional form. Note that sigma is defined as the
|
|
zero-crossing distance for the potential, not as the energy minimum at
|
|
2^(1/6) sigma.
|
|
|
|
D0 and alpha and r0 are settings for the hydrogen bond potential based
|
|
on a Morse functional form.
|
|
|
|
The last 3 coefficients for both styles are optional. If not
|
|
specified, the global n, distance cutoff, and angle cutoff specified
|
|
in the pair_style command are used. If you wish to only override the
|
|
2nd or 3rd optional parameter, you must also specify the preceding
|
|
optional parameters.
|
|
|
|
:line
|
|
|
|
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
|
|
the same as the corresponding style without the suffix. They have
|
|
been optimized to run faster, depending on your available hardware, as
|
|
discussed in "Section_accelerate"_Section_accelerate.html of the
|
|
manual. The accelerated styles take the same arguments and should
|
|
produce the same results, except for round-off and precision issues.
|
|
|
|
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
|
|
packages, respectively. They are only enabled if LAMMPS was built with
|
|
those packages. See the "Making LAMMPS"_Section_start.html#start_3
|
|
section for more info.
|
|
|
|
You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the "-suffix command-line
|
|
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
|
|
use the "suffix"_suffix.html command in your input script.
|
|
|
|
See "Section_accelerate"_Section_accelerate.html of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
:line
|
|
|
|
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
|
|
|
These pair styles do not support mixing. You must explicitly identify
|
|
each donor/acceptor type pair.
|
|
|
|
These styles do not support the "pair_modify"_pair_modify.html shift
|
|
option for the energy of the interactions.
|
|
|
|
The "pair_modify"_pair_modify.html table option is not relevant for
|
|
these pair styles.
|
|
|
|
These pair styles do not support the "pair_modify"_pair_modify.html
|
|
tail option for adding long-range tail corrections to energy and
|
|
pressure.
|
|
|
|
These pair styles do not write their information to "binary restart
|
|
files"_restart.html, so pair_style and pair_coeff commands need to be
|
|
re-specified in an input script that reads a restart file.
|
|
|
|
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 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 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 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
|
|
|
|
[Restrictions:] none
|
|
|
|
[Related commands:]
|
|
|
|
"pair_coeff"_pair_coeff.html
|
|
|
|
[Default:] none
|
|
|
|
:line
|
|
|
|
:link(Mayo)
|
|
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
|
(1990).
|
|
|
|
:link(Liu)
|
|
[(Liu)] Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
|
|
2798 (2009)
|