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