forked from lijiext/lammps
226 lines
9.5 KiB
Plaintext
226 lines
9.5 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 lj/long/coul/long command :h3
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pair_style lj/long/coul/long/omp command :h3
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pair_style lj/long/coul/long/opt command :h3
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pair_style lj/long/tip4p/long command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/long/coul/long} or {lj/long/tip4p/long}
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args = list of arguments for a particular style :ul
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{lj/long/coul/long} args = flag_lj flag_coul cutoff (cutoff2)
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flag_lj = {long} or {cut} or {off}
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{long} = use Kspace long-range summation for dispersion 1/r^6 term
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{cut} = use a cutoff on dispersion 1/r^6 term
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{off} = omit disperion 1/r^6 term entirely
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flag_coul = {long} or {off}
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{long} = use Kspace long-range summation for Coulombic 1/r term
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{off} = omit Coulombic term
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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{lj/long/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
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flag_lj = {long} or {cut}
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{long} = use Kspace long-range summation for dispersion 1/r^6 term
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{cut} = use a cutoff
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flag_coul = {long} or {off}
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{long} = use Kspace long-range summation for Coulombic 1/r term
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{off} = omit Coulombic term
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
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[Examples:]
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pair_style lj/long/coul/long cut off 2.5
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pair_style lj/long/coul/long cut long 2.5 4.0
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pair_style lj/long/coul/long long long 2.5 4.0
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pair_coeff * * 1 1
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pair_coeff 1 1 1 3 4 :pre
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pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
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pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0 :pre
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[Description:]
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Style {lj/long/coul/long} computes the standard 12/6 Lennard-Jones and
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Coulombic potentials, given by
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:c,image(Eqs/pair_lj.jpg)
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:c,image(Eqs/pair_coulomb.jpg)
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where C is an energy-conversion constant, Qi and Qj are the charges on
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the 2 atoms, epsilon is the dielectric constant which can be set by
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the "dielectric"_dielectric.html command, and Rc is the cutoff. If
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one cutoff is specified in the pair_style command, it is used for both
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the LJ and Coulombic terms. If two cutoffs are specified, they are
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used as cutoffs for the LJ and Coulombic terms respectively.
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The purpose of this pair style is to capture long-range interactions
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resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
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interactions. This is done by use of the {flag_lj} and {flag_coul}
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settings. The "In 't Veld"_#Veld paper has more details on when it is
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appropriate to include long-range 1/r^6 interactions, using this
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potential.
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Style {lj/long/tip4p/long} implements the TIP4P water model of
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"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
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short distance away from the oxygen atom along the bisector of the HOH
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angle. The atomic types of the oxygen and hydrogen atoms, the bond
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and angle types for OH and HOH interactions, and the distance to the
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massless charge site are specified as pair_style arguments.
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IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
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IDs for the O and 2 H atoms must be consecutive, with the O atom
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first. This is to enable LAMMPS to "find" the 2 H atoms associated
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with each O atom. For example, if the atom ID of an O atom in a TIP4P
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water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
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See the "howto section"_Section_howto.html#howto_8 for more
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information on how to use the TIP4P pair style. Note that the
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neighobr list cutoff for Coulomb interactions is effectively extended
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by a distance 2*qdist when using the TIP4P pair style, to account for
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the offset distance of the fictitious charges on O atoms in water
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molecules. Thus it is typically best in an efficiency sense to use a
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LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
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neighbor list. This leads to slightly larger cost for the long-range
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calculation, so you can test the trade-off for your model.
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If {flag_lj} is set to {long}, no cutoff is used on the LJ 1/r^6
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dispersion term. The long-range portion can be calculated by using
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the "kspace_style ewald/disp or pppm/disp"_kspace_style.html commands.
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The specified LJ cutoff then determines which portion of the LJ
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interactions are computed directly by the pair potential versus which
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part is computed in reciprocal space via the Kspace style. If
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{flag_lj} is set to {cut}, the LJ interactions are simply cutoff, as
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with "pair_style lj/cut"_pair_lj.html.
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If {flag_coul} is set to {long}, no cutoff is used on the Coulombic
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interactions. The long-range portion can calculated by using any of
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several "kspace_style"_kspace_style.html command options such as
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{pppm} or {ewald}. Note that if {flag_lj} is also set to long, then
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the {ewald/disp} or {pppm/disp} Kspace style needs to be used to
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perform the long-range calculations for both the LJ and Coulombic
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interactions. If {flag_coul} is set to {off}, Coulombic interactions
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are not computed.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon (energy units)
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sigma (distance units)
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cutoff1 (distance units)
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cutoff2 (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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The latter 2 coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair.
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Note that if you are using {flag_lj} set to {long}, you
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cannot specify a LJ cutoff for an atom type pair, since only one
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global LJ cutoff is allowed. Similarly, if you are using {flag_coul}
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set to {long}, you cannot specify a Coulombic cutoff for an atom type
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pair, since only one global Coulombic cutoff is allowed.
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For {lj/long/tip4p/long} only the LJ cutoff can be specified
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since a Coulombic cutoff cannot be specified for an individual I,J
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type pair. All type pairs use the same global Coulombic cutoff
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specified in the pair_style command.
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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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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/long pair styles can be mixed.
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The default mix value is {geometric}. See the "pair_modify" command
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for details.
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These pair styles support the "pair_modify"_pair_modify.html shift
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option for the energy of the Lennard-Jones portion of the pair
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interaction, assuming {flag_lj} is {cut}.
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These pair styles support the "pair_modify"_pair_modify.html table and
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table/disp options since they can tabulate the short-range portion of
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the long-range Coulombic and dispersion interactions.
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Thes pair styles do not support the "pair_modify"_pair_modify.html
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tail option for adding a long-range tail correction to the
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Lennard-Jones portion of the energy and pressure.
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These pair styles write their information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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The pair lj/long/coul/long styles support the use of the {inner},
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{middle}, and {outer} keywords of the "run_style respa"_run_style.html
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command, meaning the pairwise forces can be partitioned by distance at
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different levels of the rRESPA hierarchy. See the
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"run_style"_run_style.html command for details.
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:line
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[Restrictions:]
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These styles are part of the KSPACE package. They are only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info. Note that
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the KSPACE package is installed by default.
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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(Veld)
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[(In 't Veld)] In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
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