forked from lijiext/lammps
92 lines
3.1 KiB
Plaintext
92 lines
3.1 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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compute pe/atom command :h3
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[Syntax:]
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compute ID group-ID pe/atom keyword ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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pe/atom = style name of this compute command
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zero or more keywords may be appended
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keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
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[Examples:]
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compute 1 all pe/atom
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compute 1 all pe/atom pair
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compute 1 all pe/atom pair bond :pre
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[Description:]
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Define a computation that computes the per-atom potential energy for
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each atom in a group. See the "compute pe"_compute_pe.html command if
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you want the potential energy of the entire system.
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The per-atom energy is calculated by the various pair, bond, etc
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potentials defined for the simulation. If no extra keywords are
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listed, then the potential energy is the sum of pair, bond, angle,
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dihedral,improper, and kspace energy. If any extra keywords are
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listed, then only those components are summed to compute the potential
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energy.
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Note that the energy of each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.
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For an energy contribution produced by a small set of atoms (e.g. 4
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atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
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energy is assigned in equal portions to each atom in the set.
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E.g. 1/4 of the dihedral energy to each of the 4 atoms.
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The "dihedral_style charmm"_dihedral_charmm.html style calculates
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pairwise interactions between 1-4 atoms. The energy contribution of
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these terms is included in the pair energy, not the dihedral energy.
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The KSpace contribution is calculated using the method in
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"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
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as specified by the "kspace_style pppm"_kspace_style.html command.
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For PPPM, the calcluation requires 1 extra FFT each timestep that
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per-atom energy is calculated. Thie "document"_PDF/kspace.pdf
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describes how the long-range per-atom energy calculation is performed.
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As an example of per-atom potential energy compared to total potential
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energy, these lines in an input script should yield the same result
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in the last 2 columns of thermo output:
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compute peratom all pe/atom
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compute pe all reduce sum c_peratom
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thermo_style custom step temp etotal press pe c_pe :pre
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IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
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corrections invoked by the "pair_modify tail yes"_pair_modify.html
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command, since those are global contributions to the system energy.
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[Output info:]
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This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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"Section_howto 15"_Section_howto.html#howto_15 for an overview of
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LAMMPS output options.
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The per-atom vector values will be in energy "units"_units.html.
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[Restrictions:]
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[Related commands:]
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"compute pe"_compute_pe.html, "compute
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stress/atom"_compute_stress_atom.html
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[Default:] none
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:line
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:link(Heyes)
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[(Heyes)] Heyes, Phys Rev B 49, 755 (1994),
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