forked from lijiext/lammps
120 lines
4.9 KiB
Plaintext
120 lines
4.9 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 temp/cs command :h3
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[Syntax:]
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compute ID group-ID temp/cs group1 group2 :pre
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ID, group-ID are documented in "compute"_compute.html command
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temp/cs = style name of this compute command
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group1 = group-ID of either cores or shells
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group2 = group-ID of either shells or cores :ul
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[Examples:]
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compute oxygen_c-s all temp/cs O_core O_shell
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compute core_shells all temp/cs cores shells :pre
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[Description:]
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Define a computation that calculates the temperature of a system based
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on the center-of-mass velocity of atom pairs that are bonded to each
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other. This compute is designed to be used with the adiabatic
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core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
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"Section_howto 25"_Section_howto.html#howto_25 of the manual for an
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overview of the model as implemented in LAMMPS. Specifically, this
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compute enables correct temperature calculation and thermostatting of
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core/shell pairs where it is desirable for the internal degrees of
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freedom of the core/shell pairs to not be influenced by a thermostat.
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A compute of this style can be used by any command that computes a
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temperature via "fix_modify"_fix_modify.html e.g. "fix
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temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
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Note that this compute does not require all ions to be polarized,
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hence defined as core/shell pairs. One can mix core/shell pairs and
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ions without a satellite particle if desired. The compute will
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consider the non-polarized ions according to the physical system.
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For this compute, core and shell particles are specified by two
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respective group IDs, which can be defined using the
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"group"_group.html command. The number of atoms in the two groups
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must be the same and there should be one bond defined between a pair
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of atoms in the two groups. Non-polarized ions which might also be
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included in the treated system should not be included into either of
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these groups, they are taken into account by the {group-ID} (2nd
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argument) of the compute.
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The temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in the group, k = Boltzmann constant, and T = temperature. Note that
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the velocity of each core or shell atom used in the KE calculation is
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the velocity of the center-of-mass (COM) of the core/shell pair the
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atom is part of.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz. In contrast to the temperature, the velocity of
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each core or shell atom is taken individually.
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The change this fix makes to core/shell atom velocities is essentially
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computing the temperature after a "bias" has been removed from the
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velocity of the atoms. This "bias" is the velocity of the atom
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relative to the COM velocity of the core/shell pair. If this compute
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is used with a fix command that performs thermostatting then this bias
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will be subtracted from each atom, thermostatting of the remaining COM
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velocity will be performed, and the bias will be added back in. This
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means the thermostating will effectively be performed on the
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core/shell pairs, instead of on the individual core and shell atoms.
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Thermostatting fixes that work in this way include "fix
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nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
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temp/berendsen"_fix_temp_berendsen.html, and "fix
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langevin"_fix_langevin.html.
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The internal energy of core/shell pairs can be calculated by the
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"compute temp/chunk"_compute_temp_chunk.html command, if chunks are
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defined as core/shell pairs. See "Section_howto
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25"_Section_howto.html#howto_25 for more discussion on how to do this.
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[Output info:]
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This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input.
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The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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The scalar value will be in temperature "units"_units.html. The
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vector values will be in energy "units"_units.html.
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[Restrictions:]
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The number of core/shell pairs contributing to the temperature is
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assumed to be constant for the duration of the run. No fixes should
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be used which generate new molecules or atoms during a simulation.
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[Related commands:]
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"compute temp"_compute_temp.html, "compute
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temp/chunk"_compute_temp_chunk.html
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[Default:] none
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:line
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:link(MitchellFinchham)
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[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
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5, 1031-1038 (1993).
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