compute temp/cs command

Syntax

compute ID group-ID temp/cs group1 group2
  • ID, group-ID are documented in compute command
  • temp/cs = style name of this compute command
  • group1 = group-ID of either cores or shells
  • group2 = group-ID of either shells or cores

Examples

compute oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells

Description

Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of (Mitchell and Finchham). See the Howto coreshell doc page for an overview of the model as implemented in LAMMPS. Specifically, this compute enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of freedom of the core/shell pairs to not be influenced by a thermostat. A compute of this style can be used by any command that computes a temperature via fix_modify e.g. fix temp/rescale, fix npt, etc.

Note that this compute does not require all ions to be polarized, hence defined as core/shell pairs. One can mix core/shell pairs and ions without a satellite particle if desired. The compute will consider the non-polarized ions according to the physical system.

For this compute, core and shell particles are specified by two respective group IDs, which can be defined using the group command. The number of atoms in the two groups must be the same and there should be one bond defined between a pair of atoms in the two groups. Non-polarized ions which might also be included in the treated system should not be included into either of these groups, they are taken into account by the group-ID (2nd argument) of the compute.

The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the atom is part of.

A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as the above formula, except that v^2 is replaced by vx*vy for the xy component, etc. The 6 components of the vector are ordered xx, yy, zz, xy, xz, yz. In contrast to the temperature, the velocity of each core or shell atom is taken individually.

The change this fix makes to core/shell atom velocities is essentially computing the temperature after a “bias” has been removed from the velocity of the atoms. This “bias” is the velocity of the atom relative to the COM velocity of the core/shell pair. If this compute is used with a fix command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining COM velocity will be performed, and the bias will be added back in. This means the thermostating will effectively be performed on the core/shell pairs, instead of on the individual core and shell atoms. Thermostatting fixes that work in this way include fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin.

The internal energy of core/shell pairs can be calculated by the compute temp/chunk command, if chunks are defined as core/shell pairs. See the Howto coreshell doc page doc page for more discussion on how to do this.

Output info:

This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or vector values from a compute as input.

The scalar value calculated by this compute is “intensive”. The vector values are “extensive”.

The scalar value will be in temperature units. The vector values will be in energy units.

Restrictions

The number of core/shell pairs contributing to the temperature is assumed to be constant for the duration of the run. No fixes should be used which generate new molecules or atoms during a simulation.