compute temp/profile command¶
Syntax¶
compute ID group-ID temp/profile xflag yflag zflag binstyle args
ID, group-ID are documented in compute command
temp/profile = style name of this compute command
xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
binstyle = x or y or z or xy or yz or xz or xyz
x arg = Nx y arg = Ny z arg = Nz xy args = Nx Ny yz args = Ny Nz xz args = Nx Nz xyz args = Nx Ny Nz Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
zero or more keyword/value pairs may be appended
keyword = out
out value = tensor or bin
Examples¶
compute myTemp flow temp/profile 1 1 1 x 10
compute myTemp flow temp/profile 1 1 1 x 10 out bin
compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
Description¶
Define a computation that calculates the temperature of a group of atoms, after subtracting out a spatially-averaged center-of-mass velocity field, before computing the kinetic energy. This can be useful for thermostatting a collection of atoms undergoing a complex flow, e.g. via a profile-unbiased thermostat (PUT) as described in (Evans). A compute of this style can be used by any command that computes a temperature, e.g. thermo_modify, fix temp/rescale, fix npt, etc.
The xflag, yflag, zflag settings determine which components of average velocity are subtracted out.
The binstyle setting and its Nx, Ny, Nz arguments determine how bins are setup to perform spatial averaging. “Bins” can be 1d slabs, 2d pencils, or 3d bricks depending on which binstyle is used. The simulation box is partitioned conceptually into Nx by Ny by Nz bins. Depending on the binstyle, you may only specify one or two of these values; the others are effectively set to 1 (no binning in that dimension). For non-orthogonal (triclinic) simulation boxes, the bins are “tilted” slabs or pencils or bricks that are parallel to the tilted faces of the box. See the region prism command for a discussion of the geometry of tilted boxes in LAMMPS.
When a temperature is computed, the center-of-mass velocity for the set of atoms that are both in the compute group and in the same spatial bin is calculated. This bias velocity is then subtracted from the velocities of individual atoms in the bin to yield a thermal velocity for each atom. Note that if there is only one atom in the bin, its thermal velocity will thus be 0.0.
After the spatially-averaged velocity field has been subtracted from each atom, the temperature is calculated by the formula KE = (dim*N - dim*Nx*Ny*Nz) k T/2, 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. The dim*Nx*Ny*Nz term are degrees of freedom subtracted to adjust for the removal of the center-of-mass velocity in each of Nx*Ny*Nz bins, as discussed in the (Evans) paper.
If the out keyword is used with a tensor value, which is the default, 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.
If the out keyword is used with a bin value, the count of atoms and computed temperature for each bin are stored for output, as an array of values, as described below. The temperature of each bin is calculated as described above, where the bias velocity is subtracted and only the remaining thermal velocity of atoms in the bin contributes to the temperature. See the note below for how the temperature is normalized by the degrees-of-freedom of atoms in the bin.
The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case.
The removal of the spatially-averaged velocity field by this fix is essentially computing the temperature after a “bias” has been removed from the velocity of the atoms. 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 thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin.
This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.
Note
When using the out keyword with a value of bin, the calculated temperature for each bin does not include the degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the extra option, which is applied to each bin.
See the Howto thermostat page for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in (Evans).
Output info¶
This compute calculates a global scalar (the temperature). Depending on the setting of the out keyword, it also calculates a global vector or array. For out = tensor, it calculates a vector of length 6 (KE tensor), which can be accessed by indices 1-6. For out = bin it calculates a global array which has 2 columns and N rows, where N is the number of bins. The first column contains the number of atoms in that bin. The second contains the temperature of that bin, calculated as described above. The ordering of rows in the array is as follows. Bins in x vary fastest, then y, then z. Thus for a 10x10x10 3d array of bins, there will be 1000 rows. The bin with indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 + ix = 322, where the rows are numbered from 1 to 1000 and the bin indices are numbered from 1 to 10 in each dimension.
These values can be used by any command that uses global scalar or vector or array values from a compute as input. See the Howto output page for an overview of LAMMPS output options.
The scalar value calculated by this compute is “intensive”. The vector values are “extensive”. The array values are “intensive”.
The scalar value will be in temperature units. The vector values will be in energy units. The first column of array values are counts; the values in the second column will be in temperature units.
Restrictions¶
You should not use too large a velocity-binning grid, especially in 3d. In the current implementation, the binned velocity averages are summed across all processors, so this will be inefficient if the grid is too large, and the operation is performed every timestep, as it will be for most thermostats.
Default¶
The option default is out = tensor.
(Evans) Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).