Syntax: +
+compute ID group-ID temp/profile xflag yflag zflag binstyle args ++
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 ++ +
Examples: +
+compute myTemp flow temp/profile 1 1 1 x 10 +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 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 +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 velocity for the set of atoms that +are both in the compute group and in the same spatial bin is summed to +compute an average velocity for the bin. This bias velocity is then +subtracted from the velocities of individual atoms in the bin to yield +a thermal velocity. +
+After the spatially-averaged velocity field has been subtracted from +each atom, 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. +
+A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation 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 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. +
+See this howto section of the manual for a +discussion of different ways to compute temperature and perform +thermostatting. Using this compute in conjunction with a +thermostatting fix will effectively implement a PUT, as described in +(Evans). +
+Output info: +
+The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. The vector +values are "extensive", meaning they scale with the number of atoms in +the simulation. +
+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. +
+Related commands: +
+compute temp, compute +temp/ramp, compute +temp/deform, compute +pressure +
+Default: +
+The option default is units = lattice. +
+(Evans) Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). +
+ diff --git a/doc/compute_temp_profile.txt b/doc/compute_temp_profile.txt new file mode 100644 index 0000000000..46ed1c6655 --- /dev/null +++ b/doc/compute_temp_profile.txt @@ -0,0 +1,133 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute temp/profile command :h3 + +[Syntax:] + +compute ID group-ID temp/profile xflag yflag zflag binstyle args :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +temp/profile = style name of this compute command :l +xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :l +binstyle = {x} or {y} or {z} or {xy} or {yz} or {xz} or {xyz} :l + {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 :pre +:ule + +[Examples:] + +compute myTemp flow temp/profile 1 1 1 x 10 +compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out a spatially-averaged 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)"_#Evans. A compute of this style can be used by any command +that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, +"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc. + +The {xflag}, {yflag}, {zflag} settings determine which components of +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"_region.html +command for a discussion of the geometry of tilted boxes in LAMMPS. + +When a temperature is computed, the velocity for the set of atoms that +are both in the compute group and in the same spatial bin is summed to +compute an average velocity for the bin. This bias velocity is then +subtracted from the velocities of individual atoms in the bin to yield +a thermal velocity. + +After the spatially-averaged velocity field has been subtracted from +each atom, 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. + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation 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 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"_compute_modify.html 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_nvt.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix +temp/berendsen"_fix_temp_berendsen, and "fix +langevin"_fix_langevin.html. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as "fix shake"_fix_shake.html and +"fix rigid"_fix_rigid.html. 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"_compute_modify.html command. + +See "this howto section"_Section_howto.html#4_16 of the manual for a +discussion of different ways to compute temperature and perform +thermostatting. Using this compute in conjunction with a +thermostatting fix will effectively implement a PUT, as described in +"(Evans)"_#Evans. + +[Output info:] + +The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. The vector +values are "extensive", meaning they scale with the number of atoms in +the simulation. + +[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. + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +temp/ramp"_compute_temp_ramp.html, "compute +temp/deform"_compute_temp_deform.html, "compute +pressure"_compute_pressure.html + +[Default:] + +The option default is units = lattice. + +:line + +:link(Evans) +[(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).