fix npt/sphere command¶
Accelerator Variants: npt/sphere/omp
fix ID group-ID npt/sphere keyword value ...
ID, group-ID are documented in fix command npt/sphere = style name of this fix command zero or more keyword/value pairs may be appended
keyword = disc
disc value = none = treat particles as 2d discs, not spheres
additional thermostat and barostat related keyword/value pairs from the fix npt command can be appended
fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
Perform constant NPT integration to update position, velocity, and angular velocity each timestep for finite-sizex spherical particles in the group using a Nose/Hoover temperature thermostat and Nose/Hoover pressure barostat. P is pressure; T is temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble.
This fix differs from the fix npt command, which assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational degrees of freedom for the spherical particles, assuming a compute is used which calculates a temperature that includes the rotational degrees of freedom (see below). The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
If the disc keyword is used, then each particle is treated as a 2d disc (circle) instead of as a sphere. This is only possible for 2d simulations, as defined by the dimension keyword. The only difference between discs and spheres in this context is their moment of inertia, as used in the time integration.
Additional parameters affecting the thermostat and barostat are specified by keywords and values documented with the fix npt command. See, for example, discussion of the temp, iso, aniso, and dilate keywords.
The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the NPT integration.
Regardless of what particles are in the fix group, a global pressure is computed for all particles. Similarly, when the size of the simulation box is changed, all particles are re-scaled to new positions, unless the keyword dilate is specified with a value of partial, in which case only the particles in the fix group are re-scaled. The latter can be useful for leaving the coordinates of particles in a solid substrate unchanged and controlling the pressure of a surrounding fluid.
This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/sphere” and “pressure”, as if these commands had been issued:
compute fix-ID_temp all temp/sphere compute fix-ID_press all pressure fix-ID_temp
See the compute temp/sphere and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” since pressure is computed for the entire system.
Note that these are NOT the computes used by thermodynamic output (see the thermo_style command) with ID = thermo_temp and thermo_press. This means you can change the attributes of this fix’s temperature or pressure via the compute_modify command or print this temperature or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used with compute commands that calculate a temperature after removing a “bias” from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by default, but only if the fix_modify command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual compute commands to determine which ones include a bias. In this case, the thermostat works in the following manner: the current temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Speed packages doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See the Speed packages doc page for more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info¶
This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.
The fix_modify temp and press options are supported by this fix. You can use them to assign a compute you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note that the kinetic energy derived from the compute temperature should be consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms.
This fix computes the same global scalar and global vector of quantities as does the fix npt command.
This fix is not invoked during energy minimization.
This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the atom_style sphere command.
All particles in the group must be finite-size spheres. They cannot be point particles.
Use of the disc keyword is only allowed for 2d simulations, as defined by the dimension keyword.