fix temp/csvr command¶
fix temp/csld command¶
fix ID group-ID temp/csvr Tstart Tstop Tdamp seed fix ID group-ID temp/csld Tstart Tstop Tdamp seed
ID, group-ID are documented in fix command
temp/csvr or temp/csld = style name of this fix command
Tstart,Tstop = desired temperature at start/end of run
Tstart can be a variable (see below)
Tdamp = temperature damping parameter (time units)
seed = random number seed to use for white noise (positive integer)
fix 1 all temp/csvr 300.0 300.0 100.0 54324 fix 1 all temp/csld 100.0 300.0 10.0 123321
Adjust the temperature with a canonical sampling thermostat that uses global velocity rescaling with Hamiltonian dynamics (temp/csvr) (Bussi1), or Langevin dynamics (temp/csld) (Bussi2). In the case of temp/csvr the thermostat is similar to the empirical Berendsen thermostat in temp/berendsen, but chooses the actual scaling factor from a suitably chosen (gaussian) distribution rather than having it determined from the time constant directly. In the case of temp/csld the velocities are updated to a linear combination of the current velocities with a gaussian distribution of velocities at the desired temperature. Both thermostats are applied every timestep.
The thermostat is applied to only the translational degrees of freedom for the particles, which is an important consideration for finite-size particles which have rotational degrees of freedom are being thermostatted with these fixes. The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below.
The desired temperature at each timestep is a ramped value during the run from Tstart to Tstop. The Tdamp parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (tau or fs or ps - see the units command).
Tstart can be specified as an equal-style variable. In this case, the Tstop setting is ignored. If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature.
Equal-style variables can specify formulas with various mathematical functions, and include thermo_style command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature.
Unlike the fix nvt command which performs Nose/Hoover thermostatting AND time integration, these fixes do NOT perform time integration. They only modify velocities to effect thermostatting. Thus you must use a separate time integration fix, like fix nve to actually update the positions of atoms using the modified velocities. Likewise, these fixes should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix langevin commands.
See the Howto thermostat doc page for a discussion of different ways to compute temperature and perform thermostatting.
These fixes compute a temperature each timestep. To do this, the fix creates its own compute of style “temp”, as if this command had been issued:
compute fix-ID_temp group-ID temp
See the compute temp command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see the thermo_style command) with ID = thermo_temp. This means you can change the attributes of this fix’s temperature (e.g. its degrees-of-freedom) via the compute_modify command or print this temperature during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.
Like other fixes that perform thermostatting, these fixes 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.
An important feature of these thermostats is that they have an associated effective energy that is a constant of motion. The effective energy is the total energy (kinetic + potential) plus the accumulated kinetic energy changes due to the thermostat. The latter quantity is the global scalar computed by these fixes. This feature is useful to check the integration of the equations of motion against discretization errors. In other words, the conservation of the effective energy can be used to choose an appropriate integration timestep. This is similar to the usual paradigm of checking the conservation of the total energy in the microcanonical ensemble.
Restart, fix_modify, output, run start/stop, minimize info¶
These fixes write the cumulative global energy change and the random number generator states 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 selected fix continues in an uninterrupted fashion. The random number generator state can only be restored when the number of processors remains unchanged from what is recorded in the restart file.
The fix_modify temp option is supported by these fixes. You can use it to assign a temperature compute you have defined to these fixes which will be used in its thermostatting procedure, as described above. For consistency, the group used by these fixes and by the compute should be the same.
These fixes compute a global scalar which can be accessed by various output commands. The scalar is the same cumulative energy change due to this fix described in the previous paragraph. The scalar value calculated by this fix is “extensive”.
These fixes are not invoked during energy minimization.
These fixes are not compatible with fix shake.
The fix can be used with dynamic groups as defined by the group command. Likewise it can be used with groups to which atoms are added or deleted over time, e.g. a deposition simulation. However, the conservation properties of the thermostat and barostat are defined for systems with a static set of atoms. You may observe odd behavior if the atoms in a group vary dramatically over time or the atom count becomes very small.
(Bussi1) Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
(Bussi2) Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)