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(git:6a2e663)
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(git:6a2e663)
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Functions/Subroutines | |
| real(kind=dp) function, public | rescaling_factor (kk, sigma, ndeg, taut, rng_stream) |
| Stochastic velocity rescale, as described in Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101 (2007) More... | |
| real(kind=dp) function, public csvr_system_utils::rescaling_factor | ( | real(kind=dp), intent(in) | kk, |
| real(kind=dp), intent(in) | sigma, | ||
| integer, intent(in) | ndeg, | ||
| real(kind=dp), intent(in) | taut, | ||
| type(rng_stream_type), intent(inout) | rng_stream | ||
| ) |
Stochastic velocity rescale, as described in Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101 (2007)
This subroutine implements Eq.(A7) and returns the new value for the kinetic energy, which can be used to rescale the velocities. The procedure can be applied to all atoms or to smaller groups. If it is applied to intersecting groups in sequence, the kinetic energy that is given as an input (kk) has to be up-to-date with respect to the previous rescalings.
When applied to the entire system, and when performing standard molecular dynamics (fixed c.o.m. (center of mass)) the degrees of freedom of the c.o.m. have to be discarded in the calculation of ndeg, and the c.o.m. momentum HAS TO BE SET TO ZERO. When applied to subgroups, one can chose to: (a) calculate the subgroup kinetic energy in the usual reference frame, and count the c.o.m. in ndeg (b) calculate the subgroup kinetic energy with respect to its c.o.m. motion, discard the c.o.m. in ndeg and apply the rescale factor with respect to the subgroup c.o.m. velocity. They should be almost equivalent. If the subgroups are expected to move one respect to the other, the choice (b) should be better.
If a null relaxation time is required (taut=0.0), the procedure reduces to an istantaneous randomization of the kinetic energy, as described in paragraph IIA.
HOW TO CALCULATE THE EFFECTIVE-ENERGY DRIFT The effective-energy (htilde) drift can be used to check the integrator against discretization errors. The easiest recipe is: htilde = h + conint where h is the total energy (kinetic + potential) and conint is a quantity accumulated along the trajectory as minus the sum of all the increments of kinetic energy due to the thermostat.
Variables: kk ! present value of the kinetic energy of the atoms to be thermalized (in arbitrary units) sigma ! target average value of the kinetic energy (ndeg k_b T/2) (in the same units as kk) ndeg ! number of degrees of freedom of the atoms to be thermalized taut ! relaxation time of the thermostat, in units of 'how often this routine is called'
| kk | ... |
| sigma | ... |
| ndeg | ... |
| taut | ... |
| rng_stream | ... |
Definition at line 80 of file csvr_system_utils.F.
1.9.1