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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15161 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-06-09 21:55:26 +00:00
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12
doc/src/fix_ehex.txt
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@ -61,8 +61,8 @@ hundred (LJ and SPC/E water) with little computational overhead.
In both algorithms (non-translational) kinetic energy is constantly
swapped between regions (reservoirs) to impose a heat flux onto the
system. The equations of motion are therefore modified if a particle
\(i\) is located inside a reservoir \(\Gamma_{k}\) where \(k>0\). We
use \(\Gamma_{0}\) to label those parts of the simulation box which
\(i\) is located inside a reservoir \(\Gamma_k\) where \(k>0\). We
use \(\Gamma_0\) to label those parts of the simulation box which
are not thermostatted.) The input parameter {region-ID} of this fix
corresponds to \(k\). The energy swap is modelled by introducing an
additional thermostatting force to the equations of motion, such that
@ -77,9 +77,9 @@ The thermostatting force is given by
where \(m_i\) is the mass and \(k(\mathbf r_i)\) maps the particle
position to the respective reservoir. The quantity
\(F_{\Gamma_{k(\mathbf r_i)}}\) corresponds to the input parameter
\(F_\{\Gamma_\{k(\mathbf r_i)\}\}\) corresponds to the input parameter
{F}, which is the energy flux into the reservoir. Furthermore,
\(K_{\Gamma_{k(\mathbf r_i)}}\) and \(v_{\Gamma_{k(\mathbf r_i)}}\)
\(K_\{\Gamma_\{k(\mathbf r_i)\}\}\) and \(v_\{\Gamma_\{k(\mathbf r_i)\}\}\)
denote the non-translational kinetic energy and the centre of mass
velocity of that reservoir. The thermostatting force does not affect
the centre of mass velocities of the individual reservoirs and the
@ -131,13 +131,13 @@ constraints will be satisfied.
NOTE: Even if RATTLE is used and the keywords {com} and {constrain}
are both set, the coordinate constraints will not necessarily be
satisfied up to the target precision. The velocity constraints are
satisfied as long as all sites of a cluster are rescaled (keyyword
satisfied as long as all sites of a cluster are rescaled (keyword
{com}) and the cluster does not span adjacent reservoirs. The current
implementation of the eHEX algorithm introduces a small error in the
bond distances, which goes to zero with order three in the
timestep. For example, in a simulation of SPC/E water with a timestep
of 2 fs the maximum relative error in the bond distances was found to
be on the order of \(10^{-7}\) for relatively large
be on the order of \(10^\{-7\}\) for relatively large
temperature gradients. A higher precision can be achieved by
decreasing the timestep.