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port thread-safe temperature biasing from LAMMPS-ICMS

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This commit is contained in:
Axel Kohlmeyer
2017-05-16 18:15:13 -04:00
parent 06c151421c
commit d2810f9f83
23 changed files with 256 additions and 12 deletions
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23
src/compute_temp_ramp.cpp
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@ -234,6 +234,19 @@ void ComputeTempRamp::remove_bias(int i, double *v)
v[v_dim] -= vbias[v_dim];
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRamp::remove_bias_thr(int i, double *v, double *b)
{
double fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
b[v_dim] = v_lo + fraction*(v_hi - v_lo);
v[v_dim] -= b[v_dim];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
@ -271,6 +284,16 @@ void ComputeTempRamp::restore_bias(int i, double *v)
v[v_dim] += vbias[v_dim];
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias_thr()
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias_thr(int i, double *v, double *b)
{
v[v_dim] += b[v_dim];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called