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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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32
src/compute_temp_deform.cpp
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@ -221,6 +221,26 @@ void ComputeTempDeform::remove_bias(int i, double *v)
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempDeform::remove_bias_thr(int i, double *v, double *b)
{
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
domain->x2lamda(atom->x[i],lamda);
b[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
b[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
b[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[0] -= b[0];
v[1] -= b[1];
v[2] -= b[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
@ -266,6 +286,18 @@ void ComputeTempDeform::restore_bias(int i, double *v)
v[2] += vbias[2];
}
/* ----------------------------------------------------------------------
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 ComputeTempDeform::restore_bias_thr(int i, double *v, double *b)
{
v[0] += b[0];
v[1] += b[1];
v[2] += b[2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called