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reformat with clang-format and related changes

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This commit is contained in:
Axel Kohlmeyer
2021-05-11 19:32:57 -04:00
parent 0d4cca5af9
commit 8a507cc7da
10 changed files with 468 additions and 694 deletions
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124
src/USER-BROWNIAN/fix_brownian.cpp
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@ -19,79 +19,60 @@
#include "fix_brownian.h" #include "fix_brownian.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "force.h"
#include "update.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBrownian::FixBrownian(LAMMPS *lmp, int narg, char **arg) : FixBrownian::FixBrownian(LAMMPS *lmp, int narg, char **arg) : FixBrownianBase(lmp, narg, arg)
FixBrownianBase(lmp, narg, arg)
{ {
if (dipole_flag || gamma_t_eigen_flag || gamma_r_eigen_flag || gamma_r_flag) { if (dipole_flag || gamma_t_eigen_flag || gamma_r_eigen_flag || gamma_r_flag) {
error->all(FLERR,"Illegal fix brownian command."); error->all(FLERR, "Illegal fix brownian command.");
} }
if (!gamma_t_flag) { error->all(FLERR, "Illegal fix brownian command."); }
if (!gamma_t_flag) {
error->all(FLERR,"Illegal fix brownian command.");
}
} }
/* ---------------------------------------------------------------------- */
FixBrownian::~FixBrownian()
{
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownian::init() void FixBrownian::init()
{ {
FixBrownianBase::init(); FixBrownianBase::init();
g1 /= gamma_t;
g1 /= gamma_t;
g2 *= sqrt(gamma_t); g2 *= sqrt(gamma_t);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownian::initial_integrate(int /*vflag */) void FixBrownian::initial_integrate(int /*vflag */)
{ {
if (domain->dimension == 2) { if (domain->dimension == 2) {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,1>(); initial_integrate_templated<0, 0, 1>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,1>(); initial_integrate_templated<0, 1, 1>();
} else { } else {
initial_integrate_templated<1,0,1>(); initial_integrate_templated<1, 0, 1>();
} }
} else { } else {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,0>(); initial_integrate_templated<0, 0, 0>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,0>(); initial_integrate_templated<0, 1, 0>();
} else { } else {
initial_integrate_templated<1,0,0>(); initial_integrate_templated<1, 0, 0>();
} }
} }
return; return;
@ -99,8 +80,7 @@ void FixBrownian::initial_integrate(int /*vflag */)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void FixBrownian::initial_integrate_templated()
void FixBrownian::initial_integrate_templated()
{ {
double **x = atom->x; double **x = atom->x;
double **v = atom->v; double **v = atom->v;
@ -110,52 +90,46 @@ void FixBrownian::initial_integrate_templated()
if (igroup == atom->firstgroup) nlocal = atom->nfirst; if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dx,dy,dz; double dx, dy, dz;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (Tp_2D) { if (Tp_2D) {
dz = 0; dz = 0;
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
dx = dt * (g1 * f[i][0] + g2 * (random->uniform()-0.5)); dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
dy = dt * (g1 * f[i][1] + g2 * (random->uniform()-0.5)); dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
} else if (Tp_GAUSS) {
} else if (Tp_GAUSS) { dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
dx = dt * (g1 * f[i][0] + g2 * random->gaussian()); dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
dy = dt * (g1 * f[i][1] + g2 * random->gaussian()); } else {
} else { dx = dt * g1 * f[i][0];
dx = dt * g1 * f[i][0]; dy = dt * g1 * f[i][1];
dy = dt * g1 * f[i][1]; }
}
} else { } else {
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
dx = dt * (g1 * f[i][0] + g2 * (random->uniform()-0.5)); dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
dy = dt * (g1 * f[i][1] + g2 * (random->uniform()-0.5)); dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
dz = dt * (g1 * f[i][2] + g2 * (random->uniform()-0.5)); dz = dt * (g1 * f[i][2] + g2 * (rng->uniform() - 0.5));
} else if (Tp_GAUSS) { } else if (Tp_GAUSS) {
dx = dt * (g1 * f[i][0] + g2 * random->gaussian()); dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
dy = dt * (g1 * f[i][1] + g2 * random->gaussian()); dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
dz = dt * (g1 * f[i][2] + g2 * random->gaussian()); dz = dt * (g1 * f[i][2] + g2 * rng->gaussian());
} else { } else {
dx = dt * g1 * f[i][0]; dx = dt * g1 * f[i][0];
dy = dt * g1 * f[i][1]; dy = dt * g1 * f[i][1];
dz = dt * g1 * f[i][2]; dz = dt * g1 * f[i][2];
} }
} }
x[i][0] += dx; x[i][0] += dx;
v[i][0] = dx/dt; v[i][0] = dx / dt;
x[i][1] += dy;
v[i][1] = dy/dt;
x[i][2] += dz;
v[i][2] = dz/dt;
x[i][1] += dy;
v[i][1] = dy / dt;
x[i][2] += dz;
v[i][2] = dz / dt;
} }
} }
return; return;

14
src/USER-BROWNIAN/fix_brownian.h
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@ -12,9 +12,9 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off
FixStyle(brownian,FixBrownian) FixStyle(brownian,FixBrownian);
// clang-format on
#else #else
#ifndef LMP_FIX_BROWNIAN_H #ifndef LMP_FIX_BROWNIAN_H
@ -27,18 +27,16 @@ namespace LAMMPS_NS {
class FixBrownian : public FixBrownianBase { class FixBrownian : public FixBrownianBase {
public: public:
FixBrownian(class LAMMPS *, int, char **); FixBrownian(class LAMMPS *, int, char **);
virtual ~FixBrownian(); virtual ~FixBrownian() {};
void init(); void init();
void initial_integrate(int); void initial_integrate(int);
private: private:
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
void initial_integrate_templated(); void initial_integrate_templated();
}; };
} } // namespace LAMMPS_NS
#endif #endif
#endif #endif

275
src/USER-BROWNIAN/fix_brownian_asphere.cpp
View File

@ -19,65 +19,44 @@
#include "fix_brownian_asphere.h" #include "fix_brownian_asphere.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) : FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) :
FixBrownianBase(lmp, narg, arg) FixBrownianBase(lmp, narg, arg)
{ {
if (!gamma_t_eigen_flag || !gamma_r_eigen_flag) { if (!gamma_t_eigen_flag || !gamma_r_eigen_flag) {
error->all(FLERR,"Illegal fix brownian command."); error->all(FLERR, "Illegal fix brownian command.");
} }
if (gamma_t_flag || gamma_r_flag) { if (gamma_t_flag || gamma_r_flag) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command.");
}
if (dipole_flag && !atom->mu_flag) if (dipole_flag && !atom->mu_flag)
error->all(FLERR,"Fix brownian/asphere dipole requires atom attribute mu"); error->all(FLERR, "Fix brownian/asphere dipole requires atom attribute mu");
} }
/* ---------------------------------------------------------------------- */
FixBrownianAsphere::~FixBrownianAsphere()
{
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownianAsphere::init() void FixBrownianAsphere::init()
{ {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec) if (!avec) error->all(FLERR, "Compute brownian/asphere requires atom style ellipsoid");
error->all(FLERR,"Compute brownian/asphere requires "
"atom style ellipsoid");
// check that all particles are finite-size ellipsoids // check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK // no point particles allowed, spherical is OK
@ -88,9 +67,7 @@ void FixBrownianAsphere::init()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
if (ellipsoid[i] < 0) if (ellipsoid[i] < 0) error->one(FLERR, "Fix brownian/asphere requires extended particles");
error->one(FLERR,"Fix brownian/asphere requires extended particles");
if (dipole_flag) { if (dipole_flag) {
@ -100,67 +77,62 @@ void FixBrownianAsphere::init()
AtomVecEllipsoid::Bonus *bonus = avec->bonus; AtomVecEllipsoid::Bonus *bonus = avec->bonus;
double Q[3][3]; double Q[3][3];
double **mu = atom->mu; double **mu = atom->mu;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
quat = bonus[ellipsoid[i]].quat; quat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat( quat, Q ); MathExtra::quat_to_mat(quat, Q);
MathExtra::matvec( Q, dipole_body, f_rot ); MathExtra::matvec(Q, dipole_body, f_rot);
mu[i][0] = f_rot[0];
mu[i][1] = f_rot[1];
mu[i][2] = f_rot[2];
mu[i][0] = f_rot[0];
mu[i][1] = f_rot[1];
mu[i][2] = f_rot[2];
} }
} }
} }
FixBrownianBase::init(); FixBrownianBase::init();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownianAsphere::initial_integrate(int /*vflag */) void FixBrownianAsphere::initial_integrate(int /*vflag */)
{ {
if (domain->dimension == 2) { if (domain->dimension == 2) {
if (dipole_flag) { if (dipole_flag) {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,1,1>(); initial_integrate_templated<0, 0, 1, 1>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,1,1>(); initial_integrate_templated<0, 1, 1, 1>();
} else { } else {
initial_integrate_templated<1,0,1,1>(); initial_integrate_templated<1, 0, 1, 1>();
} }
} else { } else {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,0,1>(); initial_integrate_templated<0, 0, 0, 1>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,0,1>(); initial_integrate_templated<0, 1, 0, 1>();
} else { } else {
initial_integrate_templated<1,0,0,1>(); initial_integrate_templated<1, 0, 0, 1>();
} }
} }
} else { } else {
if (dipole_flag) { if (dipole_flag) {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,1,0>(); initial_integrate_templated<0, 0, 1, 0>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,1,0>(); initial_integrate_templated<0, 1, 1, 0>();
} else { } else {
initial_integrate_templated<1,0,1,0>(); initial_integrate_templated<1, 0, 1, 0>();
} }
} else { } else {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,0,0>(); initial_integrate_templated<0, 0, 0, 0>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,0,0>(); initial_integrate_templated<0, 1, 0, 0>();
} else { } else {
initial_integrate_templated<1,0,0,0>(); initial_integrate_templated<1, 0, 0, 0>();
} }
} }
} }
@ -169,7 +141,7 @@ void FixBrownianAsphere::initial_integrate(int /*vflag */)
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D>
void FixBrownianAsphere::initial_integrate_templated() void FixBrownianAsphere::initial_integrate_templated()
{ {
double **x = atom->x; double **x = atom->x;
@ -180,24 +152,17 @@ void FixBrownianAsphere::initial_integrate_templated()
AtomVecEllipsoid::Bonus *bonus = avec->bonus; AtomVecEllipsoid::Bonus *bonus = avec->bonus;
double **mu = atom->mu; double **mu = atom->mu;
double **torque = atom->torque; double **torque = atom->torque;
double qw[4]; double qw[4];
double *quat; double *quat;
int *ellipsoid = atom->ellipsoid; int *ellipsoid = atom->ellipsoid;
if (igroup == atom->firstgroup) nlocal = atom->nfirst; if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// project dipole along x axis of quat // project dipole along x axis of quat
double f_rot[3]; double f_rot[3];
double rotationmatrix_transpose[3][3]; double rotationmatrix_transpose[3][3];
double tmp[3]; double tmp[3];
double dv[3]; double dv[3];
@ -207,51 +172,42 @@ void FixBrownianAsphere::initial_integrate_templated()
// update orientation first // update orientation first
quat = bonus[ellipsoid[i]].quat; quat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat_trans(quat, rotationmatrix_transpose);
MathExtra::quat_to_mat_trans( quat, rotationmatrix_transpose );
// tmp holds angular velocity in body frame // tmp holds angular velocity in body frame
MathExtra::matvec(rotationmatrix_transpose,torque[i],tmp); MathExtra::matvec(rotationmatrix_transpose, torque[i], tmp);
if (Tp_2D) { if (Tp_2D) {
tmp[0] = tmp[1] = 0.0; tmp[0] = tmp[1] = 0.0;
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
tmp[2] = g1*tmp[2]*gamma_r_inv[2] + gamma_r_invsqrt[2]*(random->uniform()-0.5)*g2; tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * (rng->uniform() - 0.5) * g2;
} else if (Tp_GAUSS) {
} else if (Tp_GAUSS) { tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * rng->gaussian() * g2;
tmp[2] = g1*tmp[2]*gamma_r_inv[2] + gamma_r_invsqrt[2]*random->gaussian()*g2; } else {
tmp[2] = g1 * tmp[2] * gamma_r_inv[2];
} else { }
tmp[2] = g1*tmp[2]*gamma_r_inv[2];
}
} else { } else {
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
tmp[0] = g1 * tmp[0] * gamma_r_inv[0] + gamma_r_invsqrt[0] * (rng->uniform() - 0.5) * g2;
tmp[0] = g1*tmp[0]*gamma_r_inv[0] + gamma_r_invsqrt[0]*(random->uniform()-0.5)*g2; tmp[1] = g1 * tmp[1] * gamma_r_inv[1] + gamma_r_invsqrt[1] * (rng->uniform() - 0.5) * g2;
tmp[1] = g1*tmp[1]*gamma_r_inv[1] + gamma_r_invsqrt[1]*(random->uniform()-0.5)*g2; tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * (rng->uniform() - 0.5) * g2;
tmp[2] = g1*tmp[2]*gamma_r_inv[2] + gamma_r_invsqrt[2]*(random->uniform()-0.5)*g2; } else if (Tp_GAUSS) {
tmp[0] = g1 * tmp[0] * gamma_r_inv[0] + gamma_r_invsqrt[0] * rng->gaussian() * g2;
} else if (Tp_GAUSS) { tmp[1] = g1 * tmp[1] * gamma_r_inv[1] + gamma_r_invsqrt[1] * rng->gaussian() * g2;
tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * rng->gaussian() * g2;
tmp[0] = g1*tmp[0]*gamma_r_inv[0] + gamma_r_invsqrt[0]*random->gaussian()*g2; } else {
tmp[1] = g1*tmp[1]*gamma_r_inv[1] + gamma_r_invsqrt[1]*random->gaussian()*g2; tmp[0] = g1 * tmp[0] * gamma_r_inv[0];
tmp[2] = g1*tmp[2]*gamma_r_inv[2] + gamma_r_invsqrt[2]*random->gaussian()*g2; tmp[1] = g1 * tmp[1] * gamma_r_inv[1];
tmp[2] = g1 * tmp[2] * gamma_r_inv[2];
} else { }
tmp[0] = g1*tmp[0]*gamma_r_inv[0];
tmp[1] = g1*tmp[1]*gamma_r_inv[1];
tmp[2] = g1*tmp[2]*gamma_r_inv[2];
}
} }
// convert body frame angular velocity to quaternion // convert body frame angular velocity to quaternion
MathExtra::quatvec(quat,tmp,qw); MathExtra::quatvec(quat, tmp, qw);
quat[0] = quat[0] + 0.5*dt*qw[0]; quat[0] = quat[0] + 0.5 * dt * qw[0];
quat[1] = quat[1] + 0.5*dt*qw[1]; quat[1] = quat[1] + 0.5 * dt * qw[1];
quat[2] = quat[2] + 0.5*dt*qw[2]; quat[2] = quat[2] + 0.5 * dt * qw[2];
quat[3] = quat[3] + 0.5*dt*qw[3]; quat[3] = quat[3] + 0.5 * dt * qw[3];
// normalisation introduces the stochastic drift term // normalisation introduces the stochastic drift term
// to recover the Boltzmann distribution for the case of conservative torques // to recover the Boltzmann distribution for the case of conservative torques
@ -260,99 +216,56 @@ void FixBrownianAsphere::initial_integrate_templated()
// next, update centre of mass positions and velocities // next, update centre of mass positions and velocities
// tmp now holds force in body frame // tmp now holds force in body frame
MathExtra::matvec(rotationmatrix_transpose,f[i],tmp); MathExtra::matvec(rotationmatrix_transpose, f[i], tmp);
// and then converts to gamma_t^{-1} * F (velocity) in body frame // and then converts to gamma_t^{-1} * F (velocity) in body frame
if (Tp_2D) { if (Tp_2D) {
tmp[2] = 0.0; tmp[2] = 0.0;
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
tmp[0] = g1*tmp[0]*gamma_t_inv[0] tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * (rng->uniform() - 0.5) * g2;
+ gamma_t_invsqrt[0]*(random->uniform()-0.5)*g2; tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * (rng->uniform() - 0.5) * g2;
tmp[1] = g1*tmp[1]*gamma_t_inv[1] } else if (Tp_GAUSS) {
+ gamma_t_invsqrt[1]*(random->uniform()-0.5)*g2; tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * rng->gaussian() * g2;
tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * rng->gaussian() * g2;
} else if (Tp_GAUSS) { } else {
tmp[0] = g1*tmp[0]*gamma_t_inv[0] tmp[0] = g1 * tmp[0] * gamma_t_inv[0];
+ gamma_t_invsqrt[0]*random->gaussian()*g2; tmp[1] = g1 * tmp[1] * gamma_t_inv[1];
tmp[1] = g1*tmp[1]*gamma_t_inv[1] }
+ gamma_t_invsqrt[1]*random->gaussian()*g2;
} else {
tmp[0] = g1*tmp[0]*gamma_t_inv[0];
tmp[1] = g1*tmp[1]*gamma_t_inv[1];
}
} else { } else {
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * (rng->uniform() - 0.5) * g2;
tmp[0] = g1*tmp[0]*gamma_t_inv[0] tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * (rng->uniform() - 0.5) * g2;
+ gamma_t_invsqrt[0]*(random->uniform()-0.5)*g2; tmp[2] = g1 * tmp[2] * gamma_t_inv[2] + gamma_t_invsqrt[2] * (rng->uniform() - 0.5) * g2;
tmp[1] = g1*tmp[1]*gamma_t_inv[1] } else if (Tp_GAUSS) {
+ gamma_t_invsqrt[1]*(random->uniform()-0.5)*g2; tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * rng->gaussian() * g2;
tmp[2] = g1*tmp[2]*gamma_t_inv[2] tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * rng->gaussian() * g2;
+ gamma_t_invsqrt[2]*(random->uniform()-0.5)*g2; tmp[2] = g1 * tmp[2] * gamma_t_inv[2] + gamma_t_invsqrt[2] * rng->gaussian() * g2;
} else {
} else if (Tp_GAUSS) { tmp[0] = g1 * tmp[0] * gamma_t_inv[0];
tmp[1] = g1 * tmp[1] * gamma_t_inv[1];
tmp[0] = g1*tmp[0]*gamma_t_inv[0] tmp[2] = g1 * tmp[2] * gamma_t_inv[2];
+ gamma_t_invsqrt[0]*random->gaussian()*g2; }
tmp[1] = g1*tmp[1]*gamma_t_inv[1]
+ gamma_t_invsqrt[1]*random->gaussian()*g2;
tmp[2] = g1*tmp[2]*gamma_t_inv[2]
+ gamma_t_invsqrt[2]*random->gaussian()*g2;
} else {
tmp[0] = g1*tmp[0]*gamma_t_inv[0];
tmp[1] = g1*tmp[1]*gamma_t_inv[1];
tmp[2] = g1*tmp[2]*gamma_t_inv[2];
}
} }
// finally, convert this back to lab-frame velocity and store in dv // finally, convert this back to lab-frame velocity and store in dv
MathExtra::transpose_matvec(rotationmatrix_transpose, tmp, dv ); MathExtra::transpose_matvec(rotationmatrix_transpose, tmp, dv);
/*
if (Tp_UNIFORM) {
dv[0] = dt * (g1 * f[i][0] + g2 * (random->uniform()-0.5));
dv[1] = dt * (g1 * f[i][1] + g2 * (random->uniform()-0.5));
dv[2] = dt * (g1 * f[i][2] + g2 * (random->uniform()-0.5));
} else if (Tp_GAUSS) {
dv[0] = dt * (g1 * f[i][0] + g2 * random->gaussian());
dv[1] = dt * (g1 * f[i][1] + g2 * random->gaussian());
dv[2] = dt * (g1 * f[i][2] + g2 * random->gaussian());
} else {
dv[0] = dt * g1 * f[i][0];
dv[1] = dt * g1 * f[i][1];
dv[2] = dt * g1 * f[i][2];
}
*/
v[i][0] = dv[0]; v[i][0] = dv[0];
v[i][1] = dv[1]; v[i][1] = dv[1];
v[i][2] = dv[2]; v[i][2] = dv[2];
x[i][0] += dv[0]*dt; x[i][0] += dv[0] * dt;
x[i][1] += dv[1]*dt; x[i][1] += dv[1] * dt;
x[i][2] += dv[2]*dt; x[i][2] += dv[2] * dt;
if (Tp_DIPOLE) { if (Tp_DIPOLE) {
MathExtra::quat_to_mat_trans(quat, rotationmatrix_transpose);
MathExtra::quat_to_mat_trans( quat, rotationmatrix_transpose ); MathExtra::transpose_matvec(rotationmatrix_transpose, dipole_body, f_rot);
MathExtra::transpose_matvec(rotationmatrix_transpose, dipole_body, f_rot ); mu[i][0] = f_rot[0];
mu[i][1] = f_rot[1];
mu[i][0] = f_rot[0]; mu[i][2] = f_rot[2];
mu[i][1] = f_rot[1];
mu[i][2] = f_rot[2];
} }
} }
} }
return; return;

19
src/USER-BROWNIAN/fix_brownian_asphere.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off
FixStyle(brownian/asphere,FixBrownianAsphere) FixStyle(brownian/asphere,FixBrownianAsphere);
// clang-format on
#else #else
#ifndef LMP_FIX_BROWNIAN_ASPHERE_H #ifndef LMP_FIX_BROWNIAN_ASPHERE_H
@ -27,25 +27,18 @@ namespace LAMMPS_NS {
class FixBrownianAsphere : public FixBrownianBase { class FixBrownianAsphere : public FixBrownianBase {
public: public:
FixBrownianAsphere(class LAMMPS *, int, char **); FixBrownianAsphere(class LAMMPS *, int, char **);
virtual ~FixBrownianAsphere(); virtual ~FixBrownianAsphere() {};
void initial_integrate(int); void initial_integrate(int);
void init(); void init();
protected: protected:
class AtomVecEllipsoid *avec; class AtomVecEllipsoid *avec;
private: private:
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D>
void initial_integrate_templated(); void initial_integrate_templated();
}; };
} // namespace LAMMPS_NS
}
#endif #endif
#endif #endif

176
src/USER-BROWNIAN/fix_brownian_base.cpp
View File

@ -19,28 +19,26 @@
#include "fix_brownian.h" #include "fix_brownian.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "force.h"
#include "update.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
Fix(lmp, narg, arg)
{ {
time_integrate = 1; time_integrate = 1;
noise_flag = 1; noise_flag = 1;
@ -49,141 +47,122 @@ FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) :
gamma_t_eigen_flag = gamma_r_eigen_flag = 0; gamma_t_eigen_flag = gamma_r_eigen_flag = 0;
dipole_flag = 0; dipole_flag = 0;
if (narg < 5) if (narg < 5) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command.");
temp = utils::numeric(FLERR,arg[3],false,lmp); temp = utils::numeric(FLERR, arg[3], false, lmp);
if (temp <= 0) error->all(FLERR,"Fix brownian temp must be > 0."); if (temp <= 0) error->all(FLERR, "Fix brownian temp must be > 0.");
seed = utils::inumeric(FLERR,arg[4],false,lmp);
if (seed <= 0) error->all(FLERR,"Fix brownian seed must be > 0.");
seed = utils::inumeric(FLERR, arg[4], false, lmp);
if (seed <= 0) error->all(FLERR, "Fix brownian seed must be > 0.");
int iarg = 5; int iarg = 5;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"rng") == 0) { if (strcmp(arg[iarg], "rng") == 0) {
if (narg == iarg + 1) { if (narg == iarg + 1) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command."); if (strcmp(arg[iarg + 1], "uniform") == 0) {
} noise_flag = 1;
if (strcmp(arg[iarg + 1],"uniform") == 0) { } else if (strcmp(arg[iarg + 1], "gaussian") == 0) {
noise_flag = 1; noise_flag = 1;
} else if (strcmp(arg[iarg + 1],"gaussian") == 0) { gaussian_noise_flag = 1;
noise_flag = 1; } else if (strcmp(arg[iarg + 1], "none") == 0) {
gaussian_noise_flag = 1; noise_flag = 0;
} else if (strcmp(arg[iarg + 1],"none") == 0) {
noise_flag = 0;
} else { } else {
error->all(FLERR,"Illegal fix brownian command."); error->all(FLERR, "Illegal fix brownian command.");
} }
iarg = iarg + 2; iarg = iarg + 2;
} else if (strcmp(arg[iarg],"dipole") == 0) { } else if (strcmp(arg[iarg], "dipole") == 0) {
if (narg == iarg + 3) { if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command.");
}
dipole_flag = 1; dipole_flag = 1;
dipole_body = new double[3]; dipole_body = new double[3];
dipole_body[0] = utils::numeric(FLERR,arg[iarg+1],false,lmp); dipole_body[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
dipole_body[1] = utils::numeric(FLERR,arg[iarg+2],false,lmp); dipole_body[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
dipole_body[2] = utils::numeric(FLERR,arg[iarg+3],false,lmp); dipole_body[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
iarg = iarg + 4; iarg = iarg + 4;
} else if (strcmp(arg[iarg],"gamma_t_eigen") == 0) { } else if (strcmp(arg[iarg], "gamma_t_eigen") == 0) {
if (narg == iarg + 3) { if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command.");
}
gamma_t_eigen_flag = 1; gamma_t_eigen_flag = 1;
gamma_t_inv = new double[3]; gamma_t_inv = new double[3];
gamma_t_invsqrt = new double[3]; gamma_t_invsqrt = new double[3];
gamma_t_inv[0] = 1./utils::numeric(FLERR,arg[iarg+1],false,lmp); gamma_t_inv[0] = 1. / utils::numeric(FLERR, arg[iarg + 1], false, lmp);
gamma_t_inv[1] = 1./utils::numeric(FLERR,arg[iarg+2],false,lmp); gamma_t_inv[1] = 1. / utils::numeric(FLERR, arg[iarg + 2], false, lmp);
if (domain->dimension == 2) { if (domain->dimension == 2) {
if (strcmp(arg[iarg+3],"inf") != 0) { if (strcmp(arg[iarg + 3], "inf") != 0) {
error->all(FLERR,"Fix brownian gamma_t_eigen third value must be inf for 2D system."); error->all(FLERR, "Fix brownian gamma_t_eigen third value must be inf for 2D system.");
} }
gamma_t_inv[2] = 0; gamma_t_inv[2] = 0;
} else { } else {
gamma_t_inv[2] = 1./utils::numeric(FLERR,arg[iarg+3],false,lmp); gamma_t_inv[2] = 1.0 / utils::numeric(FLERR, arg[iarg + 3], false, lmp);
} }
if (gamma_t_inv[0] < 0 || gamma_t_inv[1] < 0 || gamma_t_inv[2] < 0) if (gamma_t_inv[0] < 0 || gamma_t_inv[1] < 0 || gamma_t_inv[2] < 0)
error->all(FLERR,"Fix brownian gamma_t_eigen values must be > 0."); error->all(FLERR, "Fix brownian gamma_t_eigen values must be > 0.");
gamma_t_invsqrt[0] = sqrt(gamma_t_inv[0]); gamma_t_invsqrt[0] = sqrt(gamma_t_inv[0]);
gamma_t_invsqrt[1] = sqrt(gamma_t_inv[1]); gamma_t_invsqrt[1] = sqrt(gamma_t_inv[1]);
gamma_t_invsqrt[2] = sqrt(gamma_t_inv[2]); gamma_t_invsqrt[2] = sqrt(gamma_t_inv[2]);
iarg = iarg + 4; iarg = iarg + 4;
} else if (strcmp(arg[iarg],"gamma_r_eigen") == 0) { } else if (strcmp(arg[iarg], "gamma_r_eigen") == 0) {
if (narg == iarg + 3) { if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
error->all(FLERR,"Illegal fix brownian command.");
}
gamma_r_eigen_flag = 1; gamma_r_eigen_flag = 1;
gamma_r_inv = new double[3]; gamma_r_inv = new double[3];
gamma_r_invsqrt = new double[3]; gamma_r_invsqrt = new double[3];
if (domain->dimension == 2) { if (domain->dimension == 2) {
if (strcmp(arg[iarg+1],"inf") != 0) { if (strcmp(arg[iarg + 1], "inf") != 0) {
error->all(FLERR,"Fix brownian gamma_r_eigen first value must be inf for 2D system."); error->all(FLERR, "Fix brownian gamma_r_eigen first value must be inf for 2D system.");
} }
gamma_r_inv[0] = 0; gamma_r_inv[0] = 0;
if (strcmp(arg[iarg+2],"inf") != 0) { if (strcmp(arg[iarg + 2], "inf") != 0) {
error->all(FLERR,"Fix brownian gamma_r_eigen second value must be inf for 2D system."); error->all(FLERR, "Fix brownian gamma_r_eigen second value must be inf for 2D system.");
} }
gamma_r_inv[1] = 0; gamma_r_inv[1] = 0;
} else { } else {
gamma_r_inv[0] = 1./utils::numeric(FLERR,arg[iarg+1],false,lmp); gamma_r_inv[0] = 1. / utils::numeric(FLERR, arg[iarg + 1], false, lmp);
gamma_r_inv[1] = 1./utils::numeric(FLERR,arg[iarg+2],false,lmp); gamma_r_inv[1] = 1. / utils::numeric(FLERR, arg[iarg + 2], false, lmp);
} }
gamma_r_inv[2] = 1./utils::numeric(FLERR,arg[iarg+3],false,lmp); gamma_r_inv[2] = 1. / utils::numeric(FLERR, arg[iarg + 3], false, lmp);
if (gamma_r_inv[0] < 0 || gamma_r_inv[1] < 0 || gamma_r_inv[2] < 0) if (gamma_r_inv[0] < 0 || gamma_r_inv[1] < 0 || gamma_r_inv[2] < 0)
error->all(FLERR,"Fix brownian gamma_r_eigen values must be > 0."); error->all(FLERR, "Fix brownian gamma_r_eigen values must be > 0.");
gamma_r_invsqrt[0] = sqrt(gamma_r_inv[0]); gamma_r_invsqrt[0] = sqrt(gamma_r_inv[0]);
gamma_r_invsqrt[1] = sqrt(gamma_r_inv[1]); gamma_r_invsqrt[1] = sqrt(gamma_r_inv[1]);
gamma_r_invsqrt[2] = sqrt(gamma_r_inv[2]); gamma_r_invsqrt[2] = sqrt(gamma_r_inv[2]);
iarg = iarg + 4; iarg = iarg + 4;
} else if (strcmp(arg[iarg],"gamma_t") == 0) { } else if (strcmp(arg[iarg], "gamma_t") == 0) {
if (narg == iarg + 1) { if (narg == iarg + 1) { error->all(FLERR, "Illegal fix brownian command."); }
error->all(FLERR,"Illegal fix brownian command.");
}
gamma_t_flag = 1; gamma_t_flag = 1;
gamma_t = utils::numeric(FLERR,arg[iarg+1],false,lmp); gamma_t = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
if (gamma_t <= 0) if (gamma_t <= 0) error->all(FLERR, "Fix brownian gamma_t must be > 0.");
error->all(FLERR,"Fix brownian gamma_t must be > 0.");
iarg = iarg + 2; iarg = iarg + 2;
} else if (strcmp(arg[iarg],"gamma_r") == 0) { } else if (strcmp(arg[iarg], "gamma_r") == 0) {
if (narg == iarg + 1) { if (narg == iarg + 1) { error->all(FLERR, "Illegal fix brownian command."); }
error->all(FLERR,"Illegal fix brownian command.");
}
gamma_r_flag = 1; gamma_r_flag = 1;
gamma_r = utils::numeric(FLERR,arg[iarg+1],false,lmp); gamma_r = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
if (gamma_r <= 0) if (gamma_r <= 0) error->all(FLERR, "Fix brownian gamma_r must be > 0.");
error->all(FLERR,"Fix brownian gamma_r must be > 0.");
iarg = iarg + 2; iarg = iarg + 2;
} else { } else {
error->all(FLERR,"Illegal fix brownian command."); error->all(FLERR, "Illegal fix brownian command.");
} }
} }
// initialize Marsaglia RNG with processor-unique seed // initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me); rng = new RanMars(lmp, seed + comm->me);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -201,24 +180,18 @@ FixBrownianBase::~FixBrownianBase()
{ {
if (gamma_t_eigen_flag) { if (gamma_t_eigen_flag) {
delete [] gamma_t_inv; delete[] gamma_t_inv;
delete [] gamma_t_invsqrt; delete[] gamma_t_invsqrt;
} }
if (gamma_r_eigen_flag) { if (gamma_r_eigen_flag) {
delete [] gamma_r_inv; delete[] gamma_r_inv;
delete [] gamma_r_invsqrt; delete[] gamma_r_invsqrt;
} }
if (dipole_flag) { if (dipole_flag) { delete[] dipole_body; }
delete [] dipole_body; delete rng;
}
delete random;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownianBase::init() void FixBrownianBase::init()
@ -226,25 +199,20 @@ void FixBrownianBase::init()
dt = update->dt; dt = update->dt;
sqrtdt = sqrt(dt); sqrtdt = sqrt(dt);
g1 = force->ftm2v; g1 = force->ftm2v;
if (noise_flag == 0) { if (noise_flag == 0) {
g2 = 0; g2 = 0;
} else if (gaussian_noise_flag == 1) { } else if (gaussian_noise_flag == 1) {
g2 = sqrt(2 * force->boltz*temp/dt/force->mvv2e); g2 = sqrt(2 * force->boltz * temp / dt / force->mvv2e);
} else { } else {
g2 = sqrt( 24 * force->boltz*temp/dt/force->mvv2e); g2 = sqrt(24 * force->boltz * temp / dt / force->mvv2e);
} }
} }
void FixBrownianBase::reset_dt() void FixBrownianBase::reset_dt()
{ {
double sqrtdt_old = sqrtdt; double sqrtdt_old = sqrtdt;
dt = update->dt; dt = update->dt;
sqrtdt = sqrt(dt); sqrtdt = sqrt(dt);
g2 *= sqrtdt_old/sqrtdt; g2 *= sqrtdt_old / sqrtdt;
} }

40
src/USER-BROWNIAN/fix_brownian_base.h
View File

@ -11,7 +11,6 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifndef LMP_FIX_BROWNIAN_BASE_H #ifndef LMP_FIX_BROWNIAN_BASE_H
#define LMP_FIX_BROWNIAN_BASE_H #define LMP_FIX_BROWNIAN_BASE_H
@ -19,7 +18,6 @@
namespace LAMMPS_NS { namespace LAMMPS_NS {
class FixBrownianBase : public Fix { class FixBrownianBase : public Fix {
public: public:
FixBrownianBase(class LAMMPS *, int, char **); FixBrownianBase(class LAMMPS *, int, char **);
@ -29,42 +27,32 @@ class FixBrownianBase : public Fix {
void reset_dt(); void reset_dt();
protected: protected:
int seed; // RNG seed int seed; // RNG seed
double dt, sqrtdt; // time step interval and its sqrt double dt, sqrtdt; // time step interval and its sqrt
int gamma_t_flag; // 0/1 if isotropic translational damping is unset/set
int gamma_r_flag; // 0/1 if isotropic rotational damping is unset/set
int gamma_t_eigen_flag; // 0/1 if anisotropic translational damping is unset/set
int gamma_r_eigen_flag; // 0/1 if anisotropic rotational damping is unset/set
int gamma_t_flag; // 0/1 if isotropic translational damping is unset/set double gamma_t, gamma_r; // translational and rotational (isotropic) damping params
int gamma_r_flag; // 0/1 if isotropic rotational damping is unset/set double *gamma_t_inv; // anisotropic damping parameter eigenvalues
double gamma_t,gamma_r; // translational and rotational (isotropic) damping params
int gamma_t_eigen_flag; // 0/1 if anisotropic translational damping is unset/set
int gamma_r_eigen_flag; // 0/1 if anisotropic rotational damping is unset/set
double *gamma_t_inv; // anisotropic damping parameter eigenvalues
double *gamma_r_inv; double *gamma_r_inv;
double *gamma_t_invsqrt; double *gamma_t_invsqrt;
double *gamma_r_invsqrt; double *gamma_r_invsqrt;
int dipole_flag; // set if dipole is used for asphere int dipole_flag; // set if dipole is used for asphere
double *dipole_body; // direction dipole is slaved to in body frame double *dipole_body; // direction dipole is slaved to in body frame
int noise_flag; // 0/1 for noise off/on int noise_flag; // 0/1 for noise off/on
int gaussian_noise_flag; // 0/1 for uniform/gaussian noise int gaussian_noise_flag; // 0/1 for uniform/gaussian noise
double temp; // temperature
double g1,g2; // prefactors in time stepping
class RanMars *random;
double temp; // temperature
double g1, g2; // prefactors in time stepping
class RanMars *rng;
}; };
} } // namespace LAMMPS_NS
#endif #endif
/* ERROR/WARNING messages: /* ERROR/WARNING messages:

201
src/USER-BROWNIAN/fix_brownian_sphere.cpp
View File

@ -19,101 +19,74 @@
#include "fix_brownian_sphere.h" #include "fix_brownian_sphere.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "force.h"
#include "update.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) : FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) :
FixBrownianBase(lmp, narg, arg) FixBrownianBase(lmp, narg, arg)
{ {
if (gamma_t_eigen_flag || gamma_r_eigen_flag) { if (gamma_t_eigen_flag || gamma_r_eigen_flag) {
error->all(FLERR,"Illegal fix brownian command."); error->all(FLERR, "Illegal fix brownian command.");
} }
if (!gamma_t_flag || !gamma_r_flag) { if (!gamma_t_flag || !gamma_r_flag) { error->all(FLERR, "Illegal fix brownian command."); }
error->all(FLERR,"Illegal fix brownian command."); if (!atom->mu_flag) error->all(FLERR, "Fix brownian/sphere requires atom attribute mu");
}
if (!atom->mu_flag)
error->all(FLERR,"Fix brownian/sphere requires atom attribute mu");
} }
/* ---------------------------------------------------------------------- */
FixBrownianSphere::~FixBrownianSphere()
{
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownianSphere::init() void FixBrownianSphere::init()
{ {
FixBrownianBase::init(); FixBrownianBase::init();
g3 = g1/gamma_r; g3 = g1 / gamma_r;
g4 = g2/sqrt(gamma_r); g4 = g2 / sqrt(gamma_r);
g1 /= gamma_t; g1 /= gamma_t;
g2 /= sqrt(gamma_t); g2 /= sqrt(gamma_t);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBrownianSphere::initial_integrate(int /*vflag */) void FixBrownianSphere::initial_integrate(int /*vflag */)
{ {
if (domain->dimension == 2) { if (domain->dimension == 2) {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,1>(); initial_integrate_templated<0, 0, 1>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,1>(); initial_integrate_templated<0, 1, 1>();
} else { } else {
initial_integrate_templated<1,0,1>(); initial_integrate_templated<1, 0, 1>();
} }
} else { } else {
if (!noise_flag) { if (!noise_flag) {
initial_integrate_templated<0,0,0>(); initial_integrate_templated<0, 0, 0>();
} else if (gaussian_noise_flag) { } else if (gaussian_noise_flag) {
initial_integrate_templated<0,1,0>(); initial_integrate_templated<0, 1, 0>();
} else { } else {
initial_integrate_templated<1,0,0>(); initial_integrate_templated<1, 0, 0>();
} }
} }
return; return;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
void FixBrownianSphere::initial_integrate_templated() void FixBrownianSphere::initial_integrate_templated()
{ {
double **x = atom->x; double **x = atom->x;
@ -121,112 +94,92 @@ void FixBrownianSphere::initial_integrate_templated()
double **f = atom->f; double **f = atom->f;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double wx,wy,wz; double wx, wy, wz;
double **torque = atom->torque; double **torque = atom->torque;
double **mu = atom->mu; double **mu = atom->mu;
double mux,muy,muz,mulen; double mux, muy, muz, mulen;
if (igroup == atom->firstgroup) nlocal = atom->nfirst; if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dx, dy, dz;
double dx,dy,dz;
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (Tp_2D) { if (Tp_2D) {
dz = 0; dz = 0;
wx = wy = 0; wx = wy = 0;
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
dx = dt * (g1 * f[i][0] + g2 * (random->uniform()-0.5)); dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
dy = dt * (g1 * f[i][1] + g2 * (random->uniform()-0.5)); dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
wz = (random->uniform()-0.5)*g4; wz = (rng->uniform() - 0.5) * g4;
} else if (Tp_GAUSS) {
} else if (Tp_GAUSS) { dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
dx = dt * (g1 * f[i][0] + g2 * random->gaussian()); dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
dy = dt * (g1 * f[i][1] + g2 * random->gaussian()); wz = rng->gaussian() * g4;
wz = random->gaussian()*g4; } else {
dx = dt * g1 * f[i][0];
dy = dt * g1 * f[i][1];
} else { wz = 0;
dx = dt * g1 * f[i][0]; }
dy = dt * g1 * f[i][1];
wz = 0;
}
} else { } else {
if (Tp_UNIFORM) { if (Tp_UNIFORM) {
dx = dt * (g1 * f[i][0] + g2 * (random->uniform()-0.5)); dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
dy = dt * (g1 * f[i][1] + g2 * (random->uniform()-0.5)); dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
dz = dt * (g1 * f[i][2] + g2 * (random->uniform()-0.5)); dz = dt * (g1 * f[i][2] + g2 * (rng->uniform() - 0.5));
wx = (random->uniform()-0.5)*g4; wx = (rng->uniform() - 0.5) * g4;
wy = (random->uniform()-0.5)*g4; wy = (rng->uniform() - 0.5) * g4;
wz = (random->uniform()-0.5)*g4; wz = (rng->uniform() - 0.5) * g4;
} else if (Tp_GAUSS) {
} else if (Tp_GAUSS) { dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
dx = dt * (g1 * f[i][0] + g2 * random->gaussian()); dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
dy = dt * (g1 * f[i][1] + g2 * random->gaussian()); dz = dt * (g1 * f[i][2] + g2 * rng->gaussian());
dz = dt * (g1 * f[i][2] + g2 * random->gaussian()); wx = rng->gaussian() * g4;
wx = random->gaussian()*g4; wy = rng->gaussian() * g4;
wy = random->gaussian()*g4; wz = rng->gaussian() * g4;
wz = random->gaussian()*g4; } else {
dx = dt * g1 * f[i][0];
dy = dt * g1 * f[i][1];
} else { dz = dt * g1 * f[i][2];
dx = dt * g1 * f[i][0]; wx = wy = wz = 0;
dy = dt * g1 * f[i][1]; }
dz = dt * g1 * f[i][2];
wx = wy = wz = 0;
}
} }
x[i][0] += dx; x[i][0] += dx;
v[i][0] = dx/dt; v[i][0] = dx / dt;
x[i][1] += dy;
v[i][1] = dy / dt;
x[i][1] += dy; x[i][2] += dz;
v[i][1] = dy/dt; v[i][2] = dz / dt;
x[i][2] += dz;
v[i][2] = dz/dt;
wx += g3*torque[i][0];
wy += g3*torque[i][1];
wz += g3*torque[i][2];
wx += g3 * torque[i][0];
wy += g3 * torque[i][1];
wz += g3 * torque[i][2];
// store length of dipole as we need to convert it to a unit vector and // store length of dipole as we need to convert it to a unit vector and
// then back again // then back again
mulen = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]); mulen = sqrt(mu[i][0] * mu[i][0] + mu[i][1] * mu[i][1] + mu[i][2] * mu[i][2]);
// unit vector at time t // unit vector at time t
mux = mu[i][0]/mulen; mux = mu[i][0] / mulen;
muy = mu[i][1]/mulen; muy = mu[i][1] / mulen;
muz = mu[i][2]/mulen; muz = mu[i][2] / mulen;
// un-normalised unit vector at time t + dt // un-normalised unit vector at time t + dt
mu[i][0] = mux + (wy*muz - wz*muy)*dt; mu[i][0] = mux + (wy * muz - wz * muy) * dt;
mu[i][1] = muy + (wz*mux - wx*muz)*dt; mu[i][1] = muy + (wz * mux - wx * muz) * dt;
mu[i][2] = muz + (wx*muy - wy*mux)*dt; mu[i][2] = muz + (wx * muy - wy * mux) * dt;
// normalisation introduces the stochastic drift term due to changing from // normalisation introduces the stochastic drift term due to changing from
// Stratonovich to Ito interpretation // Stratonovich to Ito interpretation
MathExtra::norm3(mu[i]); MathExtra::norm3(mu[i]);
// multiply by original magnitude to obtain dipole of same length // multiply by original magnitude to obtain dipole of same length
mu[i][0] = mu[i][0]*mulen; mu[i][0] = mu[i][0] * mulen;
mu[i][1] = mu[i][1]*mulen; mu[i][1] = mu[i][1] * mulen;
mu[i][2] = mu[i][2]*mulen; mu[i][2] = mu[i][2] * mulen;
} }
} }
return;
} }

18
src/USER-BROWNIAN/fix_brownian_sphere.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off
FixStyle(brownian/sphere,FixBrownianSphere) FixStyle(brownian/sphere,FixBrownianSphere);
// clang-format on
#else #else
#ifndef LMP_FIX_BROWNIAN_SPHERE_H #ifndef LMP_FIX_BROWNIAN_SPHERE_H
@ -27,18 +27,16 @@ namespace LAMMPS_NS {
class FixBrownianSphere : public FixBrownianBase { class FixBrownianSphere : public FixBrownianBase {
public: public:
FixBrownianSphere(class LAMMPS *, int, char **); FixBrownianSphere(class LAMMPS *, int, char **);
virtual ~FixBrownianSphere(); virtual ~FixBrownianSphere() {};
void init(); void init();
void initial_integrate(int /*vflag */); void initial_integrate(int);
private: private:
template < int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D > template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
void initial_integrate_templated(); void initial_integrate_templated();
double g3,g4; double g3, g4;
}; };
} // namespace LAMMPS_NS
}
#endif #endif
#endif #endif

165
src/USER-BROWNIAN/fix_propel_self.cpp
View File

@ -36,60 +36,54 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
enum{DIPOLE,VELOCITY,QUAT}; enum { DIPOLE, VELOCITY, QUAT };
#define TOL 1e-14 #define TOL 1e-14
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
Fix(lmp, narg, arg)
{ {
virial_global_flag = virial_peratom_flag = 1; virial_global_flag = virial_peratom_flag = 1;
if (narg != 5 && narg != 9) if (narg != 5 && narg != 9) error->all(FLERR, "Illegal fix propel/self command");
error->all(FLERR,"Illegal fix propel/self command");
if (strcmp(arg[3], "velocity") == 0) {
if (strcmp(arg[3],"velocity") == 0) {
mode = VELOCITY; mode = VELOCITY;
thermo_virial = 0; thermo_virial = 0;
} else if (strcmp(arg[3],"dipole") == 0) { } else if (strcmp(arg[3], "dipole") == 0) {
mode = DIPOLE; mode = DIPOLE;
thermo_virial = 1; thermo_virial = 1;
} else if (strcmp(arg[3],"quat") == 0) { } else if (strcmp(arg[3], "quat") == 0) {
mode = QUAT; mode = QUAT;
thermo_virial = 1; thermo_virial = 1;
} else { } else {
error->all(FLERR,"Illegal fix propel/self command"); error->all(FLERR, "Illegal fix propel/self command");
} }
magnitude = utils::numeric(FLERR,arg[4],false,lmp); magnitude = utils::numeric(FLERR, arg[4], false, lmp);
// check for keyword // check for keyword
if (narg == 9) { if (narg == 9) {
if (mode != QUAT) { if (mode != QUAT) { error->all(FLERR, "Illegal fix propel/self command"); }
error->all(FLERR,"Illegal fix propel/self command"); if (strcmp(arg[5], "qvector") == 0) {
} sx = utils::numeric(FLERR, arg[6], false, lmp);
if (strcmp(arg[5],"qvector") == 0) { sy = utils::numeric(FLERR, arg[7], false, lmp);
sx = utils::numeric(FLERR,arg[6],false,lmp); sz = utils::numeric(FLERR, arg[8], false, lmp);
sy = utils::numeric(FLERR,arg[7],false,lmp); double snorm = sqrt(sx * sx + sy * sy + sz * sz);
sz = utils::numeric(FLERR,arg[8],false,lmp); sx = sx / snorm;
double snorm = sqrt(sx*sx + sy*sy + sz*sz); sy = sy / snorm;
sx = sx/snorm; sz = sz / snorm;
sy = sy/snorm;
sz = sz/snorm;
} else { } else {
error->all(FLERR,"Illegal fix propel/self command"); error->all(FLERR, "Illegal fix propel/self command");
} }
} else { } else {
sx = 1.0; sx = 1.0;
sy = 0.0; sy = 0.0;
sz = 0.0; sz = 0.0;
} }
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -101,27 +95,16 @@ int FixPropelSelf::setmask()
return mask; return mask;
} }
/* ---------------------------------------------------------------------- */
FixPropelSelf::~FixPropelSelf()
{
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixPropelSelf::init() void FixPropelSelf::init()
{ {
if (mode == DIPOLE && !atom->mu_flag) if (mode == DIPOLE && !atom->mu_flag)
error->all(FLERR,"Fix propel/self requires atom attribute mu " error->all(FLERR, "Fix propel/self requires atom attribute mu with option dipole");
"with option dipole.");
if (mode == QUAT) { if (mode == QUAT) {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec) if (!avec) error->all(FLERR, "Fix propel/self requires atom style ellipsoid with option quat");
error->all(FLERR,"Fix propel/self requires "
"atom style ellipsoid with option quat.");
// check that all particles are finite-size ellipsoids // check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK // no point particles allowed, spherical is OK
@ -133,17 +116,19 @@ void FixPropelSelf::init()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
if (ellipsoid[i] < 0) if (ellipsoid[i] < 0)
error->one(FLERR,"Fix propel/self requires extended particles " error->one(FLERR, "Fix propel/self requires extended particles with option quat");
"with option quat.");
} }
} }
/* ---------------------------------------------------------------------- */
void FixPropelSelf::setup(int vflag) void FixPropelSelf::setup(int vflag)
{ {
post_force(vflag); post_force(vflag);
} }
/* ---------------------------------------------------------------------- */
void FixPropelSelf::post_force(int vflag) void FixPropelSelf::post_force(int vflag)
{ {
if (mode == DIPOLE) if (mode == DIPOLE)
@ -152,9 +137,9 @@ void FixPropelSelf::post_force(int vflag)
post_force_velocity(vflag); post_force_velocity(vflag);
else if (mode == QUAT) else if (mode == QUAT)
post_force_quaternion(vflag); post_force_quaternion(vflag);
} }
/* ---------------------------------------------------------------------- */
void FixPropelSelf::post_force_dipole(int vflag) void FixPropelSelf::post_force_dipole(int vflag)
{ {
@ -163,13 +148,14 @@ void FixPropelSelf::post_force_dipole(int vflag)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double **x = atom->x; double **x = atom->x;
double **mu = atom->mu; double **mu = atom->mu;
double fx,fy,fz; double fx, fy, fz;
// energy and virial setup // energy and virial setup
double vi[6]; double vi[6];
if (vflag) v_setup(vflag); if (vflag)
else evflag = 0; v_setup(vflag);
else
evflag = 0;
// if domain has PBC, need to unwrap for virial // if domain has PBC, need to unwrap for virial
double unwrap[3]; double unwrap[3];
@ -179,26 +165,27 @@ void FixPropelSelf::post_force_dipole(int vflag)
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
fx = magnitude*mu[i][0]; fx = magnitude * mu[i][0];
fy = magnitude*mu[i][1]; fy = magnitude * mu[i][1];
fz = magnitude*mu[i][2]; fz = magnitude * mu[i][2];
f[i][0] += fx; f[i][0] += fx;
f[i][1] += fy; f[i][1] += fy;
f[i][2] += fz; f[i][2] += fz;
if (evflag) { if (evflag) {
domain->unmap(x[i],image[i],unwrap); domain->unmap(x[i], image[i], unwrap);
vi[0] = fx*unwrap[0]; vi[0] = fx * unwrap[0];
vi[1] = fy*unwrap[1]; vi[1] = fy * unwrap[1];
vi[2] = fz*unwrap[2]; vi[2] = fz * unwrap[2];
vi[3] = fx*unwrap[1]; vi[3] = fx * unwrap[1];
vi[4] = fx*unwrap[2]; vi[4] = fx * unwrap[2];
vi[5] = fy*unwrap[2]; vi[5] = fy * unwrap[2];
v_tally(i, vi); v_tally(i, vi);
} }
} }
} }
/* ---------------------------------------------------------------------- */
void FixPropelSelf::post_force_velocity(int vflag) void FixPropelSelf::post_force_velocity(int vflag)
{ {
@ -207,23 +194,24 @@ void FixPropelSelf::post_force_velocity(int vflag)
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double nv2,fnorm,fx,fy,fz; double nv2, fnorm, fx, fy, fz;
// energy and virial setup // energy and virial setup
double vi[6]; double vi[6];
if (vflag) v_setup(vflag); if (vflag)
else evflag = 0; v_setup(vflag);
else
evflag = 0;
// if domain has PBC, need to unwrap for virial // if domain has PBC, need to unwrap for virial
double unwrap[3]; double unwrap[3];
imageint *image = atom->image; imageint *image = atom->image;
// Add the active force to the atom force: // Add the active force to the atom force:
for(int i = 0; i < nlocal; ++i) { for (int i = 0; i < nlocal; ++i) {
if(mask[i] & groupbit) { if (mask[i] & groupbit) {
nv2 = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; nv2 = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
fnorm = 0.0; fnorm = 0.0;
if (nv2 > TOL) { if (nv2 > TOL) {
@ -242,69 +230,72 @@ void FixPropelSelf::post_force_velocity(int vflag)
f[i][2] += fz; f[i][2] += fz;
if (evflag) { if (evflag) {
domain->unmap(x[i],image[i],unwrap); domain->unmap(x[i], image[i], unwrap);
vi[0] = fx*unwrap[0]; vi[0] = fx * unwrap[0];
vi[1] = fy*unwrap[1]; vi[1] = fy * unwrap[1];
vi[2] = fz*unwrap[2]; vi[2] = fz * unwrap[2];
vi[3] = fx*unwrap[1]; vi[3] = fx * unwrap[1];
vi[4] = fx*unwrap[2]; vi[4] = fx * unwrap[2];
vi[5] = fy*unwrap[2]; vi[5] = fy * unwrap[2];
v_tally(i, vi); v_tally(i, vi);
} }
} }
} }
} }
/* ---------------------------------------------------------------------- */
void FixPropelSelf::post_force_quaternion(int vflag) void FixPropelSelf::post_force_quaternion(int vflag)
{ {
double **f = atom->f; double **f = atom->f;
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int* ellipsoid = atom->ellipsoid; int *ellipsoid = atom->ellipsoid;
// ellipsoidal properties // ellipsoidal properties
AtomVecEllipsoid::Bonus *bonus = avec->bonus; AtomVecEllipsoid::Bonus *bonus = avec->bonus;
double f_act[3] = { sx, sy, sz }; double f_act[3] = {sx, sy, sz};
double f_rot[3]; double f_rot[3];
double *quat; double *quat;
double Q[3][3]; double Q[3][3];
double fx,fy,fz; double fx, fy, fz;
// energy and virial setup // energy and virial setup
double vi[6]; double vi[6];
if (vflag) v_setup(vflag); if (vflag)
else evflag = 0; v_setup(vflag);
else
evflag = 0;
// if domain has PBC, need to unwrap for virial // if domain has PBC, need to unwrap for virial
double unwrap[3]; double unwrap[3];
imageint *image = atom->image; imageint *image = atom->image;
// Add the active force to the atom force: // Add the active force to the atom force:
for(int i = 0; i < nlocal; ++i) { for (int i = 0; i < nlocal; ++i) {
if(mask[i] & groupbit) { if (mask[i] & groupbit) {
quat = bonus[ellipsoid[i]].quat; quat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat(quat, Q); MathExtra::quat_to_mat(quat, Q);
MathExtra::matvec(Q, f_act, f_rot); MathExtra::matvec(Q, f_act, f_rot);
fx = magnitude*f_rot[0]; fx = magnitude * f_rot[0];
fy = magnitude*f_rot[1]; fy = magnitude * f_rot[1];
fz = magnitude*f_rot[2]; fz = magnitude * f_rot[2];
f[i][0] += fx; f[i][0] += fx;
f[i][1] += fy; f[i][1] += fy;
f[i][2] += fz; f[i][2] += fz;
if (evflag) { if (evflag) {
domain->unmap(x[i],image[i],unwrap); domain->unmap(x[i], image[i], unwrap);
vi[0] = fx*unwrap[0]; vi[0] = fx * unwrap[0];
vi[1] = fy*unwrap[1]; vi[1] = fy * unwrap[1];
vi[2] = fz*unwrap[2]; vi[2] = fz * unwrap[2];
vi[3] = fx*unwrap[1]; vi[3] = fx * unwrap[1];
vi[4] = fx*unwrap[2]; vi[4] = fx * unwrap[2];
vi[5] = fy*unwrap[2]; vi[5] = fy * unwrap[2];
v_tally(i, vi); v_tally(i, vi);
} }
} }

14
src/USER-BROWNIAN/fix_propel_self.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off
FixStyle(propel/self,FixPropelSelf) FixStyle(propel/self,FixPropelSelf);
// clang-format on
#else #else
#ifndef LMP_FIX_PROPEL_SELF_H #ifndef LMP_FIX_PROPEL_SELF_H
@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class FixPropelSelf : public Fix { class FixPropelSelf : public Fix {
public: public:
FixPropelSelf(class LAMMPS *, int, char **); FixPropelSelf(class LAMMPS *, int, char **);
virtual ~FixPropelSelf(); virtual ~FixPropelSelf() {};
void init(); void init();
void post_force(int); void post_force(int);
void setup(int); void setup(int);
@ -34,7 +34,7 @@ class FixPropelSelf : public Fix {
private: private:
double magnitude; double magnitude;
double sx,sy,sz; double sx, sy, sz;
int mode; int mode;
void post_force_dipole(int); void post_force_dipole(int);
@ -42,10 +42,8 @@ class FixPropelSelf : public Fix {
void post_force_quaternion(int); void post_force_quaternion(int);
class AtomVecEllipsoid *avec; class AtomVecEllipsoid *avec;
}; };
} // namespace LAMMPS_NS
}
#endif #endif
#endif #endif