(d8ac4b82) · Commits · 郑智淋 / lammps

src/ASPHERE/fix_npt_asphere.cpp

+72 −23

Original line number	Diff line number	Diff line
		@@ -27,9 +27,12 @@
		#include "kspace.h"
		#include "update.h"
		#include "domain.h"
		#include "error.h"

		using namespace LAMMPS_NS;

		enum{NOBIAS,BIAS};

		/* ---------------------------------------------------------------------- */

		FixNPTASphere::FixNPTASphere(LAMMPS lmp, int narg, char *arg) :
		@@ -41,6 +44,14 @@ FixNPTASphere::FixNPTASphere(LAMMPS lmp, int narg, char *arg) :
		"quat, angmom, torque, shape");
		}

		/* ---------------------------------------------------------------------- */

		void FixNPTASphere::init()
		{
		FixNPT::init();
		dtq = 0.5 * update->dt;
		}

		/* ----------------------------------------------------------------------
		1st half of Verlet update
		------------------------------------------------------------------------- */
		@@ -48,6 +59,7 @@ FixNPTASphere::FixNPTASphere(LAMMPS lmp, int narg, char *arg) :
		void FixNPTASphere::initial_integrate(int vflag)
		{
		int i;
		double dtfm;

		double delta = update->ntimestep - update->beginstep;
		delta /= update->endstep - update->beginstep;
		@@ -77,9 +89,9 @@ void FixNPTASphere::initial_integrate(int vflag)
		factor[i] = exp(-dthalf*(eta_dot+omega_dot[i]));
		dilation[i] = exp(dthalf*omega_dot[i]);
		}
		ang_factor = exp(-dthalf*eta_dot);
		factor_rotate = exp(-dthalf*eta_dot);

		// v update only for atoms in group
		// update v of only atoms in group

		double **x = atom->x;
		double **v = atom->v;
		@@ -93,7 +105,7 @@ void FixNPTASphere::initial_integrate(int vflag)
		int nlocal = atom->nlocal;
		if (igroup == atom->firstgroup) nlocal = atom->nfirst;

		double dtfm;
		if (which == NOBIAS) {
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		dtfm = dtf / mass[type[i]];
		@@ -102,6 +114,18 @@ void FixNPTASphere::initial_integrate(int vflag)
		v[i][2] = v[i][2]factor[2] + dtfmf[i][2];
		}
		}
		} else if (which == BIAS) {
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		temperature->remove_bias(i,v[i]);
		dtfm = dtf / mass[type[i]];
		v[i][0] = v[i][0]factor[0] + dtfmf[i][0];
		v[i][1] = v[i][1]factor[1] + dtfmf[i][1];
		v[i][2] = v[i][2]factor[2] + dtfmf[i][2];
		temperature->restore_bias(v[i]);
		}
		}
		}

		// remap simulation box and all owned atoms by 1/2 step

		@@ -120,11 +144,12 @@ void FixNPTASphere::initial_integrate(int vflag)
		// update angular momentum by 1/2 step
		// update quaternion a full step via Richardson iteration
		// returns new normalized quaternion

		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		angmom[i][0] = angmom[i][0] * ang_factor + dtf * torque[i][0];
		angmom[i][1] = angmom[i][1] * ang_factor + dtf * torque[i][1];
		angmom[i][2] = angmom[i][2] * ang_factor + dtf * torque[i][2];
		angmom[i][0] = angmom[i][0]factor_rotate + dtftorque[i][0];
		angmom[i][1] = angmom[i][1]factor_rotate + dtftorque[i][1];
		angmom[i][2] = angmom[i][2]factor_rotate + dtftorque[i][2];

		double inertia[3];
		calculate_inertia(atom->mass[type[i]],atom->shape[type[i]],inertia);
		@@ -146,8 +171,9 @@ void FixNPTASphere::initial_integrate(int vflag)
		void FixNPTASphere::final_integrate()
		{
		int i;
		double dtfm;

		// v update only for atoms in group
		// update v of only atoms in group

		double **v = atom->v;
		double **f = atom->f;
		@@ -159,16 +185,31 @@ void FixNPTASphere::final_integrate()
		int nlocal = atom->nlocal;
		if (igroup == atom->firstgroup) nlocal = atom->nfirst;

		double dtfm;
		if (which == NOBIAS) {
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		dtfm = dtf / mass[type[i]];
		v[i][0] = (v[i][0] + dtfmf[i][0]) factor[0];
		v[i][1] = (v[i][1] + dtfmf[i][1]) factor[1];
		v[i][2] = (v[i][2] + dtfmf[i][2]) factor[2];
		angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * ang_factor;
		angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * ang_factor;
		angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * ang_factor;
		angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * factor_rotate;
		angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * factor_rotate;
		angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate;
		}
		}
		} else if (which == BIAS) {
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		temperature->remove_bias(i,v[i]);
		dtfm = dtf / mass[type[i]];
		v[i][0] = (v[i][0] + dtfmf[i][0]) factor[0];
		v[i][1] = (v[i][1] + dtfmf[i][1]) factor[1];
		v[i][2] = (v[i][2] + dtfmf[i][2]) factor[2];
		temperature->restore_bias(v[i]);
		angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * factor_rotate;
		angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * factor_rotate;
		angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate;
		}
		}
		}

		@@ -208,6 +249,14 @@ void FixNPTASphere::final_integrate()
		}
		}

		/* ---------------------------------------------------------------------- */

		void FixNPTASphere::reset_dt()
		{
		FixNPT::reset_dt();
		dtq = 0.5 * update->dt;
		}

		/* ----------------------------------------------------------------------
		Richardson iteration to update quaternion accurately
		------------------------------------------------------------------------- */

src/ASPHERE/fix_npt_asphere.h

+4 −2

Original line number	Diff line number	Diff line
		@@ -21,12 +21,14 @@ namespace LAMMPS_NS {
		class FixNPTASphere : public FixNPT {
		public:
		FixNPTASphere(class LAMMPS , int, char *);
		~FixNPTASphere() {}
		void init();
		void initial_integrate(int);
		void final_integrate();
		void reset_dt();

		private:
		double ang_factor;
		double dtq;
		double factor_rotate;

		void richardson(double , double , double *);
		void omega_from_mq(double , double , double , double );

src/ASPHERE/fix_nvt_asphere.cpp

+93 −30

Original line number	Diff line number	Diff line
		@@ -32,6 +32,8 @@

		using namespace LAMMPS_NS;

		enum{NOBIAS,BIAS};

		/* ---------------------------------------------------------------------- */

		FixNVTASphere::FixNVTASphere(LAMMPS lmp, int narg, char *arg) :
		@@ -45,6 +47,14 @@ FixNVTASphere::FixNVTASphere(LAMMPS lmp, int narg, char *arg) :

		/* ---------------------------------------------------------------------- */

		void FixNVTASphere::init()
		{
		FixNVT::init();
		dtq = 0.5 * update->dt;
		}

		/* ---------------------------------------------------------------------- */

		void FixNVTASphere::initial_integrate(int vflag)
		{
		double dtfm;
		@@ -75,12 +85,40 @@ void FixNVTASphere::initial_integrate(int vflag)
		int nlocal = atom->nlocal;
		if (igroup == atom->firstgroup) nlocal = atom->nfirst;

		if (which == NOBIAS) {
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		dtfm = dtf / mass[type[i]];
		v[i][0] = v[i][0]factor + dtfmf[i][0];
		v[i][1] = v[i][1]factor + dtfmf[i][1];
		v[i][2] = v[i][2]factor + dtfmf[i][2];
		x[i][0] += dtv * v[i][0];
		x[i][1] += dtv * v[i][1];
		x[i][2] += dtv * v[i][2];

		// update angular momentum by 1/2 step
		// update quaternion a full step via Richardson iteration
		// returns new normalized quaternion

		angmom[i][0] = angmom[i][0]factor + dtftorque[i][0];
		angmom[i][1] = angmom[i][1]factor + dtftorque[i][1];
		angmom[i][2] = angmom[i][2]factor + dtftorque[i][2];

		double inertia[3];
		calculate_inertia(atom->mass[type[i]],atom->shape[type[i]],inertia);
		richardson(quat[i],angmom[i],inertia);
		}
		}

		} else if (which == BIAS) {
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		temperature->remove_bias(i,v[i]);
		dtfm = dtf / mass[type[i]];
		v[i][0] = v[i][0]factor + dtfmf[i][0];
		v[i][1] = v[i][1]factor + dtfmf[i][1];
		v[i][2] = v[i][2]factor + dtfmf[i][2];
		temperature->restore_bias(v[i]);
		x[i][0] += dtv * v[i][0];
		x[i][1] += dtv * v[i][1];
		x[i][2] += dtv * v[i][2];
		@@ -99,6 +137,7 @@ void FixNVTASphere::initial_integrate(int vflag)
		}
		}
		}
		}

		/* ---------------------------------------------------------------------- */

		@@ -118,16 +157,32 @@ void FixNVTASphere::final_integrate()
		int nlocal = atom->nlocal;
		if (igroup == atom->firstgroup) nlocal = atom->nfirst;

		if (which == NOBIAS) {
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		dtfm = dtf / mass[type[i]] * factor;
		v[i][0] = v[i][0]factor + dtfmf[i][0];
		v[i][1] = v[i][1]factor + dtfmf[i][1];
		v[i][2] = v[i][2]factor + dtfmf[i][2];
		angmom[i][0] = (angmom[i][0] + dtftorque[i][0]) factor;
		angmom[i][1] = (angmom[i][1] + dtftorque[i][1]) factor;
		angmom[i][2] = (angmom[i][2] + dtftorque[i][2]) factor;
		}
		}

		angmom[i][0] = angmom[i][0] * factor + dtf * torque[i][0];
		angmom[i][1] = angmom[i][1] * factor + dtf * torque[i][1];
		angmom[i][2] = angmom[i][2] * factor + dtf * torque[i][2];
		} else if (which == BIAS) {
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		temperature->remove_bias(i,v[i]);
		dtfm = dtf / mass[type[i]] * factor;
		v[i][0] = v[i][0]factor + dtfmf[i][0];
		v[i][1] = v[i][1]factor + dtfmf[i][1];
		v[i][2] = v[i][2]factor + dtfmf[i][2];
		temperature->restore_bias(v[i]);
		angmom[i][0] = (angmom[i][0] + dtftorque[i][0]) factor;
		angmom[i][1] = (angmom[i][1] + dtftorque[i][1]) factor;
		angmom[i][2] = (angmom[i][2] + dtftorque[i][2]) factor;
		}
		}
		}

		@@ -142,6 +197,14 @@ void FixNVTASphere::final_integrate()
		eta_dot *= drag_factor;
		}

		/* ---------------------------------------------------------------------- */

		void FixNVTASphere::reset_dt()
		{
		FixNVT::reset_dt();
		dtq = 0.5 * update->dt;
		}

		/* ----------------------------------------------------------------------
		Richardson iteration to update quaternion accurately
		------------------------------------------------------------------------- */

src/ASPHERE/fix_nvt_asphere.h

+4 −1

Original line number	Diff line number	Diff line
		@@ -21,11 +21,14 @@ namespace LAMMPS_NS {
		class FixNVTASphere : public FixNVT {
		public:
		FixNVTASphere(class LAMMPS , int, char *);
		~FixNVTASphere() {}
		void init();
		void initial_integrate(int);
		void final_integrate();
		void reset_dt();

		private:
		double dtq;

		void richardson(double , double , double *);
		void omega_from_mq(double , double , double , double );
		void calculate_inertia(double mass, double shape, double inertia);

src/compute.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -175,4 +175,3 @@ void Compute::restore_bias(double *v)
		v[1] += vbias[1];
		v[2] += vbias[2];
		}

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