Added two modes, one via velocity and one via quaternion. (920ea89c) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_propel_self.cpp

+104 −18

Original line number	Diff line number	Diff line
		@@ -51,24 +51,34 @@ static constexpr const bool debug_out = false;
		FixPropelSelf::FixPropelSelf( LAMMPS lmp, int narg, char *argv )
		: Fix(lmp, narg, argv)
		{
		// if( lmp->citeme) lmp->citeme->add(cite_fix_active);
		if( narg < 4 ) error->all(FLERR, "Illegal fix propel/self command");
		if( narg < 5 ) error->all(FLERR, "Illegal fix propel/self command");

		AtomVecEllipsoid av = static_cast<AtomVecEllipsoid>(atom->avec);
		if (!av) error->all(FLERR, "FixPropelSelf requires atom_style ellipsoid");
		// The fix is to support the following cases:
		// 1. Simple atoms, in which case the force points along the velocity
		// 2. Cases where the atoms have an internal ellipsoid. Currently those
		// styles are only body and aspherical particles.
		// The first argument (mode) is used to differentiate between these.

		if( debug_out && comm->me == 0 ){
		fprintf(screen, "This is fix active, narg is %d\n", narg );
		fprintf(screen, "args:");
		for( int i = 0; i < narg; ++i ){
		fprintf(screen, " %s", argv[i]);
		// args: fix ID all propel/self mode magnitude
		// Optional args are
		const char *mode_str = argv[3];
		if (strncmp(mode_str, "velocity", 8) == 0) {
		mode = VELOCITY;
		} else if (strncmp(mode_str, "quaternion", 10) == 0) {
		// This mode should only be supported if the atom style has
		// a quaternion (and if all atoms in the group have it)
		if (verify_atoms_have_quaternion()) {
		error->all(FLERR, "All atoms need a quaternion");
		}
		fprintf(screen, "\n");
		mode = QUATERNION;
		} else {
		char msg[2048];
		sprintf(msg, "Illegal mode \"%s\" for fix propel/self", mode_str);
		error->all(FLERR, msg);
		}

		// args: fix ID all propel/self magnitude prop1 prop2 prop3
		// Optional args are
		magnitude = force->numeric( FLERR, argv[3] );

		magnitude = force->numeric( FLERR, argv[4] );
		}


		@@ -92,17 +102,29 @@ double FixPropelSelf::memory_usage()
		}


		void FixPropelSelf::post_force(int vflag )
		{
		switch(mode) {
		case QUATERNION:
		post_force_quaternion(vflag);
		break;
		case VELOCITY:
		post_force_velocity(vflag);
		break;
		default:
		error->all(FLERR, "reached statement that should be unreachable");
		}
		}



		void FixPropelSelf::post_force(int /* vflag */ )
		void FixPropelSelf::post_force_quaternion(int /* vflag */ )
		{
		// Then do the rest:
		double **f = atom->f;

		AtomVecEllipsoid av = static_cast<AtomVecEllipsoid>(atom->avec);

		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		if (igroup == atom->firstgroup) nlocal = atom->nfirst;

		AtomVecEllipsoid::Bonus *bonus = av->bonus;
		// Add the active force to the atom force:
		@@ -141,7 +163,71 @@ void FixPropelSelf::post_force(int /* vflag */ )
		f[i][0] += magnitude * f_rot[0];
		f[i][1] += magnitude * f_rot[1];
		f[i][2] += magnitude * f_rot[2];
		}
		}
		}



		void FixPropelSelf::post_force_velocity(int /vflag/ )
		{
		double **f = atom->f;
		double **v = atom->v;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		tagint *tag = atom->tag;

		// Add the active force to the atom force:
		for( int i = 0; i < nlocal; ++i ){
		if( mask[i] & groupbit ){
		const double *vi = v[i];
		double f_act[3] = { vi[0], vi[1], vi[2] };
		double nv2 = vi[0]vi[0] + vi[1]vi[1] + vi[2]*vi[2];
		double fnorm = magnitude / sqrt(nv2);

		if (debug_out && comm->me == 0) {
		// Magical reference particle:
		if (tag[i] == 12) {
		fprintf(screen, "Active force on atom %d: (%f %f %f)\n",
		tag[i], f_act[0], f_act[1], f_act[2]);
		fprintf(screen, " Total force before: (%f %f %f)\n",
		f[i][0], f[i][1], f[i][2]);
		}
		}

		f[i][0] += fnorm * f_act[0];
		f[i][1] += fnorm * f_act[1];
		f[i][2] += fnorm * f_act[2];
		}
		}
		}


		int FixPropelSelf::verify_atoms_have_quaternion()
		{
		int ellipsoid_flag = atom->ellipsoid_flag;
		int body_flag = atom->body_flag;
		int *mask = atom->mask;
		if (! (ellipsoid_flag \|\| body_flag) ){
		error->all(FLERR, "mode quaternion requires body or ellipsoid atoms");
		}

		// Make sure all atoms have ellipsoid or body set:
		for (int i = 0; i < atom->nlocal; ++i) {
		if (mask[i] & groupbit) {
		if (ellipsoid_flag && atom->ellipsoid[i] < 0) {
		error->all(FLERR, "Got atom without ellipsoid set");
		// Kind-of pointless but silences some compiler warnings:
		return 1;
		}
		if (body_flag && atom->body[i] < 0) {
		error->all(FLERR, "Got atom without body set");
		// Kind-of pointless but silences some compiler warnings:
		return 1;
		}
		}
		}

		return 0;
		}

src/USER-MISC/fix_propel_self.h

+14 −1

Original line number	Diff line number	Diff line
		@@ -26,6 +26,12 @@ namespace LAMMPS_NS {

		class FixPropelSelf : public Fix {
		public:

		enum operation_modes {
		VELOCITY = 0,
		QUATERNION = 1
		};

		FixPropelSelf(class LAMMPS , int, char *);
		virtual ~FixPropelSelf();
		virtual int setmask();
		@@ -34,9 +40,16 @@ class FixPropelSelf : public Fix {

		double memory_usage();

		protected:
		private:
		double magnitude;
		int thermostat_orient;
		int mode;

		int verify_atoms_have_quaternion();
		void post_force_velocity(int);
		void post_force_quaternion(int);


		};

		}

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