(7e77b5a9) · Commits · 郑智淋 / lammps

src/delete_atoms.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -231,7 +231,6 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
		// only ever delete owned atom I, never J even if owned

		int *tag = atom->tag;
		int *type = atom->type;
		int *mask = atom->mask;
		double **x = atom->x;
		int nall = atom->nlocal + atom->nghost;

src/fix_msd.cpp

+65 −11

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ using namespace LAMMPS_NS;
		FixMSD::FixMSD(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg)
		{
		if (narg != 5) error->all("Illegal fix msd command");
		if (narg != 5 && narg != 7) error->all("Illegal fix msd command");
		nevery = atoi(arg[3]);
		if (nevery <= 0) error->all("Illegal fix msd command");
		first = 1;
		@@ -51,6 +51,21 @@ FixMSD::FixMSD(LAMMPS lmp, int narg, char *arg) :
		fprintf(fp,"# TimeStep x y z total\n");
		}

		// optional args

		comflag = 0;

		int iarg = 5;
		while (iarg < narg) {
		if (strcmp(arg[iarg],"com") == 0) {
		if (iarg+2 > narg) error->all("Illegal fix msd command");
		if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
		else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
		else error->all("Illegal fix msd command");
		iarg += 2;
		} else error->all("Illegal fix msd command");
		}

		// perform initial allocation of atom-based array
		// register with Atom class

		@@ -59,7 +74,17 @@ FixMSD::FixMSD(LAMMPS lmp, int narg, char *arg) :
		atom->add_callback(0);
		atom->add_callback(1);

		// cm = original center of mass

		double cm[3];

		if (comflag) {
		masstotal = group->mass(igroup);
		group->xcm(igroup,masstotal,cm);
		}

		// xoriginal = initial unwrapped positions of atoms
		// relative to center of mass if comflag is set

		double **x = atom->x;
		int *mask = atom->mask;
		@@ -67,8 +92,14 @@ FixMSD::FixMSD(LAMMPS lmp, int narg, char *arg) :
		int nlocal = atom->nlocal;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
		else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
		if (mask[i] & groupbit) {
		domain->unmap(x[i],image[i],xoriginal[i]);
		if (comflag) {
		xoriginal[i][0] -= cm[0];
		xoriginal[i][1] -= cm[1];
		xoriginal[i][2] -= cm[2];
		}
		} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
		}

		// nmsd = # of atoms in group
		@@ -133,6 +164,15 @@ void FixMSD::setup(int vflag)

		void FixMSD::end_of_step()
		{
		// cm = current center of mass

		double cm[3];

		if (comflag) {
		group->mass(igroup);
		group->xcm(igroup,masstotal,cm);
		}

		double **x = atom->x;
		int *mask = atom->mask;
		int *image = atom->image;
		@@ -148,6 +188,7 @@ void FixMSD::end_of_step()
		msd[0] = msd[1] = msd[2] = msd[3] = 0.0;

		// dx,dy,dz = displacement of atom from original position
		// relative to center of mass if comflag is set
		// for triclinic, need to unwrap current atom coord via h matrix

		if (domain->triclinic == 0) {
		@@ -156,9 +197,15 @@ void FixMSD::end_of_step()
		xbox = (image[i] & 1023) - 512;
		ybox = (image[i] >> 10 & 1023) - 512;
		zbox = (image[i] >> 20) - 512;
		if (comflag) {
		dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
		dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
		dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
		} else {
		dx = x[i][0] + xbox*xprd - xoriginal[i][0];
		dy = x[i][1] + ybox*yprd - xoriginal[i][1];
		dz = x[i][2] + zbox*zprd - xoriginal[i][2];
		}
		msd[0] += dx*dx;
		msd[1] += dy*dy;
		msd[2] += dz*dz;
		@@ -171,9 +218,16 @@ void FixMSD::end_of_step()
		xbox = (image[i] & 1023) - 512;
		ybox = (image[i] >> 10 & 1023) - 512;
		zbox = (image[i] >> 20) - 512;
		if (comflag) {
		dx = x[i][0] + h[0]xbox + h[5]ybox + h[4]*zbox -
		cm[0] - xoriginal[i][0];
		dy = x[i][1] + h[1]ybox + h[3]zbox - cm[1] - xoriginal[i][1];
		dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
		} else {
		dx = x[i][0] + h[0]xbox + h[5]ybox + h[4]*zbox - xoriginal[i][0];
		dy = x[i][1] + h[1]ybox + h[3]zbox - xoriginal[i][1];
		dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
		}
		msd[0] += dx*dx;
		msd[1] += dy*dy;
		msd[2] += dz*dz;

src/fix_msd.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -39,8 +39,10 @@ class FixMSD : public Fix {
		int maxsize_restart();

		private:
		int me,first;
		int me,first,comflag;
		FILE *fp;
		double masstotal;

		int nmsd; // # of atoms in group
		double **xoriginal; // original coords of atoms
		};

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