(b2af7fb8) · Commits · 郑智淋 / lammps

src/domain.cpp

+24 −1

Original line number	Diff line number	Diff line
		@@ -678,7 +678,7 @@ void Domain::remap(double *x, int &image)

		/* ----------------------------------------------------------------------
		unmap the point via image flags
		don't reset image flag
		x overwritten with result, don't reset image flag
		for triclinic, use h[] to add in tilt factors in other dims as needed
		------------------------------------------------------------------------- */

		@@ -699,6 +699,29 @@ void Domain::unmap(double *x, int image)
		}
		}

		/* ----------------------------------------------------------------------
		unmap the point via image flags
		result returned in y, don't reset image flag
		for triclinic, use h[] to add in tilt factors in other dims as needed
		------------------------------------------------------------------------- */

		void Domain::unmap(double x, int image, double y)
		{
		int xbox = (image & 1023) - 512;
		int ybox = (image >> 10 & 1023) - 512;
		int zbox = (image >> 20) - 512;

		if (triclinic == 0) {
		y[0] = x[0] + xbox*xprd;
		y[1] = x[1] + ybox*yprd;
		y[2] = x[2] + zbox*zprd;
		} else {
		y[0] = x[0] + h[0]xbox + h[5]ybox + h[4]*zbox;
		y[1] = x[1] + h[1]ybox + h[3]zbox;
		y[2] = x[2] + h[2]*zbox;
		}
		}

		/* ----------------------------------------------------------------------
		create a lattice
		delete it if style = none

src/domain.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -91,6 +91,7 @@ class Domain : protected Pointers {
		void pbc();
		void remap(double *, int &);
		void unmap(double *, int);
		void unmap(double , int, double );
		void minimum_image(double &, double &, double &);
		void minimum_image(double *);
		void set_lattice(int, char **);

src/fix_msd.cpp

+36 −21

Original line number	Diff line number	Diff line
		@@ -72,14 +72,8 @@ FixMSD::FixMSD(LAMMPS lmp, int narg, char *arg) :
		int xbox,ybox,zbox;

		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		xbox = (image[i] & 1023) - 512;
		ybox = (image[i] >> 10 & 1023) - 512;
		zbox = (image[i] >> 20) - 512;
		xoriginal[i][0] = x[i][0] + xbox*xprd;
		xoriginal[i][1] = x[i][1] + ybox*yprd;
		xoriginal[i][2] = x[i][2] + zbox*zprd;
		} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
		if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
		else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
		}

		// nmsd = # of atoms in group
		@@ -149,6 +143,7 @@ void FixMSD::end_of_step()
		int *image = atom->image;
		int nlocal = atom->nlocal;

		double *h = domain->h;
		double xprd = domain->xprd;
		double yprd = domain->yprd;
		double zprd = domain->zprd;
		@@ -157,6 +152,10 @@ void FixMSD::end_of_step()
		double msd[4];
		msd[0] = msd[1] = msd[2] = msd[3] = 0.0;

		// dx,dy,dz = displacement of atom from original position
		// for triclinic, need to unwrap current atom coord via h matrix

		if (domain->triclinic == 0) {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		xbox = (image[i] & 1023) - 512;
		@@ -171,6 +170,22 @@ void FixMSD::end_of_step()
		msd[3] += dxdx + dydy + dz*dz;
		}

		} else {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		xbox = (image[i] & 1023) - 512;
		ybox = (image[i] >> 10 & 1023) - 512;
		zbox = (image[i] >> 20) - 512;
		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;
		msd[3] += dxdx + dydy + dz*dz;
		}
		}

		double msd_all[4];
		MPI_Allreduce(msd,msd_all,4,MPI_DOUBLE,MPI_SUM,world);
		msd_all[0] /= nmsd;

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