(efea2a18) · Commits · 郑智淋 / lammps

src/domain.cpp

+46 −0

Original line number	Diff line number	Diff line
		@@ -676,6 +676,52 @@ void Domain::remap(double *x, int &image)
		if (triclinic) lamda2x(coord,x);
		}

		/* ----------------------------------------------------------------------
		remap the point into the periodic box no matter how far away
		resulting coord must satisfy lo <= coord < hi
		MAX is important since coord - prd < lo can happen when coord = hi
		for triclinic, point is converted to lamda coords (0-1) before doing remap
		------------------------------------------------------------------------- */

		void Domain::remap(double *x)
		{
		double lo,hi,period,coord;
		double lamda[3];

		if (triclinic == 0) {
		lo = boxlo;
		hi = boxhi;
		period = prd;
		coord = x;
		} else {
		lo = boxlo_lamda;
		hi = boxhi_lamda;
		period = prd_lamda;
		x2lamda(x,lamda);
		coord = lamda;
		}

		if (xperiodic) {
		while (coord[0] < lo[0]) coord[0] += period[0];
		while (coord[0] >= hi[0]) coord[0] -= period[0];
		coord[0] = MAX(coord[0],lo[0]);
		}

		if (yperiodic) {
		while (coord[1] < lo[1]) coord[1] += period[1];
		while (coord[1] >= hi[1]) coord[1] -= period[1];
		coord[1] = MAX(coord[1],lo[1]);
		}

		if (zperiodic) {
		while (coord[2] < lo[2]) coord[2] += period[2];
		while (coord[2] >= hi[2]) coord[2] -= period[2];
		coord[2] = MAX(coord[2],lo[2]);
		}

		if (triclinic) lamda2x(coord,x);
		}

		/* ----------------------------------------------------------------------
		unmap the point via image flags
		x overwritten with result, don't reset image flag

src/domain.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -90,6 +90,7 @@ class Domain : protected Pointers {
		void reset_box();
		void pbc();
		void remap(double *, int &);
		void remap(double *);
		void unmap(double *, int);
		void unmap(double , int, double );
		void minimum_image(double &, double &, double &);

src/fix_indent.cpp

+33 −22

Original line number	Diff line number	Diff line
		@@ -171,12 +171,15 @@ void FixIndent::post_force(int vflag)

		if (istyle == SPHERE) {

		// x1,y1,z1 = current position of indenter from original x0,y0,z0
		// ctr = current indenter center from original x0,y0,z0
		// remap into periodic box

		double ctr[3];
		double delta = (update->ntimestep - update->beginstep) * update->dt;
		double x1 = x0 + delta*vx;
		double y1 = y0 + delta*vy;
		double z1 = z0 + delta*vz;
		ctr[0] = x0 + delta*vx;
		ctr[1] = y0 + delta*vy;
		ctr[2] = z0 + delta*vz;
		domain->remap(ctr);

		double **x = atom->x;
		double **f = atom->f;
		@@ -187,9 +190,10 @@ void FixIndent::post_force(int vflag)

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		delx = x[i][0] - x1;
		dely = x[i][1] - y1;
		delz = x[i][2] - z1;
		delx = x[i][0] - ctr[0];
		dely = x[i][1] - ctr[1];
		delz = x[i][2] - ctr[2];
		domain->minimum_image(delx,dely,delz);
		r = sqrt(delxdelx + delydely + delz*delz);
		if (side == OUTSIDE) {
		dr = r - r0;
		@@ -215,20 +219,26 @@ void FixIndent::post_force(int vflag)

		} else if (istyle == CYLINDER) {

		// c1new,c2new = current coords of indenter axis from original c1,c2
		// ctr = current indenter axis from original c1,c2
		// remap into periodic box
		// 3rd coord is just near box for remap(), since isn't used

		double ctr[3];
		double delta = (update->ntimestep - update->beginstep) * update->dt;
		double c1new,c2new;
		if (cdim == 0) {
		c1new = c1 + delta*vy;
		c2new = c2 + delta*vz;
		ctr[0] = domain->boxlo[0];
		ctr[1] = c1 + delta*vy;
		ctr[2] = c2 + delta*vz;
		} else if (cdim == 1) {
		c1new = c1 + delta*vx;
		c2new = c2 + delta*vz;
		ctr[0] = c1 + delta*vx;
		ctr[1] = domain->boxlo[1];
		ctr[2] = c2 + delta*vz;
		} else {
		c1new = c1 + delta*vx;
		c2new = c2 + delta*vy;
		ctr[0] = c1 + delta*vx;
		ctr[1] = c2 + delta*vy;
		ctr[2] = domain->boxlo[2];
		}
		domain->remap(ctr);

		double **x = atom->x;
		double **f = atom->f;
		@@ -241,17 +251,18 @@ void FixIndent::post_force(int vflag)
		if (mask[i] & groupbit) {
		if (cdim == 0) {
		delx = 0;
		dely = x[i][1] - c1new;
		delz = x[i][2] - c2new;
		dely = x[i][1] - ctr[1];
		delz = x[i][2] - ctr[2];
		} else if (cdim == 1) {
		delx = x[i][0] - c1new;
		delx = x[i][0] - ctr[0];
		dely = 0;
		delz = x[i][2] - c2new;
		delz = x[i][2] - ctr[2];
		} else {
		delx = x[i][0] - c1new;
		dely = x[i][1] - c2new;
		delx = x[i][0] - ctr[0];
		dely = x[i][1] - ctr[1];
		delz = 0;
		}
		domain->minimum_image(delx,dely,delz);
		r = sqrt(delxdelx + delydely + delz*delz);
		if (side == OUTSIDE) {
		dr = r - r0;

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