remove content of PR #723 from this branch to avoid merge issues (97e59b16) · Commits · 郑智淋 / lammps

doc/src/replicate.txt

+2 −10

Original line number	Diff line number	Diff line
		@@ -10,11 +10,9 @@ replicate command :h3

		[Syntax:]

		replicate nx ny nz {keyword} :pre
		replicate nx ny nz :pre

		nx,ny,nz = replication factors in each dimension :ulb
		optional {keyword} = {bbox} :l
		{bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
		nx,ny,nz = replication factors in each dimension :ul

		[Examples:]

		@@ -45,12 +43,6 @@ file that crosses a periodic boundary should be between two atoms with
		image flags that differ by 1. This will allow the bond to be
		unwrapped appropriately.

		The optional keyword {bbox} uses a bounding box to only check atoms
		in replicas that overlap with a processor's subdomain when assigning
		atoms to processors, and thus can result in substantial speedups for
		calculations using a large number of processors. It does require
		temporarily using more memory.

		[Restrictions:]

		A 2d simulation cannot be replicated in the z dimension.

src/replicate.cpp

+73 −407

Original line number	Diff line number	Diff line
		@@ -44,7 +44,7 @@ void Replicate::command(int narg, char **arg)

		if (domain->box_exist == 0)
		error->all(FLERR,"Replicate command before simulation box is defined");
		if (narg < 3 \|\| narg > 4) error->all(FLERR,"Illegal replicate command");
		if (narg != 3) error->all(FLERR,"Illegal replicate command");

		int me = comm->me;
		int nprocs = comm->nprocs;
		@@ -58,10 +58,6 @@ void Replicate::command(int narg, char **arg)
		int nz = force->inumeric(FLERR,arg[2]);
		int nrep = nxnynz;

		int bbox_flag = 0;
		if (narg == 4)
		if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1;

		// error and warning checks

		if (nx <= 0 \|\| ny <= 0 \|\| nz <= 0)
		@@ -103,37 +99,6 @@ void Replicate::command(int narg, char **arg)
		maxmol = maxmol_all;
		}

		// check image flags maximum extent; only efficient small image flags compared to new system

		int _imagelo[3], _imagehi[3];
		_imagelo[0] = 0;
		_imagelo[1] = 0;
		_imagelo[2] = 0;
		_imagehi[0] = 0;
		_imagehi[1] = 0;
		_imagehi[2] = 0;

		if (bbox_flag) {

		for (i=0; i<atom->nlocal; ++i) {
		imageint image = atom->image[i];
		int xbox = (image & IMGMASK) - IMGMAX;
		int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
		int zbox = (image >> IMG2BITS) - IMGMAX;

		if (xbox < _imagelo[0]) _imagelo[0] = xbox;
		if (ybox < _imagelo[1]) _imagelo[1] = ybox;
		if (zbox < _imagelo[2]) _imagelo[2] = zbox;

		if (xbox > _imagehi[0]) _imagehi[0] = xbox;
		if (ybox > _imagehi[1]) _imagehi[1] = ybox;
		if (zbox > _imagehi[2]) _imagehi[2] = zbox;
		}

		MPI_Allreduce(MPI_IN_PLACE, &(_imagelo[0]), 3, MPI_INT, MPI_MIN, world);
		MPI_Allreduce(MPI_IN_PLACE, &(_imagehi[0]), 3, MPI_INT, MPI_MAX, world);
		}

		// unmap existing atoms via image flags

		for (i = 0; i < atom->nlocal; i++)
		@@ -315,304 +280,6 @@ void Replicate::command(int narg, char **arg)
		double *coord;
		int tag_enable = atom->tag_enable;

		if (bbox_flag) {

		// allgather size of buf on each proc

		n = 0;
		for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);

		int * size_buf_rnk;
		memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk");

		MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world);

		// size of buf_all

		int size_buf_all = 0;
		MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world);

		if (me == 0 && screen) {
		fprintf(screen," bounding box image = (%i %i %i) to (%i %i %i)\n",
		_imagelo[0],_imagelo[1],_imagelo[2],_imagehi[0],_imagehi[1],_imagehi[2]);
		fprintf(screen," bounding box extra memory = %.2f MB\n",
		(double)size_buf_all*sizeof(double)/1024/1024);
		}

		// rnk offsets

		int * disp_buf_rnk;
		memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk");
		disp_buf_rnk[0] = 0;
		for (i=1; i<nprocs; ++i) disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1];

		// allgather buf_all

		double * buf_all;
		memory->create(buf_all, size_buf_all, "replicate:buf_all");

		MPI_Allgatherv(buf, n, MPI_DOUBLE, buf_all, size_buf_rnk, disp_buf_rnk, MPI_DOUBLE, world);

		// bounding box of original unwrapped system

		double _orig_lo[3], _orig_hi[3];
		if (triclinic) {
		_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz;
		_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd + _imagelo[2] * old_yz;
		_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;

		_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd + (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz;
		_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz;
		_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
		} else {
		_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd;
		_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd;
		_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;

		_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd;
		_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd;
		_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
		}

		double _lo[3], _hi[3];

		int num_replicas_added = 0;

		for (ix = 0; ix < nx; ix++) {
		for (iy = 0; iy < ny; iy++) {
		for (iz = 0; iz < nz; iz++) {

		// domain->remap() overwrites coordinates, so always recompute here

		if (triclinic) {
		_lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz;
		_hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz;

		_lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz;
		_hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz;

		_lo[2] = _orig_lo[2] + iz * old_zprd;
		_hi[2] = _orig_hi[2] + iz * old_zprd;
		} else {
		_lo[0] = _orig_lo[0] + ix * old_xprd;
		_hi[0] = _orig_hi[0] + ix * old_xprd;

		_lo[1] = _orig_lo[1] + iy * old_yprd;
		_hi[1] = _orig_hi[1] + iy * old_yprd;

		_lo[2] = _orig_lo[2] + iz * old_zprd;
		_hi[2] = _orig_hi[2] + iz * old_zprd;
		}

		// test if bounding box of shifted replica overlaps sub-domain of proc
		// if not, then skip testing atoms

		int xoverlap = 1;
		int yoverlap = 1;
		int zoverlap = 1;
		if (triclinic) {
		double _llo[3];
		domain->x2lamda(_lo,_llo);
		double _lhi[3];
		domain->x2lamda(_hi,_lhi);

		if (_llo[0] > (subhi[0] - EPSILON)
		\|\| _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
		if (_llo[1] > (subhi[1] - EPSILON)
		\|\| _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
		if (_llo[2] > (subhi[2] - EPSILON)
		\|\| _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
		} else {
		if (_lo[0] > (subhi[0] - EPSILON)
		\|\| _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0;
		if (_lo[1] > (subhi[1] - EPSILON)
		\|\| _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0;
		if (_lo[2] > (subhi[2] - EPSILON)
		\|\| _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0;
		}

		int overlap = 0;
		if (xoverlap && yoverlap && zoverlap) overlap = 1;

		// if no overlap, test if bounding box wrapped back into new system

		if (!overlap) {

		// wrap back into cell

		imageint imagelo = ((imageint) IMGMAX << IMG2BITS) \|
		((imageint) IMGMAX << IMGBITS) \| IMGMAX;
		domain->remap(&(_lo[0]), imagelo);
		int xboxlo = (imagelo & IMGMASK) - IMGMAX;
		int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX;
		int zboxlo = (imagelo >> IMG2BITS) - IMGMAX;

		imageint imagehi = ((imageint) IMGMAX << IMG2BITS) \|
		((imageint) IMGMAX << IMGBITS) \| IMGMAX;
		domain->remap(&(_hi[0]), imagehi);
		int xboxhi = (imagehi & IMGMASK) - IMGMAX;
		int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX;
		int zboxhi = (imagehi >> IMG2BITS) - IMGMAX;

		if (triclinic) {
		double _llo[3];
		_llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2];
		domain->x2lamda(_llo,_lo);

		double _lhi[3];
		_lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2];
		domain->x2lamda(_lhi,_hi);
		}

		// test all fragments for any overlap; ok to include false positives

		int _xoverlap1 = 0;
		int _xoverlap2 = 0;
		if (!xoverlap) {
		if (xboxlo < 0) {
		_xoverlap1 = 1;
		if ( _lo[0] > (subhi[0] - EPSILON) ) _xoverlap1 = 0;
		}

		if (xboxhi > 0) {
		_xoverlap2 = 1;
		if ( _hi[0] < (sublo[0] + EPSILON) ) _xoverlap2 = 0;
		}

		if (_xoverlap1 \|\| _xoverlap2) xoverlap = 1;
		}

		int _yoverlap1 = 0;
		int _yoverlap2 = 0;
		if (!yoverlap) {
		if (yboxlo < 0) {
		_yoverlap1 = 1;
		if ( _lo[1] > (subhi[1] - EPSILON) ) _yoverlap1 = 0;
		}

		if (yboxhi > 0) {
		_yoverlap2 = 1;
		if ( _hi[1] < (sublo[1] + EPSILON) ) _yoverlap2 = 0;
		}

		if (_yoverlap1 \|\| _yoverlap2) yoverlap = 1;
		}


		int _zoverlap1 = 0;
		int _zoverlap2 = 0;
		if (!zoverlap) {
		if (zboxlo < 0) {
		_zoverlap1 = 1;
		if ( _lo[2] > (subhi[2] - EPSILON) ) _zoverlap1 = 0;
		}

		if (zboxhi > 0) {
		_zoverlap2 = 1;
		if ( _hi[2] < (sublo[2] + EPSILON) ) _zoverlap2 = 0;
		}

		if (_zoverlap1 \|\| _zoverlap2) zoverlap = 1;
		}

		// does either fragment overlap w/ sub-domain

		if (xoverlap && yoverlap && zoverlap) overlap = 1;
		}

		// while loop over one proc's atom list

		if (overlap) {
		num_replicas_added++;

		m = 0;
		while (m < size_buf_all) {
		image = ((imageint) IMGMAX << IMG2BITS) \|
		((imageint) IMGMAX << IMGBITS) \| IMGMAX;
		if (triclinic == 0) {
		x[0] = buf_all[m+1] + ix*old_xprd;
		x[1] = buf_all[m+2] + iy*old_yprd;
		x[2] = buf_all[m+3] + iz*old_zprd;
		} else {
		x[0] = buf_all[m+1] + ixold_xprd + iyold_xy + iz*old_xz;
		x[1] = buf_all[m+2] + iyold_yprd + izold_yz;
		x[2] = buf_all[m+3] + iz*old_zprd;
		}
		domain->remap(x,image);
		if (triclinic) {
		domain->x2lamda(x,lamda);
		coord = lamda;
		} else coord = x;

		if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
		coord[1] >= sublo[1] && coord[1] < subhi[1] &&
		coord[2] >= sublo[2] && coord[2] < subhi[2]) {

		m += avec->unpack_restart(&buf_all[m]);

		i = atom->nlocal - 1;
		if (tag_enable)
		atom_offset = iznynxmaxtag + iynxmaxtag + ixmaxtag;
		else atom_offset = 0;
		mol_offset = iznynxmaxmol + iynxmaxmol + ixmaxmol;

		atom->x[i][0] = x[0];
		atom->x[i][1] = x[1];
		atom->x[i][2] = x[2];

		atom->tag[i] += atom_offset;
		atom->image[i] = image;

		if (atom->molecular) {
		if (atom->molecule[i] > 0)
		atom->molecule[i] += mol_offset;
		if (atom->molecular == 1) {
		if (atom->avec->bonds_allow)
		for (j = 0; j < atom->num_bond[i]; j++)
		atom->bond_atom[i][j] += atom_offset;
		if (atom->avec->angles_allow)
		for (j = 0; j < atom->num_angle[i]; j++) {
		atom->angle_atom1[i][j] += atom_offset;
		atom->angle_atom2[i][j] += atom_offset;
		atom->angle_atom3[i][j] += atom_offset;
		}
		if (atom->avec->dihedrals_allow)
		for (j = 0; j < atom->num_dihedral[i]; j++) {
		atom->dihedral_atom1[i][j] += atom_offset;
		atom->dihedral_atom2[i][j] += atom_offset;
		atom->dihedral_atom3[i][j] += atom_offset;
		atom->dihedral_atom4[i][j] += atom_offset;
		}
		if (atom->avec->impropers_allow)
		for (j = 0; j < atom->num_improper[i]; j++) {
		atom->improper_atom1[i][j] += atom_offset;
		atom->improper_atom2[i][j] += atom_offset;
		atom->improper_atom3[i][j] += atom_offset;
		atom->improper_atom4[i][j] += atom_offset;
		}
		}
		}
		} else m += static_cast<int> (buf_all[m]);
		}
		} // if (overlap)

		}
		}
		}

		memory->destroy(size_buf_rnk);
		memory->destroy(disp_buf_rnk);
		memory->destroy(buf_all);

		int sum = 0;
		MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world);
		double avg = (double) sum / nprocs;
		if (me == 0 && screen)
		fprintf(screen," average # of replicas added to proc = %.2f out of %i (%.2f %%)\n",
		avg,nxnynz,avg/(nxnynz)*100.0);

		} else {

		for (int iproc = 0; iproc < nprocs; iproc++) {
		if (me == iproc) {
		n = 0;
		@@ -700,7 +367,6 @@ void Replicate::command(int narg, char **arg)
		}
		}
		}
		} // if (bbox_flag)

		// free communication buffer and old atom class

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