added triclinic support (a69a99a9) · Commits · 郑智淋 / lammps

src/replicate.cpp

+60 −18

Original line number	Diff line number	Diff line
		@@ -356,6 +356,15 @@ void Replicate::command(int narg, char **arg)
		// 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;
		@@ -363,6 +372,7 @@ void Replicate::command(int narg, char **arg)
		_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];

		@@ -374,6 +384,16 @@ void Replicate::command(int narg, char **arg)

		// 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;

		@@ -382,6 +402,7 @@ void Replicate::command(int narg, char **arg)

		_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
		@@ -389,9 +410,20 @@ void Replicate::command(int narg, char **arg)
		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;
		@@ -416,6 +448,16 @@ void Replicate::command(int narg, char **arg)
		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;

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