(6fbbb515) · Commits · 郑智淋 / lammps

src/PERI/fix_peri_neigh.cpp

+11 −0

Original line number	Diff line number	Diff line
		@@ -119,6 +119,17 @@ void FixPeriNeigh::init()
		neighbor->requests[irequest]->half = 0;
		neighbor->requests[irequest]->full = 1;
		neighbor->requests[irequest]->occasional = 1;

		// compute PD scale factor, stored in Atom class, used by DumpCFG

		int nlocal = atom->nlocal;
		double vone = 0.0;
		for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
		double vave;
		MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
		if (atom->natoms) vave /= atom->natoms;
		if (vave > 0.0) atom->pdscale = 1.44 / pow(vave,1.0/3.0);
		else atom->pdscale = 1.0;
		}

		/* ---------------------------------------------------------------------- */

+4 −0

Original line number	Diff line number	Diff line
		@@ -140,6 +140,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		cs_flag = csforce_flag = vforce_flag = ervelforce_flag= etag_flag = 0;
		rho_flag = e_flag = cv_flag = vest_flag = 0;

		// Peridynamic scale factor

		pdscale = 1.0;

		// ntype-length arrays

		mass = NULL;

+4 −0

Original line number	Diff line number	Diff line
		@@ -114,6 +114,10 @@ class Atom : protected Pointers {
		int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
		int rho_flag,e_flag,cv_flag,vest_flag;

		// Peridynamics scale factor, used by dump cfg

		double pdscale;

		// molecule templates
		// each template can be a set of consecutive molecules
		// each with same ID (stored in molecules)

+10 −16

Original line number	Diff line number	Diff line
		@@ -130,22 +130,16 @@ void DumpCFG::init_style()

		void DumpCFG::write_header(bigint n)
		{
		// special handling for atom style peri
		// use average volume of particles to scale particles to mimic C atoms
		// scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
		// special handling for unwrapped coordinates

		double scale;
		if (atom->peri_flag) {
		int nlocal = atom->nlocal;
		double vone = 0.0;
		for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
		double vave;
		MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
		if (atom->natoms) vave /= atom->natoms;
		if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
		} else if (unwrapflag == 1) scale = UNWRAPEXPAND;
		else scale = 1.0;
		// set scale factor used by AtomEye for CFG viz
		// default = 1.0
		// for peridynamics, set to pre-computed PD scale factor
		// so PD particles mimic C atoms
		// for unwrapped coords, set to UNWRAPEXPAND (10.0)
		// so molecules are not split across periodic box boundaries

		double scale = 1.0;
		if (atom->peri_flag) scale = atom->pdscale;
		else if (unwrapflag == 1) scale = UNWRAPEXPAND;

		char str[64];
		sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);