(bd37304a) · Commits · 郑智淋 / lammps

src/ASPHERE/compute_temp_asphere.cpp

+3 −2

Original line number	Diff line number	Diff line
		@@ -133,7 +133,6 @@ void ComputeTempAsphere::setup()
		{
		dynamic = 0;
		if (dynamic_user \|\| group->dynamic[igroup]) dynamic = 1;
		fix_dof = -1;
		dof_compute();
		}

		@@ -141,7 +140,7 @@ void ComputeTempAsphere::setup()

		void ComputeTempAsphere::dof_compute()
		{
		if (fix_dof) adjust_dof_fix();
		fix_dof = modify->adjust_dof_fix(igroup);

		// 6 dof for 3d, 3 dof for 2d
		// which dof are included also depends on mode
		@@ -268,6 +267,8 @@ double ComputeTempAsphere::compute_scalar()

		MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
		if (dynamic \|\| tempbias == 2) dof_compute();
		if (tfactor == 0.0 && scalar != 0.0)
		error->all(FLERR,"Temperature compute degrees of freedom < 0");
		scalar *= tfactor;
		return scalar;
		}

+3 −2

Original line number	Diff line number	Diff line
		@@ -201,7 +201,6 @@ void ComputeTempCS::setup()

		// calculate DOF for temperature

		fix_dof = -1;
		dof_compute();
		}

		@@ -209,7 +208,7 @@ void ComputeTempCS::setup()

		void ComputeTempCS::dof_compute()
		{
		if (fix_dof) adjust_dof_fix();
		fix_dof = modify->adjust_dof_fix(igroup);
		int nper = domain->dimension;
		double natoms = group->count(igroup);
		dof = nper * natoms;
		@@ -257,6 +256,8 @@ double ComputeTempCS::compute_scalar()

		MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
		if (dynamic) dof_compute();
		if (tfactor == 0.0 && scalar != 0.0)
		error->all(FLERR,"Temperature compute degrees of freedom < 0");
		scalar *= tfactor;
		return scalar;
		}

+37 −1

Original line number	Diff line number	Diff line
		@@ -249,6 +249,41 @@ void FixDeposit::init()
		error->all(FLERR,"Fix deposit and fix shake not using "
		"same molecule template ID");
		}

		// for finite size spherical particles:
		// warn if near < 2 * maxrad of existing and inserted particles
		// since may lead to overlaps
		// if inserted molecule does not define diameters,
		// use AtomVecSphere::create_atom() default radius = 0.5

		if (atom->radius_flag) {
		double *radius = atom->radius;
		int nlocal = atom->nlocal;

		double maxrad = 0.0;
		for (int i = 0; i < nlocal; i++)
		maxrad = MAX(maxrad,radius[i]);

		double maxradall;
		MPI_Allreduce(&maxrad,&maxradall,1,MPI_DOUBLE,MPI_MAX,world);

		double maxradinsert = 0.0;
		if (mode == MOLECULE) {
		for (int i = 0; i < nmol; i++) {
		if (onemols[i]->radiusflag)
		maxradinsert = MAX(maxradinsert,onemols[i]->maxradius);
		else maxradinsert = MAX(maxradinsert,0.5);
		}
		} else maxradinsert = 0.5;

		double separation = MAX(2.0*maxradinsert,maxradall+maxradinsert);
		if (sqrt(nearsq) < separation && comm->me == 0) {
		char str[128];
		sprintf(str,"Fix deposit near setting < possible overlap separation %g",
		separation);
		error->warning(FLERR,str);
		}
		}
		}

		/* ----------------------------------------------------------------------
		@@ -389,7 +424,8 @@ void FixDeposit::pre_exchange()
		}
		}

		// if distance to any inserted atom is less than near, try again
		// check distance between any existing atom and any inserted atom
		// if less than near, try again
		// use minimum_image() to account for PBC

		double **x = atom->x;

+1 −0

Original line number	Diff line number	Diff line
		@@ -71,6 +71,7 @@ FixPOEMS::FixPOEMS(LAMMPS lmp, int narg, char *arg) :
		time_integrate = 1;
		rigid_flag = 1;
		virial_flag = 1;
		dof_flag = 1;

		MPI_Comm_rank(world,&me);

+1 −0

Original line number	Diff line number	Diff line
		@@ -66,6 +66,7 @@ FixRigid::FixRigid(LAMMPS lmp, int narg, char *arg) :
		rigid_flag = 1;
		virial_flag = 1;
		create_attribute = 1;
		dof_flag = 1;

		MPI_Comm_rank(world,&me);
		MPI_Comm_size(world,&nprocs);