Examples - new local option (124641dc) · Commits · 郑智淋 / lammps

doc/src/compute_pair_entropy_atom.txt

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Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ The advantage of this parameter over others is that no a priori
		information about the solid structure is required.

		This parameter for atom i is computed using the following formula from
		"(Piaggi)"_#Piaggi
		"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton

		:c,image(Eqs/pair_entropy.jpg)

		@@ -119,3 +119,6 @@ The default value for the optional keyword is avg = no.

		:link(Piaggi)
		[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).

		:link(Nettleton}
		[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958).

examples/USER/misc/pair_entropy/Na_MendelevM_2014.eam.fs

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examples/USER/misc/pair_entropy/data.interface

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examples/USER/misc/pair_entropy/start.lmp

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Original line number	Diff line number	Diff line
		echo both

		units metal
		atom_style full

		read_data data.interface
		mass 1 22.98977

		neigh_modify delay 10 every 1
		pair_style eam/fs
		pair_coeff * * Na_MendelevM_2014.eam.fs Na
		timestep 0.002
		thermo 500

		neighbor 4. bin

		# Define computes
		# Global density, no average
		compute 1 all pentropy/atom 0.25 7.75
		# Local density, no average
		compute 2 all pentropy/atom 0.25 7.75 local yes
		# Global density, average over neighbors
		compute 3 all pentropy/atom 0.25 7.75 avg yes 5.
		# Local density, average over neighbors
		compute 4 all pentropy/atom 0.25 7.75 avg yes 5. local yes

		dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4


		fix 1 all nph x 1. 1. 10.
		fix 2 all temp/csvr 350. 350. 0.1 64582

		run 100000

src/compute_pair_entropy_atom.cpp

+15 −3

Original line number	Diff line number	Diff line
		@@ -44,7 +44,7 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		Compute(lmp, narg, arg),
		pair_entropy(NULL), pair_entropy_avg(NULL)
		{
		if (narg < 5 \|\| narg > 8)
		if (narg < 5 \|\| narg > 10)
		error->all(FLERR,"Illegal compute pentropy/atom command");

		// Arguments are: sigma cutoff avg yes/no cutoff2
		@@ -59,6 +59,7 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		if (cutoff < 0.0) error->all(FLERR,"Illegal compute pentropy/atom command; negative cutoff");

		avg_flag = 0;
		local_flag = 0;

		// optional keywords
		int iarg = 5;
		@@ -73,7 +74,12 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute pentropy/atom command; negative cutoff2");
		cutsq2 = cutoff2*cutoff2;
		iarg += 3;
		} else error->all(FLERR,"Illegal compute pentropy/atom argument after sigma and cutoff should be avg");
		} else if (strcmp(arg[iarg],"local") == 0) {
		if (strcmp(arg[iarg+1],"yes") == 0) local_flag = 1;
		else if (strcmp(arg[iarg+1],"no") == 0) local_flag = 0;
		else error->all(FLERR,"Illegal compute pentropy/atom argument after local should be yes or no");
		iarg += 2;
		} else error->all(FLERR,"Illegal compute pentropy/atom argument after sigma and cutoff should be avg or local");
		}


		@@ -209,6 +215,12 @@ void ComputePairEntropyAtom::compute_peratom()
		jlist = firstneigh[i];
		jnum = numneigh[i];

		// If local density is used, calculate it
		if (local_flag) {
		double neigh_cutoff = force->pair->cutforce + neighbor->skin;
		double volume = (4./3.)MY_PIneigh_cutoffneigh_cutoffneigh_cutoff;
		density = jnum / volume;
		}

		// calculate kernel normalization
		double normConstantBase = 4MY_PIdensity; // Normalization of g(r)

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