resolution of cutoff issues (44bda245) · Commits · 郑智淋 / lammps

doc/src/pair_atm.txt

+5 −8

Original line number	Diff line number	Diff line
		@@ -10,8 +10,6 @@ pair_style atm command :h3

		[Syntax:]

		SJP: add an arg

		pair_style atm cutoff cutoff_triple :pre

		cutoff = cutoff for each pair in 3-body interaction (distance units)
		@@ -19,11 +17,10 @@ cutoff_triple = additional cutoff applied to product of 3 pairwise distances (di

		[Examples:]

		SJP: is 1.5 a good value?
		pair_style atm 2.5 1.5
		pair_style atm 4.5 2.5
		pair_coeff * * * 0.072 :pre

		pair_style hybrid/overlay lj/cut 6.5 atm 2.5 1.5
		pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5
		pair_coeff * * lj/cut 1.0 1.0
		pair_coeff 1 1 atm 1 0.064
		pair_coeff 1 1 atm 2 0.080
		@@ -55,9 +52,9 @@ command as in the example above.

		The potential for a triplet of atom is calculated only if all 3
		distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
		SJP: In addition, the product of the 3 distances r12r23r31 <
		cutoff_triple^3 is required, which limits the contribution of the
		potential to ???
		In addition, the product of the 3 distances r12r23r31 <
		cutoff_triple^3 is required, which excludes from calculation the
		triplets with small contribution to the interaction.

		The following coefficients must be defined for each pair of atoms
		types via the "pair_coeff"_pair_coeff.html command as in the examples

examples/atm/in.atm

+1 −1

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ region box block 0 ${xx} 0 ${yy} 0 ${zz}
		create_box 1 box
		create_atoms 1 box

		pair_style hybrid/overlay lj/cut 4.5 atm 2.5
		pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
		pair_coeff * * lj/cut 1.0 1.0
		pair_coeff * * atm * 0.072

examples/atm/log.9Jul18.atm.g++.1→examples/atm/log.23Aug18.atm.g++.1

+18 −18

Original line number	Diff line number	Diff line
		LAMMPS (29 Jun 2018)
		LAMMPS (22 Aug 2018)
		# Axilrod-Teller-Muto potential example

		variable x index 1
		@@ -26,9 +26,9 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
		1 by 1 by 1 MPI processor grid
		create_atoms 1 box
		Created 4000 atoms
		Time spent = 0.00125098 secs
		Time spent = 0.00126314 secs

		pair_style hybrid/overlay lj/cut 4.5 atm 2.5
		pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
		pair_coeff * * lj/cut 1.0 1.0
		pair_coeff * * atm * 0.072

		@@ -60,26 +60,26 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 11.47 \| 11.47 \| 11.47 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 1.033 -4.733482 0 -3.1843694 -3.924644
		5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
		10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
		15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
		20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
		25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
		Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms
		0 1.033 -4.8899813 0 -3.3408686 -4.2298176
		5 1.0337853 -4.8928208 0 -3.3425304 -4.2233154
		10 1.0358056 -4.8953304 0 -3.3420104 -4.1897183
		15 1.0380938 -4.8990457 0 -3.3422942 -4.1310148
		20 1.0389566 -4.9014345 0 -3.3433892 -4.0406616
		25 1.0358313 -4.8989663 0 -3.3456079 -3.9093019
		Loop time of 12.2062 on 1 procs for 25 steps with 4000 atoms

		Performance: 155.167 tau/day, 0.898 timesteps/s
		100.0% CPU use with 1 MPI tasks x no OpenMP threads
		Performance: 353.920 tau/day, 2.048 timesteps/s
		99.9% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 27.837 \| 27.837 \| 27.837 \| 0.0 \| 99.99
		Pair \| 12.202 \| 12.202 \| 12.202 \| 0.0 \| 99.96
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.0015321 \| 0.0015321 \| 0.0015321 \| 0.0 \| 0.01
		Output \| 0.00016594 \| 0.00016594 \| 0.00016594 \| 0.0 \| 0.00
		Modify \| 0.001785 \| 0.001785 \| 0.001785 \| 0.0 \| 0.01
		Other \| \| 0.0006731 \| \| \| 0.00
		Comm \| 0.0015621 \| 0.0015621 \| 0.0015621 \| 0.0 \| 0.01
		Output \| 0.00020814 \| 0.00020814 \| 0.00020814 \| 0.0 \| 0.00
		Modify \| 0.0019698 \| 0.0019698 \| 0.0019698 \| 0.0 \| 0.02
		Other \| \| 0.0007734 \| \| \| 0.01

		Nlocal: 4000 ave 4000 max 4000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -97,4 +97,4 @@ Dangerous builds = 0

		Please see the log.cite file for references relevant to this simulation

		Total wall time: 0:00:29
		Total wall time: 0:00:13

examples/atm/log.9Jul18.atm.g++.4→examples/atm/log.23Aug18.atm.g++.4

+17 −17

Original line number	Diff line number	Diff line
		LAMMPS (29 Jun 2018)
		LAMMPS (22 Aug 2018)
		# Axilrod-Teller-Muto potential example

		variable x index 1
		@@ -26,9 +26,9 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
		1 by 2 by 2 MPI processor grid
		create_atoms 1 box
		Created 4000 atoms
		Time spent = 0.000769138 secs
		Time spent = 0.000785112 secs

		pair_style hybrid/overlay lj/cut 4.5 atm 2.5
		pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
		pair_coeff * * lj/cut 1.0 1.0
		pair_coeff * * atm * 0.072

		@@ -60,26 +60,26 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 5.532 \| 5.532 \| 5.532 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 1.033 -4.733482 0 -3.1843694 -3.924644
		5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
		10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
		15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
		20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
		25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
		Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms
		0 1.033 -4.8921547 0 -3.343042 -4.2340557
		5 1.0337949 -4.8947881 0 -3.3444835 -4.2271456
		10 1.0358286 -4.8973178 0 -3.3439632 -4.1935779
		15 1.0381322 -4.9010593 0 -3.3442503 -4.134913
		20 1.0390107 -4.9034854 0 -3.3453589 -4.0446162
		25 1.0358988 -4.9010506 0 -3.3475908 -3.9133006
		Loop time of 3.20632 on 4 procs for 25 steps with 4000 atoms

		Performance: 598.314 tau/day, 3.462 timesteps/s
		Performance: 1347.340 tau/day, 7.797 timesteps/s
		100.0% CPU use with 4 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 7.1346 \| 7.1684 \| 7.1863 \| 0.8 \| 99.28
		Pair \| 3.1207 \| 3.1553 \| 3.1859 \| 1.5 \| 98.41
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.032945 \| 0.0509 \| 0.084664 \| 9.1 \| 0.70
		Output \| 0.00010133 \| 0.00011051 \| 0.00013804 \| 0.0 \| 0.00
		Modify \| 0.00059557 \| 0.00060683 \| 0.00061274 \| 0.0 \| 0.01
		Other \| \| 0.000318 \| \| \| 0.00
		Comm \| 0.019466 \| 0.05009 \| 0.084602 \| 12.0 \| 1.56
		Output \| 7.1049e-05 \| 8.2076e-05 \| 0.00011325 \| 0.0 \| 0.00
		Modify \| 0.00056338 \| 0.00057292 \| 0.00058413 \| 0.0 \| 0.02
		Other \| \| 0.0003092 \| \| \| 0.01

		Nlocal: 1000 ave 1000 max 1000 min
		Histogram: 4 0 0 0 0 0 0 0 0 0
		@@ -97,4 +97,4 @@ Dangerous builds = 0

		Please see the log.cite file for references relevant to this simulation

		Total wall time: 0:00:07
		Total wall time: 0:00:03

src/MANYBODY/pair_atm.cpp

+5 −16

Original line number	Diff line number	Diff line
		@@ -15,9 +15,7 @@
		Contributing author: Sergey Lishchuk
		------------------------------------------------------------------------- */


		#include <cmath>

		#include "pair_atm.h"
		#include "atom.h"
		#include "citeme.h"
		@@ -92,7 +90,6 @@ void PairATM::compute(int eflag, int vflag)
		int *type = atom->type;

		double cutoff_squared = cut_global*cut_global;
		// SJP: new cutoff
		double triple = cut_triplecut_triplecut_triple;
		double cutoff_triple_sixth = triple*triple;

		@@ -142,15 +139,14 @@ void PairATM::compute(int eflag, int vflag)
		rik2 = rik[0]rik[0] + rik[1]rik[1] + rik[2]*rik[2];
		if (rik2 > cutoff_squared) continue;

		// SJP: add this line?

		if (rij2rjk2rik2 > cutoff_triple_sixth) continue;
		double r6 = rij2rjk2rik2;
		if (r6 > cutoff_triple_sixth) continue;

		nu_local = nu[type[i]][type[j]][type[k]];
		if (nu_local == 0.0) continue;

		interaction_ddd(nu_local,
		rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
		r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);

		f[i][0] -= fj[0] + fk[0];
		f[i][1] -= fj[1] + fk[1];
		@@ -200,14 +196,10 @@ void PairATM::allocate()

		void PairATM::settings(int narg, char **arg)
		{
		// SJP: change to 2 args, require triple <= global

		if (narg != 2) error->all(FLERR,"Illegal pair_style command");

		cut_global = force->numeric(FLERR,arg[0]);
		cut_triple = force->numeric(FLERR,arg[1]);

		if (cut_triple > cut_global) error->all(FLERR,"Illegal pair_style command");
		}

		/* ----------------------------------------------------------------------
		@@ -324,7 +316,6 @@ void PairATM::read_restart(FILE *fp)
		void PairATM::write_restart_settings(FILE *fp)
		{
		fwrite(&cut_global,sizeof(double),1,fp);
		// SJP: 2nd arg
		fwrite(&cut_triple,sizeof(double),1,fp);
		}

		@@ -334,7 +325,6 @@ void PairATM::write_restart_settings(FILE *fp)

		void PairATM::read_restart_settings(FILE *fp)
		{
		// SJP: 2nd arg
		int me = comm->me;
		if (me == 0) {
		fread(&cut_global,sizeof(double),1,fp);
		@@ -348,13 +338,12 @@ void PairATM::read_restart_settings(FILE *fp)
		Axilrod-Teller-Muto (dipole-dipole-dipole) potential
		------------------------------------------------------------------------- */

		void PairATM::interaction_ddd(double nu,
		void PairATM::interaction_ddd(double nu, double r6,
		double rij2, double rik2, double rjk2,
		double rij, double rik, double *rjk,
		double fj, double fk, int eflag, double &eng)
		{
		double r6,r5inv,rri,rrj,rrk,rrr;
		r6 = rij2rik2rjk2;
		double r5inv,rri,rrj,rrk,rrr;
		r5inv = nu / (r6r6sqrt(r6));
		rri = rik[0]rij[0] + rik[1]rij[1] + rik[2]*rij[2];
		rrj = rij[0]rjk[0] + rij[1]rjk[1] + rij[2]*rjk[2];

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