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resolution of cutoff issues

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This commit is contained in:
Steven J. Plimpton
2018-08-24 09:36:39 -06:00
parent 59d3af44f2
commit 44bda245a6
6 changed files with 47 additions and 62 deletions
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13
doc/src/pair_atm.txt
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@ -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 r12*r23*r31 <
cutoff_triple^3 is required, which limits the contribution of the
potential to ???
In addition, the product of the 3 distances r12*r23*r31 <
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

2
examples/atm/in.atm
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@ -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

36
examples/atm/log.9Jul18.atm.g++.1 → examples/atm/log.23Aug18.atm.g++.1
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@ -1,4 +1,4 @@
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

34
examples/atm/log.9Jul18.atm.g++.4 → examples/atm/log.23Aug18.atm.g++.4
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@ -1,4 +1,4 @@
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

21
src/MANYBODY/pair_atm.cpp
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@ -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_triple*cut_triple*cut_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 (rij2*rjk2*rik2 > cutoff_triple_sixth) continue;
double r6 = rij2*rjk2*rik2;
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 = rij2*rik2*rjk2;
double r5inv,rri,rrj,rrk,rrr;
r5inv = nu / (r6*r6*sqrt(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];

3
src/MANYBODY/pair_atm.h
View File

@ -39,12 +39,11 @@ class PairATM : public Pair {
void read_restart_settings(FILE *);
protected:
// SJP: add 2nd cutoff
double cut_global,cut_triple;
double ***nu;
void allocate();
void interaction_ddd(double, double, double, double, double *,
void interaction_ddd(double, double, double, double, double, double *,
double *, double *, double *, double *, int, double &);
};