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Merge pull request #1309 from PabloPiaggi/pair_entropy

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compute entropy/atom - enhancement/optimization
This commit is contained in:
Axel Kohlmeyer
2019-01-31 09:36:44 +01:00
committed by GitHub
parent 8cc593fe6b ccdfde4978
commit 0e1c6082b0
2 changed files with 45 additions and 39 deletions
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72
examples/USER/misc/entropy/log.entropy
View File

@ -1,4 +1,4 @@
LAMMPS (30 Mar 2018)
LAMMPS (4 Jan 2019)
units metal
atom_style full
@ -45,10 +45,10 @@ fix 1 all nph x 1. 1. 10.
fix 2 all temp/csvr 350. 350. 0.1 64582
run 1000
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -56,27 +56,27 @@ Neighbor list info ...
ghost atom cutoff = 13.2
binsize = 6.6, bins = 21 6 6
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs, perpetual
(1) pair eam/fs, perpetual, half/full from (2)
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
pair build: halffull/newton
stencil: none
bin: none
(2) compute entropy/atom, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(3) compute entropy/atom, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(4) compute entropy/atom, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) compute entropy/atom, perpetual, copy from (2)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
(4) compute entropy/atom, perpetual, copy from (2)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
(5) compute entropy/atom, perpetual, copy from (2)
(5) compute entropy/atom, perpetual, copy from (4)
attributes: full, newton on, ghost
pair build: copy
stencil: none
@ -85,34 +85,34 @@ Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.002
Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes
Per MPI rank memory allocation (min/avg/max) = 19.6 | 19.6 | 19.6 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75
500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18
1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18
Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms
500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09
1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86
Loop time of 4.4394 on 4 procs for 1000 steps with 4096 atoms
Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95
Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00
Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96
Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06
Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66
Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16
Other | | 0.01161 | | | 0.22
Pair | 3.5298 | 3.5931 | 3.6669 | 2.6 | 80.94
Bond | 8.2099e-05 | 0.00011444 | 0.00014673 | 0.0 | 0.00
Neigh | 0.43384 | 0.4445 | 0.45558 | 1.4 | 10.01
Comm | 0.048904 | 0.11122 | 0.16728 | 12.7 | 2.51
Output | 0.22595 | 0.22595 | 0.22596 | 0.0 | 5.09
Modify | 0.053103 | 0.053795 | 0.054549 | 0.3 | 1.21
Other | | 0.01068 | | | 0.24
Nlocal: 1024 ave 1040 max 1001 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 4614.25 ave 4700 max 4540 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 121747 ave 126398 max 116931 min
Neighs: 121747 ave 126398 max 116930 min
Histogram: 1 0 0 1 0 0 1 0 0 1
FullNghs: 243494 ave 252523 max 233842 min
FullNghs: 243494 ave 252523 max 233841 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 973974
@ -121,4 +121,4 @@ Ave special neighs/atom = 0
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:04

12
src/USER-MISC/compute_entropy_atom.cpp
View File

@ -65,6 +65,7 @@ ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; cutoff must be positive");
cutoff2 = 0.;
avg_flag = 0;
local_flag = 0;
@ -137,15 +138,20 @@ void ComputeEntropyAtom::init()
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute entropy/atom");
// need a full neighbor list with neighbors of the ghost atoms
// Request neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 0;
neighbor->requests[irequest]->ghost = 1;
if (avg_flag) {
// need a full neighbor list with neighbors of the ghost atoms
neighbor->requests[irequest]->ghost = 1;
} else {
// need a full neighbor list
neighbor->requests[irequest]->ghost = 0;
}
}