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rerun updated examples and record log files

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This commit is contained in:
Axel Kohlmeyer
2023-03-07 14:36:56 -05:00
parent a3c9029664
commit c2d0734bc4
13 changed files with 729 additions and 73 deletions
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2
examples/PACKAGES/dielectric/in.nopbc
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@ -27,7 +27,7 @@ neigh_modify one 5000
#compute ef all efield/atom #compute ef all efield/atom
#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] #dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
# #
dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] #dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
#dump_modify 1 sort id #dump_modify 1 sort id
fix 1 ions nve fix 1 ions nve

192
examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.1 Normal file
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@ -0,0 +1,192 @@
LAMMPS (8 Feb 2023)
using 1 OpenMP thread(s) per MPI task
# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1
# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2
# bottom interface: n = (0, 0, 1)
# top interface: n = (0, 0, -1)
# so that ed's are the same for both interfaces
# Dielectric constants can be set to be different from the input data file
variable epsilon1 index 20
variable epsilon2 index 10
variable data index data.confined
newton off
units lj
atom_style dielectric
atom_modify map array
dimension 3
boundary p p f
variable method index gmres # gmres = BEM/GMRES
# icc = BEM/ICC*
# dof = Direct optimization of the functional
# none
# compute the relevant values for the interface particles
variable ed equal "v_epsilon2 - v_epsilon1"
variable em equal "(v_epsilon2 + v_epsilon1)/2"
variable epsilon equal 1.0 # epsilon at the patch, not used for now
variable area equal 0.866 # patch area, same as in the data file
read_data ${data}
read_data data.confined
Reading data file ...
orthogonal box = (0 0 0) to (40.000006 43.301277 40)
1 by 1 by 1 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ...
4002 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.013 seconds
group interface type 1
4000 atoms in group interface
group ions type 2 3
2 atoms in group ions
group cations type 2
1 atoms in group cations
group anions type 3
1 atoms in group anions
# set the dielectric constant of the medium where the ions reside
set group cations epsilon ${epsilon2}
set group cations epsilon 10
Setting atom values ...
1 settings made for epsilon
set group anions epsilon ${epsilon2}
set group anions epsilon 10
Setting atom values ...
1 settings made for epsilon
pair_style lj/cut/coul/long/dielectric 1.122 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.0 1.0
kspace_style pppm/dielectric 0.0001
kspace_modify slab 3.0
neigh_modify every 1 delay 0 check yes one 5000
#compute ef all efield/atom
#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
#dump_modify 1 sort id
#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3]
fix 1 ions nve
# fix modify is used to set the properties of the interface particle group
if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' "
fix 3 interface polarize/functional 1 0.0001
fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 ${em} ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 15 ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 15 1 ${area} NULL
fix_modify 3 dielectrics -10 15 1 0.866 NULL
thermo 1000
thermo_style custom step evdwl ecoul elong epair #f_3
thermo_modify flush yes
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006
@Article{TrungCPC19,
author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica}
title = {Incorporating Surface Polarization Effects Into Large-Scale
Coarse-Grained Molecular Dynamics Simulation},
journal = {Comput.\ Phys.\ Commun.},
year = 2019,
volume = 241,
pages = {80--91}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.24260797
grid = 12 12 36
stencil order = 5
estimated absolute RMS force accuracy = 2.5219574e-07
estimated relative force accuracy = 2.5219574e-07
using double precision KISS FFT
3d grid and FFT values/proc = 10982 5184
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Direct solver using a variational approach for 4000 induced charges
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 8 9 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long/dielectric, perpetual
attributes: full, newton off
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) fix polarize/functional, perpetual, copy from (1)
attributes: full, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 753.9 | 753.9 | 753.9 Mbytes
Step E_vdwl E_coul E_long E_pair
0 0 0 -1.8534698e-05 -1.8534698e-05
Loop time of 1.622e-06 on 1 procs for 0 steps with 4002 atoms
185.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.622e-06 | | |100.00
Nlocal: 4002 ave 4002 max 4002 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4832 ave 4832 max 4832 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.51316e+06 ave 1.51316e+06 max 1.51316e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1513160
Ave neighs/atom = 378.10095
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

192
examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.4 Normal file
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@ -0,0 +1,192 @@
LAMMPS (8 Feb 2023)
using 1 OpenMP thread(s) per MPI task
# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1
# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2
# bottom interface: n = (0, 0, 1)
# top interface: n = (0, 0, -1)
# so that ed's are the same for both interfaces
# Dielectric constants can be set to be different from the input data file
variable epsilon1 index 20
variable epsilon2 index 10
variable data index data.confined
newton off
units lj
atom_style dielectric
atom_modify map array
dimension 3
boundary p p f
variable method index gmres # gmres = BEM/GMRES
# icc = BEM/ICC*
# dof = Direct optimization of the functional
# none
# compute the relevant values for the interface particles
variable ed equal "v_epsilon2 - v_epsilon1"
variable em equal "(v_epsilon2 + v_epsilon1)/2"
variable epsilon equal 1.0 # epsilon at the patch, not used for now
variable area equal 0.866 # patch area, same as in the data file
read_data ${data}
read_data data.confined
Reading data file ...
orthogonal box = (0 0 0) to (40.000006 43.301277 40)
2 by 2 by 1 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ...
4002 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.013 seconds
group interface type 1
4000 atoms in group interface
group ions type 2 3
2 atoms in group ions
group cations type 2
1 atoms in group cations
group anions type 3
1 atoms in group anions
# set the dielectric constant of the medium where the ions reside
set group cations epsilon ${epsilon2}
set group cations epsilon 10
Setting atom values ...
1 settings made for epsilon
set group anions epsilon ${epsilon2}
set group anions epsilon 10
Setting atom values ...
1 settings made for epsilon
pair_style lj/cut/coul/long/dielectric 1.122 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.0 1.0
kspace_style pppm/dielectric 0.0001
kspace_modify slab 3.0
neigh_modify every 1 delay 0 check yes one 5000
#compute ef all efield/atom
#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3]
#dump_modify 1 sort id
#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3]
fix 1 ions nve
# fix modify is used to set the properties of the interface particle group
if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' "
fix 3 interface polarize/functional 1 0.0001
fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 ${em} ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 15 ${epsilon} ${area} NULL
fix_modify 3 dielectrics -10 15 1 ${area} NULL
fix_modify 3 dielectrics -10 15 1 0.866 NULL
thermo 1000
thermo_style custom step evdwl ecoul elong epair #f_3
thermo_modify flush yes
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006
@Article{TrungCPC19,
author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica}
title = {Incorporating Surface Polarization Effects Into Large-Scale
Coarse-Grained Molecular Dynamics Simulation},
journal = {Comput.\ Phys.\ Commun.},
year = 2019,
volume = 241,
pages = {80--91}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.24260797
grid = 12 12 36
stencil order = 5
estimated absolute RMS force accuracy = 2.5219574e-07
estimated relative force accuracy = 2.5219574e-07
using double precision KISS FFT
3d grid and FFT values/proc = 4598 1296
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Direct solver using a variational approach for 4000 induced charges
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 8 9 8
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long/dielectric, perpetual
attributes: full, newton off
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) fix polarize/functional, perpetual, copy from (1)
attributes: full, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 744 | 744 | 744 Mbytes
Step E_vdwl E_coul E_long E_pair
0 0 0 -1.8534698e-05 -1.8534698e-05
Loop time of 2.36225e-06 on 4 procs for 0 steps with 4002 atoms
148.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.362e-06 | | |100.00
Nlocal: 1000.5 ave 1001 max 1000 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2889.5 ave 2890 max 2889 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 378290 ave 378465 max 378117 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1513160
Ave neighs/atom = 378.10095
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

8
examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1
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@ -47,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors 0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.013 seconds read_data CPU = 0.013 seconds
group interface type 1 group interface type 1
@ -149,9 +149,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 381.6 | 381.6 | 381.6 Mbytes Per MPI rank memory allocation (min/avg/max) = 381.6 | 381.6 | 381.6 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05
Loop time of 1.872e-06 on 1 procs for 0 steps with 4002 atoms Loop time of 1.939e-06 on 1 procs for 0 steps with 4002 atoms
160.3% CPU use with 1 MPI tasks x 1 OpenMP threads 103.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -163,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.872e-06 | | |100.00 Other | | 1.939e-06 | | |100.00
Nlocal: 4002 ave 4002 max 4002 min Nlocal: 4002 ave 4002 max 4002 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

8
examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4
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@ -48,7 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.001 seconds
read_data CPU = 0.011 seconds read_data CPU = 0.012 seconds
group interface type 1 group interface type 1
4000 atoms in group interface 4000 atoms in group interface
@ -149,9 +149,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 376.2 | 376.2 | 376.2 Mbytes Per MPI rank memory allocation (min/avg/max) = 376.2 | 376.2 | 376.2 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05
Loop time of 1.49983e-05 on 4 procs for 0 steps with 4002 atoms Loop time of 1.6531e-05 on 4 procs for 0 steps with 4002 atoms
85.0% CPU use with 4 MPI tasks x 1 OpenMP threads 102.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -163,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.5e-05 | | |100.00 Other | | 1.653e-05 | | |100.00
Nlocal: 1000.5 ave 1001 max 1000 min Nlocal: 1000.5 ave 1001 max 1000 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2

6
examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1
View File

@ -151,9 +151,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 14.99 | 14.99 | 14.99 Mbytes Per MPI rank memory allocation (min/avg/max) = 14.99 | 14.99 | 14.99 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05
Loop time of 1.573e-06 on 1 procs for 0 steps with 4002 atoms Loop time of 1.823e-06 on 1 procs for 0 steps with 4002 atoms
190.7% CPU use with 1 MPI tasks x 1 OpenMP threads 109.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.573e-06 | | |100.00 Other | | 1.823e-06 | | |100.00
Nlocal: 4002 ave 4002 max 4002 min Nlocal: 4002 ave 4002 max 4002 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

8
examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4
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@ -47,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors 0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds read_data CPU = 0.012 seconds
group interface type 1 group interface type 1
@ -151,9 +151,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 9.647 | 9.647 | 9.647 Mbytes Per MPI rank memory allocation (min/avg/max) = 9.647 | 9.647 | 9.647 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05
Loop time of 1.23127e-05 on 4 procs for 0 steps with 4002 atoms Loop time of 2.29425e-06 on 4 procs for 0 steps with 4002 atoms
103.6% CPU use with 4 MPI tasks x 1 OpenMP threads 141.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.231e-05 | | |100.00 Other | | 2.294e-06 | | |100.00
Nlocal: 1000.5 ave 1001 max 1000 min Nlocal: 1000.5 ave 1001 max 1000 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2

136
examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.1 Normal file
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@ -0,0 +1,136 @@
LAMMPS (8 Feb 2023)
using 1 OpenMP thread(s) per MPI task
# Interface
newton off
units lj
atom_style dielectric
atom_modify map array
dimension 3
boundary f f f
variable method index gmres # gmres = BEM/GMRES
# icc = BEM/ICC*
# dof = Direct optimization of the functional
# none
variable data index data.sphere
read_data ${data}
read_data data.sphere
Reading data file ...
orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ...
643 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
group interface type 1
642 atoms in group interface
group ions type 2 3
1 atoms in group ions
pair_style lj/cut/coul/cut/dielectric 1.122 20.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.0 1.0
neigh_modify one 5000
#compute ef all efield/atom
#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
#
#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
#dump_modify 1 sort id
fix 1 ions nve
if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' "
fix 3 interface polarize/functional 1 1.0e-4
thermo 1000
thermo_style custom step evdwl ecoul elong epair
thermo_modify flush yes
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006
@Article{TrungCPC19,
author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica}
title = {Incorporating Surface Polarization Effects Into Large-Scale
Coarse-Grained Molecular Dynamics Simulation},
journal = {Comput.\ Phys.\ Commun.},
year = 2019,
volume = 241,
pages = {80--91}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Direct solver using a variational approach for 642 induced charges
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000
master list distance cutoff = 20.3
ghost atom cutoff = 20.3
binsize = 10.15, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/cut/dielectric, perpetual
attributes: full, newton off
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) fix polarize/functional, perpetual, copy from (1)
attributes: full, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 29.83 | 29.83 | 29.83 Mbytes
Step E_vdwl E_coul E_long E_pair
0 0 -0.011053355 0 -0.011053355
Loop time of 1.691e-06 on 1 procs for 0 steps with 643 atoms
177.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.691e-06 | | |100.00
Nlocal: 643 ave 643 max 643 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 412806 ave 412806 max 412806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 412806
Ave neighs/atom = 642
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

136
examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.4 Normal file
View File

@ -0,0 +1,136 @@
LAMMPS (8 Feb 2023)
using 1 OpenMP thread(s) per MPI task
# Interface
newton off
units lj
atom_style dielectric
atom_modify map array
dimension 3
boundary f f f
variable method index gmres # gmres = BEM/GMRES
# icc = BEM/ICC*
# dof = Direct optimization of the functional
# none
variable data index data.sphere
read_data ${data}
read_data data.sphere
Reading data file ...
orthogonal box = (0 0 0) to (100 100 100)
1 by 2 by 2 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ...
643 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.004 seconds
group interface type 1
642 atoms in group interface
group ions type 2 3
1 atoms in group ions
pair_style lj/cut/coul/cut/dielectric 1.122 20.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.0 1.0
neigh_modify one 5000
#compute ef all efield/atom
#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
#
#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3]
#dump_modify 1 sort id
fix 1 ions nve
if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' "
fix 3 interface polarize/functional 1 1.0e-4
thermo 1000
thermo_style custom step evdwl ecoul elong epair
thermo_modify flush yes
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006
@Article{TrungCPC19,
author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica}
title = {Incorporating Surface Polarization Effects Into Large-Scale
Coarse-Grained Molecular Dynamics Simulation},
journal = {Comput.\ Phys.\ Commun.},
year = 2019,
volume = 241,
pages = {80--91}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Direct solver using a variational approach for 642 induced charges
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000
master list distance cutoff = 20.3
ghost atom cutoff = 20.3
binsize = 10.15, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/cut/dielectric, perpetual
attributes: full, newton off
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) fix polarize/functional, perpetual, copy from (1)
attributes: full, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 26.9 | 27.48 | 27.67 Mbytes
Step E_vdwl E_coul E_long E_pair
0 0 -0.011053355 0 -0.011053355
Loop time of 2.96225e-06 on 4 procs for 0 steps with 643 atoms
143.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.962e-06 | | |100.00
Nlocal: 160.75 ave 178 max 145 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 482.25 ave 498 max 465 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 103202 ave 114276 max 93090 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 412806
Ave neighs/atom = 642
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

26
examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1
View File

@ -22,7 +22,7 @@ Reading data file ...
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ... reading atoms ...
2563 atoms 643 atoms
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0 special bond factors lj: 0 0 0
special bond factors coul: 0 0 0 special bond factors coul: 0 0 0
@ -31,10 +31,10 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds read_data CPU = 0.004 seconds
group interface type 1 group interface type 1
2562 atoms in group interface 642 atoms in group interface
group ions type 2 3 group ions type 2 3
1 atoms in group ions 1 atoms in group ions
@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited:
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors BEM/GMRES solver for 642 induced charges using maximum 641 q-vectors
Neighbor list info ... Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000 max neighbors/atom: 5000, page size: 100000
@ -93,12 +93,12 @@ Neighbor list info ...
pair build: full/bin pair build: full/bin
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 183.5 | 183.5 | 183.5 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.6 | 18.6 | 18.6 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 2.1870454e-07 0 2.1870454e-07 0 0 -0.011226675 0 -0.011226675
Loop time of 1.538e-06 on 1 procs for 0 steps with 2563 atoms Loop time of 1.659e-06 on 1 procs for 0 steps with 643 atoms
195.1% CPU use with 1 MPI tasks x 1 OpenMP threads 120.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -109,19 +109,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.538e-06 | | |100.00 Other | | 1.659e-06 | | |100.00
Nlocal: 2563 ave 2563 max 2563 min Nlocal: 643 ave 643 max 643 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min FullNghs: 412806 ave 412806 max 412806 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6565612 Total # of neighbors = 412806
Ave neighs/atom = 2561.6902 Ave neighs/atom = 642
Ave special neighs/atom = 0 Ave special neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0

30
examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4
View File

@ -22,7 +22,7 @@ Reading data file ...
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ... reading atoms ...
2563 atoms 643 atoms
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0 special bond factors lj: 0 0 0
special bond factors coul: 0 0 0 special bond factors coul: 0 0 0
@ -30,11 +30,11 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors 0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds read_data CPU = 0.003 seconds
group interface type 1 group interface type 1
2562 atoms in group interface 642 atoms in group interface
group ions type 2 3 group ions type 2 3
1 atoms in group ions 1 atoms in group ions
@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited:
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors BEM/GMRES solver for 642 induced charges using maximum 641 q-vectors
Neighbor list info ... Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 5000, page size: 100000 max neighbors/atom: 5000, page size: 100000
@ -93,12 +93,12 @@ Neighbor list info ...
pair build: full/bin pair build: full/bin
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 164.6 | 164.7 | 165 Mbytes Per MPI rank memory allocation (min/avg/max) = 17.2 | 17.49 | 17.58 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 2.1870454e-07 0 2.1870454e-07 0 0 -0.011226675 0 -0.011226675
Loop time of 2.4415e-06 on 4 procs for 0 steps with 2563 atoms Loop time of 6.7975e-06 on 4 procs for 0 steps with 643 atoms
133.1% CPU use with 4 MPI tasks x 1 OpenMP threads 80.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -109,19 +109,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.442e-06 | | |100.00 Other | | 6.797e-06 | | |100.00
Nlocal: 640.75 ave 674 max 609 min Nlocal: 160.75 ave 178 max 145 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 1922.25 ave 1954 max 1889 min Nghost: 482.25 ave 498 max 465 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min FullNghs: 103202 ave 114276 max 93090 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 6565612 Total # of neighbors = 412806
Ave neighs/atom = 2561.6902 Ave neighs/atom = 642
Ave special neighs/atom = 0 Ave special neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0

28
examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1
View File

@ -22,7 +22,7 @@ Reading data file ...
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ... reading atoms ...
2563 atoms 643 atoms
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0 special bond factors lj: 0 0 0
special bond factors coul: 0 0 0 special bond factors coul: 0 0 0
@ -31,10 +31,10 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds read_data CPU = 0.004 seconds
group interface type 1 group interface type 1
2562 atoms in group interface 642 atoms in group interface
group ions type 2 3 group ions type 2 3
1 atoms in group ions 1 atoms in group ions
@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited:
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
BEM/ICC solver for 2562 induced charges BEM/ICC solver for 642 induced charges
using pair style lj/cut/coul/cut/dielectric using pair style lj/cut/coul/cut/dielectric
Neighbor list info ... Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes update: every = 1 steps, delay = 0 steps, check = yes
@ -94,12 +94,12 @@ Neighbor list info ...
pair build: full/bin pair build: full/bin
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 32.96 | 32.96 | 32.96 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.898 | 8.898 | 8.898 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 2.1870503e-07 0 2.1870503e-07 0 0 -0.011226707 0 -0.011226707
Loop time of 1.536e-06 on 1 procs for 0 steps with 2563 atoms Loop time of 1.532e-06 on 1 procs for 0 steps with 643 atoms
195.3% CPU use with 1 MPI tasks x 1 OpenMP threads 130.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -110,23 +110,23 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.536e-06 | | |100.00 Other | | 1.532e-06 | | |100.00
Nlocal: 2563 ave 2563 max 2563 min Nlocal: 643 ave 643 max 643 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min FullNghs: 412806 ave 412806 max 412806 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6565612 Total # of neighbors = 412806
Ave neighs/atom = 2561.6902 Ave neighs/atom = 642
Ave special neighs/atom = 0 Ave special neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:01 Total wall time: 0:00:00

30
examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4
View File

@ -22,7 +22,7 @@ Reading data file ...
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620)
reading atoms ... reading atoms ...
2563 atoms 643 atoms
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0 special bond factors lj: 0 0 0
special bond factors coul: 0 0 0 special bond factors coul: 0 0 0
@ -30,11 +30,11 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors 0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors 0 = max # of 1-4 neighbors
1 = max # of special neighbors 1 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds read_data CPU = 0.004 seconds
group interface type 1 group interface type 1
2562 atoms in group interface 642 atoms in group interface
group ions type 2 3 group ions type 2 3
1 atoms in group ions 1 atoms in group ions
@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited:
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
BEM/ICC solver for 2562 induced charges BEM/ICC solver for 642 induced charges
using pair style lj/cut/coul/cut/dielectric using pair style lj/cut/coul/cut/dielectric
Neighbor list info ... Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes update: every = 1 steps, delay = 0 steps, check = yes
@ -94,12 +94,12 @@ Neighbor list info ...
pair build: full/bin pair build: full/bin
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.03 | 14.12 | 14.41 Mbytes Per MPI rank memory allocation (min/avg/max) = 7.496 | 7.783 | 7.878 Mbytes
Step E_vdwl E_coul E_long E_pair Step E_vdwl E_coul E_long E_pair
0 0 2.1870503e-07 0 2.1870503e-07 0 0 -0.011226707 0 -0.011226707
Loop time of 2.408e-06 on 4 procs for 0 steps with 2563 atoms Loop time of 6.43925e-06 on 4 procs for 0 steps with 643 atoms
135.0% CPU use with 4 MPI tasks x 1 OpenMP threads 93.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
@ -110,19 +110,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.408e-06 | | |100.00 Other | | 6.439e-06 | | |100.00
Nlocal: 640.75 ave 674 max 609 min Nlocal: 160.75 ave 178 max 145 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 1922.25 ave 1954 max 1889 min Nghost: 482.25 ave 498 max 465 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min FullNghs: 103202 ave 114276 max 93090 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 6565612 Total # of neighbors = 412806
Ave neighs/atom = 2561.6902 Ave neighs/atom = 642
Ave special neighs/atom = 0 Ave special neighs/atom = 0
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0