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add madelung logs

This commit is contained in:
srtee 2022-12-01 16:35:57 +10:00
parent ad68eb8a59
commit 8951aceecb
6 changed files with 805 additions and 0 deletions
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131
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LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-8
kspace_modify slab 8.0 # ew3dc
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on algo cg 1e-6
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.32261103
estimated absolute RMS force accuracy = 3.8272011e-06
estimated relative force accuracy = 1.1525502e-08
KSpace vectors: actual max1d max3d = 52 50 515150
kxmax kymax kzmax = 1 1 50
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
139.943964815502, 0.279214485147241
Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes
Step PotEng c_qbot c_qtop
0 139.94396 -0.27921449 0.27921449
Loop time of 1.092e-06 on 1 procs for 0 steps with 4 atoms
91.6% CPU use with 1 MPI tasks x no 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 | | 1.092e-06 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Average conjugate gradient steps: 1
Total wall time: 0:00:00

130
examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ew2d.g++.1 Normal file
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LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-8
kspace_modify slab ew2d
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.002 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.32261103
estimated absolute RMS force accuracy = 9.9990544e-06
estimated relative force accuracy = 3.0111855e-08
KSpace vectors: actual max1d max3d = 2 8 2456
kxmax kymax kzmax = 1 1 8
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
139.946125020193, 0.279214126709814
Per MPI rank memory allocation (min/avg/max) = 20.42 | 20.42 | 20.42 Mbytes
Step PotEng c_qbot c_qtop
0 139.94613 -0.27921413 0.27921413
Loop time of 1.082e-06 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no 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 | | 1.082e-06 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

130
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LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-8
kspace_modify slab 8.0 # ew3dc
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.32261103
estimated absolute RMS force accuracy = 3.8272011e-06
estimated relative force accuracy = 1.1525502e-08
KSpace vectors: actual max1d max3d = 52 50 515150
kxmax kymax kzmax = 1 1 50
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
139.943964815502, 0.279214485147238
Per MPI rank memory allocation (min/avg/max) = 144.1 | 144.1 | 144.1 Mbytes
Step PotEng c_qbot c_qtop
0 139.94396 -0.27921449 0.27921449
Loop time of 7.31e-07 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no 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 | | 7.31e-07 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

129
examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-ewald-ffield.g++.1 Normal file
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LAMMPS (3 Nov 2022)
boundary p p p
kspace_style ewald/electrode 1.0e-8
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.002 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.32261103
estimated absolute RMS force accuracy = 9.9990544e-06
estimated relative force accuracy = 3.0111855e-08
KSpace vectors: actual max1d max3d = 10 8 2456
kxmax kymax kzmax = 1 1 8
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
138.299024320284, 0.287160231879378
Per MPI rank memory allocation (min/avg/max) = 21.19 | 21.19 | 21.19 Mbytes
Step PotEng c_qbot c_qtop
0 138.29902 -0.28716023 0.28716023
Loop time of 1.804e-06 on 1 procs for 0 steps with 4 atoms
55.4% CPU use with 1 MPI tasks x no 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 | | 1.804e-06 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10796 ave 10796 max 10796 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

143
examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ew3dc.g++.1 Normal file
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@ -0,0 +1,143 @@
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style pppm/electrode 1.0e-10
kspace_modify slab 8.0 # ew3dc
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.003 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on write_inv inv.csv write_vec vec.csv
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.37216302
grid = 12 12 375
stencil order = 5
estimated absolute RMS force accuracy = 9.4312865e-06
estimated relative force accuracy = 2.8402039e-08
using double precision MKL FFT
3d grid and FFT values/proc = 637099 54000
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
139.946107219358, 0.279214187928028
Per MPI rank memory allocation (min/avg/max) = 40.22 | 40.22 | 40.22 Mbytes
Step PotEng c_qbot c_qtop
0 139.94611 -0.27921419 0.27921419
Loop time of 8.32e-07 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no 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 | | 8.32e-07 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

142
examples/PACKAGES/electrode/madelung/log.1Dec2022.madelung-pppm-ffield.g++.1 Normal file
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@ -0,0 +1,142 @@
LAMMPS (3 Nov 2022)
boundary p p p
kspace_style pppm/electrode 1.0e-10
include "settings.mod" # styles, computes, groups and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 12
read_data "data.au-elyt"
Reading data file ...
orthogonal box = (0 0 -10) to (1 1 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.002 seconds
group bot type 1
1 atoms in group bot
group top type 2
1 atoms in group top
# get electrode charges
variable q atom q
compute qbot bot reduce sum v_q
compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
thermo_style custom step pe c_qbot c_qtop
fix conp bot electrode/conp 0 2 couple top 1 symm on ffield yes write_inv inv.csv write_vec vec.csv
2 atoms in group conp_group
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
G vector (1/distance) = 0.37297537
grid = 12 12 90
stencil order = 5
estimated absolute RMS force accuracy = 9.4312758e-06
estimated relative force accuracy = 2.8402007e-08
using double precision MKL FFT
3d grid and FFT values/proc = 174824 12960
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 1 1 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conp, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:966)
138.298994634846, 0.287160247352281
Per MPI rank memory allocation (min/avg/max) = 16.7 | 16.7 | 16.7 Mbytes
Step PotEng c_qbot c_qtop
0 138.29899 -0.28716025 0.28716025
Loop time of 1.022e-06 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no 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 | | 1.022e-06 | | |100.00
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10796 ave 10796 max 10796 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4790 ave 4790 max 4790 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4790
Ave neighs/atom = 1197.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00