Logs for eta mix example
This commit is contained in:
Ludwig Ahrens
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1
Normal file
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1
Normal file
@ -0,0 +1,138 @@
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
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using 1 OpenMP thread(s) per MPI task
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boundary p p f
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kspace_style ewald/electrode 1.0e-8
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kspace_modify slab 8.0 # ew3dc
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include "settings.mod" # styles, computes, groups and fixes
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# set boundary in main script because ffield is periodic
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units real
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# distribute electrode atoms among all processors:
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if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
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atom_style full
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pair_style lj/cut/coul/long 12
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read_data "data.au-elyt"
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Reading data file ...
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orthogonal box = (0 0 -10) to (1 1 10)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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group bot type 1
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1 atoms in group bot
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group top type 2
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1 atoms in group top
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# get electrode charges
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variable q atom q
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compute qbot bot reduce sum v_q
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compute qtop top reduce sum v_q
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||||||
|
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||||||
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compute compute_pe all pe
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||||||
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variable vpe equal c_compute_pe
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variable charge equal c_qtop
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||||||
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fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
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||||||
|
|
||||||
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thermo_style custom step pe c_qbot c_qtop
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||||||
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 2.0
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Setting atom values ...
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1 settings made for d_eta
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set group top d_eta 2.0
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Setting atom values ...
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1 settings made for d_eta
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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2 atoms in group conp_group
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run 0
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||||||
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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
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||||||
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author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
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||||||
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doi = {10.1063/5.0099239},
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||||||
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title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
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||||||
|
journal = {The Journal of Chemical Physics},
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||||||
|
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)
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||||||
|
Ewald/electrode initialization ...
|
||||||
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
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|
G vector (1/distance) = 0.32261103
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estimated absolute RMS force accuracy = 3.8272011e-06
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estimated relative force accuracy = 1.1525502e-08
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||||||
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KSpace vectors: actual max1d max3d = 52 50 515150
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||||||
|
kxmax kymax kzmax = 1 1 50
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||||||
|
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
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||||||
|
Neighbor list info ...
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||||||
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update: every = 1 steps, delay = 0 steps, check = yes
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||||||
|
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
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||||||
|
stencil: half/bin/3d
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||||||
|
bin: standard
|
||||||
|
(2) fix electrode/conp, perpetual, copy from (1)
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||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
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||||||
|
stencil: none
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||||||
|
bin: none
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|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:965)
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139.943964815502, 0.279214485147238
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Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
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Step PotEng c_qbot c_qtop
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0 139.94396 -0.27921449 0.27921449
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Loop time of 2.191e-06 on 1 procs for 0 steps with 4 atoms
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91.3% CPU use with 1 MPI tasks x 1 OpenMP threads
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|
|
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|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
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|
---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Kspace | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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||||||
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Output | 0 | 0 | 0 | 0.0 | 0.00
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||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.191e-06 | | |100.00
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|
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|
Nlocal: 4 ave 4 max 4 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3596 ave 3596 max 3596 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4790 ave 4790 max 4790 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
|
|
||||||
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Total # of neighbors = 4790
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Ave neighs/atom = 1197.5
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||||||
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Ave special neighs/atom = 0
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||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
139
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1
Normal file
139
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1
Normal file
@ -0,0 +1,139 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
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 = 0.000 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 feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
set group top d_eta 3.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta 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:965)
|
||||||
|
165.519373910316, 0.29521534552818
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
|
||||||
|
Step PotEng c_qbot c_qtop
|
||||||
|
0 165.51937 -0.29521535 0.29521535
|
||||||
|
Loop time of 2.797e-06 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
71.5% 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 | | 2.797e-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
|
||||||
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1
Normal file
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1
Normal file
@ -0,0 +1,138 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
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 = 0.000 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 feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
set group top d_eta 3.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta 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:965)
|
||||||
|
165.519373910316, 0.295215345528172
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
|
||||||
|
Step PotEng c_qbot c_qtop
|
||||||
|
0 165.51937 -0.29521535 0.29521535
|
||||||
|
Loop time of 2.18e-06 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
91.7% 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 | | 2.18e-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
|
||||||
Reference in New Issue
Block a user