diff --git a/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1 b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1 new file mode 100644 index 0000000000..daf0563799 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1 @@ -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 2.0 +Setting atom values ... + 1 settings made for d_eta +set group top d_eta 2.0 +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) +139.943964815502, 0.279214485147238 +Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes + Step PotEng c_qbot c_qtop + 0 139.94396 -0.27921449 0.27921449 +Loop time of 2.191e-06 on 1 procs for 0 steps with 4 atoms + +91.3% 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 | | 2.191e-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 diff --git a/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1 b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1 new file mode 100644 index 0000000000..edb2e434e6 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1 @@ -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 diff --git a/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1 b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1 new file mode 100644 index 0000000000..51eda0d870 --- /dev/null +++ b/examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1 @@ -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