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Add APIP package.

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This commit is contained in:
David Immel
2025-04-08 15:26:45 +02:00
parent 16db8e1515
commit 535d08895a
75 changed files with 99196 additions and 8 deletions
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34
examples/PACKAGES/apip/Cu-1.yace Normal file
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NOTE: This is a simple potential for the example. Production usage without testing is not recommended. Provided by Yury Lysogorskiy (ICAMS, RUB, Germany).
elements: [Cu]
E0: [0]
deltaSplineBins: 0.001
embeddings:
0: {ndensity: 2, FS_parameters: [1, 1, 1, 0.5], npoti: FinnisSinclairShiftedScaled, rho_core_cutoff: 100000, drho_core_cutoff: 250}
bonds:
[0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 15, radbasename: ChebPow, radparameters: [2], radcoefficients: [[[0.99440439385969503, -0.085048653403583918, -0.23248632054717755, -0.22732701549371864, 0.026354948476648921, 0.21853318667456997, 0.05745747498169812, -0.19717925712228765, -0.11474256770370879, 0.12738668745839368, 0.053777769435472259, -0.11094768379576209, 0.072620812391582482, -0.058715761632824881, 0.030359986427775303], [0.96259704765772924, -0.10129488003029259, -0.10345557604916655, -0.020393848425879282, 0.076671442494272601, 0.10318554794001746, 0.0555341702761026, 0.00083194423680727696, -0.018184436957498409, -0.021866885826555403, -0.020179969116479776, 0.021880011516616484, 0.053112509345249602, -0.083707026393616657, 0.020611714544479017], [1.001530579978529, -0.030080648426358471, -0.13318582671063051, -0.24371635685809706, -0.22760541127468878, -0.041144767051648642, 0.18080289144697201, 0.24543156067198274, 0.11014559411659355, -0.069512010077804498, -0.1172049950938457, -0.027509386703874331, 0.056985864219913585, 0.037536629112081353, -0.044222474537374087]], [[0.25716120576634355, 1.7485527550537943, 0.91889737965719875, 0.50902244208852199, -0.15895537149482841, -0.48109723575282892, -0.17843605933015286, 0.39450608859531944, 0.59293909285591195, 0.18268386912819001, -0.34706543720907351, -0.3210061634328315, 0.21678650779400246, 0.39500148786376449, -0.31820913370341625], [0.0079213202761679105, 1.0212489038630681, 0.011530454475879359, -0.049445152058907642, -0.15268524878755677, -0.2319378608755131, -0.20612580998548105, -0.067027395211212315, 0.08241096034972574, 0.11288597065081186, 0.01355948960244063, -0.074722461388416803, -0.022724332047049267, 0.088871664887057056, 0.031667459613258314], [-0.0069872405356639312, 0.9939655327342134, 0.035044055182587928, 0.099765277857093104, 0.11687607289674087, 0.030241996404391416, -0.12367698594314165, -0.22480900218170197, -0.17727517861619441, -0.015144941558075584, 0.11375495728241894, 0.090680932947050971, -0.041190210394591399, -0.10085768296286811, 0.055789864104988186]]], prehc: 0, lambdahc: 0, rcut: 3.8999999999999999, dcut: 0.01, rcut_in: 0, dcut_in: 0, inner_cutoff_type: density}
functions:
0:
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [0.26072556900842869, -0.03073189825062177]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [0.64429175483702295, -0.1630534353246999]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [3], ls: [0], ms_combs: [0], ctildes: [0.51856313423563594, -0.4259316875879266]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [4], ls: [0], ms_combs: [0], ctildes: [-0.078113533662468398, -0.70352070540668643]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [5], ls: [0], ms_combs: [0], ctildes: [-0.45633111544093646, -0.7859368117550467]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [6], ls: [0], ms_combs: [0], ctildes: [-0.19608401600520556, -0.59151667874441172]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [7], ls: [0], ms_combs: [0], ctildes: [0.30580228338697285, -0.29248216980800118]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [8], ls: [0], ms_combs: [0], ctildes: [0.40167461008815436, -0.15647925731818518]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [9], ls: [0], ms_combs: [0], ctildes: [0.053519057558225343, -0.25900906688118652]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [10], ls: [0], ms_combs: [0], ctildes: [-0.20446546815457517, -0.40019216010057629]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [11], ls: [0], ms_combs: [0], ctildes: [-0.070020661105060208, -0.33441939205411986]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [12], ls: [0], ms_combs: [0], ctildes: [0.15734064575001952, -0.055233119903794807]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [13], ls: [0], ms_combs: [0], ctildes: [0.10021406559793103, 0.18641744536767416]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [14], ls: [0], ms_combs: [0], ctildes: [-0.14066730990975543, 0.14711096149210373]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [15], ls: [0], ms_combs: [0], ctildes: [0.031100766650549283, -0.13720067925313634]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [1, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0984212008195524, 0.49756623164565855]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.2591109116320176, 0.21348077494861176, -0.5182218232640351, -0.4269615498972234]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.015905361441871636, 0.023783303055646809, -0.031810722883743273, -0.047566606111293624, 0.031810722883743286, 0.047566606111293638]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.63958612617724186, 1.6623415103929948]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.14199022782503917, 0.0069900458821809735, -0.28398045565007829, -0.013980091764361944]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.028732470496968317, -0.037173039560267927, -0.05746494099393664, 0.074346079120535868, 0.057464940993936654, -0.074346079120535882]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 2], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.056442895466964321, 0.0054387873274233034]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.025326283180140272, -0.19511149476156769, -0.050652566360280531, 0.39022298952313533]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.012754475331985416, -0.058934602152610385, -0.025508950663970836, 0.11786920430522078, 0.025508950663970843, -0.11786920430522081]}

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The APIP package is based on the paper:
David Immel, Ralf Drautz, Godehard Sutmann; Adaptive-precision potentials for large-scale atomistic simulations. J. Chem. Phys. 14 March 2025; 162 (11): 114119. https://doi.org/10.1063/5.0245877
The pair_style pace/apip requires the installation of lib/pace of the ML-PACE package.
The installation of lib/pace is described in src/ML-PACE/README .
Examples of how to use an adaptive-precision potential are provided in examples/PACKAGES/apip .
in.vacancy contains a small example that can be used to visualize the transition region and get a visual impression of the selected parameters.
in.surface.balance in a more realistic example, in which a surface is simulated and the benefit of fix apip_atom_weight and fix balance for adaptive-precision interatomic potentials is demonstrated.

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##################################################
# parameters of the adaptive-precision potential #
##################################################
# We couple an EAM potential with an ACE potential.
variable eamfs_file string "Cu_300K_Immel_2023.eam.fs"
variable ace_file1 string "Cu-1.yace"
variable ace_file2 string "../../../potentials/Cu-PBE-core-rep.ace"
# The csp is used as detection mechanism for atoms of interest.
variable csp_lattice string "fcc"
variable csp_cutoff equal 6.0
# The range [r_sw_lo, r_sw_hi] determines where the switching parameter changes from 0 to 1.
variable r_sw_lo equal 4.0
variable r_sw_hi equal 12.0
# Thresholds between which the switching parameter changes from 1 to 0 based on the csp.
variable lambda_input_thr_lo equal 7.5
variable lambda_input_thr_hi equal 8.0
# Number of averaged steps.
variable lambda_input_histlen equal 110
variable lambda_histlen equal 110
# Minimum required change of the switching parameter
variable min_delta_lambda equal 1/${lambda_histlen}
# number of atoms rescaled by the lambda_thermostat
variable N_rescaling equal 600
# basic stuff
units metal
dimension 3
boundary p p s
atom_style apip # own atom style required for APIP
timestep 0.001
read_data data.surface.balance
fix nve all nve
comm_style tiled
# Only the upper surface should be treated precisely.
# Thus, we create group, for whose atoms the csp is ignored, as the corresponding
# argument of fix lambda is used.
region bottom block INF INF INF INF INF 0 units box
group group_ignore_csp region bottom
# use adaptive-precision eam-ace potential with lambda_thermostat
pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file2} Cu
pair_coeff * * lambda_input/csp
pair_coeff * * lambda/zone
fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda} group_ignore_lambda_input group_ignore_csp
fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling}
fix weight_atom all apip_atom_weight 10 eam ace lambda_input lambda/zone all
# store weight in variable
fix property_atom all property/atom d_usedweight
variable myweight atom f_weight_atom
#dump 1 all custom 10 dump/surface_ap_balance.dump.* id type x y z lambda lambda_input f_weight_atom proc d_usedweight
## apply load balancing
## no load-balancing
#fix balance all balance 10 0.9 report weight time 1.0 weight store usedweight
## load balancing with times per atom per processor
#fix balance all balance 10 0.9 rcb weight time 1.0 weight store usedweight
## load balancing with an approximated load per atom by fix apip_atom_weight
fix balance all balance 10 0.9 rcb weight var myweight weight store usedweight
thermo_style custom step f_balance spcpu f_weight_atom[*]
thermo 10
run 100

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##################################################
# parameters of the adaptive-precision potential #
##################################################
# We couple an EAM potential with an ACE potential.
variable eamfs_file string "Cu_300K_Immel_2023.eam.fs"
variable ace_file1 string "Cu-1.yace"
variable ace_file2 string "../../../potentials/Cu-PBE-core-rep.ace"
# The csp is used as detection mechanism for atoms of interest.
variable csp_lattice string "fcc"
variable csp_cutoff equal 6.0
# The range [r_sw_lo, r_sw_hi] determines where the switching parameter changes from 0 to 1.
variable r_sw_lo equal 4.0
variable r_sw_hi equal 12.0
# Thresholds between which the switching parameter changes from 1 to 0 based on the csp.
variable lambda_input_thr_lo equal 2.5
variable lambda_input_thr_hi equal 3.0
# Number of averaged steps.
variable lambda_input_histlen equal 110
variable lambda_histlen equal 110
# Minimum required change of the switching parameter
variable min_delta_lambda equal 1/${lambda_histlen}
# number of atoms rescaled by the lambda_thermostat
variable N_rescaling equal 600
## basic stuff
units metal
atom_style apip # own atom style required for APIP
timestep 0.001
# copper at room temperature with a vacancy
read_data data.vacancy
fix nve all nve
## Use adaptive-precision ace-ace potential without lambda_thermostat.
## Calculate atomic weight that could be used for load balancing.
#pair_style hybrid/overlay pace/apip/fast pace/apip/precise lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
#pair_coeff * * pace/apip/fast ${ace_file1} Cu
#pair_coeff * * pace/apip/precise ${ace_file2} Cu
#pair_coeff * * lambda_input/csp
#pair_coeff * * lambda/zone
#fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
#fix weight_atom all apip_atom_weight 100 ace ace lambda_input lambda/zone all
# Use adaptive-precision eam-ace potential without lambda_thermostat.
# Calculate atomic weight that could be used for load balancing.
pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp ${csp_lattice} cutoff ${csp_cutoff} lambda/zone ${r_sw_hi}
pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file2} Cu
pair_coeff * * lambda_input/csp
pair_coeff * * lambda/zone
fix lambda all lambda ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
fix weight_atom all apip_atom_weight 100 eam ace lambda_input lambda/zone all
## One can comment out fix lambda_thermostat to see the energy change caused by the neglection of the
## gradient of the switching function. This neglection can be compensated by the local thermostat and the
## energy can be conserved within numerical precision.
fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling} store_atomic_forces 100
thermo_style custom step etotal
thermo 1
run 100
# dump atoms
#write_dump all custom dump/vacancy.dump.* id type x y z fx fy fz lambda lambda_input f_weight_atom f_lambda_thermostat[*]
## A smooth restart of the simulation is possible as the history of lambda and lambda_input is stored.
#write_restart vacancy_ap.restart
#clear
#read_restart vacancy_ap.restart
#pair_style hybrid/overlay eam/fs/apip pace/apip lambda_input/csp fcc cutoff 6.0 lambda/zone 12.0
#pair_coeff * * eam/fs/apip "Cu_300K_Immel_2023.eam.fs" Cu
#pair_coeff * * pace/apip "../../../potentials/Cu-PBE-core-rep.ace" Cu
#pair_coeff * * lambda_input/csp
#pair_coeff * * lambda/zone
#fix lambda all lambda 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda $(1/110)
#fix lambda_thermostat all lambda_thermostat N_rescaling ${N_rescaling} store_atomic_forces 100
#fix nve all nve
#thermo_style custom step etotal
#thermo 1
#run 10
#shell rm vacancy_ap.restart

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LAMMPS (4 Feb 2025 - Development - )
Reading data file ...
orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
1 by 1 by 4 MPI processor grid
reading atoms ...
40200 atoms
reading velocities ...
40200 velocities
read_data CPU = 1.143 seconds
200 atoms in group group_ignore_csp
ACE version: 2023.11.25
Recursive evaluator is used by ACE
Loading ../../../potentials/Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
atomic load lambda:
fast potential: extract eam/apip:time_per_atom
precise potential: extract pace/apip:time_per_atom
lambda_input: extract lambda_input:time_per_atom
lambda: extract lambda_zone:time_per_atom
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lambda command: doi.org/10.1063/5.0245877
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 6 6 52
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs/apip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair pace/apip, perpetual, trim from (4)
attributes: full, newton on, cut 9.4
pair build: trim
stencil: none
bin: none
(3) pair lambda_input/csp, perpetual, trim from (2)
attributes: full, newton on, cut 8
pair build: trim
stencil: none
bin: none
(4) pair lambda/zone, perpetual
attributes: full, newton on, ghost, cut 14
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(5) fix lambda_thermostat, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 297.9 | 306.9 | 315.9 Mbytes
Step f_balance S/CPU f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
0 1.0139303 0 0 0 0 0
10 2.4606058 1.8697255 5.5957166e-06 0.0002553649 2.7500342e-06 4.6802407e-06
20 2.0765883 1.7644069 5.9864867e-06 0.0002751227 2.9574758e-06 5.078614e-06
30 2.0955022 1.729507 5.9541701e-06 0.00028593742 3.1165205e-06 5.2349106e-06
40 2.1015667 1.7241359 6.0115135e-06 0.00028640643 3.1154236e-06 5.2528746e-06
50 2.0981491 1.6201337 6.0470102e-06 0.00028778687 3.1443635e-06 5.2497711e-06
60 2.1327959 1.3101362 7.7658865e-06 0.00037855901 4.1641447e-06 6.9162514e-06
70 2.098134 1.3357863 7.5378657e-06 0.00037046011 4.0510159e-06 6.9345367e-06
80 2.1000138 1.3475583 7.5679751e-06 0.00036818876 4.0188623e-06 6.7257237e-06
90 2.0966073 1.1728052 7.6393621e-06 0.00036755436 4.0052073e-06 6.6818754e-06
100 1.8896711 1.3506386 7.5946481e-06 0.00036649967 3.984174e-06 6.6518701e-06
Loop time of 67.2407 on 4 procs for 100 steps with 40200 atoms
Performance: 0.128 ns/day, 186.780 hours/ns, 1.487 timesteps/s, 59.785 katom-step/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.34 | 21.891 | 56.059 | 421.6 | 32.56
Neigh | 8.1064 | 9.1925 | 10.667 | 33.9 | 13.67
Comm | 1.3105 | 23.525 | 45.141 | 437.6 | 34.99
Output | 0.00053598 | 0.73462 | 2.8834 | 144.7 | 1.09
Modify | 1.4504 | 2.6152 | 5.8041 | 114.0 | 3.89
Other | | 9.282 | | | 13.80
Nlocal: 10050 ave 10180 max 10000 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 27854.5 ave 30385 max 25525 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: 9.49222e+06 ave 9.76687e+06 max 9.29466e+06 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 37968882
Ave neighs/atom = 944.49955
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:01:11

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LAMMPS (4 Feb 2025 - Development - )
Reading data file ...
orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
1 by 1 by 4 MPI processor grid
reading atoms ...
40200 atoms
reading velocities ...
40200 velocities
read_data CPU = 1.141 seconds
200 atoms in group group_ignore_csp
ACE version: 2023.11.25
Recursive evaluator is used by ACE
Loading ../../../potentials/Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
atomic load lambda:
fast potential: extract eam/apip:time_per_atom
precise potential: extract pace/apip:time_per_atom
lambda_input: extract lambda_input:time_per_atom
lambda: extract lambda_zone:time_per_atom
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lambda command: doi.org/10.1063/5.0245877
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 6 6 52
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs/apip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair pace/apip, perpetual, trim from (4)
attributes: full, newton on, cut 9.4
pair build: trim
stencil: none
bin: none
(3) pair lambda_input/csp, perpetual, trim from (2)
attributes: full, newton on, cut 8
pair build: trim
stencil: none
bin: none
(4) pair lambda/zone, perpetual
attributes: full, newton on, ghost, cut 14
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(5) fix lambda_thermostat, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 298.1 | 306.3 | 314.5 Mbytes
Step f_balance S/CPU f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
0 1 0 0 0 0 0
10 1.0010585 1.8144651 5.3526071e-06 0.00025703793 2.7730117e-06 4.7190461e-06
20 1.0016587 3.0895281 6.0547706e-06 0.00030627156 2.9311147e-06 2.8627034e-06
30 1.0006595 2.1815977 7.7086095e-06 0.00034346642 3.4831025e-06 3.6494203e-06
40 1.0003702 2.7847348 6.9889341e-06 0.00031605872 3.2092228e-06 2.9177266e-06
50 1.0013639 2.8085372 7.1723284e-06 0.00032050748 3.2148509e-06 2.9280764e-06
60 1.001567 2.7692583 7.3191318e-06 0.00032348311 3.2792367e-06 3.0731907e-06
70 1.0008473 2.7848811 7.4547446e-06 0.00032207119 3.2487866e-06 3.0045227e-06
80 1.0008791 2.1902426 8.8463371e-06 0.00037692301 3.878561e-06 3.5166374e-06
90 1.0005633 2.0207998 1.0049193e-05 0.00043004983 4.4508803e-06 4.0369005e-06
100 1.0011185 2.11148 9.5552543e-06 0.00040548477 4.282726e-06 4.0021617e-06
Loop time of 41.9356 on 4 procs for 100 steps with 40200 atoms
Performance: 0.206 ns/day, 116.488 hours/ns, 2.385 timesteps/s, 95.861 katom-step/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.856 | 23.33 | 25.627 | 29.8 | 55.63
Neigh | 12.078 | 12.235 | 12.335 | 2.8 | 29.18
Comm | 1.8098 | 3.4438 | 5.8848 | 91.3 | 8.21
Output | 0.0013883 | 0.0067437 | 0.010676 | 4.1 | 0.02
Modify | 1.7044 | 1.8301 | 1.9304 | 7.0 | 4.36
Other | | 1.09 | | | 2.60
Nlocal: 10050 ave 10381 max 9892 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 52763 ave 52921 max 52432 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9.49222e+06 ave 9.80751e+06 max 9.34231e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 37968882
Ave neighs/atom = 944.49955
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:46

108
examples/PACKAGES/apip/log.04Feb25.surface.balance.rcb.time.g++.4 Normal file
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@ -0,0 +1,108 @@
LAMMPS (4 Feb 2025 - Development - )
Reading data file ...
orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
1 by 1 by 4 MPI processor grid
reading atoms ...
40200 atoms
reading velocities ...
40200 velocities
read_data CPU = 1.549 seconds
200 atoms in group group_ignore_csp
ACE version: 2023.11.25
Recursive evaluator is used by ACE
Loading ../../../potentials/Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
atomic load lambda:
fast potential: extract eam/apip:time_per_atom
precise potential: extract pace/apip:time_per_atom
lambda_input: extract lambda_input:time_per_atom
lambda: extract lambda_zone:time_per_atom
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lambda command: doi.org/10.1063/5.0245877
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 6 6 52
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs/apip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair pace/apip, perpetual, trim from (4)
attributes: full, newton on, cut 9.4
pair build: trim
stencil: none
bin: none
(3) pair lambda_input/csp, perpetual, trim from (2)
attributes: full, newton on, cut 8
pair build: trim
stencil: none
bin: none
(4) pair lambda/zone, perpetual
attributes: full, newton on, ghost, cut 14
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(5) fix lambda_thermostat, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 298.1 | 306.3 | 314.5 Mbytes
Step f_balance S/CPU f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
0 1 0 0 0 0 0
10 1.0001725 1.7198837 5.5314343e-06 0.00025930431 2.7883957e-06 4.707143e-06
20 1.0001862 1.8265719 5.6099429e-06 0.00027931903 2.9758981e-06 5.002563e-06
30 1.00056 1.8317507 5.9076763e-06 0.0002894911 3.1109902e-06 5.1394341e-06
40 1.0004862 2.5730799 6.243133e-06 0.00030439841 3.1674858e-06 3.784468e-06
50 1.0001422 1.7867846 6.1734458e-06 0.00029065411 3.1286655e-06 5.1705237e-06
60 1.0008942 1.4365047 7.2226216e-06 0.00035501193 3.8052887e-06 6.42234e-06
70 1.0001463 1.9946081 8.1287731e-06 0.00038928999 4.1631973e-06 4.9840279e-06
80 1.0004234 1.4099223 7.8487793e-06 0.00037185703 4.022587e-06 6.8562431e-06
90 1.000166 1.6477504 1.1740135e-05 0.00039310073 4.5190508e-06 5.9037201e-06
100 1.0004352 1.3977939 7.9664586e-06 0.00037057101 4.0412051e-06 6.8616558e-06
Loop time of 58.5219 on 4 procs for 100 steps with 40200 atoms
Performance: 0.148 ns/day, 162.561 hours/ns, 1.709 timesteps/s, 68.692 katom-step/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.129 | 22.408 | 43.047 | 253.7 | 38.29
Neigh | 2.9649 | 8.8754 | 14.209 | 175.4 | 15.17
Comm | 4.4729 | 19.561 | 38.596 | 306.3 | 33.43
Output | 0.0076245 | 0.28239 | 0.93926 | 72.3 | 0.48
Modify | 1.0567 | 2.2026 | 4.445 | 92.5 | 3.76
Other | | 5.192 | | | 8.87
Nlocal: 10050 ave 16633 max 2176 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 27619 ave 42218 max 8849 min
Histogram: 1 0 0 1 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: 9.49222e+06 ave 1.56603e+07 max 1.80672e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 37968882
Ave neighs/atom = 944.49955
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:01:02

193
examples/PACKAGES/apip/log.04Feb25.vacancy.lambda.no.thermostat.g++.4 Normal file
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@ -0,0 +1,193 @@
LAMMPS (4 Feb 2025 - Development - )
Reading data file ...
orthogonal box = (0 0 0) to (28.92 28.92 28.92)
1 by 2 by 2 MPI processor grid
reading atoms ...
2047 atoms
reading velocities ...
2047 velocities
read_data CPU = 0.037 seconds
ACE version: 2023.11.25
Recursive evaluator is used by ACE
Loading ../../../potentials/Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
atomic load lambda:
fast potential: extract eam/apip:time_per_atom
precise potential: extract pace/apip:time_per_atom
lambda_input: extract lambda_input:time_per_atom
lambda: extract lambda_zone:time_per_atom
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lambda command: doi.org/10.1063/5.0245877
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: The energy is not conserved when lambda changes as fix lambda_thermostat is not used. (../fix_lambda.cpp:247)
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 = 5 5 5
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair eam/fs/apip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair pace/apip, perpetual, trim from (4)
attributes: full, newton on, cut 9.4
pair build: trim
stencil: none
bin: none
(3) pair lambda_input/csp, perpetual, trim from (2)
attributes: full, newton on, cut 8
pair build: trim
stencil: none
bin: none
(4) pair lambda/zone, perpetual
attributes: full, newton on, ghost, cut 14
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 58.65 | 58.75 | 59.03 Mbytes
Step TotEng
0 -7409.9869
1 -7409.9869
2 -7409.987
3 -7409.987
4 -7409.987
5 -7409.987
6 -7409.987
7 -7409.987
8 -7409.987
9 -7409.987
10 -7409.9871
11 -7409.9876
12 -7409.9876
13 -7409.9876
14 -7409.988
15 -7409.9876
16 -7409.9864
17 -7409.9864
18 -7409.9853
19 -7409.9847
20 -7409.9865
21 -7409.9852
22 -7409.9867
23 -7409.9864
24 -7409.9869
25 -7409.9844
26 -7409.9849
27 -7409.9856
28 -7409.9851
29 -7409.9835
30 -7409.9843
31 -7409.9861
32 -7409.9862
33 -7409.9869
34 -7409.9863
35 -7409.9885
36 -7409.9924
37 -7409.9945
38 -7409.9942
39 -7409.9903
40 -7409.9909
41 -7409.9962
42 -7409.996
43 -7409.9959
44 -7410.0004
45 -7410.0044
46 -7409.9993
47 -7409.9948
48 -7409.9923
49 -7409.9844
50 -7409.9861
51 -7409.9849
52 -7409.986
53 -7409.9828
54 -7409.9799
55 -7409.9804
56 -7409.9782
57 -7409.9777
58 -7409.9777
59 -7409.9781
60 -7409.982
61 -7409.982
62 -7409.9824
63 -7409.9844
64 -7409.9826
65 -7409.9816
66 -7409.9788
67 -7409.9769
68 -7409.9727
69 -7409.9716
70 -7409.9693
71 -7409.9674
72 -7409.9691
73 -7409.9693
74 -7409.9682
75 -7409.9664
76 -7409.9678
77 -7409.966
78 -7409.9674
79 -7409.9654
80 -7409.9649
81 -7409.9636
82 -7409.967
83 -7409.9693
84 -7409.9655
85 -7409.9654
86 -7409.9644
87 -7409.961
88 -7409.9609
89 -7409.9594
90 -7409.96
91 -7409.9643
92 -7409.9603
93 -7409.9622
94 -7409.9603
95 -7409.9584
96 -7409.9555
97 -7409.9596
98 -7409.9587
99 -7409.9585
100 -7409.9602
Loop time of 10.6279 on 4 procs for 100 steps with 2047 atoms
Performance: 0.813 ns/day, 29.522 hours/ns, 9.409 timesteps/s, 19.261 katom-step/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.4326 | 8.9455 | 10.524 | 49.4 | 84.17
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.089305 | 1.6676 | 3.18 | 114.5 | 15.69
Output | 0.0028034 | 0.0041679 | 0.0061404 | 1.9 | 0.04
Modify | 0.0040779 | 0.0053928 | 0.0062702 | 1.1 | 0.05
Other | | 0.005266 | | | 0.05
Nlocal: 511.75 ave 529 max 502 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 7684.25 ave 7693 max 7668 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 490648 ave 507159 max 481313 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 1962590
Ave neighs/atom = 958.76404
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:12

197
examples/PACKAGES/apip/log.04Feb25.vacancy.lambda.thermostat.g++.4 Normal file
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@ -0,0 +1,197 @@
LAMMPS (4 Feb 2025 - Development - )
Reading data file ...
orthogonal box = (0 0 0) to (28.92 28.92 28.92)
1 by 2 by 2 MPI processor grid
reading atoms ...
2047 atoms
reading velocities ...
2047 velocities
read_data CPU = 0.041 seconds
ACE version: 2023.11.25
Recursive evaluator is used by ACE
Loading ../../../potentials/Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
atomic load lambda:
fast potential: extract eam/apip:time_per_atom
precise potential: extract pace/apip:time_per_atom
lambda_input: extract lambda_input:time_per_atom
lambda: extract lambda_zone:time_per_atom
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lambda command: doi.org/10.1063/5.0245877
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 5 5 5
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs/apip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair pace/apip, perpetual, trim from (4)
attributes: full, newton on, cut 9.4
pair build: trim
stencil: none
bin: none
(3) pair lambda_input/csp, perpetual, trim from (2)
attributes: full, newton on, cut 8
pair build: trim
stencil: none
bin: none
(4) pair lambda/zone, perpetual
attributes: full, newton on, ghost, cut 14
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(5) fix lambda_thermostat, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 61.44 | 61.63 | 62.2 Mbytes
Step TotEng
0 -7409.9869
1 -7409.9869
2 -7409.987
3 -7409.987
4 -7409.987
5 -7409.987
6 -7409.987
7 -7409.987
8 -7409.987
9 -7409.987
10 -7409.987
11 -7409.9871
12 -7409.9871
13 -7409.9871
14 -7409.9871
15 -7409.9871
16 -7409.9871
17 -7409.9871
18 -7409.9871
19 -7409.9872
20 -7409.9872
21 -7409.9872
22 -7409.9872
23 -7409.9872
24 -7409.9872
25 -7409.9872
26 -7409.9872
27 -7409.9872
28 -7409.9872
29 -7409.9872
30 -7409.9872
31 -7409.9872
32 -7409.9872
33 -7409.9872
34 -7409.9872
35 -7409.9872
36 -7409.9872
37 -7409.9873
38 -7409.9873
39 -7409.9873
40 -7409.9873
41 -7409.9873
42 -7409.9874
43 -7409.9874
44 -7409.9874
45 -7409.9874
46 -7409.9875
47 -7409.9875
48 -7409.9875
49 -7409.9875
50 -7409.9875
51 -7409.9876
52 -7409.9876
53 -7409.9876
54 -7409.9876
55 -7409.9876
56 -7409.9876
57 -7409.9876
58 -7409.9876
59 -7409.9876
60 -7409.9876
61 -7409.9876
62 -7409.9875
63 -7409.9875
64 -7409.9875
65 -7409.9875
66 -7409.9874
67 -7409.9874
68 -7409.9874
69 -7409.9873
70 -7409.9873
71 -7409.9873
72 -7409.9873
73 -7409.9872
74 -7409.9872
75 -7409.9872
76 -7409.9872
77 -7409.9872
78 -7409.9871
79 -7409.9871
80 -7409.9871
81 -7409.9871
82 -7409.9871
83 -7409.9871
84 -7409.9871
85 -7409.9871
86 -7409.9871
87 -7409.9871
88 -7409.9871
89 -7409.9871
90 -7409.9871
91 -7409.9871
92 -7409.9871
93 -7409.9872
94 -7409.9872
95 -7409.9872
96 -7409.9872
97 -7409.9872
98 -7409.9872
99 -7409.9872
100 -7409.9872
Loop time of 11.8395 on 4 procs for 100 steps with 2047 atoms
Performance: 0.730 ns/day, 32.887 hours/ns, 8.446 timesteps/s, 17.290 katom-step/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.1066 | 9.7912 | 11.642 | 53.8 | 82.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.057574 | 1.9086 | 3.5932 | 121.8 | 16.12
Output | 0.022525 | 0.027196 | 0.031414 | 2.2 | 0.23
Modify | 0.10334 | 0.10795 | 0.11223 | 1.2 | 0.91
Other | | 0.004525 | | | 0.04
Nlocal: 511.75 ave 529 max 502 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 7684.25 ave 7693 max 7668 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 490648 ave 507159 max 481313 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 1962590
Ave neighs/atom = 958.76404
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:13